f455a0b1104b883c44c9d5bd9a3f1bee7c25a9a2
HIV-1 epidemic in Western Europe is largely due to subtype B. Little is known about the HIV-1 in Eastern Europe, but a few studies have shown that non-B subtypes are quite common. In Albania, where a recent study estimated a ten-fold increase of AIDS incidence during the last six years, subtype A and B account for 90\% of the know infections.
Methodology/Principal FindingsWe investigated the demographic history of HIV-1 subtype A and B in Albania by using a statistical framework based on coalescent theory and phylogeography. High-resolution phylogenetic and molecular clock analysis showed a limited introduction to the Balkan country of subtype A during the late 1980s followed by an epidemic outburst in the early 1990s. In contrast, subtype B was apparently introduced multiple times between the mid-1970s and mid-1980s. Both subtypes are growing exponentially, although the HIV-1A epidemic displays a faster growth rate, and a significantly higher basic reproductive number R0. HIV-1A gene flow occurs primarily from the capital Tirane, in the center of the country, to the periphery, while HIV-1B flow is characterized by a balanced exchange between center and periphery. Finally, we calculated that the actual number of infections in Albania is at least two orders of magnitude higher than previously thought.
Conclusions/SignificanceOur analysis demonstrates the power of recently developed computational tools to investigate molecular epidemiology of pathogens, and emphasize the complex factors involved in the establishment of HIV-1 epidemics. We suggest that a significant correlation exists between HIV-1 exponential spread and the socio-political changes occurred during the Balkan wars. The fast growth of a relatively new non-B epidemic in the Balkans may have significant consequences for the evolution of HIV-1 epidemiology in neighboring countries in Eastern and Western Europe.
}, Author = {Salemi, Marco and de Oliveira, Tulio and Ciccozzi, Massimo and Rezza, Giovanni and Goodenow, Maureen M.}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Doi = {10.1371/journal.pone.0001390}, Journal = {PLoS ONE}, Month = {01}, Number = {1}, Pages = {e1390}, Publisher = {Public Library of Science}, Title = {High-Resolution Molecular Epidemiology and Evolutionary History of HIV-1 Subtypes in Albania}, Url = {http://dx.plos.org/10.1371%2Fjournal.pone.0001390}, Volume = {3}, Year = {2008}, Bdsk-Url-1 = {http://dx.plos.org/10.1371/journal.pone.0001390}, Bdsk-Url-2 = {http://dx.doi.org/10.1371/journal.pone.0001390}} @article{salminen:1995:id, Annote = {{PMID:} 8573403}, Author = {Salminen, M.O. and Carr, J.K. and Burke, D.S. and McCutchan, F.E.}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Journal = {{AIDS} Research and Human Retroviruses}, Number = {11}, Pages = {1423--1425}, Title = {Identification of Breakpoints in Intergenotypic Recombinants of {HIV} Type 1 by Bootscanning}, Url = {http://dx.doi.org/10.1089/aid.1995.11.1423}, Volume = {11}, Year = {1995}, Bdsk-Url-1 = {http://dx.doi.org/10.1089/aid.1995.11.1423}} @article{sanderson:1997no, Author = {Sanderson, {MJ}}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Journal = {Molecular Biology and Evolution}, Month = dec, Number = {12}, Pages = {1218--1231}, Title = {A Nonparametric Approach to Estimating Divergence Times in the Absence of Rate Constancy}, Url = {http://mbe.oxfordjournals.org.ezproxy.auckland.ac.nz/cgi/reprint/14/12/1218}, Volume = {14}, Year = {1997}, Bdsk-Url-1 = {http://mbe.oxfordjournals.org.ezproxy.auckland.ac.nz/cgi/reprint/14/12/1218}} @article{sanderson:2002es, Abstract = {Rates of molecular evolution vary widely between lineages, but quantification of how rates change has proven difficult. Recently proposed estimation procedures have mainly adopted highly parametric approaches that model rate evolution explicitly. In this study, a semiparametric smoothing method is developed using penalized likelihood. A saturated model in which every lineage has a separate rate is combined with a roughness penalty that discourages rates from varying too much across a phylogeny. A data-driven cross-validation criterion is then used to determine an optimal level of smoothing. This criterion is based on an estimate of the average prediction error associated with pruning lineages from the tree. The methods are applied to three data sets of six genes across a sample of land plants. Optimally smoothed estimates of absolute rates entailed 2- to 10-fold variation across lineages.}, Author = {Sanderson, Michael J.}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Journal = {Molecular Biology and Evolution}, Month = jan, Number = {1}, Pages = {101--109}, Title = {Estimating Absolute Rates of Molecular Evolution and Divergence Times: A Penalized Likelihood Approach}, Url = {http://mbe.oxfordjournals.org/cgi/content/abstract/19/1/101}, Volume = {19}, Year = {2002}, Bdsk-Url-1 = {http://mbe.oxfordjournals.org/cgi/content/abstract/19/1/101}} @article{sanmartin:2008in, Abstract = {Aim Oceanic islands represent a special challenge to historical biogeographers because dispersal is typically the dominant process while most existing methods are based on vicariance. Here, we describe a new Bayesian approach to island biogeography that estimates island carrying capacities and dispersal rates based on simple Markov models of biogeographical processes. This is done in the context of simultaneous analysis of phylogenetic and distributional data across groups, accommodating phylogenetic uncertainty and making parameter estimates more robust. We test our models on an empirical data set of published phylogenies of Canary Island organisms to examine overall dispersal rates and correlation of rates with explanatory factors such as geographic proximity and area {size.Location} Oceanic archipelagos with special reference to the Atlantic Canary {Islands.Methods} The Canary Islands were divided into three island-groups, corresponding to the main magmatism periods in the formation of the archipelago, while {non-Canarian} distributions were grouped into a fourth 'mainland-island'. Dispersal between island groups, which were assumed constant through time, was modelled as a homogeneous, time-reversible Markov process, analogous to the standard models of {DNA} evolution. The stationary state frequencies in these models reflect the relative carrying capacity of the islands, while the exchangeability (rate) parameters reflect the relative dispersal rates between islands. We examined models of increasing complexity: {Jukes2013Cantor} {(JC),} Equal-in, and General Time Reversible {(GTR),} with or without the assumption of stepping-stone dispersal. The data consisted of 13 Canarian phylogenies: 954 individuals representing 393 taxonomic (morphological) entities. Each group was allowed to evolve under its own {DNA} model, with the island-model shared across groups. Posterior distributions on island model parameters were estimated using Markov Chain Monte Carlo {(MCMC)} sampling, as implemented in {MrBayes} 4.0, and Bayes Factors were used to compare {models.Results} The Equal-in step, the {GTR,} and the {GTR} step dispersal models showed the best fit to the data. In the Equal-in and {GTR} models, the largest carrying capacity was estimated for the mainland, followed by the central islands and the western islands, with the eastern islands having the smallest carrying capacity. The relative dispersal rate was highest between the central and eastern islands, and between the central and western islands. The exchange with the mainland was rare in {comparison.Main} conclusions Our results confirm those of earlier studies suggesting that inter-island dispersal within the Canary Island archipelago has been more important in explaining diversification within lineages than dispersal between the continent and the islands, despite the close proximity to North Africa. The low carrying capacity of the eastern islands, uncorrelated with their size or age, fits well with the idea of a historically depauperate biota in these islands but more sophisticated models are needed to address the possible influence of major recent extinction events. The island models explored here can easily be extended to address other problems in historical biogeography, such as dispersal among areas in continental settings or reticulate area relationships.}, Author = {Sanmart{\'\i}n, Isabel and van der Mark, Paul and Ronquist, Fredrik}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Doi = {10.1111/j.1365-2699.2008.01885.x}, Journal = {Journal of Biogeography}, Number = {3}, Pages = {428--449}, Shorttitle = {Inferring dispersal}, Title = {Inferring dispersal: a Bayesian approach to phylogeny-based island biogeography, with special reference to the Canary Islands}, Url = {http://dx.doi.org.ezproxy.auckland.ac.nz/10.1111/j.1365-2699.2008.01885.x}, Volume = {35}, Year = {2008}, Bdsk-Url-1 = {http://dx.doi.org.ezproxy.auckland.ac.nz/10.1111/j.1365-2699.2008.01885.x}, Bdsk-Url-2 = {http://dx.doi.org/10.1111/j.1365-2699.2008.01885.x}} @article{santiago:2002si, Author = {Santiago, Mario L. and Rodenburg, Cynthia M. and Kamenya, Shadrack and {Bibollet-Ruche}, Frederic and Gao, Feng and Bailes, Elizabeth and Meleth, Sreelatha and Soong, {Seng-Jaw} and Kilby, J. Michael and Moldoveanu, Zina and Fahey, Babette and Muller, Martin N. and Ayouba, Ahidjo and Nerrienet, Eric and {McClure}, Harold M. and Heeney, Jonathan L. and Pusey, Anne E. and Collins, D. Anthony and Boesch, Christophe and Wrangham, Richard W. and Goodall, Jane and Sharp, Paul M. and Shaw, George M. and Hahn, Beatrice H.}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Doi = {10.1126/science.295.5554.465}, Journal = {Science}, Month = jan, Number = {5554}, Pages = {465}, Title = {{SIVcpz} in Wild Chimpanzees}, Url = {http://www.sciencemag.org}, Volume = {295}, Year = {2002}, Bdsk-Url-1 = {http://www.sciencemag.org}, Bdsk-Url-2 = {http://dx.doi.org/10.1126/science.295.5554.465}} @article{santiago:2005si, Abstract = {Simian immunodeficiency virus of sooty mangabeys {(SIVsmm)} is recognized as the progenitor of human immunodeficiency virus type 2 {(HIV-2)} and has been transmitted to humans on multiple occasions, yet the epidemiology and genetic diversity of {SIVsmm} infection in wild-living populations remain largely unknown. Here, we report the first molecular epidemiological survey of {SIVsmm} in a community of [{\textasciitilde}]120 free-ranging sooty mangabeys in the Tai Forest, Cote {d'Ivoire.} Fecal samples (n = 39) were collected from 35 habituated animals (27 females and 8 males) and tested for {SIVsmm} virion {RNA} {(vRNA).} Viral gag (800 bp) and/or env (490 bp) sequences were amplified from 11 different individuals (eight females and three males). Based on the sensitivity of fecal {vRNA} detection and the numbers of samples analyzed, the prevalence of {SIVsmm} infection was estimated to be 59\% (95\% confidence interval, 0.35 to 0.88). Behavioral data collected from this community indicated that {SIVsmm} infection occurred preferentially in high-ranking females. Phylogenetic analysis of gag and env sequences revealed an extraordinary degree of genetic diversity, including evidence for frequent recombination events in both the recent and distant past. Some sooty mangabeys harbored near-identical viruses ({\textless}2\% interstrain distance), indicating epidemiologically linked infections. These transmissions were identified by microsatellite analyses to involve both related (mother/daughter) and unrelated individuals, thus providing evidence for vertical and horizontal transmission in the wild. Finally, evolutionary tree analyses revealed significant clustering of the Tai {SIVsmm} strains with five of the eight recognized groups of {HIV-2,} including the epidemic groups A and B, thus pointing to a likely geographic origin of these human infections in the eastern part of the sooty mangabey range.}, Author = {Santiago, Mario L. and Range, Friederike and Keele, Brandon F. and Li, Yingying and Bailes, Elizabeth and {Bibollet-Ruche}, Frederic and Fruteau, Cecile and Noe, Ronald and Peeters, Martine and Brookfield, John F. Y. and Shaw, George M. and Sharp, Paul M. and Hahn, Beatrice H.}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Doi = {10.1128/JVI.79.19.12515-12527.2005}, Journal = {The Journal of Virology}, Month = oct, Number = {19}, Pages = {12515--12527}, Title = {Simian Immunodeficiency Virus Infection in {Free-Ranging} Sooty Mangabeys {(Cercocebus} atys atys) from the Tai Forest, Cote {d'Ivoire:} Implications for the Origin of Epidemic Human Immunodeficiency Virus Type 2}, Url = {http://jvi.asm.org/cgi/content/abstract/79/19/12515}, Volume = {79}, Year = {2005}, Bdsk-Url-1 = {http://jvi.asm.org/cgi/content/abstract/79/19/12515}, Bdsk-Url-2 = {http://dx.doi.org/10.1128/JVI.79.19.12515-12527.2005}} @article{schwartz:2010br, Abstract = {{BACKGROUND:Estimates} of divergence dates between species improve our understanding of processes ranging from nucleotide substitution to speciation. Such estimates are frequently based on molecular genetic differences between species; therefore, they rely on accurate estimates of the number of such differences (i.e. substitutions per site, measured as branch length on phylogenies). We used simulations to determine the effects of dataset size, branch length heterogeneity, branch depth, and analytical framework on branch length estimation across a range of branch lengths. We then reanalyzed an empirical dataset for plethodontid salamanders to determine how inaccurate branch length estimation can affect estimates of divergence {dates.RESULTS:The} accuracy of branch length estimation varied with branch length, dataset size (both number of taxa and sites), branch length heterogeneity, branch depth, dataset complexity, and analytical framework. For simple phylogenies analyzed in a Bayesian framework, branches were increasingly underestimated as branch length increased; in a maximum likelihood framework, longer branch lengths were somewhat overestimated. Longer datasets improved estimates in both frameworks; however, when the number of taxa was increased, estimation accuracy for deeper branches was less than for tip branches. Increasing the complexity of the dataset produced more misestimated branches in a Bayesian framework; however, in an {ML} framework, more branches were estimated more accurately. Using {ML} branch length estimates to re-estimate plethodontid salamander divergence dates generally resulted in an increase in the estimated age of older nodes and a decrease in the estimated age of younger {nodes.CONCLUSIONS:Branch} lengths are misestimated in both statistical frameworks for simulations of simple datasets. However, for complex datasets, length estimates are quite accurate in {ML} (even for short datasets), whereas few branches are estimated accurately in a Bayesian framework. Our reanalysis of empirical data demonstrates the magnitude of effects of Bayesian branch length misestimation on divergence date estimates. Because the length of branches for empirical datasets can be estimated most reliably in an {ML} framework when branches are {\textless}1 substitution/site and datasets are [greater than or equal to]1 kb, we suggest that divergence date estimates using datasets, branch lengths, and/or analytical techniques that fall outside of these parameters should be interpreted with caution.}, Author = {Schwartz, Rachel and Mueller, Rachel}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Journal = {{BMC} Evolutionary Biology}, Number = {1}, Pages = {5}, Title = {Branch length estimation and divergence dating: estimates of error in Bayesian and maximum likelihood frameworks}, Url = {http://www.biomedcentral.com/1471-2148/10/5}, Volume = {10}, Year = {2010}, Bdsk-Url-1 = {http://www.biomedcentral.com/1471-2148/10/5}} @article{seo:2002vi, Abstract = {Motivation: The high pace of viral sequence change means that variation in the times at which sequences are sampled can have a profound effect both on the ability to detect trends over time in evolutionary rates and on the power to reject the Molecular Clock Hypothesis {(MCH).} Trends in viral evolutionary rates are of particular interest because their detection may allow connections to be established between a patient's treatment or condition and the process of evolution. Variation in sequence isolation times also impacts the uncertainty associated with estimates of divergence times and evolutionary rates. Variation in isolation times can be intentionally adjusted to increase the power of hypothesis tests and to reduce the uncertainty of evolutionary parameter estimates, but this fact has received little previous {attention.Results:} We provide approximations for the power to reject the {MCH} when the alternative is that rates change in a linear fashion over time and when the alternative is that rates differ randomly among branches. In addition, we approximate the standard deviation of estimated evolutionary rates and divergence times. We illustrate how these approximations can be exploited to determine which viral sample to sequence when samples representing different dates are {available.Contact:} [email protected]; [email protected]; [email protected]; [email protected]}, Author = {Seo, Tae-{K}un and Thorne, Jeffrey L. and Hasegawa, Masami and Kishino, Hirohisa}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2014-07-06 03:45:03 +0000}, Doi = {10.1093/bioinformatics/18.1.115}, Journal = {Bioinformatics}, Month = jan, Number = {1}, Pages = {115 --123}, Title = {A viral sampling design for testing the molecular clock and for estimating evolutionary rates and divergence times}, Volume = {18}, Year = {2002}, Bdsk-Url-1 = {http://bioinformatics.oxfordjournals.org/content/18/1/115.abstract}, Bdsk-Url-2 = {http://dx.doi.org/10.1093/bioinformatics/18.1.115}} @article{shapiro:2010ba, Author = {Shapiro, B. and Ho, S. Y. W. and Drummond, A. J. and Suchard, M. A. and Pybus, O. G. and Rambaut, A.}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2014-07-06 00:55:00 +0000}, Issn = {0737-4038}, Journal = {Molecular Biology and Evolution}, Publisher = {SMBE}, Title = {{A Bayesian phylogenetic method to estimate unknown sequence ages}}, Year = {2010}} @article{sharp:2000or, Author = {Sharp, P. and Bailes, E. and Gao, F. and Beer, B. and Hirsch, V. and Hahn, B.}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Journal = {Biochemical society transactions}, Number = {part 2}, Pages = {275--282}, Title = {{Origins and evolution of AIDS viruses: estimating the time-scale}}, Volume = {28}, Year = {2000}} @article{sharp:2001or, Abstract = {In the absence of direct epidemiological evidence, molecular evolutionary studies of primate lentiviruses provide the most definitive information about the origins of human immunodeficiency virus {(HIV)--1} and {HIV--2.} Related lentiviruses have been found infecting numerous species of primates in {sub--Saharan} Africa. The only species naturally infected with viruses closely related to {HIV--2} is the sooty mangabey {(Cercocebus} atys) from western Africa, the region where {HIV--2} is known to be endemic. Similarly, the only viruses very closely related to {HIV--1} have been isolated from chimpanzees {(Pan} troglodytes), and in particular those from western equatorial Africa, again coinciding with the region that appears to be the hearth of the {HIV--1} pandemic. {HIV--1} and {HIV--2} have each arisen several times: in the case of {HIV--1,} the three groups {(M,} N and O) are the result of independent cross--species transmission events. Consistent with the phylogenetic position of a `fossil' virus from 1959, molecular clock analyses using realistic models of {HIV--1} sequence evolution place the last common ancestor of the M group prior to 1940, and several lines of evidence indicate that the jump from chimpanzees to humans occurred before then. Both the inferred geographical origin of {HIV--1} and the timing of the cross--species transmission are inconsistent with the suggestion that oral polio vaccines, putatively contaminated with viruses from chimpanzees in eastern equatorial Africa in the late 1950s, could be responsible for the origin of acquired immune deficiency syndrome.}, Author = {Sharp, Paul M. and Bailes, Elizabeth and Chaudhuri, Roy R. and Rodenburg, Cynthia M. and Santiago, Mario O. and Hahn, Beatrice H.}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Doi = {10.1098/rstb.2001.0863}, Journal = {Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences}, Month = jun, Number = {1410}, Pages = {867 --876}, Title = {The origins of acquired immune deficiency syndrome viruses: where and when?}, Url = {http://rstb.royalsocietypublishing.org/content/356/1410/867.abstract}, Volume = {356}, Year = {2001}, Bdsk-Url-1 = {http://rstb.royalsocietypublishing.org/content/356/1410/867.abstract}, Bdsk-Url-2 = {http://dx.doi.org/10.1098/rstb.2001.0863}} @article{sharp:2010ev, Abstract = {The major cause of acquired immune deficiency syndrome {(AIDS)} is human immunodeficiency virus type 1 {(HIV-1).} We have been using evolutionary comparisons to trace (i) the origin(s) of {HIV-1} and (ii) the origin(s) of {AIDS.} The closest relatives of {HIV-1} are simian immunodeficiency viruses {(SIVs)} infecting wild-living chimpanzees {(Pan} troglodytes troglodytes) and gorillas {(Gorilla} gorilla gorilla) in west central Africa. Phylogenetic analyses have revealed the origins of {HIV-1:} chimpanzees were the original hosts of this clade of viruses; four lineages of {HIV-1} have arisen by independent cross-species transmissions to humans and one or two of those transmissions may have been via gorillas. However, {SIVs} are primarily monkey viruses: more than 40 species of African monkeys are infected with their own, species-specific, {SIV} and in at least some host species, the infection seems non-pathogenic. Chimpanzees acquired from monkeys two distinct forms of {SIVs} that recombined to produce a virus with a unique genome structure. We have found that {SIV} infection causes {CD4+} T-cell depletion and increases mortality in wild chimpanzees, and so the origin of {AIDS} is more ancient than the origin of {HIV-1.} Tracing the genetic changes that occurred as monkey viruses adapted to infect first chimpanzees and then humans may provide insights into the causes of the pathogenicity of these viruses.}, Author = {Sharp, Paul M. and Hahn, Beatrice H.}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Doi = {10.1098/rstb.2010.0031}, Journal = {Philosophical Transactions of the Royal Society B: Biological Sciences}, Number = {1552}, Pages = {2487 --2494}, Title = {The evolution of {HIV-1} and the origin of {AIDS}}, Url = {http://rstb.royalsocietypublishing.org/content/365/1552/2487.abstract}, Volume = {365}, Year = {2010}, Bdsk-Url-1 = {http://rstb.royalsocietypublishing.org/content/365/1552/2487.abstract}, Bdsk-Url-2 = {http://dx.doi.org/10.1098/rstb.2010.0031}} @article{Siebenga:2010fk, Abstract = {Noroviruses are the most common cause of viral gastroenteritis. An increase in the number of globally reported norovirus outbreaks was seen the past decade, especially for outbreaks caused by successive genogroup II genotype 4 (GII.4) variants. Whether this observed increase was due to an upswing in the number of infections, or to a surveillance artifact caused by heightened awareness and concomitant improved reporting, remained unclear. Therefore, we set out to study the population structure and changes thereof of GII.4 strains detected through systematic outbreak surveillance since the early 1990s. We collected 1383 partial polymerase and 194 full capsid GII.4 sequences. A Bayesian MCMC coalescent analysis revealed an increase in the number of GII.4 infections during the last decade. The GII.4 strains included in our analyses evolved at a rate of 4.3-9.0x10(-3) mutations per site per year, and share a most recent common ancestor in the early 1980s. Determinants of adaptation in the capsid protein were studied using different maximum likelihood approaches to identify sites subject to diversifying or directional selection and sites that co-evolved. While a number of the computationally determined adaptively evolving sites were on the surface of the capsid and possible subject to immune selection, we also detected sites that were subject to constrained or compensatory evolution due to secondary RNA structures, relevant in virus-replication. We highlight codons that may prove useful in identifying emerging novel variants, and, using these, indicate that the novel 2008 variant is more likely to cause a future epidemic than the 2007 variant. While norovirus infections are generally mild and self-limiting, more severe outcomes of infection frequently occur in elderly and immunocompromized people, and no treatment is available. The observed pattern of continually emerging novel variants of GII.4, causing elevated numbers of infections, is therefore a cause for concern.}, Author = {Siebenga, J Joukje and Lemey, Philippe and Kosakovsky Pond, Sergei L and Rambaut, Andrew and Vennema, Harry and Koopmans, Marion}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Doi = {10.1371/journal.ppat.1000884}, Journal = {PLoS Pathog}, Journal-Full = {PLoS pathogens}, Mesh = {Amino Acid Substitution; Bayes Theorem; Caliciviridae Infections; Capsid Proteins; Dimerization; Disease Outbreaks; Epistasis, Genetic; Evolution, Molecular; Gastroenteritis; Models, Genetic; Norovirus; Nucleic Acid Conformation; Open Reading Frames; Phylogeny; RNA, Viral; Virus Replication}, Month = {May}, Number = {5}, Pages = {e1000884}, Pmc = {PMC2865530}, Pmid = {20463813}, Pst = {epublish}, Title = {Phylodynamic reconstruction reveals norovirus GII.4 epidemic expansions and their molecular determinants}, Volume = {6}, Year = {2010}, Bdsk-Url-1 = {http://dx.doi.org/10.1371/journal.ppat.1000884}} @article{simmonds:2001or, Author = {Simmonds, P.}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Journal = {The Journal of general virology}, Number = {Pt 4}, Pages = {693}, Title = {{The origin and evolution of hepatitis viruses in humans.}}, Volume = {82}, Year = {2001}} @article{slatkin:1989cl, Author = {Slatkin, M. and Maddison, W. P.}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-09-27 15:57:41 +1300}, Journal = {Genetics}, Month = nov, Number = {3}, Pages = {603--613}, Title = {A Cladistic Measure of Gene Flow Inferred from the Phylogenies of Alleles}, Volume = {123}, Year = {1989}, Bdsk-Url-1 = {http://www.genetics.org/cgi/content/abstract/123/3/603}} @article{smith:1992:an, Author = {Smith, {JohnMaynard}}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Doi = {10.1007/BF00182389}, Issn = {0022-2844}, Journal = {Journal of Molecular Evolution}, Number = {2}, Title = {Analyzing the mosaic structure of genes}, Url = {http://www.springerlink.com.ezproxy.auckland.ac.nz/content/n185628502116551/}, Volume = {34}, Year = {1992}, Bdsk-Url-1 = {http://www.springerlink.com.ezproxy.auckland.ac.nz/content/n185628502116551/}, Bdsk-Url-2 = {http://dx.doi.org/10.1007/BF00182389}} @article{Smith:2009fv, Abstract = {In March and early April 2009, a new swine-origin influenza A (H1N1) virus (S-OIV) emerged in Mexico and the United States. During the first few weeks of surveillance, the virus spread worldwide to 30 countries (as of May 11) by human-to-human transmission, causing the World Health Organization to raise its pandemic alert to level 5 of 6. This virus has the potential to develop into the first influenza pandemic of the twenty-first century. Here we use evolutionary analysis to estimate the timescale of the origins and the early development of the S-OIV epidemic. We show that it was derived from several viruses circulating in swine, and that the initial transmission to humans occurred several months before recognition of the outbreak. A phylogenetic estimate of the gaps in genetic surveillance indicates a long period of unsampled ancestry before the S-OIV outbreak, suggesting that the reassortment of swine lineages may have occurred years before emergence in humans, and that the multiple genetic ancestry of S-OIV is not indicative of an artificial origin. Furthermore, the unsampled history of the epidemic means that the nature and location of the genetically closest swine viruses reveal little about the immediate origin of the epidemic, despite the fact that we included a panel of closely related and previously unpublished swine influenza isolates. Our results highlight the need for systematic surveillance of influenza in swine, and provide evidence that the mixing of new genetic elements in swine can result in the emergence of viruses with pandemic potential in humans.}, Author = {Smith, Gavin J D and Vijaykrishna, Dhanasekaran and Bahl, Justin and Lycett, Samantha J and Worobey, Michael and Pybus, Oliver G and Ma, Siu Kit and Cheung, Chung Lam and Raghwani, Jayna and Bhatt, Samir and Peiris, J S Malik and Guan, Yi and Rambaut, Andrew}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Doi = {10.1038/nature08182}, Journal = {Nature}, Journal-Full = {Nature}, Mesh = {Animals; Disease Outbreaks; Evolution, Molecular; Genome, Viral; Humans; Influenza A Virus, H1N1 Subtype; Influenza, Human; Molecular Sequence Data; Orthomyxoviridae Infections; Phylogeny; Reassortant Viruses; Swine; Swine Diseases; Time Factors}, Month = {Jun}, Number = {7250}, Pages = {1122-5}, Pmid = {19516283}, Pst = {ppublish}, Title = {Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic}, Volume = {459}, Year = {2009}, Bdsk-Url-1 = {http://dx.doi.org/10.1038/nature08182}} @article{Smith:2009ss, Abstract = {Pandemic influenza viruses cause significant mortality in humans. In the 20th century, 3 influenza viruses caused major pandemics: the 1918 H1N1 virus, the 1957 H2N2 virus, and the 1968 H3N2 virus. These pandemics were initiated by the introduction and successful adaptation of a novel hemagglutinin subtype to humans from an animal source, resulting in antigenic shift. Despite global concern regarding a new pandemic influenza, the emergence pathway of pandemic strains remains unknown. Here we estimated the evolutionary history and inferred date of introduction to humans of each of the genes for all 20th century pandemic influenza strains. Our results indicate that genetic components of the 1918 H1N1 pandemic virus circulated in mammalian hosts, i.e., swine and humans, as early as 1911 and was not likely to be a recently introduced avian virus. Phylogenetic relationships suggest that the A/Brevig Mission/1/1918 virus (BM/1918) was generated by reassortment between mammalian viruses and a previously circulating human strain, either in swine or, possibly, in humans. Furthermore, seasonal and classic swine H1N1 viruses were not derived directly from BM/1918, but their precursors co-circulated during the pandemic. Mean estimates of the time of most recent common ancestor also suggest that the H2N2 and H3N2 pandemic strains may have been generated through reassortment events in unknown mammalian hosts and involved multiple avian viruses preceding pandemic recognition. The possible generation of pandemic strains through a series of reassortment events in mammals over a period of years before pandemic recognition suggests that appropriate surveillance strategies for detection of precursor viruses may abort future pandemics.}, Author = {Smith, Gavin J D and Bahl, Justin and Vijaykrishna, Dhanasekaran and Zhang, Jinxia and Poon, Leo L M and Chen, Honglin and Webster, Robert G and Peiris, J S Malik and Guan, Yi}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Doi = {10.1073/pnas.0904991106}, Journal = {Proc Natl Acad Sci U S A}, Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America}, Mesh = {Bayes Theorem; Cluster Analysis; Disease Outbreaks; Evolution, Molecular; History, 20th Century; Humans; Influenza A virus; Influenza, Human; Models, Genetic; Phylogeny}, Month = {Jul}, Number = {28}, Pages = {11709-12}, Pmc = {PMC2709671}, Pmid = {19597152}, Pst = {ppublish}, Title = {Dating the emergence of pandemic influenza viruses}, Volume = {106}, Year = {2009}, Bdsk-Url-1 = {http://dx.doi.org/10.1073/pnas.0904991106}} @article{sneath:1973:nu, Author = {Sneath, P.H.A. and Sokal, R.R.}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Journal = {San Francisco}, Title = {{Numerical taxonomy: the principles and practice of numerical classification}}, Volume = {21}, Year = {1973}} @article{Stack:2010fk, Abstract = {With more emphasis being put on global infectious disease monitoring, viral genetic data are being collected at an astounding rate, both within and without the context of a long-term disease surveillance plan. Concurrent with this increase have come improvements to the sophisticated and generalized statistical techniques used for extracting population-level information from genetic sequence data. However, little research has been done on how the collection of these viral sequence data can or does affect the efficacy of the phylogenetic algorithms used to analyse and interpret them. In this study, we use epidemic simulations to consider how the collection of viral sequence data clarifies or distorts the picture, provided by the phylogenetic algorithms, of the underlying population dynamics of the simulated viral infection over many epidemic cycles. We find that sampling protocols purposefully designed to capture sequences at specific points in the epidemic cycle, such as is done for seasonal influenza surveillance, lead to a significantly better view of the underlying population dynamics than do less-focused collection protocols. Our results suggest that the temporal distribution of samples can have a significant effect on what can be inferred from genetic data, and thus highlight the importance of considering this distribution when designing or evaluating protocols and analysing the data collected thereunder.}, Author = {Stack, J Conrad and Welch, J David and Ferrari, Matt J and Shapiro, Beth U and Grenfell, Bryan T}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Doi = {10.1098/rsif.2009.0530}, Journal = {J R Soc Interface}, Journal-Full = {Journal of the Royal Society, Interface / the Royal Society}, Mesh = {Base Sequence; Disease Outbreaks; Humans; Influenza, Human; Population Dynamics}, Month = {Jul}, Number = {48}, Pages = {1119-27}, Pmc = {PMC2880085}, Pmid = {20147314}, Pst = {ppublish}, Title = {Protocols for sampling viral sequences to study epidemic dynamics}, Volume = {7}, Year = {2010}, Bdsk-Url-1 = {http://dx.doi.org/10.1098/rsif.2009.0530}} @article{Stadler:2009fk, Abstract = {The constant rate birth-death process is used as a stochastic model for many biological systems, for example phylogenies or disease transmission. As the biological data are usually not fully available, it is crucial to understand the effect of incomplete sampling. In this paper, we analyze the constant rate birth-death process with incomplete sampling. We derive the density of the bifurcation events for trees on n leaves which evolved under this birth-death-sampling process. This density is used for calculating prior distributions in Bayesian inference programs and for efficiently simulating trees. We show that the birth-death-sampling process can be interpreted as a birth-death process with reduced rates and complete sampling. This shows that joint inference of birth rate, death rate and sampling probability is not possible. The birth-death-sampling process is compared to the sampling-based population genetics model, the coalescent. It is shown that despite many similarities between these two models, the distribution of bifurcation times remains different even in the case of very large population sizes. We illustrate these findings on an Hepatitis C virus dataset from Egypt. We show that the transmission times estimates are significantly different-the widely used Gamma statistic even changes its sign from negative to positive when switching from the coalescent to the birth-death process.}, Author = {Stadler, Tanja}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2014-07-04 01:58:49 +0000}, Doi = {10.1016/j.jtbi.2009.07.018}, Journal = {J Theor Biol}, Journal-Full = {Journal of theoretical biology}, Mesh = {Animals; Birth Rate; Egypt; Hepatitis C; Humans; Models, Biological; Phylogeny; Population Density; Population Dynamics; Stochastic Processes}, Month = {11}, Number = {1}, Pages = {58-66}, Pmid = {19631666}, Pst = {ppublish}, Title = {On incomplete sampling under birth-death models and connections to the sampling-based coalescent}, Volume = {261}, Year = {2009}, Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.jtbi.2009.07.018}} @article{Stadler:2010kx, Abstract = {I consider the constant rate birth-death process with incomplete sampling. I calculate the density of a given tree with sampled extant and extinct individuals. This density is essential for analyzing datasets which are sampled through time. Such datasets are common in virus epidemiology as viruses in infected individuals are sampled through time. Further, such datasets appear in phylogenetics when extant and extinct species data is available. I show how the derived tree density can be used (i) as a tree prior in a Bayesian method to reconstruct the evolutionary past of the sequence data on a calender-timescale, (ii) to infer the birth- and death-rates for a reconstructed evolutionary tree, and (iii) for simulating trees with a given number of sampled extant and extinct individuals which is essential for testing evolutionary hypotheses for the considered datasets.}, Author = {Stadler, Tanja}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2014-07-04 01:59:03 +0000}, Doi = {10.1016/j.jtbi.2010.09.010}, Journal = {J Theor Biol}, Journal-Full = {Journal of theoretical biology}, Month = {12}, Number = {3}, Pages = {396-404}, Pmid = {20851708}, Pst = {ppublish}, Title = {Sampling-through-time in birth-death trees}, Volume = {267}, Year = {2010}, Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.jtbi.2010.09.010}} @article{stanhope:2004ev, Annote = {The origins and evolutionary history of the Severe Acute Respiratory Syndrome {(SARS)} coronavirus {(SARS-CoV)} remain an issue of uncertainty and debate. Based on evolutionary analyses of coronavirus {DNA} sequences, encompassing an approximately 13�kb stretch of the {SARS-TOR2} genome, we provide evidence that {SARS-CoV} has a recombinant history with lineages of types I and {III} coronavirus. We identified a minimum of five recombinant regions ranging from 83 to 863�bp in length and including the polymerase, nsp9, nsp10, and nsp14. Our results are consistent with a hypothesis of viral host jumping events, concomitant with the reassortment of bird and mammalian coronaviruses, a scenario analogous to earlier outbreaks of influenzae.}, Author = {Stanhope, Michael J. and Brown, James R. and {Amrine-Madsen}, Heather}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Doi = {doi: DOI: 10.1016/j.meegid.2003.10.001}, Issn = {1567-1348}, Journal = {Infection, Genetics and Evolution}, Keywords = {Coronavirus, Phylogeny, recombination, Severe acute respiratory syndrome, Viral host-shift}, Number = {1}, Pages = {15--19}, Title = {Evidence from the evolutionary analysis of nucleotide sequences for a recombinant history of {SARS-CoV}}, Url = {http://www.sciencedirect.com/science/article/B6W8B-4B7Y1FV-1/2/8b3c7f9095b6b149f8886c3a1d8c69c8}, Volume = {4}, Year = {2004}, Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6W8B-4B7Y1FV-1/2/8b3c7f9095b6b149f8886c3a1d8c69c8}, Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.meegid.2003.10.001}} @article{stephens:1998da, Annote = {Summary The {CCR5-[Delta]32} deletion obliterates the {CCR5} chemokine and the human immunodeficiency virus {(HIV)-1} coreceptor on lymphoid cells, leading to strong resistance against {HIV-1} infection and {AIDS.} A genotype survey of 4,166 individuals revealed a cline of {CCR5-[Delta]32} allele frequencies of 0\%-14\% across Eurasia, whereas the variant is absent among native African, American Indian, and East Asian ethnic groups. Haplotype analysis of 192 Caucasian chromosomes revealed strong linkage disequilibrium between {CCR5} and two microsatellite loci. By use of coalescence theory to interpret modern haplotype genealogy, we estimate the origin of the {CCR5-[Delta]32-containing} ancestral haplotype to be {\textasciitilde}700 years ago, with an estimated range of 275-1,875 years. The geographic cline of {CCR5-[Delta]32} frequencies and its recent emergence are consistent with a historic strong selective event (e.g., an epidemic of a pathogen that, like {HIV-1,} utilizes {CCR5),} driving its frequency upward in ancestral Caucasian populations.}, Author = {Stephens, J. Claiborne and Reich, David E. and Goldstein, David B. and Shin, Hyoung Doo and Smith, Michael W. and Carrington, Mary and Winkler, Cheryl and Huttley, Gavin A. and Allikmets, Rando and Schriml, Lynn and Gerrard, Bernard and Malasky, Michael and Ramos, Maria D. and Morlot, Susanne and Tzetis, Maria and Oddoux, Carole and di Giovine, Francesco S. and Nasioulas, Georgios and Chandler, David and Aseev, Michael and Hanson, Matthew and Kalaydjieva, Luba and Glavac, Damjan and Gasparini, Paolo and Kanavakis, E. and Claustres, Mireille and Kambouris, Marios and Ostrer, Harry and Duff, Gordon and Baranov, Vladislav and Sibul, Hiljar and Metspalu, Andres and Goldman, David and Martin, Nick and Duffy, David and Schmidtke, Jorg and Estivill, Xavier and {O'Brien}, Stephen J. and Dean, Michael}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Doi = {doi: DOI: 10.1086/301867}, Issn = {0002-9297}, Journal = {The American Journal of Human Genetics}, Keywords = {{AIDS} resistance, Ancestral haplotype, Coalescence of haplotypes, Phylogenetic analysis, Short tandem-repeat polymorphism}, Month = jun, Number = {6}, Pages = {1507--1515}, Title = {Dating the Origin of the {CCR5-[Delta]32} {AIDS-Resistance} Allele by the Coalescence of Haplotypes}, Url = {http://www.sciencedirect.com/science/article/B8JDD-4RDBM6M-12/2/9f79fd03bd3f44faba8404aef2a6c5c8}, Volume = {62}, Year = {1998}, Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B8JDD-4RDBM6M-12/2/9f79fd03bd3f44faba8404aef2a6c5c8}, Bdsk-Url-2 = {http://dx.doi.org/10.1086/301867}} @article{Streftaris:2004uq, Abstract = {We consider continuous-time stochastic compartmental models that can be applied in veterinary epidemiology to model the within-herd dynamics of infectious diseases. We focus on an extension of Markovian epidemic models, allowing the infectious period of an individual to follow a Weibull distribution, resulting in a more flexible model for many diseases. Following a Bayesian approach we show how approximation methods can be applied to design efficient MCMC algorithms with favourable mixing properties for fitting non-Markovian models to partial observations of epidemic processes. The methodology is used to analyse real data concerning a smallpox outbreak in a human population, and a simulation study is conducted to assess the effects of the frequency and accuracy of diagnostic tests on the information yielded on the epidemic process.}, Address = {338 EUSTON ROAD, LONDON NW1 3BH, ENGLAND}, Author = {Streftaris, G and Gibson, GJ}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Doi = {DOI 10.1191/1471082X04st065oa}, Isi = {000220682400004}, Isi-Recid = {134152689}, Isi-Ref-Recids = {103368257 95300111 65170366 70601182 126329392 107431130 72811647 101030461 104569679 107031825 98580464 94466653 33771207 127210831 108835391 78069508 91296799}, Journal = {Statistical Modelling}, Keywords = {Bayesian inference; diagnostic tests; Markov chain Monte Carlo; Metropolis-Hastings acceptance rate; non-Markovian model; stochastic epidemic modelling}, Month = apr, Number = {1}, Pages = {63--75}, Publisher = {ARNOLD, HODDER HEADLINE PLC}, Times-Cited = {10}, Title = {Bayesian inference for stochastic epidemics in closed populations}, Volume = {4}, Year = {2004}, Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000220682400004}} @article{Strimmer:2001vn, Abstract = {We present an intuitive visual framework, the generalized skyline plot, to explore the demographic history of sampled DNA sequences. This approach is based on a genealogy inferred from the sequences and provides a nonparametric estimate of effective population size through time. In contrast to previous related procedures, the generalized skyline plot is more applicable to cases where the underlying tree is not fully resolved and the data is not highly variable. This is achieved by the grouping of adjacent coalescent intervals. We employ a small-sample Akaike information criterion to objectively choose the optimal grouping strategy. We investigate the performance of our approach using simulation and subsequently apply it to HIV-1 sequences from central Africa and mtDNA sequences from red pandas.}, Author = {Strimmer, K and Pybus, O G}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2014-07-04 01:59:20 +0000}, Journal = {Mol Biol Evol}, Journal-Full = {Molecular biology and evolution}, Mesh = {Africa; Animals; Base Sequence; China; DNA; DNA, Mitochondrial; Data Interpretation, Statistical; Genetics, Population; HIV-1; Humans; Models, Genetic; Phylogeny; Ursidae}, Month = {12}, Number = {12}, Pages = {2298-305}, Pmid = {11719579}, Pst = {ppublish}, Title = {Exploring the demographic history of DNA sequences using the generalized skyline plot}, Volume = {18}, Year = {2001}} @article{suchard:2009ma, Abstract = {Motivation: Statistical phylogenetics is computationally intensive, resulting in considerable attention meted on techniques for parallelization. Codon-based models allow for independent rates of synonymous and replacement substitutions and have the potential to more adequately model the process of protein-coding sequence evolution with a resulting increase in phylogenetic accuracy. Unfortunately, due to the high number of codon states, computational burden has largely thwarted phylogenetic reconstruction under codon models, particularly at the genomic-scale. Here, we describe novel algorithms and methods for evaluating phylogenies under arbitrary molecular evolutionary models on graphics processing units {(GPUs),} making use of the large number of processing cores to efficiently parallelize calculations even for large state-size models. Results: We implement the approach in an existing Bayesian framework and apply the algorithms to estimating the phylogeny of 62 complete mitochondrial genomes of carnivores under a 60-state codon model. We see a near 90-fold speed increase over an optimized {CPU-based} computation and a {\textgreater}140-fold increase over the currently available implementation, making this the first practical use of codon models for phylogenetic inference over whole mitochondrial or microorganism genomes. Availability and implementation: Source code provided in {BEAGLE:} Broad-platform Evolutionary Analysis General Likelihood Evaluator, a cross-platform/processor library for phylogenetic likelihood computation (http://beagle-lib.googlecode.com/). We employ a {BEAGLE-implementation} using the Bayesian phylogenetics framework {BEAST} (http://beast.bio.ed.ac.uk/). Contact: [email protected]; [email protected]}, Author = {Suchard, Marc A. and Rambaut, Andrew}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-09-27 15:57:30 +1300}, Doi = {10.1093/bioinformatics/btp244}, Journal = {Bioinformatics}, Month = jun, Number = {11}, Pages = {1370--1376}, Title = {Many-core algorithms for statistical phylogenetics}, Volume = {25}, Year = {2009}, Bdsk-Url-1 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/11/1370}, Bdsk-Url-2 = {http://dx.doi.org/10.1093/bioinformatics/btp244}} @article{suzuki:2010ph, Annote = {When multiple strains of viruses with segmented genomes co-infect a single cell, strains with novel genomic constellations may be created. This mutational process, called reassortment, has caused pandemics of influenza A virus in 1957 and 1968. Here a phylogenetic approach to detecting reassortments, which can be used even when the phylogenetic tree constructed for all strains analyzed is unreliable, is presented. A quartet of strains is examined at a time, where a phylogenetic tree is constructed for each genomic segment and the topology is compared among segments only when all quartet trees are supported with a statistical significance. The occurrence of reassortment and the segments involved in the reassortment event are inferred according to the pattern of topological difference among segments. The reassortment point for a pattern is inferred by superimposing the exterior branches of relevant quartet trees on the all-strains trees. In the analysis of {H1N1} and {H3N2} human influenza A viruses, a topological difference was observed for all pairs of genomic segments, suggesting that there is no pair of segments that has always co-segregated in reassortment during the evolutionary history of these viruses. When the reassortment point was inferred for the pattern of topological difference that was supported with the largest number of quartets for each virus, the results appeared to be mostly correct, suggesting that the method was largely reliable.}, Author = {Suzuki, Yoshiyuki}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Doi = {doi: DOI: 10.1016/j.gene.2010.05.002}, Issn = {0378-1119}, Journal = {Gene}, Keywords = {phylogenetic tree, quartet, Reassortment, segmented genome, virus}, Number = {1-2}, Pages = {11--16}, Title = {A phylogenetic approach to detecting reassortments in viruses with segmented genomes}, Url = {http://www.sciencedirect.com/science/article/B6T39-505Y0NP-1/2/0c14c4f98adfad5f4ed95aa2014ec0e9}, Volume = {464}, Year = {2010}, Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6T39-505Y0NP-1/2/0c14c4f98adfad5f4ed95aa2014ec0e9}, Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.gene.2010.05.002}} @article{swofford:2003pa, Author = {Swofford, D. L.}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2014-07-06 03:16:46 +0000}, Journal = {Massachusetts: Sinauer Associates, Sunderland}, Keywords = {bibtex-import, likelihood, parsimony, Phylogeny, phyloinformatics, Software}, Shorttitle = {{PAUP*}}, Title = {{PAUP*:} phylogenetic analysis using parsimony (* and other methods). Version 4}, Year = {2003}} @article{Takahata:1987kx, Abstract = {Rates of molecular evolution at some loci are more irregular than described by simple Poisson processes. Three situations under which molecular evolution would not follow simple Poisson processes are reevaluated from the viewpoint of the neutrality hypothesis: concomitant or multiple substitutions in a gene, fluctuating substitution rates in time caused by coupled effects of deleterious mutations and bottlenecks, and changes in the degree of selective constraints against a gene (neutral space) caused by successive substitutions. The common underlying assumption that these causes are lineage nonspecific excludes the case where mutation rates themselves change systematically among lineages or taxonomic groups, and severely limits the extent of variation in the number of substitutions among lineages. Even under this stringent condition, however, the third hypothesis, the fluctuating neutral space model, can generate fairly large variation. This is described by a time-dependent renewal process, which does not exhibit any episodic nature of molecular evolution. It is argued that the observed elevated variances in the number of nucleotide or amino acid substitutions do not immediately call for positive Darwinian selection in molecular evolution.}, Author = {Takahata, N}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Journal = {Genetics}, Journal-Full = {Genetics}, Mesh = {Animals; Biological Evolution; Biometry; Models, Genetic; Stochastic Processes; Time Factors}, Month = {May}, Number = {1}, Pages = {169-79}, Pmc = {PMC1203115}, Pmid = {3596230}, Pst = {ppublish}, Title = {On the overdispersed molecular clock}, Volume = {116}, Year = {1987}} @article{takahata:1991ge, Abstract = {In a geographically structured population, the interplay among gene migration, genetic drift and natural selection raises intriguing evolutionary problems, but the rigorous mathematical treatment is often very difficult. Therefore several approximate formulas were developed concerning the coalescence process of neutral genes and the fixation process of selected mutations in an island model, and their accuracy was examined by computer simulation. When migration is limited, the coalescence (or divergence) time for sampled neutral genes can be described by the convolution of exponential functions, as in a panmictic population, but it is determined mainly by migration rate and the number of demes from which the sample is taken. This time can be much longer than that in a panmictic population with the same number of breeding individuals. For a selected mutation, the spreading over the entire population was formulated as a birth and death process, in which the fixation probability within a deme plays a key role. With limited amounts of migration, even advantageous mutations take a large number of generations to spread. Furthermore, it is likely that these mutations which are temporarily fixed in some demes may be swamped out again by non-mutant immigrants from other demes unless selection is strong enough. These results are potentially useful for testing quantitatively various hypotheses that have been proposed for the origin of modern human populations.}, Author = {Takahata, N.}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Journal = {Genetics}, Number = {2}, Pages = {585--595}, Title = {Genealogy of neutral genes and spreading of selected mutations in a geographically structured population}, Url = {http://www.scopus.com.ezproxy.auckland.ac.nz/inward/record.url?eid=2-s2.0-0025945698&partnerID=40&md5=6014dfbeabcb13874041073152fff452}, Volume = {129}, Year = {1991}, Bdsk-Url-1 = {http://www.scopus.com.ezproxy.auckland.ac.nz/inward/record.url?eid=2-s2.0-0025945698&partnerID=40&md5=6014dfbeabcb13874041073152fff452}} @article{Takahata:1991vn, Abstract = {The most commonly used statistical model to describe the rate constancy of molecular evolution (molecular clock) is a simple Poisson process in which the variance of the number of amino acid or nucleotide substitutions in a particular gene should be equal to the mean and henceforth the dispersion index, the ratio of the variance to the mean, should be equal to one. Recent sequence data, however, have shown that the substitutional process in molecular evolution is often considerably overdispersed and have called into question the generality of using a simple Poisson process. Several efforts have been made to develop more realistic models of molecular evolution. In this paper, I will show that the spatial (site-specific) variation in the rate of molecular evolution is an improbable cause of the overdispersion and then review various statistical models which take the temporal variation into account. Although these models do not immediately specify what the mechanisms of molecular evolution might be, they do make qualitatively different predictions and give some insight into their inference. One way to distinguish them is suggested. In addition, effects of selected substitutions that presumably occur after a major change in a molecule are quasi-quantitatively examined. It is most likely that the overdispersion of molecular clock is due either to a major molecular reconfiguration (fluctuating neutral space) led by a series of subliminal neutral changes or to selected substitutions fine-tuning a molecule after a major molecular change. Although the latter possibility, of course, violates the simplest neutrality assumption, it would not impair the neutral theory as a whole.}, Author = {Takahata, N}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Journal = {Theor Popul Biol}, Journal-Full = {Theoretical population biology}, Mesh = {Biological Evolution; Humans; Models, Statistical; Molecular Biology; Poisson Distribution}, Month = {Jun}, Number = {3}, Pages = {329-44}, Pmid = {1896948}, Pst = {ppublish}, Title = {Statistical models of the overdispersed molecular clock}, Volume = {39}, Year = {1991}} @article{takebe:2003hi, Abstract = {Objectives: To investigate the molecular epidemiology and genetic structure of {HIV-1s} causing the epidemic in Central Myanmar and to explore the genesis of {HIV} epidemic in this area. Design: A molecular epidemiological investigation was conducted in 1999-2000 in the city of Mandalay among high-risk populations and the structural features of circulating {HIV-1s} were analyzed. Methods: {HIV-1} genotypes of 59 specimens were screened based on gag (p17) and env {(C2/V3)} regions. Near full-length nucleotide sequences of {HIV-1} isolates with subtype discordance were determined and their recombinant structures were characterized. Results: Three lineages of {HIV-1} strains, including {CRF01\_AE} (27, 45.8\%), subtype B' {(Thailand} variant of subtype B) (15, 25.4\%) and subtype C (8, 13.6\%), were distributed in Mandalay, while substantial portions (9, 15.3\%) of specimens showed various patterns of subtype discordance in different regions of {HIV-1} genomes. The study on six {HIV-1} isolates with subtype discordance revealed that they were highly diverse types of unique recombinant forms {(URFs)} comprised of various combinations of three circulating subtypes. One {URF} was a particularly complex mosaic that contained 13 recombination breakpoints between three {HIV-1} subtypes. Approximately half of recombinants showed 'pseudotype' virion structures, in which the external portions of envelope glycoproteins were exchanged with different lineages of {HIV-1} strains, suggesting the potential selective advantage of 'pseudotype' viruses over parental strains. Conclusion: The study revealed the unique geographical hot spot in Central Myanmar where extensive recombination events appeared to be taking place continually. This reflects the presence of highly exposed individuals and social networks of {HIV-1} transmission. {(C)} 2003 Lippincott Williams \& Wilkins, Inc.}, Author = {Takebe, Yutaka and Motomura, Kazushi and Tatsumi, Masashi and Lwin, Hla Htut and Zaw, Myint and Kusagawa, Shigeru}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Issn = {0269-9370}, Journal = {{AIDS}}, Keywords = {{HIV-1,} injecting drug users, molecular epidemiology, Myanmar, recombination, unique recombinant forms {(URFs)}}, Number = {14}, Title = {High prevalence of diverse forms of {HIV-1} intersubtype recombinants in Central Myanmar: geographical hot spot of extensive recombination}, Url = {http://journals.lww.com/aidsonline/Fulltext/2003/09260/High_prevalence_of_diverse_forms_of_HIV_1.9.aspx}, Volume = {17}, Year = {2003}, Bdsk-Url-1 = {http://journals.lww.com/aidsonline/Fulltext/2003/09260/High_prevalence_of_diverse_forms_of_HIV_1.9.aspx}} @article{takehisa:2009or, Abstract = {Western lowland gorillas {(Gorilla} gorilla gorilla) are infected with a simian immunodeficiency virus {(SIVgor)} that is closely related to chimpanzee and human immunodeficiency viruses {(SIVcpz} and {HIV-1,} respectively) in west central Africa. Although existing data suggest a chimpanzee origin for {SIVgor,} a paucity of available sequences has precluded definitive conclusions. Here, we report the molecular characterization of one partial {(BQ664)} and three full-length {(CP684,} {CP2135,} and {CP2139)} {SIVgor} genomes amplified from fecal {RNAs} of wild-living gorillas at two field sites in Cameroon. Phylogenetic analyses showed that all {SIVgor} strains clustered together, forming a monophyletic lineage throughout their genomes. Interestingly, the closest relatives of {SIVgor} were not {SIVcpzPtt} strains from west central African chimpanzees {(Pan} troglodytes troglodytes) but human viruses belonging to {HIV-1} group O. In trees derived from most genomic regions, {SIVgor} and {HIV-1} group O formed a sister clade to the {SIVcpzPtt} lineage. However, in a tree derived from 5' pol sequences ([{\textasciitilde}]900 bp), {SIVgor} and {HIV-1} group O fell within the {SIVcpzPtt} radiation. The latter was due to two {SIVcpzPtt} strains that contained mosaic pol sequences, pointing to the existence of a divergent {SIVcpzPtt} lineage that gave rise to {SIVgor} and {HIV-1} group O. Gorillas appear to have acquired this lineage at least 100 to 200 years ago. To examine the biological properties of {SIVgor,} we synthesized a full-length provirus from fecal consensus sequences. Transfection of the resulting clone {(CP2139.287)} into {293T} cells yielded infectious virus that replicated efficiently in both human and chimpanzee {CD4+} T cells and used {CCR5} as the coreceptor for viral entry. Together, these results provide strong evidence that P. t. troglodytes apes were the source of {SIVgor.} These same apes may also have spawned the group O epidemic; however, the possibility that gorillas served as an intermediary host cannot be excluded.}, Author = {Takehisa, Jun and Kraus, Matthias H. and Ayouba, Ahidjo and Bailes, Elizabeth and {Van Heuverswyn}, Fran and Decker, Julie M. and Li, Yingying and Rudicell, Rebecca S. and Learn, Gerald H. and Neel, Cecile and Ngole, Eitel Mpoudi and Shaw, George M. and Peeters, Martine and Sharp, Paul M. and Hahn, Beatrice H.}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Doi = {10.1128/JVI.02311-08}, Journal = {The Journal of Virology}, Month = feb, Number = {4}, Pages = {1635--1648}, Title = {Origin and Biology of Simian Immunodeficiency Virus in {Wild-Living} Western Gorillas}, Url = {http://jvi.asm.org/cgi/content/abstract/83/4/1635}, Volume = {83}, Year = {2009}, Bdsk-Url-1 = {http://jvi.asm.org/cgi/content/abstract/83/4/1635}, Bdsk-Url-2 = {http://dx.doi.org/10.1128/JVI.02311-08}} @article{Tanaka:2006fk, Abstract = {Tuberculosis can be studied at the population level by genotyping strains of Mycobacterium tuberculosis isolated from patients. We use an approximate Bayesian computational method in combination with a stochastic model of tuberculosis transmission and mutation of a molecular marker to estimate the net transmission rate, the doubling time, and the reproductive value of the pathogen. This method is applied to a published data set from San Francisco of tuberculosis genotypes based on the marker IS6110. The mutation rate of this marker has previously been studied, and we use those estimates to form a prior distribution of mutation rates in the inference procedure. The posterior point estimates of the key parameters of interest for these data are as follows: net transmission rate, 0.69/year [95\% credibility interval (C.I.) 0.38, 1.08]; doubling time, 1.08 years (95\% C.I. 0.64, 1.82); and reproductive value 3.4 (95\% C.I. 1.4, 79.7). These figures suggest a rapidly spreading epidemic, consistent with observations of the resurgence of tuberculosis in the United States in the 1980s and 1990s.}, Author = {Tanaka, Mark M and Francis, Andrew R and Luciani, Fabio and Sisson, S A}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Doi = {10.1534/genetics.106.055574}, Journal = {Genetics}, Journal-Full = {Genetics}, Mesh = {Algorithms; Bayes Theorem; Computational Biology; Genetic Markers; Genotype; Humans; Mutation; Risk Factors; San Francisco; Tuberculosis}, Month = {Jul}, Number = {3}, Pages = {1511-20}, Pmc = {PMC1526704}, Pmid = {16624908}, Pst = {ppublish}, Title = {Using approximate Bayesian computation to estimate tuberculosis transmission parameters from genotype data}, Volume = {173}, Year = {2006}, Bdsk-Url-1 = {http://dx.doi.org/10.1534/genetics.106.055574}} @article{taubenberger:2005ch, Author = {Taubenberger, Jeffery K. and Reid, Ann H. and Lourens, Raina M. and Wang, Ruixue and Jin, Guozhong and Fanning, Thomas G.}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Doi = {10.1038/nature04230}, Issn = {0028-0836}, Journal = {Nature}, Number = {7060}, Pages = {889--893}, Title = {Characterization of the 1918 influenza virus polymerase genes}, Url = {http://www.nature.com/doifinder/10.1038/nature04230}, Volume = {437}, Year = {2005}, Bdsk-Url-1 = {http://www.nature.com/doifinder/10.1038/nature04230}, Bdsk-Url-2 = {http://dx.doi.org/10.1038/nature04230}} @article{Taylor:2005cq, Abstract = {Because recombination between a pair of viral genomes can occur only when both viruses are present in the same host, genealogical evidence of recombination is influenced by the rate of viral migration between infected hosts. If superinfection is rare, then recombining viral genomes will usually be more closely related to each other than to viral genomes present in other hosts and the impact of recombination on the genealogy of a sample of viruses from different hosts may be weak. We used this relationship to estimate the relative rate of intra-subtype HIV-1 superinfection in six urban populations. Comparisons of the population recombination rates estimated from the HIV-1 sequence data with population recombination rates estimated for sets of sequences simulated using a structured coalescent process suggest that intra-subtype superinfection rates in all but one of these populations may be as high as 15\% of the corresponding infection rate. However, we caution that these estimates might be upwardly biased if variation in contact and mixing rates between infected hosts causes viral lineages to be concentrated in groups with higher than average superinfection rates.}, Author = {Taylor, Jesse E and Korber, Bette T}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Doi = {10.1016/j.meegid.2004.07.001}, Journal = {Infect Genet Evol}, Journal-Full = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, Mesh = {Evolution, Molecular; Genetic Variation; HIV Infections; HIV-1; Humans; Models, Genetic; Molecular Epidemiology; Mutation; Recombination, Genetic; Superinfection}, Month = {Jan}, Number = {1}, Pages = {85-95}, Pmid = {15567142}, Pst = {ppublish}, Title = {HIV-1 intra-subtype superinfection rates: estimates using a structured coalescent with recombination}, Volume = {5}, Year = {2005}, Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.meegid.2004.07.001}} @article{tee:2009es, Annote = {{HIV} is capable of frequent genetic exchange through recombination. Despite the pandemic spread of {HIV-1} recombinants, their times of origin are not well understood. We investigate the epidemic history of a {HIV-1} circulating recombinant form {(CRF)} by estimating the time of the recombination event that lead to the emergence of {CRF33\_01B,} a recently described recombinant descended from {CRF01\_AE} and subtype B. The gag, pol and env genes were analyzed using a combined coalescent and relaxed molecular clock model, implemented in a Bayesian Markov chain Monte Carlo framework. Using linked genealogical trees we calculated the time interval between the common ancestor of {CRF33\_01B} and the ancestors it shares with closely related parental lineages. The recombination event that generated {CRF33\_01B} (trec) occurred sometime between 1991 and 1993, suggesting that recombination is common in the early evolutionary history of {HIV-1.} The proof-of-concept approach provides a new tool for the investigation of {HIV} molecular epidemiology and evolution.}, Author = {Tee, Kok Keng and Pybus, Oliver G. and Parker, Joe and Ng, Kee Peng and Kamarulzaman, Adeeba and Takebe, Yutaka}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Doi = {doi: DOI: 10.1016/j.virol.2009.02.020}, Issn = {0042-6822}, Journal = {Virology}, Keywords = {Coalescence, Genesis, {HIV,} recombination, Reticulate evolution}, Month = apr, Number = {1}, Pages = {229--234}, Title = {Estimating the date of origin of an {HIV-1} circulating recombinant form}, Url = {http://www.sciencedirect.com/science/article/B6WXR-4VT17M3-5/2/b82934708b0b649c5d4690766239d00b}, Volume = {387}, Year = {2009}, Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6WXR-4VT17M3-5/2/b82934708b0b649c5d4690766239d00b}, Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.virol.2009.02.020}} @article{templeton:2004st, Abstract = {Nested clade phylogeographical analysis {(NCPA)} has become a common tool in intraspecific phylogeography. To evaluate the validity of its inferences, {NCPA} was applied to actual data sets with 150 strong a priori expectations, the majority of which had not been analysed previously by {NCPA.} {NCPA} did well overall, but it sometimes failed to detect an expected event and less commonly resulted in a false positive. An examination of these errors suggested some alterations in the {NCPA} inference key, and these modifications reduce the incidence of false positives at the cost of a slight reduction in power. Moreover, {NCPA} does equally well in inferring events regardless of the presence or absence of other, unrelated events. A reanalysis of some recent computer simulations that are seemingly discordant with these results revealed that {NCPA} performed appropriately in these simulated samples and was not prone to a high rate of false positives under sampling assumptions that typify real data sets. {NCPA} makes a posteriori use of an explicit inference key for biological interpretation after statistical hypothesis testing. Alternatives to {NCPA} that claim that biological inference emerges directly from statistical testing are shown in fact to use an a priori inference key, albeit implicitly. It is argued that the a priori and a posteriori approaches to intraspecific phylogeography are complementary, not contradictory. Finally, cross-validation using multiple {DNA} regions is shown to be a powerful method of minimizing inference errors. A likelihood ratio hypothesis testing framework has been developed that allows testing of phylogeographical hypotheses, extends {NCPA} to testing specific hypotheses not within the formal inference key (such as the {out-of-Africa} replacement hypothesis of recent human evolution) and integrates intra- and interspecific phylogeographical inference.}, Author = {Templeton, Alan R.}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Doi = {10.1046/j.1365-294X.2003.02041.x}, Journal = {Molecular Ecology}, Number = {4}, Pages = {789--809}, Shorttitle = {Statistical phylogeography}, Title = {Statistical phylogeography: methods of evaluating and minimizing inference errors}, Url = {http://dx.doi.org.ezproxy.auckland.ac.nz/10.1046/j.1365-294X.2003.02041.x}, Volume = {13}, Year = {2004}, Bdsk-Url-1 = {http://dx.doi.org.ezproxy.auckland.ac.nz/10.1046/j.1365-294X.2003.02041.x}, Bdsk-Url-2 = {http://dx.doi.org/10.1046/j.1365-294X.2003.02041.x}} @article{thorne:1998es, Author = {Thorne, J. L. and Kishino, H and Painter, I. S.}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2014-07-06 03:44:20 +0000}, Journal = {Molecular Biology and Evolution}, Number = {12}, Pages = {1647--1657}, Title = {Estimating the rate of evolution of the rate of molecular evolution}, Volume = {15}, Year = {1998}, Bdsk-Url-1 = {http://mbe.oxfordjournals.org/cgi/content/abstract/15/12/1647}} @article{Toni:2009uq, Abstract = {Approximate Bayesian computation (ABC) methods can be used to evaluate posterior distributions without having to calculate likelihoods. In this paper, we discuss and apply an ABC method based on sequential Monte Carlo (SMC) to estimate parameters of dynamical models. We show that ABC SMC provides information about the inferability of parameters and model sensitivity to changes in parameters, and tends to perform better than other ABC approaches. The algorithm is applied to several well-known biological systems, for which parameters and their credible intervals are inferred. Moreover, we develop ABC SMC as a tool for model selection; given a range of different mathematical descriptions, ABC SMC is able to choose the best model using the standard Bayesian model selection apparatus.}, Author = {Toni, Tina and Welch, David and Strelkowa, Natalja and Ipsen, Andreas and Stumpf, Michael P H}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Journal = {J R Soc Interface}, Journal-Full = {Journal of the Royal Society, Interface / the Royal Society}, Mesh = {Algorithms; Bayes Theorem; Common Cold; Communicable Diseases; Computer Simulation; Models, Biological; Models, Statistical; Monte Carlo Method}, Month = {Feb}, Number = {31}, Pages = {187-202}, Pmc = {PMC2658655}, Pmid = {19205079}, Pst = {ppublish}, Title = {Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems}, Volume = {6}, Year = {2009}} @article{van:2006hu, Annote = {10.1038/444164a}, Author = {{Van Heuverswyn}, Fran and Li, Yingying and Neel, Cecile and Bailes, Elizabeth and Keele, Brandon F. and Liu, Weimin and Loul, Severin and Butel, Christelle and Liegeois, Florian and Bienvenue, Yanga and Ngolle, Eitel Mpoudi and Sharp, Paul M. and Shaw, George M. and Delaporte, Eric and Hahn, Beatrice H. and Peeters, Martine}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Doi = {10.1038/444164a}, Issn = {0028-0836}, Journal = {Nature}, Month = nov, Number = {7116}, Pages = {164}, Title = {Hum2006mmunodeficiency viruses: {SIV} infection in wild gorillas}, Url = {http://dx.doi.org/10.1038/444164a}, Volume = {444}, Year = {2006}, Bdsk-Url-1 = {http://dx.doi.org/10.1038/444164a}} @article{van:spreadas, Annote = {{PMID:} 14722895}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Journal = {The Journal of Infectious Diseases}, Month = jan, Number = {2}, Pages = {292--302}, Title = {Spread of Hepatitis C Virus among European Injection Drug Users Infected with {HIV:} A Phylogenetic Analysis}, Url = {http://dx.doi.org/10.1086/380821}, Volume = {189}, Year = {2004}, Bdsk-Url-1 = {http://dx.doi.org/10.1086/380821}} @article{vanden:1996se, Author = {Vanden Haesevelde, M.M. and Peeters, M. and Jannes, G. and Janssens, W. and Van Der Greon, G. and Sharp, P.M. and Saman, E.}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Issn = {0042-6822}, Journal = {Virology}, Number = {2}, Pages = {346--350}, Publisher = {Elsevier}, Title = {{Sequence analysis of a highly divergent HIV-1-related lentivirus isolated from a wild captured chimpanzee}}, Volume = {221}, Year = {1996}} @article{Viboud:2006fk, Abstract = {Quantifying long-range dissemination of infectious diseases is a key issue in their dynamics and control. Here, we use influenza-related mortality data to analyze the between-state progression of interpandemic influenza in the United States over the past 30 years. Outbreaks show hierarchical spatial spread evidenced by higher pairwise synchrony between more populous states. Seasons with higher influenza mortality are associated with higher disease transmission and more rapid spread than are mild ones. The regional spread of infection correlates more closely with rates of movement of people to and from their workplaces (workflows) than with geographical distance. Workflows are described in turn by a gravity model, with a rapid decay of commuting up to around 100 km and a long tail of rare longer range flow. A simple epidemiological model, based on the gravity formulation, captures the observed increase of influenza spatial synchrony with transmissibility; high transmission allows influenza to spread rapidly beyond local spatial constraints.}, Author = {Viboud, C{\'e}cile and Bj{\o}rnstad, Ottar N and Smith, David L and Simonsen, Lone and Miller, Mark A and Grenfell, Bryan T}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Doi = {10.1126/science.1125237}, Journal = {Science}, Journal-Full = {Science (New York, N.Y.)}, Mesh = {Adult; Algorithms; Child; Disease Outbreaks; Hospitalization; Humans; Incidence; Influenza A Virus, H1N1 Subtype; Influenza A Virus, H3N2 Subtype; Influenza B virus; Influenza, Human; Models, Statistical; Population Density; Seasons; Stochastic Processes; Time Factors; Travel; United States; Workplace}, Month = {Apr}, Number = {5772}, Pages = {447-51}, Pmid = {16574822}, Pst = {ppublish}, Title = {Synchrony, waves, and spatial hierarchies in the spread of influenza}, Volume = {312}, Year = {2006}, Bdsk-Url-1 = {http://dx.doi.org/10.1126/science.1125237}} @article{Vijaykrishna:2008fc, Abstract = {The highly pathogenic avian influenza (HPAI) H5N1 virus lineage has undergone extensive genetic reassortment with viruses from different sources to produce numerous H5N1 genotypes, and also developed into multiple genetically distinct sublineages in China. From there, the virus has spread to over 60 countries. The ecological success of this virus in diverse species of both poultry and wild birds with frequent introduction to humans suggests that it is a likely source of the next human pandemic. Therefore, the evolutionary and ecological characteristics of its emergence from wild birds into poultry are of considerable interest. Here, we apply the latest analytical techniques to infer the early evolutionary dynamics of H5N1 virus in the population from which it emerged (wild birds and domestic poultry). By estimating the time of most recent common ancestors of each gene segment, we show that the H5N1 prototype virus was likely introduced from wild birds into poultry as a non-reassortant low pathogenic avian influenza H5N1 virus and was not generated by reassortment in poultry. In contrast, more recent H5N1 genotypes were generated locally in aquatic poultry after the prototype virus (A/goose/Guangdong/1/96) introduction occurred, i.e., they were not a result of additional emergence from wild birds. We show that the H5N1 virus was introduced into Indonesia and Vietnam 3-6 months prior to detection of the first outbreaks in those countries. Population dynamics analyses revealed a rapid increase in the genetic diversity of A/goose/Guangdong/1/96 lineage viruses from mid-1999 to early 2000. Our results suggest that the transmission of reassortant viruses through the mixed poultry population in farms and markets in China has selected HPAI H5N1 viruses that are well adapted to multiple hosts and reduced the interspecies transmission barrier of those viruses.}, Author = {Vijaykrishna, Dhanasekaran and Bahl, Justin and Riley, Steven and Duan, Lian and Zhang, Jin Xia and Chen, Honglin and Peiris, J S Malik and Smith, Gavin J D and Guan, Yi}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Doi = {10.1371/journal.ppat.1000161}, Journal = {PLoS Pathog}, Journal-Full = {PLoS pathogens}, Mesh = {Animals; Birds; Communicable Diseases, Emerging; Evolution; Genotype; Humans; Influenza A Virus, H5N1 Subtype; Phylogeny; Poultry; Species Specificity; Zoonoses}, Number = {9}, Pages = {e1000161}, Pmc = {PMC2533123}, Pmid = {18818732}, Pst = {epublish}, Title = {Evolutionary dynamics and emergence of panzootic H5N1 influenza viruses}, Volume = {4}, Year = {2008}, Bdsk-Url-1 = {http://dx.doi.org/10.1371/journal.ppat.1000161}} @article{Volz:2009pr, Abstract = {We present a formalism for unifying the inference of population size from genetic sequences and mathematical models of infectious disease in populations. Virus phylogenies have been used in many recent studies to infer properties of epidemics. These approaches rely on coalescent models that may not be appropriate for infectious diseases. We account for phylogenetic patterns of viruses in susceptible-infected (SI), susceptible-infected-susceptible (SIS), and susceptible-infected-recovered (SIR) models of infectious disease, and our approach may be a viable alternative to demographic models used to reconstruct epidemic dynamics. The method allows epidemiological parameters, such as the reproductive number, to be estimated directly from viral sequence data. We also describe patterns of phylogenetic clustering that are often construed as arising from a short chain of transmissions. Our model reproduces the moments of the distribution of phylogenetic cluster sizes and may therefore serve as a null hypothesis for cluster sizes under simple epidemiological models. We examine a small cross-sectional sample of human immunodeficiency (HIV)-1 sequences collected in the United States and compare our results to standard estimates of effective population size. Estimated prevalence is consistent with estimates of effective population size and the known history of the HIV epidemic. While our model accurately estimates prevalence during exponential growth, we find that periods of decline are harder to identify.}, Author = {Volz, Erik M and Kosakovsky Pond, Sergei L and Ward, Melissa J and Leigh Brown, Andrew J and Frost, Simon D W}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Doi = {10.1534/genetics.109.106021}, Journal = {Genetics}, Journal-Full = {Genetics}, Mesh = {Communicable Diseases; Disease Outbreaks; Disease Susceptibility; Evolution, Molecular; HIV; HIV Infections; Models, Biological; Phylogeny; Virus Diseases; Viruses}, Month = {Dec}, Number = {4}, Pages = {1421-30}, Pmc = {PMC2787429}, Pmid = {19797047}, Pst = {ppublish}, Title = {Phylodynamics of infectious disease epidemics}, Volume = {183}, Year = {2009}, Bdsk-Url-1 = {http://dx.doi.org/10.1534/genetics.109.106021}} @article{wallace:2007st, Author = {Wallace, R.G. and HoDac, H.M. and Lathrop, R.H. and Fitch, W.M.}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Journal = {Proceedings of the National Academy of Sciences}, Number = {11}, Pages = {4473}, Publisher = {National Acad Sciences}, Title = {{A statistical phylogeography of influenza A H5N1}}, Volume = {104}, Year = {2007}} @article{Wallinga:2007ve, Abstract = {Mathematical models of transmission have become invaluable management tools in planning for the control of emerging infectious diseases. A key variable in such models is the reproductive number R. For new emerging infectious diseases, the value of the reproductive number can only be inferred indirectly from the observed exponential epidemic growth rate r. Such inference is ambiguous as several different equations exist that relate the reproductive number to the growth rate, and it is unclear which of these equations might apply to a new infection. Here, we show that these different equations differ only with respect to their assumed shape of the generation interval distribution. Therefore, the shape of the generation interval distribution determines which equation is appropriate for inferring the reproductive number from the observed growth rate. We show that by assuming all generation intervals to be equal to the mean, we obtain an upper bound to the range of possible values that the reproductive number may attain for a given growth rate. Furthermore, we show that by taking the generation interval distribution equal to the observed distribution, it is possible to obtain an empirical estimate of the reproductive number.}, Author = {Wallinga, J and Lipsitch, M}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Journal = {Proc Biol Sci}, Journal-Full = {Proceedings. Biological sciences / The Royal Society}, Mesh = {Cohort Effect; Disease Outbreaks; Humans; Influenza, Human; Models, Biological}, Month = {Feb}, Number = {1609}, Pages = {599-604}, Pmc = {PMC1766383}, Pmid = {17476782}, Pst = {ppublish}, Title = {How generation intervals shape the relationship between growth rates and reproductive numbers}, Volume = {274}, Year = {2007}} @article{webby:2000ev, Abstract = {During 1998, severe outbreaks of influenza were observed in four swine herds in the United States. This event was unique because the causative agents, {H3N2} influenza viruses, are infrequently isolated from swine in North America. Two antigenically distinct reassortant viruses {(H3N2)} were isolated from infected animals: a double-reassortant virus containing genes similar to those of human and swine viruses, and a triple-reassortant virus containing genes similar to those of human, swine, and avian influenza viruses {(N.} N. Zhou, D. A. Senne, J. S. Landgraf, S. L. Swenson, G. Erickson, K. Rossow, L. Liu, {K.-J.} Yoon, S. Krauss, and R. G. Webster, J. Virol. 73:8851-8856, 1999). Because the {U.S.} pig population was essentially naive in regard to {H3N2} viruses, it was important to determine the extent of viral spread. Hemagglutination inhibition {(HI)} assays of 4,382 serum samples from swine in 23 states indicated that 28.3\% of these animals had been exposed to classical swine-like {H1N1} viruses and 20.5\% had been exposed to the triple-reassortant-like {H3N2} viruses. The {HI} data suggested that viruses antigenically related to the double-reassortant {H3N2} virus have not become widespread in the {U.S.} swine population. The seroreactivity levels in swine serum samples and the nucleotide sequences of six additional 1999 isolates, all of which were of the triple-reassortant genotype, suggested that {H3N2} viruses containing avian {PA} and {PB2} genes had spread throughout much of the country. These avian-like genes cluster with genes from North American avian viruses. The worldwide predominance of swine viruses containing an avian-like internal gene component suggests that these genes may confer a selective advantage in pigs. Analysis of the 1999 swine {H3N2} isolates showed that the internal gene complex of the triple-reassortant viruses was associated with three recent phylogenetically distinct human-like hemagglutinin {(HA)} molecules. Acquisition of {HA} genes from the human virus reservoir will significantly affect the efficacy of the current swine {H3N2} vaccines. This finding supports continued surveillance of {U.S.} swine populations for influenza virus activity.}, Author = {Webby, Richard J. and Swenson, Sabrina L. and Krauss, Scott L. and Gerrish, Philip J. and Goyal, Sagar M. and Webster, Robert G.}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Doi = {10.1128/JVI.74.18.8243-8251.2000}, Journal = {The Journal of Virology}, Month = sep, Number = {18}, Pages = {8243--8251}, Title = {Evolution of Swine {H3N2} Influenza Viruses in the United States}, Url = {http://jvi.asm.org/cgi/content/abstract/74/18/8243}, Volume = {74}, Year = {2000}, Bdsk-Url-1 = {http://jvi.asm.org/cgi/content/abstract/74/18/8243}, Bdsk-Url-2 = {http://dx.doi.org/10.1128/JVI.74.18.8243-8251.2000}} @article{Wei:1995ly, Abstract = {The dynamics of HIV-1 replication in vivo are largely unknown yet they are critical to our understanding of disease pathogenesis. Experimental drugs that are potent inhibitors of viral replication can be used to show that the composite lifespan of plasma virus and virus-producing cells is remarkably short (half-life approximately 2 days). Almost complete replacement of wild-type virus in plasma by drug-resistant variants occurs after fourteen days, indicating that HIV-1 viraemia is sustained primarily by a dynamic process involving continuous rounds of de novo virus infection and replication and rapid cell turnover.}, Author = {Wei, X and Ghosh, S K and Taylor, M E and Johnson, V A and Emini, E A and Deutsch, P and Lifson, J D and Bonhoeffer, S and Nowak, M A and Hahn, B H}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Doi = {10.1038/373117a0}, Journal = {Nature}, Journal-Full = {Nature}, Mesh = {Antiviral Agents; Base Sequence; CD4 Lymphocyte Count; CD4-Positive T-Lymphocytes; Cell Survival; DNA, Viral; Drug Resistance, Microbial; Genotype; HIV Infections; HIV Protease Inhibitors; HIV Reverse Transcriptase; HIV-1; Humans; Leukocytes, Mononuclear; Molecular Sequence Data; Mutation; Phenotype; RNA, Viral; RNA-Directed DNA Polymerase; Reverse Transcriptase Inhibitors; Viremia; Virus Replication}, Month = {Jan}, Number = {6510}, Pages = {117-22}, Pmid = {7529365}, Pst = {ppublish}, Title = {Viral dynamics in human immunodeficiency virus type 1 infection}, Volume = {373}, Year = {1995}, Bdsk-Url-1 = {http://dx.doi.org/10.1038/373117a0}} @article{Welch2005, Annote = {We model the genealogies of coupled haploid host-virus populations. Hosts reproduce and replace other hosts as in the Moran model. The virus can be transmitted between individuals of the same and succeeding generations. The epidemic model allows a selective advantage for susceptible over infected hosts. The coupled host-virus ancestry of a sample of hosts is embedded in a branching and coalescing structure that we call the Ancestral Infection and Selection Graph, a direct analogue to the Ancestral Selection Graph of Krone and Neuhauser [1997. Theoret. Population Biol. 51, 210-237]. We prove this and discuss various special cases. We show that the inter-host viral genealogy is a scaled coalescent. Using simulations, we compare the viral genealogy under this model to earlier published models and investigate the estimatability of the selection and infectious contact rates. We use simulations to compare the persistence of the disease with the time to the ultimate ancestor.}, Author = {Welch, David and Nicholls, Geoff K. and Rodrigo, Allen G. and Solomon, Wiremu}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2014-07-06 01:01:07 +0000}, Doi = {doi: DOI: 10.1016/j.tpb.2005.03.003}, Issn = {0040-5809}, Journal = {Theoretical Population Biology}, Keywords = {Ancestral selection graph, Coalescent, Epidemiology, Host-virus genealogy, Moran model, Population genetics}, Month = jul, Number = {1}, Pages = {65--75}, Title = {Integrating genealogy and epidemiology: The ancestral infection and selection graph as a model for reconstructing host virus histories}, Url = {http://www.sciencedirect.com/science/article/B6WXD-4G94HM9-2/2/0a9c431ab39a017d7a200aa5d24952c7}, Volume = {68}, Year = {2005}, Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6WXD-4G94HM9-2/2/0a9c431ab39a017d7a200aa5d24952c7}, Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.tpb.2005.03.003}} @article{welch2011statistical, Author = {Welch, D. and Bansal, S. and Hunter, D.R.}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Issn = {1755-4365}, Journal = {Epidemics}, Number = {1}, Pages = {38--45}, Publisher = {Elsevier}, Title = {Statistical inference to advance network models in epidemiology}, Volume = {3}, Year = {2011}} @article{wertheim:????re, Abstract = {In 1977, {H1N1} influenza A virus reappeared after a 20-year absence. Genetic analysis indicated that this strain was missing decades of nucleotide sequence evolution, suggesting an accidental release of a frozen laboratory strain into the general population. Recently, this strain and its descendants were included in an analysis attempting to date the origin of pandemic influenza virus without accounting for the missing decades of evolution. Here, we investigated the effect of using viral isolates with biologically unrealistic sampling dates on estimates of divergence dates. Not accounting for missing sequence evolution produced biased results and increased the variance of date estimates of the most recent common ancestor of the re-emergent lineages and across the entire phylogeny. Reanalysis of the {H1N1} sequences excluding isolates with unrealistic sampling dates indicates that the 1977 re-emergent lineage was circulating for approximately one year before detection, making it difficult to determine the geographic source of reintroduction. We suggest that a new method is needed to account for viral isolates with unrealistic sampling dates.}, Author = {Wertheim, Joel O.}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Doi = {10.1371/journal.pone.0011184}, Journal = {{PLoS} One}, Number = {6}, Title = {The {Re-Emergence} of {H1N1} Influenza Virus in 1977: A Cautionary Tale for Estimating Divergence Times Using Biologically Unrealistic Sampling Dates}, Volume = {5}, Bdsk-Url-1 = {http://dx.doi.org/10.1371/journal.pone.0011184}} @article{wertheim:2007ch, Abstract = {While the circumstances surrounding the origin and spread of {HIV} are becoming clearer, the particulars of the origin of simian immunodeficiency virus {(SIV)} are still unknown. Specifically, the age of {SIV,} whether it is an ancient or recent infection, has not been resolved. Although many instances of cross-species transmission of {SIV} have been documented, the similarity between the African green monkey {(AGM)} and {SIVagm} phylogenies has long been held as suggestive of ancient codivergence between {SIVs} and their primate hosts. Here, we present well-resolved phylogenies based on full-length {AGM} mitochondrial genomes and seven previously published {SIVagm} genomes; these allowed us to perform the first rigorous phylogenetic test to our knowledge of the hypothesis that {SIVagm} codiverged with the {AGMs.} Using the {Shimodaira--Hasegawa} test, we show that the {AGM} mitochondrial genomes and {SIVagm} did not evolve along the same topology. Furthermore, we demonstrate that the {SIVagm} topology can be explained by a pattern of west-to-east transmission of the virus across existing {AGM} geographic ranges. Using a relaxed molecular clock, we also provide a date for the most recent common ancestor of the {AGMs} at approximately 3 million years ago. This study substantially weakens the theory of ancient {SIV} infection followed by codivergence with its primate hosts.}, Author = {Wertheim, Joel O and Worobey, Michael}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Doi = {10.1371/journal.ppat.0030095}, Issn = {1553-7366}, Journal = {{PLoS} Pathogens}, Month = jul, Note = {{PMID:} 17616975 {PMCID:} 1904472}, Number = {7}, Title = {A Challenge to the Ancient Origin of {SIVagm} Based on African Green Monkey Mitochondrial Genomes}, Volume = {3}, Year = {2007}, Bdsk-Url-1 = {http://dx.doi.org/10.1371/journal.ppat.0030095}} @article{wertheim:2009da, Abstract = {{HIV/AIDS} continues to be a major health problem worldwide. An understanding of the evolution of {HIV} in humans may be greatly improved by detailed knowledge of its predecessor, simian immunodeficiency virus {(SIV),} in non-human primates. While {HIV} causes {AIDS} in humans, {SIV} generally produces a benign infection in its natural hosts. This avirulence is often attributed to coevolution between the virus and its host, possibly due to codivergence over millions of years. Here, we provide a temporal reference for evolution of {SIV} in its natural primate hosts. Using state-of-the-art molecular clock dating techniques, we estimate the time of most recent common ancestor for {SIV} in sooty mangabeys and chimpanzees at 1809 (1729{\^a}€``1875) and 1492 (1266{\^a}€``1685), respectively. These ages indicate that {SIV} may have infected these natural hosts for only hundreds of years before giving rise to {HIV.} This short duration suggests that viral{\^a}€``host coevolution over millions of years is not a likely explanation for the widespread avirulence of {SIV.} Finally, despite differences between {SIV} and {HIV} in host biology and viral pathogenicity, we have found clear and direct evidence that {SIV} evolves at a rapid rate in its natural hosts, an evolutionary rate that is indistinguishable from that of {HIV} in humans.}, Author = {Wertheim, Joel O. and Worobey, Michael}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Journal = {{PLoS} Comput Biol}, Month = may, Number = {5}, Pages = {e1000377}, Title = {Dating the Age of the {SIV} Lineages That Gave Rise to {HIV-1} and {HIV-2}}, Url = {http://dx.doi.org/10.1371%2Fjournal.pcbi.1000377}, Volume = {5}, Year = {2009}, Bdsk-Url-1 = {http://dx.doi.org/10.1371/journal.pcbi.1000377}} @article{wertheim:2010re, Author = {Wertheim, J.O.}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Journal = {PLoS ONE}, Number = {6}, Pages = {e11184}, Publisher = {Public Library of Science}, Title = {{The Re-Emergence of H1N1 Influenza Virus in 1977: A Cautionary Tale for Estimating Divergence Times Using Biologically Unrealistic Sampling Dates}}, Volume = {5}, Year = {2010}} @article{worobey:2001no, Author = {Worobey, Michael}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Journal = {Molecular Biology and Evolution}, Number = {8}, Pages = {1425 --1434}, Title = {A Novel Approach to Detecting and Measuring Recombination: New Insights into Evolution in Viruses, Bacteria, and Mitochondria}, Url = {http://mbe.oxfordjournals.org/content/18/8/1425.abstract}, Volume = {18}, Year = {2001}, Bdsk-Url-1 = {http://mbe.oxfordjournals.org/content/18/8/1425.abstract}} @article{worobey:2004or, Author = {Worobey, M. and Santiago, M.L. and Keele, B.F. and Ndjango, J.B.N. and Joy, J.B. and Labama, B.L. and Dhed'a, B.D. and Rambaut, A. and Sharp, P.M. and Shaw, G.M. and others}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Issn = {0028-0836}, Journal = {Nature}, Number = {6985}, Pages = {820}, Publisher = {Nature Publishing Group}, Title = {{Origin of AIDS: contaminated polio vaccine theory refuted}}, Volume = {428}, Year = {2004}} @article{worobey:2008di, Annote = {10.1038/nature07390}, Author = {Worobey, Michael and Gemmel, Marlea and Teuwen, Dirk E. and Haselkorn, Tamara and Kunstman, Kevin and Bunce, Michael and Muyembe, {Jean-Jacques} and Kabongo, {Jean-Marie} M. and Kalengayi, Raphael M. and Marck, Eric Van and Gilbert, M. Thomas P. and Wolinsky, Steven M.}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-09-27 23:30:05 +1300}, Doi = {10.1038/nature07390}, Issn = {0028-0836}, Journal = {Nature}, Month = oct, Number = {7213}, Pages = {661--664}, Title = {Direct evidence of extensive diversity of {HIV-1} in Kinshasa by 1960}, Volume = {455}, Year = {2008}, Bdsk-Url-1 = {http://dx.doi.org/10.1038/nature07390}} @article{worobey:2010is, Abstract = {Simian immunodeficiency virus {(SIV)} lineages have been identified that are endemic to Bioko Island. The time the island formed offers a geological time scale calibration point for dating the most recent common ancestor of {SIV.} The Bioko viruses cover the whole range of {SIV} genetic diversity, and each Bioko {SIV} clade is most closely related to viruses circulating in hosts of the same genus on the African mainland rather than to {SIVs} of other Bioko species. Our phylogeographic approach establishes that {SIV} is ancient and at least 32,000 years old. Our conservative calibration point and analyses of gene sequence saturation and dating bias suggest it may be much older.}, Author = {Worobey, Michael and Telfer, Paul and Souquiere, Sandrine and Hunter, Meredith and Coleman, Clint A. and Metzger, Michael J. and Reed, Patricia and Makuwa, Maria and Hearn, Gail and Honarvar, Shaya and Roques, Pierre and Apetrei, Cristian and Kazanji, Mirdad and Marx, Preston A.}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Doi = {10.1126/science.1193550}, Journal = {Science}, Month = sep, Number = {5998}, Pages = {1487}, Title = {Island Biogeography Reveals the Deep History of {SIV}}, Url = {http://www.sciencemag.org.ezproxy.auckland.ac.nz/cgi/content/abstract/329/5998/1487}, Volume = {329}, Year = {2010}, Bdsk-Url-1 = {http://www.sciencemag.org.ezproxy.auckland.ac.nz/cgi/content/abstract/329/5998/1487}, Bdsk-Url-2 = {http://dx.doi.org/10.1126/science.1193550}} @article{Wright:1931ev, Author = {Wright, S.}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Journal = {Genetics}, Number = {2}, Pages = {97--159}, Title = {{Evolution in Mendelian populations}}, Volume = {16}, Year = {1931}} @article{yang:1994ma, Author = {Yang, Ziheng}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Doi = {10.1007/BF00160154}, Journal = {Journal of Molecular Evolution}, Number = {3}, Pages = {306--314}, Title = {Maximum likelihood phylogenetic estimation from {DNA} sequences with variable rates over sites: Approximate methods}, Url = {http://dx.doi.org/10.1007/BF00160154}, Volume = {39}, Year = {1994}, Bdsk-Url-1 = {http://dx.doi.org/10.1007/BF00160154}} @article{Yip:2009ys, Abstract = {Severe Acute Respiratory Syndrome (SARS) is a respiratory disease caused by a zoonotic coronavirus (CoV) named SARS-CoV (SCoV), which rapidly swept the globe after its emergence in rural China during late 2002. The origins of SCoV have been mysterious and controversial, until the recent discovery of SARS-like CoV (SLCoV) in bats and the proposal of bats as the natural reservior of the Coronaviridae family. In this article, we focused on discussing how phylogenetics contributed to our understanding towards the emergence and transmission of SCoV. We first reviewed the epidemiology of SCoV from a phylogenetic perspective and discussed the controversies over its phylogenetic origins. Then, we summarized the phylogenetic findings in relation to its zoonotic origins and the proposed inter-species viral transmission events. Finally, we also discussed how the discoveries of SCoV and SLCoV expanded our knowledge on the evolution of the Coronaviridae family as well as its implications on the possible future re-emergence of SCoV.}, Author = {Yip, Chi Wai and Hon, Chung Chau and Shi, Mang and Lam, Tommy Tsan-Yuk and Chow, Ken Yan-Ching and Zeng, Fanya and Leung, Frederick Chi-Ching}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Doi = {10.1016/j.meegid.2009.09.015}, Journal = {Infect Genet Evol}, Journal-Full = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, Mesh = {Animals; Coronavirus; Disease Reservoirs; Evolution, Molecular; Genetic Variation; Genome, Viral; Humans; Phylogeny; SARS Virus; Severe Acute Respiratory Syndrome}, Month = {Dec}, Number = {6}, Pages = {1185-96}, Pmid = {19800030}, Pst = {ppublish}, Title = {Phylogenetic perspectives on the epidemiology and origins of SARS and SARS-like coronaviruses}, Volume = {9}, Year = {2009}, Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.meegid.2009.09.015}} @article{yusim:2001us, Author = {Yusim, K. and Peeters, M. and Pybus, O.G. and Bhattacharya, T. and Korber, B.}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Issn = {0962-8436}, Journal = {Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences}, Number = {1410}, Pages = {855}, Publisher = {The Royal Society}, Title = {{Using human immunodeficiency virus type 1 sequences to infer historical features of the acquired immune deficiency syndrome epidemic and human immunodeficiency virus evolution}}, Volume = {356}, Year = {2001}} @article{zhang:????ro, Author = {Zhang, Ming and Foley, Brian and Schultz, {Anne-Kathrin} and Macke, Jennifer P and Bulla, Ingo and Stanke, Mario and Morgenstern, Burkhard and Korber, Bette and Leitner, Thomas}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Doi = {10.1186/1742-4690-7-25}, Note = {{PMID:} 20331894 {PMCID:} 2855530}, Pages = {25--25}, Title = {The role of recombination in the emergence of a complex and dynamic {HIV} epidemic}, Volume = {7}, Bdsk-Url-1 = {http://dx.doi.org/10.1186/1742-4690-7-25}} @article{zimmer:2009hi, Author = {Zimmer, S.M. and Burke, D.S.}, Date-Added = {2011-04-22 15:18:57 +1200}, Date-Modified = {2011-04-22 15:18:57 +1200}, Journal = {New England Journal of Medicine}, Publisher = {Mass Med Soc}, Title = {{Historical perspective--Emergence of influenza A (H1N1) viruses}}, Year = {2009}} @article{A.Zanotto, Author = {de A. Zanotto, P. M. and Gould, E. A. and Gao, G. F. and Harvey, P. H. and Holmes, E. C.}, Date-Modified = {2014-07-06 03:57:38 +0000}, Journal = {Proceedings of the National Academy of Sciences, USA}, Pages = {548--553}, Title = {Population dynamics of flaviviruses revealed by molecular phylogeny}, Volume = {93}} @article{Aach2001, Author = {Aach, J. and Church, G.M.}, Journal = {Bioinformatics}, Notes = {expression}, Pages = {495--508}, Title = {Aligning gene expression time series with time warping algorithms}, Volume = {17}, Year = {2001}} @article{Adachi1996, Author = {Adachi, J. and Hasegawa, M.}, Journal = {Journal of Molecular Evolution}, Pages = {459--468}, Title = {Model of amino acid substitution in proteins encoded by mitochondrial DNA}, Volume = {42}, Year = {1996}} @article{Adeleke1996, Author = {Adeleke, A. and Prucklet, J. and Benson, R. and Rowbotham, T. and Halablab, M. and Fields, B.}, Journal = {Emerging Infectious Diseases}, Pages = {225--230}, Title = {Legionella-like amebal pathogens -- phylogenetic status and possible role in respiratory disease}, Volume = {2}, Year = {1996}} @article{Agapow2002, Author = {Agapow, P. and Purvis, A.}, Journal = {Systematic Biology}, Pages = {866--872}, Title = {Power of eight tree shape statistics to detect nonrandom diversification: a comparison by simulation of two models of cladogenesis}, Volume = {51}, Year = {2002}} @article{Aguilar2000, Author = {Aguilar, O. and West, M.}, Journal = {Journal of Business and Economic Statistics}, Pages = {338--357}, Title = {Bayesian dynamic factor models and portfolio allocation}, Volume = {18}, Year = {2000}} @article{Ai2003, Author = {Ai, Bao-Quan and Wang, Xian-Ju and Liu, Guo-Tao and Liu, Liang-Gang}, Doi = {10.1103/PhysRevE.67.022903}, Journal = {Phys. Rev. E}, Month = {Feb}, Number = {2}, Numpages = {3}, Pages = {022903}, Publisher = {American Physical Society}, Title = {Correlated noise in a logistic growth model}, Volume = {67}, Year = {2003}, Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevE.67.022903}} @article{Albert1993, Author = {Albert, J. and Chib, S.}, Journal = {Journal of the American Statistical Association}, Pages = {657--667}, Title = {Bayesian regression analysis of binary and polychotomous response data}, Volume = {88}, Year = {1993}} @article{Aldous2001, Author = {Aldous, D.J.}, Journal = {Statistical Science}, Pages = {23--34}, Title = {Stochastic models and descriptive statistics for phylogenetic trees, from Yule to today}, Volume = {16}, Year = {2001}} @incollection{Aldous1996, Author = {Aldous, D.}, Booktitle = {Random Discrete Structures,\}, Editors = {D. Aldous and P. Pemantle}, Notes = {tree shape}, Pages = {1--18}, Publisher = {Springer (IMA Volumes Math.\ Appl.\ 76)}, Title = {Probability distributions on cladograms}, Year = {1996}} @book{Aldousinpreparation, Address = {http://stat-www.berkeley.edu/users/aldous/RWG/book.html}, Author = {Aldous, D. and Fill, J.}, Publisher = {University of California, Berkeley, Department of Statistics}, Title = {Reversible Markov Chains and Random Walks on Graphs}, Year = {in preparation}} @article{Allard1996, Author = {Allard, M.W. and Carpenter, J.M.}, Journal = {Cladistics}, Pages = {183--198}, Title = {On weighting and congruence}, Volume = {12}, Year = {1996}} @article{Allard1999, Author = {Allard, M.W. and Farris, J.S. and Carpenter, J.M.}, Journal = {Cladistics}, Pages = {75--84}, Title = {Congruence among mammalian mitochondrial genes}, Volume = {15}, Year = {1999}} @article{Allen2001, Author = {Allen, B.L. and Steel, M.}, Journal = {Annals of Combinatorics}, Pages = {1--15}, Title = {Subtree transfer operations and their induced matrics on evolutionary trees}, Volume = {5}, Year = {2001}} @article{Allison1994, Author = {Allison, L. and Wallace, C.S.}, Journal = {Journal of Molecular Evolution}, Notes = {alignment}, Pages = {418--430}, Title = {The posterior probability distribution of alignments and its application to parameter estimation of evolutionary trees and to optimization of multiple alignments}, Volume = {39}, Year = {1994}} @article{Allison1992, Author = {Allison, L. and Wallace, C.S. and Yee, SC.N.}, Journal = {Journal of Molecular Evolution}, Notes = {alignment}, Pages = {77--89}, Title = {Finite-state models in the alignment of macro-molecules}, Volume = {35}, Year = {1992}} @article{Alter2000, Author = {Alter, O. and Brown, P.O. and Botstein, D.}, Journal = {Proceedings of the National Academy of Science, USA}, Notes = {SVD}, Pages = {10101--10106}, Title = {Singular value decomposition for genome-wide expression data processing and modeling}, Volume = {97}, Year = {2000}} @article{Altfeld2001, Author = {Altfeld, M. and Rosenburg, E.S. and Shankarappa, R. and Mukherjee, J.S. and Hecht, F.M. and Eldridge, R.L. and Eddo, M.M. and Poon, S.H. and Phillips, M.N. and Robbins, G.K. and Sax, P.E. and Boswell, S. and Kahn, J.O. and Brander, C. and Goulder, P.J.R. and Levy, J.A. and Mullins, J.I. and Walker, B.D.}, Journal = jem, Notes = {cr}, Pages = {169--180}, Title = {Cellular Immune Responses and Viral Diversity in Individuals treated during acute and early HIV-1 infection}, Volume = {193}, Year = {2001}} @article{Altman2000, Author = {Altman, D.G.}, Journal = {Statistics in Medicine}, Pages = {3275--3289}, Title = {Statistics in medical journals: some recent trends}, Volume = {19}, Year = {2000}} @article{Altschul1990, Author = {Altschul, S.F. and Gish, W. and Miller, W. and Myers, E.W. and Lipman, D.J.}, Journal = {Journal of Molecular Biology}, Notes = {urosenor,blast}, Pages = {403--410}, Title = {Basic local aligment search tool}, Volume = {215}, Year = {1990}} @article{Andrieu1999, Author = {Andrieu, C. and Doucet, A.}, Journal = {IEEE Transactions on Signal Processing}, Pages = {2667--2676}, Title = {Joint Bayesian model selection and estimation of noisy sinusoids via MCMC}, Volume = {47}, Year = {1999}} @article{Anesubmitted, Author = {Ane, C. and Larget, B. and Baum, D.A. and Smith, S.D. and Rokas, A.}, Journal = {Molecular Biology and Evolution}, Title = {Bayesian estimation of concordance among gene trees}, Year = {submitted}} @article{Anisimova2002, Author = {Anisimova, M. and Bielawski, J.P. and Yang, Z.}, Journal = {Molecular Biology and Evolution}, Pages = {950--958}, Title = {Accuracy and power of Bayesian prediction of amino acid sites under positive selection}, Volume = {19}, Year = {2002}} @article{Anisimova2001, Author = {Anisimova, M. and Bielawski, J.P. and Yang, Z.}, Journal = {Molecular Biology and Evolution}, Pages = {1585--1592}, Title = {Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution}, Volume = {18}, Year = {2001}} @article{Archibald2002, Author = {Archibald, J.M. and Roger, A.J.}, Journal = {Journal of Molecular Biology}, Pages = {1041--1050}, Title = {Gene duplication and gene conversion shape the evolution of archaeal chaperonins}, Volume = {316}, Year = {2002}} @article{Archibald2002a, Author = {Archibald, J.M. and Roger, A.J.}, Journal = {Journal of Molecular Evolution}, Pages = {232--245}, Title = {Gene conversion and the evolution of euryarchaeal chaperonins: a maximum likelihood-based method for detecting conflicting phylogenetic signal}, Volume = {55}, Year = {2002}} @article{Awadalla1999, Author = {Awadalla, P. and Eyre-Walker, A. and Smith, J.M.}, Journal = {Science}, Pages = {2524--2525}, Title = {Linkage disequilibrium and recombination in hominid mitochondrial DNA}, Volume = {286}, Year = {1999}} @article{Ayala1996, Author = {Ayala, F.J. and Barrio, E. and Kwiatowski, J.}, Journal = {Proceedings of the National Academy of Sciences 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By deriving stochastic analogues to difference equations from first principles, we show that the form of these models depends on whether noise in the population process is demographic or environmental. When noise is demographic, we argue that variance around the expectation is proportional to the expectation. When noise is environmental the variance depends in a non-trivial way on how variation enters into model parameters, but we argue that if the environment affects the population multiplicatively then variance is proportional to the square of the expectation. We compare various stochastic analogues of the Ricker map model by fitting them, using maximum likelihood estimation, to data generated from an individual-based model and the weevil data of Utida. Our demographic models are significantly better than our environmental models at fitting noise generated by population processes where noise is mainly demographic. However, the traditionally chosen stochastic analogues to deterministic models--additive normally distributed noise and multiplicative lognormally distributed noise--generally fit all data sets well. Thus, the form of the variance does play a role in the fitting of models to ecological time series, but may not be important in practice as first supposed.}, Address = {Mathematics Department, Umea University, Sweden. [email protected]}, Au = {Brannstrom, A and Sumpter, DJ}, Author = {Brannstrom, A and Sumpter, D J T}, Da = {20060502}, Date-Added = {2008-04-13 17:20:00 +1200}, Date-Modified = {2008-04-13 17:31:58 +1200}, Dcom = {20061005}, Dep = {20060310}, Doi = {10.1016/j.tpb.2006.01.006}, Edat = {2006/03/15 09:00}, Issn = {0040-5809 (Print)}, Jid = {0256422}, Journal = {Theor Popul Biol}, Jt = {Theoretical population biology}, Language = {eng}, Lr = {20061115}, Mhda = {2006/10/06 09:00}, Number = {4}, Own = {NLM}, Pages = {442--451}, Pii = {S0040-5809(06)00014-1}, Pl = {United States}, Pmid = {16530798}, Pst = {ppublish}, Pt = {Journal article; Research Support, Non-U.S. Gov't}, Pubm = {Print-Electronic}, Sb = {IM}, So = {Theor Popul Biol. 2006 Jun;69(4):442-51. Epub 2006 Mar 10.}, Stat = {MEDLINE}, Title = {Stochastic analogues of deterministic single-species population models.}, Volume = {69}, Year = {2006}, Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.tpb.2006.01.006}} @article{Breiman1995, Author = {Breiman, L.}, Journal = {Technometrics}, Pages = {373--384}, Title = {Better subset regression using nonnegative garrote}, Volume = {37}, Year = {1995}} @article{Britten2002, Author = {Britten, R.J.}, Journal = {Proceedings of the National Academy of Sciences, USA}, Notes = {indel}, Pages = {13633--13635}, Title = {Divergence between samples of chimpanzee and human DNA sequences is 5\%, counting indels}, Volume = {99}, Year = {2002}} @article{Britten1969, Author = {Britten, R.J. and Davidson, E.H.}, Journal = {Science}, Notes = {expression}, Pages = {349--357}, Title = {Gene regulation for higher cells: a theory}, Volume = {165}, Year = {1969}} @article{Britten2003, Author = {Britten, R.J. and Rowen, L. and Williams, J. and Cameron, R.A.}, Journal = {Proceedings of the National Academy of Sciences, USA}, Notes = {indel}, Pages = {4661-4665}, Title = {Majority of divergence between closely related DNA samples is due to indels}, Volume = {100}, Year = {2003}} @article{Bromham2003, Author = {Bromham, L.}, Journal = {Palenontologia Electronica}, Pages = {1.2E}, Title = {Into focus, molecular dates for the Cambrian explosion: is the light at the end of the tunnel an oncoming train?}, Volume = {9}, Year = {2003}} @article{Bromham2003a, Author = {Bromham, L. and Penny, D.}, Journal = {Nature Reviews Genetics}, Notes = {relaxed clocks}, Pages = {216--224}, Title = {The modern molecular clock}, Volume = {4}, Year = {2003}} @article{Bromham2004, Author = {Bromham, L. and Woolfit, M.}, Journal = {Syst Biol}, Notes = {relaxed clocks}, Pages = {758--766}, Title = {Explosive radiations and the reliability of molecular clocks: island endemic radiations as a test case}, Volume = {53}, Year = {2004}} @article{Brooks1998, Author = {Brooks, S.P. and Gelman, A.}, Journal = {Journal of Computational and Graphical Statistics}, Pages = {434--455}, Title = {Assessing convergence of Markov chain Monte Carlo algorithms}, Volume = {7}, Year = {1998}} @incollection{Brooks1999, Address = {New York, NY}, Author = {Brooks, S. 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While the mathematical theory of such processes is very well-developed, they may be difficult to work with when attempting to estimate parameters or expected times to extinction. Hence, we focus on diffusion and other approximations to these models, presenting new and recent developments in parameter estimation for density dependent processes, and the calculation of extinction times for processes subject to catastrophes. We illustrate these and other methods using data from simulated and real time series. We give particular attention to a procedure, due to Ross et al. [Ross, J.V., Taimre, T., Pollett, P.K. On parameter estimation in population models, Theor. Popul. Biol., in press], for estimating the parameters of the stochastic SIS logistic model, and demonstrate ways in which these parameters may be used to estimate expected extinction times. Although the stochastic SIS logistic model is strictly density dependent and allows only for birth and death events, it nonetheless may be used to predict extinction times with some accuracy even for populations that are only weakly density dependent, or that are subject to catastrophes. (c) 2006 Elsevier B.V. All rights reserved.}, Author = {Cairns, B. J. and Ross, J. 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This supposition is based on analyses of models exhibiting exponential growth or stable equilibria. Using two quantitative measures, we extend the scaling rule to situations in which population densities fluctuate due to nonlinear deterministic dynamics. These measures are applied to populations of the flour beetle Tribolium castaneum that display chaotic dynamics in both 20-g and 60-g habitats. Populations cultured in the larger habitat exhibit a clarification of the deterministic dynamics, which follows the inverse square root rule. Lattice effects, a deterministic phenomenon caused by the discrete nature of individuals, can cause deviations from the scaling rule when population numbers are small. 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hypotheses about chances, the order of a Markov chain}, Volume = {41}, Year = {1970}} @article{Diebolt1994, Author = {Diebolt, J. and Robert, C.}, Journal = {Journal of the Royal Statistical Society, Series B}, Pages = {363--375}, Title = {Estimation of finite mixture distributions through Bayesian sampling}, Volume = {56}, Year = {1994}} @article{Diggle1984, Author = {Diggle, P.J. and Gratton, R.J.}, Journal = {Journal of Royal Statistical Society, B}, Pages = {193--227}, Title = {Monte Carlo methods of inference for implicit statistical models}, Volume = {46}, Year = {1984}} @article{DiMatteo2001, Author = {DiMatteo, I. and Genovese, C.R. and Kass, R.E.}, Journal = {Biometrika}, Notes = {reversible jump MCMC}, Pages = {1055--1071}, Title = {Bayesian curve fitting with free-knot splines}, Volume = {88}, Year = {2001}} @techreport{DiMatteo2000, Author = {DiMatteo, I. and Genovese, C.R. and Kass, R.E.}, Institution = {Department of Statistics, Carnegie Mellon University}, Number = {716}, Title = {Bayesian curve fitting with free-knot splines}, Year = {2000}} @book{Dobbins1987, Address = {Springfield, IL}, Author = {Dobbins, W.O.}, Publisher = {Thomas}, Title = {Whipple's Disease}, Year = {1987}} @article{Doering2005, Author = {Doering, C.R. and Sargsyan, K.V. and Sanders, L.M.}, Date-Added = {2008-03-28 16:31:18 +1300}, Date-Modified = {2008-03-28 16:32:27 +1300}, Journal = {SIAM Journal of Multiscale Modeling and simulation}, Pages = {283-299}, Title = {Extinction times for birth-death processes: exact results, continuum asymptotics, and the failure of the Fokker-Planck approximation}, Volume = {3}, Year = {2005}} @article{Dong2001, Author = {Dong, W.L. and Caldeira, S. and Sehr, P. and Pawlita, M. and Tommasino, M.}, Journal = {Journal of Virological Methods}, Notes = {HPV}, Pages = {91--98}, Title = {Determination of the binding affinity of different human papillomavirus E7 proteins for the tumor suppressor prb by a plate-binding assay}, Volume = {98}, Year = {2001}} @article{Donnelly1999, Author = {Donnelly, P. and Kurtz, T.G.}, Journal = {Annals of Applied Probability}, Pages = {1091--1148}, Title = {Genealogical processes for Fleming-Viot models with selections and recombination}, Volume = {9}, Year = {1999}} @article{Doolittle2000, Author = {Doolittle, W.F.}, Journal = {Scientific American}, Notes = {HGT}, Pages = {90--95}, Title = {Uprooting the tree of life}, Volume = {February}, Year = {2000}} @article{Doolittle1999, Author = {Doolittle, W.F.}, Journal = {Science}, Notes = {HGT}, Pages = {1443a}, Title = {Lateral gene transfer, genome surveys and the phylogeny of prokaryotes [technical comments]}, Volume = {286}, Year = {1999}} @article{Doolittle1999a, Author = {Doolittle, W.F.}, Journal = {Science}, Notes = {HGT}, Pages = {2124--2128}, Title = {Phylogenetic classification and the universal tree}, Volume = {284}, Year = {1999}} @article{Dorman2001, Author = {Dorman, K.S. and Kaplan, A.H. and Lange, K. and Sinsheimer, J.S.}, Journal = {Journal of Acquired Immune Deficiency Symdromes}, Pages = {398--402}, Title = {Mutation takes no vacation: can structed treatment interruptions increase the risk of drug-resistant HIV-1?}, Volume = {25}, Year = {2001}} @article{Dorman2002, Author = {Dorman, K.S. and Kaplan, A.H. and Sinsheimer, J.S.}, Journal = {Journal of Molecular Evolution}, Pages = {200--209}, Title = {Bootstrap confidence levels for HIV-1 recombination}, Volume = {54}, Year = {2002}} @article{Dorman2004, Author = {Dorman, K.S. and Sinsheimer, J.S. and Lange, K.}, Journal = {SIAM Review}, Pages = {202--229}, Title = {In the garden of branching processes}, Volume = {46}, Year = {2004}} @article{Douzery2003, Author = {Douzery, E.J.P. and Delsuc, P. and Stanhope, M.J. and Huchon, D.}, Journal = {Journal of Molecular Evolution}, Pages = {S201-S213}, Title = {Local molecular clocks in three nuclear genes: divergence times for rodents and other mammals and incompatibility among fossil calibrations}, Volume = {57}, Year = {2003}} @article{Dowson1989, Author = {Dowson, C.G. and Hutchison, A. and Brannigan, J.A. and George, R.C. and Hansman, D. and Linares, J. and Tomasz, A. and Smith, J. Maynard and Spratt, B.G.}, Journal = {Proceedings of the National Academy of Sciences, USA}, Pages = {8842-8846}, Title = {Horizontal transfer of penicillin-binding protein genes in penicillin-resistant clinical isolates of Streptococcus pneumoniae}, Volume = {86}, Year = {1989}} @article{Doyle1992, Author = {Doyle, J.J.}, Journal = {Systematic Botany}, Notes = {incongruence}, Pages = {144--163}, Title = {Gene trees and species trees: molecular systematics as one-character taxonomy}, Volume = {17}, Year = {1992}} @article{Drake2006, Abstract = {Predicting population extinctions is a key element of quantitative conservation biology and population ecology. Although stochastic population theories have long been used to obtain theoretical distributions of population extinction times, model-based predictions have rarely been tested. Here I report results from a quantitative analysis of extinction time in 281 experimental populations of water fleas (Daphnia magna) in variable environments. To my knowledge, this is the first quantitative estimate of the shape of the distribution of population extinction times based on extinction data for any species. The finding that the distribution of population extinction times was extraordinarily peaked is consistent with theoretical predictions for density-independent populations, but inconsistent with predictions for density-dependent populations. The tail of the extinction time distribution was not exponential. These results imply that our current theories of extinction are inadequate. Future work should focus on how demographic stochasticity scales with population size and effects of nonrandom variable environments on population growth and decline.}, Address = {National Center for Ecological Analysis and Synthesis, 735 State Street, Ste. 300, Santa Barbara, California 93101, USA. [email protected]}, Au = {Drake, JM}, Author = {Drake, John M}, Da = {20060925}, Date-Added = {2008-04-13 17:20:00 +1200}, Date-Modified = {2008-04-13 17:27:45 +1200}, Edat = {2006/09/26 09:00}, Issn = {0012-9658 (Print)}, Jid = {0043541}, Journal = {Ecology}, Jt = {Ecology}, Language = {eng}, Mhda = {2006/09/26 09:00}, Number = {9}, Own = {NLM}, Pages = {2215--2220}, Pl = {United States}, Pmid = {16995621}, Pst = {ppublish}, Pt = {Comparative Study; Journal article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.}, Pubm = {Print}, Sb = {IM}, So = {Ecology. 2006 Sep;87(9):2215-20.}, Stat = {In-Process}, Title = {Extinction times in experimental populations.}, Volume = {87}, Year = {2006}} @article{Drummond2001, Author = {Drummond, A. J. and Forsberg, R. and Rodrigo, A. G.}, Date-Modified = {2014-07-06 01:00:40 +0000}, Journal = {Molecular Biology and Evolution}, Notes = {serial}, Pages = {1365--1371}, Title = {The inference of stepwise changes in substitution rates using serial sequence samples}, Volume = {18}, Year = {2001}} @article{Drummond2003, Author = {Drummond, A. J. and Pybus, O. G. and Rambaut, A. and Forsberg, R. and Rodrigo, A. G.}, Date-Modified = {2014-07-06 00:50:13 +0000}, Journal = {Trends in Ecology \& Evolution}, Pages = {481--488}, Title = {Measurably evolving populations}, Volume = {18}, Year = {2003}} @article{Drummond2000, Author = {Drummond, A. J. and Rodrigo, A. G.}, Date-Modified = {2014-07-06 00:49:07 +0000}, Journal = {Molecular Biology and Evolution}, Notes = {serial}, Number = {12}, Pages = {1807--1815}, Title = {Reconstructing genealogies of serial samples under the assumption of a molecular clock using serial-sample UPGMA}, Volume = {17}, Year = {2000}} @article{Drummond2004, Author = {Drummond, P. D.}, Date-Added = {2008-04-12 21:34:38 +1200}, Date-Modified = {2014-07-06 00:51:05 +0000}, Journal = {European Physical Journal B}, Number = {4}, Pages = {617-634}, Title = {Gauge Poisson representations for birth/death master equations}, Volume = {38}, Year = {2004}} @article{Drummond2003a, Author = {Drummond, P. D. and Deuar, P.}, Date-Added = {2008-04-12 21:30:37 +1200}, Date-Modified = {2014-07-06 00:49:19 +0000}, Journal = {Journal of Optics B: Quantum and Semiclassical Optics}, Pages = {S281-S289}, Title = {Quantum dynamics with stochastic gauge simulations}, Volume = {5}, Year = {2003}} @article{Dudoit2002, Author = {Dudoit, S. and Fridlyand, F. and Speed, T.P.}, Journal = {Journal of the American Statistical Association}, Pages = {77--87}, Title = {Comparison of discrimination methods for the classification of tumors using gene expression data}, Volume = {97}, Year = {2002}} @book{Durbin1998, Address = {Cambridge}, Author = {Durbin, R. and Eddy, S. and Krogh, A. and Mitchinson, G.}, Publisher = {Cambridge University Press}, Title = {Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids}, Year = {1998}} @article{Dushoff2000, Abstract = {The stochastic logistic model is the simplest model that combines individual-level demography with density dependence. It explicitly or implicitly underlies many models of biodiversity of competing species, as well as non-spatial or metapopulation models of persistence of individual species. The model has also been used to study persistence in simple disease models. The stochastic logistic model has direct relevance for questions of limiting similarity in ecological systems. This paper uses a biased random walk heuristic to derive a scaling relationship for the persistence of a population under this model, and discusses its implications for models of biodiversity and persistence. Time to extinction of a species under the stochastic logistic model is approximated by the exponential of the scaling quantity U=(R-1)(2) N/R(R+1), where N is the habitat size and R is the basic reproductive number.}, Address = {Institute of Physics, Academia Sinica, Nankang 105, Taipei, Taiwan.}, Au = {Dushoff, J}, Author = {Dushoff, J}, Ci = {Copyright 2000 Academic Press.}, Da = {20000413}, Date-Added = {2008-03-28 15:30:44 +1300}, Date-Modified = {2008-03-28 15:42:35 +1300}, Dcom = {20000413}, Doi = {10.1006/tpbi.1999.1434}, Edat = {2000/03/10 09:00}, Issn = {0040-5809 (Print)}, Jid = {0256422}, Journal = {Theor Popul Biol}, Jt = {Theoretical population biology}, Keywords = {stochastic logistic}, Language = {eng}, Lr = {20031114}, Mh = {Animals; Bias (Epidemiology); Competitive Behavior/*physiology; *Demography; *Ecosystem; Finite Element Analysis; *Logistic Models; *Population Density; Reproduction; Selection (Genetics); Species Specificity; *Stochastic Processes; Time Factors}, Mhda = {2000/04/15 09:00}, Number = {1}, Own = {NLM}, Pages = {59--65}, Pii = {S0040-5809(99)91434-X}, Pl = {UNITED STATES}, Pmid = {10708629}, Pst = {ppublish}, Pt = {Journal article}, Pubm = {Print}, Sb = {IM}, So = {Theor Popul Biol. 2000 Feb;57(1):59-65.}, Stat = {MEDLINE}, Title = {Carrying capacity and demographic stochasticity: scaling behavior of the stochastic logistic model.}, Volume = {57}, Year = {2000}, Bdsk-Url-1 = {http://dx.doi.org/10.1006/tpbi.1999.1434}} @article{Dyk, Author = {Dyk, D.A. Van and Meng, X.-L.}, Journal = {Journal of Computational and Graphical Statistics}, Pages = {1--50}, Title = {The art of data augmentation}, Volume = {10}} @article{Editor-Nature1999, Author = {Sen-Editor-Nature}, Journal = {Nature}, Pages = {843}, Title = {Combating the exploiters of creationism}, Volume = {402}, Year = {1999}} @article{Edwards1970, Author = {Edwards, A.W.F.}, Journal = {Journal of the Royal Statistical Society, Series B}, Notes = {tree shape}, Pages = {155--174}, Title = {Estimation of the branch points of a branching diffusion process (with discussion)}, Volume = {32}, Year = {1970}} @article{Efron1996, Author = {Efron, B. and Halloran, E. and Holmes, S.}, Journal = {Proceedings of the National Academy of Sciences, USA}, Pages = {13429--13434}, Title = {Bootstrap confidence levels for phylogenetic trees}, Volume = {93}, Year = {1996}} @article{Efron2002, Author = {Efron, B. and Tibshirani, R.}, Journal = {Genetic Epidemiology}, Notes = {FDR}, Pages = {70-86}, Title = {Empirical Bayes methods and false discovery rates for microarrays}, Volume = {23}, Year = {2002}} @book{Efron1993, Address = {New York}, Author = {Efron, B. and Tibshirani, R.J.}, Publisher = {Chapman \& Hall}, Series = {Monographs on Statistics and Applied Probability 57}, Title = {An Introduction to the Bootstrap}, Year = {1993}} @incollection{Efroymson1960, Address = {New York}, Author = {Efroymson, M.A.}, Booktitle = {Mathematical Methods for Digital Computers}, Editor = {Ralston, A. and Wilf, H.S.}, Pages = {191--203}, Publisher = {Wiley}, Title = {Multiple regression analysis}, Year = {1960}} @article{Eilers1996, Author = {Eilers, P.H.C. and Marx, B.D.}, Journal = {Statistical Science}, Notes = {splines}, Pages = {89--121}, Title = {Flexible smoothing with B-splines and penalties}, Volume = {11}, Year = {1996}} @article{Eisen1998, Author = {Eisen, M.B. and Spellman, P.T. and Brown, P.O. and Botstein, D.}, Journal = {Proceedings of the National Academies of Science, USA}, Notes = {yeast expression}, Pages = {14863--14868}, Title = {Cluster analysis and display of genome-wide expression patterns}, Volume = {95}, Year = {1998}} @conference{El-Sadr2006, Address = {,\ Denver, CO}, Author = {El-Sadr, W. and Neaton, J. and Team, SMART Study}, Booktitle = {13th Conference on Retroviruses and Opportunistic Infections}, Month = {February}, Title = {Strategies for management of antiretroviral therapy study}, Year = {2006}} @article{Engen2007, Abstract = {We derive formulas that can be applied to estimate the effective population size N(e) for organisms with two sexes reproducing once a year and having constant adult mean vital rates independent of age. Temporal fluctuations in population size are generated by demographic and environmental stochasticity. For populations with even sex ratio at birth, no deterministic population growth and identical mean vital rates for both sexes, the key parameter determining N(e) is simply the mean value of the demographic variance for males and females considered separately. In this case Crow and Kimura's generalization of Wright's formula for N(e) with two sexes, in terms of the effective population sizes for each sex, is applicable even for fluctuating populations with different stochasticity in vital rates for males and females. If the mean vital rates are different for the sexes then a simple linear combination of the demographic variances determines N(e), further extending Wright's formula. For long-lived species an expression is derived for N(e) involving the generation times for both sexes. In the general case with nonzero population growth and uneven sex ratio of newborns, we use the model to investigate numerically the effects of different population parameters on N(e). We also estimate the ratio of effective to actual population size in six populations of house sparrows on islands off the coast of northern Norway. This ratio showed large interisland variation because of demographic differences among the populations. Finally, we calculate how N(e) in a growing house sparrow population will change over time.}, Address = {Population Biology Center, Department of Mathematical Sciences, Norwegian University of Science and Technology, N-7491 Trondheim, Norway. [email protected]}, Au = {Engen, S and Ringsby, TH and Saether, BE and Lande, R and Jensen, H and Lillegard, M and Ellegren, H}, Author = {Engen, Steinar and Ringsby, Thor Harald and Saether, Bernt-Erik and Lande, Russell and Jensen, Henrik and Lillegard, Magnar and Ellegren, Hans}, Da = {20070808}, Date-Added = {2008-04-13 17:20:00 +1200}, Date-Modified = {2008-04-13 17:22:21 +1200}, Dcom = {20071108}, Doi = {10.1111/j.1558-5646.2007.00155.x}, Edat = {2007/08/09 09:00}, Issn = {0014-3820 (Print)}, Jid = {0373224}, Journal = {Evolution Int J Org Evolution}, Jt = {Evolution; international journal of organic evolution}, Language = {eng}, Mh = {Animals; Female; Male; *Models, Biological; Population Density; Population Dynamics; *Reproduction; Sex Factors; *Sparrows; Time Factors}, Mhda = {2007/11/09 09:00}, Number = {8}, Own = {NLM}, Pages = {1873--1885}, Pii = {EVO155}, Pl = {United States}, Pmid = {17683430}, Pst = {ppublish}, Pt = {Journal article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.; Validation Studies}, Pubm = {Print}, Sb = {IM}, So = {Evolution Int J Org Evolution. 2007 Aug;61(8):1873-85.}, Stat = {MEDLINE}, Title = {Effective size of fluctuating populations with two sexes and overlapping generations.}, Volume = {61}, Year = {2007}, Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.1558-5646.2007.00155.x}} @article{Engen2000, Abstract = {Populations threatened by extinction are often far below their carrying capacity. A population collapse or quasi-extinction is defined to occur when the population size reaches some given lower density. If this density is chosen to be large enough for the demographic stochasticity to be ignored compared to environmental stochasticity, then the logarithm of the population size may be modelled by a Brownian motion until quasi-extinction occurs. The normal-gamma mixture of inverse Gaussian distributions can then be applied to define prediction intervals for the time to quasi-extinction in such processes. A similar mixture is used to predict the population size at a finite time for the same process provided that quasi-extinction has not occurred before that time. Stochastic simulations indicate that the coverage of the prediction interval is very close to the probability calculated theoretically. As an illustration, the method is applied to predict the time to extinction of a declining population of white stork in southwestern Germany.}, Address = {Department of Mathematical Sciences, Norwegian University of Science and Technology, Trondheim, N-7491, Norway.}, Au = {Engen, S and Saether, BE}, Author = {Engen, S and Saether, B E}, Ci = {Copyright 2000 Academic Press.}, Da = {20000914}, Date-Added = {2008-04-13 17:32:20 +1200}, Date-Modified = {2008-04-13 17:38:07 +1200}, Dcom = {20000914}, Doi = {10.1006/jtbi.2000.2094}, Edat = {2000/08/10 11:00}, Issn = {0022-5193 (Print)}, Jid = {0376342}, Journal = {J Theor Biol}, Jt = {Journal of theoretical biology}, Language = {eng}, Lr = {20061115}, Mh = {Animals; *Birds; *Models, Statistical; *Population Dynamics; Time Factors}, Mhda = {2000/09/19 11:01}, Number = {4}, Own = {NLM}, Pages = {649--658}, Pii = {S0022-5193(00)92094-0}, Pl = {ENGLAND}, Pmid = {10931759}, Pst = {ppublish}, Pt = {Journal article; Research Support, Non-U.S. Gov't}, Pubm = {Print}, Sb = {IM}, So = {J Theor Biol. 2000 Aug 21;205(4):649-58.}, Stat = {MEDLINE}, Title = {Predicting the time to quasi-extinction for populations far below their carrying capacity.}, Volume = {205}, Year = {2000}, Bdsk-Url-1 = {http://dx.doi.org/10.1006/jtbi.2000.2094}} @article{Equils2000, Author = {Equils, O. and Garratty, E. and Wei, L.S. and Plaeger, S. and Tapia, M. and Deville, J. and Krogstad, P. and Sim, M-S and Nielksen, K. and Bryson, Y.}, Journal = {Journal of Infectious Diseases}, Pages = {751--7}, Title = {Recovery of replication-competent virus from CD4 T cell reservoirs and change in coreceptor use in HIV-1 infected children responding to HAART.}, Volume = {182}, Year = {2000}} @article{Eron2004, Author = {Eron, J.J. and Barlett, J.A. and Santana, J.L. and Bellos, N.C. and Johnson, J. and Keller, A. and Kuritzkes, D.R. and St.~Clair, M.H. and Johnson, V.A.}, Journal = {Journal of Acquired Immune Deficiency Syndromes}, Pages = {1581--1583}, Title = {Persistent antiretroviral activity of nucleoside analogues after prolonged zidovudine and lamivudine therapy as demonstrated by rapid loss of activity after discontinuation}, Volume = {37}, Year = {2004}} @article{Escobar1995, Author = {Escobar, M.D. and West, M.}, Journal = {Journal of the American Statistical Assocation}, Notes = {mixture}, Pages = {577-588}, Title = {Bayesian density estimation and inference using mixtures}, Volume = {90}, Year = {1995}} @article{Este1999, Author = {Este, J.A. and Cabrera, C. and Blanco, J. and Gutierrez, A. and Bridger, G. and Henson, G. and Schols, D. and DeClercq, E.}, Journal = {Journal of Virology}, Pages = {5577--5585}, Title = {Shift of clinical human immunodeficiency virus type 1 isolates from X4 to R5 and prevention of emergence of the syncytium-inducing phenotype by blockade of CXCR4}, Volume = {73}, Year = {1999}} @book{Eubank1999, Address = {New York, NY}, Author = {Eubank, R.L.}, Publisher = {Marcel Dekker, Inc.}, Title = {Nonparametric Regression and Spline Smoothing}, Year = {1999}} @article{Eyre-Walker1999, Author = {Eyre-Walker, A. and Smith, N.H. and Smith, J.M.}, Journal = {Proceedings of the Royal Society of London, B}, Pages = {477--483}, Title = {How clonal are human mitochondria?}, Volume = {266}, Year = {1999}} @article{Fang2004, Author = {Fang, G. and Weiser, B. and Kuiken, C. and Phipott, S.M. and Rowland-Jones, S. and Plummer, F. and Kimani, J. and Shi, B. and Kaul, R. and Bwayo, J. and Anzala, O. and Burger, H.}, Journal = {AIDS}, Pages = {153--159}, Title = {Recombination following superinfection by HIV-1}, Volume = {18}, Year = {2004}} @article{Fang1998, Author = {Fang, G. and Zhu, G. and Burger, H. and Keithly, J. and Weiser, B.}, Journal = {Journal of Virology Methods}, Pages = {139--148}, Title = {Minimizing DNA recombination during long RT-PCR}, Volume = {76}, Year = {1998}} @article{Farci2000, Author = {Farci, P. and Shimoda, A. and Coiana, A. and Diaz, G. and Peddis, G. and Melpolder, J.C. and Strazzera, A. and Chien, D.Y. and Munoz, S.J. and Balestrieri, A. and Purcell, R.H. and Alter, H.J.}, Journal = {Science}, Notes = {beta-prior}, Number = {5464}, Pages = {339--344}, Title = {The outcome of acute hepatitis C predicted by the evolution of the viral quasispecies}, Volume = {288}, Year = {2000}} @article{Farci2002, Author = {Farci, P. and Strazzera, R. and Alter, H.J. and Farci, S. and Degioannis, D. and Coiana, A. and Peddis, G. and Usai, F. and Serra, G. and Diaz, G. and Balestrieri, A. and Purcell, R.H.}, Journal = {Proceedings of the National Academy of Sciences, USA}, Pages = {3081--3086}, Title = {Early changes in hepatitis C viral quasispecies during interferon therapy predict the therapeutic outcome}, Volume = {99}, Year = {2002}} @article{fearnhead2001, Author = {Fearnhead, P. and Donnelly, P.}, Journal = {Genetics}, Number = {3}, Pages = {1299}, Publisher = {Genetics Soc America}, Title = {{Estimating recombination rates from population genetic data}}, Volume = {159}, Year = {2001}} @book{Feller1971, Address = {New York}, Author = {Feller, W.}, Edition = {2nd}, Publisher = {John Wiley \& Sons}, Title = {An Introduction to Probability Theory and Its Applications, Vol. II}, Year = {1971}} @book{Feller1968, Author = {Feller, W.}, Edition = {3rd}, Location = {New York, NY}, Publisher = {John Wiley \& Sons, Inc.}, Title = {An Introduction to Probability Theory and Its Applications, Volume 1}, Year = {1968}} @book{Feller1968a, Address = {New York}, Author = {Feller, W.}, Edition = {3rd}, Publisher = {John Wiley and Sons}, Title = {An Introduction to Probability Theory and Its Applications, Vol. II}, Year = {1968}} @inproceedings{Feller1951, Address = {Berkeley}, Author = {Feller, W.}, Booktitle = {Proc. Second Berkeley Symp. Math. Statist. Probab.}, Date-Added = {2008-03-28 16:44:30 +1300}, Date-Modified = {2008-03-28 16:46:12 +1300}, Pages = {227-246}, Publisher = {Univ. California Press}, Title = {Diffusion processes in genetics}, Year = {1951}} @article{Feller1939, Author = {Feller, W.}, Date-Added = {2008-03-28 16:21:11 +1300}, Date-Modified = {2008-03-28 16:22:07 +1300}, Journal = {Acta Biotheor.}, Pages = {11-40}, Title = {Die Grundlagen der Volterraschen Theorie des Kampfes ums Dasein in wahrscheinlichkeitstheoretiseher Be.handlung}, Volume = {5}, Year = {1939}} @article{Felsenstein2005, Author = {Felsenstein, J.}, Journal = {Philosophical Transactions of the Royal Society of London, Series B}, Pages = {1427--1434}, Title = {Using the quantitative genetic threshold model for inferences between and within species}, Volume = {360}, Year = {2005}} @book{Felsenstein2004, Address = {Sunderland, MA}, Author = {Felsenstein, J.}, Publisher = {Sinauer Associates, Inc.}, Title = {Inferring Phylogenies}, Year = {2004}} @book{Felsenstein1993, Address = {Seattle, WA}, Author = {Felsenstein, J.}, Publisher = {Distributed by the author. Department of Genetics, University of Washington}, Title = {PHYLIP (Phylogenetic Inference Package), Version 3.5}, Year = {1993}} @article{Felsenstein1992, Author = {Felsenstein, J.}, Journal = {Genetical Research}, Pages = {139--147}, Title = {Estimating effective population size from samples of sequences: inefficiency of pairwise and segregating sites as compared to phylogenetic estimates}, Volume = {59}, Year = {1992}} @article{Felsenstein1989, Author = {Felsenstein, J.}, Journal = {Cladistics}, Pages = {164--166}, Title = {PHYLIP -- phylogenetic inference package (version 3.2)}, Volume = {5}, Year = {1989}} @article{Felsenstein1988, Author = {Felsenstein, J.}, Journal = {Annual Review of Genetics}, Pages = {521--565}, Title = {Phylogenies from molecular sequences: inference and reliability}, Volume = {22}, Year = {1988}} @article{Felsenstein1985, Author = {Felsenstein, J.}, Journal = {Evolution}, Pages = {783--791}, Title = {Confidence limits on phylogenies: an approach using the bootstrap}, Volume = {39}, Year = {1985}} @article{Felsenstein1985a, Author = {Felsenstein, J.}, Journal = {American Naturalist}, Pages = {1--15}, Title = {Phylogenies and the comparative method}, Volume = {125}, Year = {1985}} @article{Felsenstein1981, Author = {Felsenstein, J.}, Journal = {Journal of Molecular Evolution}, Pages = {368--376}, Title = {Evolutionary trees from DNA sequences: a maximum likelihood approach}, Volume = {17}, Year = {1981}} @article{Felsenstein1978, Author = {Felsenstein, J.}, Journal = {Systematic Zoology}, Pages = {27--33}, Title = {The number of evolutionary trees}, Volume = {27}, Year = {1978}} @article{Felsenstein1978a, Author = {Felsenstein, J.}, Journal = {Systematic Zoology}, Notes = {long branch problem}, Pages = {401--410}, Title = {Cases in which parsimony or compatibility methods will be positively misleading}, Volume = {27}, Year = {1978}} @article{Felsenstein1973, Author = {Felsenstein, J.}, Journal = {American Journal of Human Genetics}, Notes = {Brownian motion}, Pages = {471--492}, Title = {Maximum likelihood estimation of evolutionary trees from continuous characters}, Volume = {25}, Year = {1973}} @article{Felsenstein1996, Author = {Felsenstein, J. and Churchill, G.A.}, Journal = {Molecular Biology and Evolution}, Pages = {93--104}, Title = {A hidden Markov model approach to variation among sites in rate of evolution}, Volume = {13}, Year = {1996}} @article{Feng1997, Author = {Feng, D.F. and Cho, G. and Doolittle, R.F.}, Journal = {Proceedings of the National Academy of Sciences, USA}, Pages = {13028--13033}, Title = {Determining divergence times with a protein clock: update and reevaluation}, Volume = {94}, Year = {1997}} @article{Feng1988, Author = {Feng, S. and Holland, E.C.}, Journal = {Nature}, Pages = {165-167}, Title = {HIV-1 tat trans-activation requires the loop sequence within TAR}, Volume = {334}, Year = {1988}} @article{Feng2003, Author = {Feng, X. and Buell, D.A. and Rose, J.R. and Waddell, P.J.}, Journal = {Journal of Parallel and Distributed Computing}, Pages = {707-718}, Title = {Parallel algorithms for Bayesian phylogenetic inference}, Volume = {63}, Year = {2003}} @article{Ferguson1973, Author = {Ferguson, T.S.}, Journal = {Annals of Statistics}, Pages = {209--230}, Title = {A Bayesian analysis of some nonparametric problems}, Volume = {1}, Year = {1973}} @article{Figlerowicz2000, Author = {Figlerowicz, M. and Bibillo, A.}, Journal = {RNA}, Pages = {339-351}, Title = {RNA motifs mediating in vivo site-specific nonhomologous recombination in (+) RNA virus enforce in vitro nonhomologous crossovers with HIV-1 reverse transcriptase}, Volume = {6}, Year = {2000}} @book{Fisher1930, Address = {Oxford}, Author = {Fisher, R.A.}, Date-Added = {2008-03-28 16:55:14 +1300}, Date-Modified = {2008-03-28 16:56:23 +1300}, Publisher = {Clarendon Press}, Title = {The Genetical Theory of Natural Selection}, Year = {1930}} @article{Fisher1918, Author = {Fisher, R.A.}, Date-Added = {2008-03-28 16:52:54 +1300}, Date-Modified = {2008-03-28 16:53:36 +1300}, Journal = {Trans. Roy. Soc. Edinb.}, Pages = {399-433}, Title = {The correlation between relatives on the supposition of Mendelian inheritance}, Volume = {52}, Year = {1918}} @article{Foca2006, Author = {Foca, M. and Moye, J. and Chu, C. and Matthews, Y. and Rich, K. and et al}, Journal = {Pediatrics}, Pages = {146--155}, Title = {Gender differences in lymphocyte populations, plasma HIV RNA levels and disease progression in a cohort of children born to women infected with HIV}, Volume = {118}, Year = {2006}} @article{FOLEY2000, Abstract = {It is a vexing problem to achieve a consensus about the proper scientific way to assess population viability for habitat conservation plans. Rather than a hypothesis-testing approach, here it is proposed to select population models, estimate extinction parameters, and assess prediction uncertainty using a pragmatic, empirical Bayesian approach. The simplest usable models include the effects of population growth, r; carrying capacity, K; Allee threshold, N(A); and environmental stochasticity, v(r). Analytic predictions of expected extinction times are available for such models. Models that are more complex can be elaborated from this basis. Selection from a hierarchy of nesting population models can often be done through the evaluation of parameters. The estimation of the most important extinction parameters can be undertaken in a variety of ways. Time series can be analyzed to estimate r(d), v(r), rho, and K. Habitat models and individualistic population models may help estimate N(A) and K and demographic stochasticity. Fine-scale biogeography and climatological data may be useful in the estimation of a variety of parameters. Because it takes many years to estimate extinction parameters accurately for a given population of interest, the most efficient estimation procedures are desirable. I propose the use of prior information from an (as yet nonexistent) population biology database. The accumulation of local information through monitoring will improve our estimates allowing adaptive management. Uncertainty in the estimates will always remain, but it may be quantified by the posterior distributions. A crude example is discussed using treefrog population data. Although the motivations, beliefs, and biases of competing stakeholders will differ, a habitat conservation plan could accommodate this variation in the prior distributions. Field experience from monitoring will increasingly clear up any discrepancies between the opposing beliefs and the real ecosystem. As the world is an uncertain place and because there is no universal scientific method, there will always be controversy and surprises. The best we can do is (1) agree about our prior information, (2) agree about the strategy of model selection and parameter estimation, and (3) agree about our strategy for adaptive management. Perhaps the greatest impediment to such prior agreements for HCPs is the likely paranoia inspired by the use of unfamiliar statistical methodology. We need to train students of ecology in a more flexible and deeper understanding of statistics and philosophy of science.}, Address = {Department of Biological Sciences, California State University, Sacramento, California 95819-6077, USA}, Author = {Foley, P}, Da = {20000509}, Date-Added = {2008-04-13 17:32:20 +1200}, Date-Modified = {2014-07-06 00:57:32 +0000}, Edat = {2000/05/10}, Issn = {0364-152X (Print)}, Jid = {7703893}, Journal = {Environ Manage}, Jt = {Environmental management}, Language = {ENG}, Mhda = {2000/05/10}, Number = {S1}, Own = {NLM}, Pages = {S55-S73}, Pii = {10.1007/s002670010062}, Pmid = {10801990}, Pst = {ppublish}, Pt = {JOURNAL ARTICLE}, Pubm = {Print}, So = {Environ Manage. 2000 Jul;26(S1):S55-S73.}, Stat = {Publisher}, Title = {Problems in Extinction Model Selection and Parameter Estimation.}, Volume = {26}, Year = {2000}} @article{Foley1994, Abstract = {Managers of small populations often need to estimate the expected time to extinction T(e) of their charges. Useful models for extinction times must be ecologically realistic and depend on measurable parameters. Many populations become extinct due to environmental stochasticity, even when the carrying capacity K is stable and the expected growth rate is positive. A model is proposed that gives T(e) by diffusion analysis of the log population size n(t) (= log(e) N(t)). The model population grows according to the equation N(t+1) = R(t)N(t), with K as a ceiling. Application of the model requires estimation of the parameters k = logK, r(d) = the expected change in n, v(r) = Variance(log R), and rho the autocorrelation of the r(t). These are readily calculable from annual census data (r(d) is trickiest to estimate). General formulas for T(e) are derived. As a special case, when environmental fluctuations overwhelm expected growth (that is r(d) almost-equal-to 0), T(e) = 2n0(k - n0/2)/v(r). If the r(t) are autocorrelated, then the effective variance is v(re) almost-equal-to v(r) (1 + rho)/(1 - rho). The theory is applied to populations of checkerspot butterfly, grizzly bear, wolf and mountain lion.}, Author = {Foley, P}, Date-Added = {2008-05-23 11:05:18 +1200}, Date-Modified = {2008-05-23 11:06:34 +1200}, Journal = {Conservation Biology}, Pages = {124-137}, Timescited = {0}, Title = {Predicting Extinction Times from Environmental Stochasticity and Carrying Capacity}, Volume = {8}, Year = {1994}} @techreport{Fonseca2006, Author = {Fonseca, T. C. O. and Ferreira, M. A. R. and Migon, H. S.}, Institution = {Departamento de M\'etodos Estat\'\i sticos - Universidade Federal do Rio de Janeiro}, Number = {187}, Title = {Objective Bayesian analysis for the Student-t regression model}, Year = {2006}} @techreport{Forster????, Author = {Forster, J.J.}, Notes = {model selection}, Title = {Bayesian inference for Poisson and multinomial log-linear models}, Year = {????}} @book{Foster1995, Author = {Foster, I.}, Publisher = {Wesley, Addison}, Title = {Designing and Building Parallel Programs}, Year = {1995}} @other{Foundation2003, Author = {Foundation, San Francisco AIDS}, Publisher = {Public Policy Department}, Title = {HIV/AIDS statistics}, Year = {2003}} @other{Foundation2003a, Author = {Foundation, San Francisco AIDS}, Publisher = {Public Policy Department}, Title = {HIV/AIDS statistics}, Year = {2003}} @article{Foxman2000, Author = {Foxman, B. and Barlow, R. and D'Arcy, H. and Gillespie, B. and Sobel, J.D.}, Journal = {Annals of Epidemiology}, Notes = {urosenor}, Pages = {509--515}, Title = {Urinary tract infection: self-reported incidence and associated costs}, Volume = {10}, Year = {2000}} @article{Fredricks2001, Author = {Fredricks, D.N. and Relman, D.A.}, Journal = {Journal of Infectious Diseases}, Notes = {id}, Pages = {1299--1237}, Title = {Localization of \textit{Tropheryma whippelii} rRNA in tissues from patients with Whipple's disease}, Volume = {183}, Year = {2001}} @article{Fredricks1999, Author = {Fredricks, D.N. and Relman, D.A.}, Journal = {Clinical Infectious Dieases}, Notes = {urosensor}, Pages = {475--486}, Title = {Application of polymerase chain reaction to the diagnosis of infectious diseases}, Volume = {29}, Year = {1999}} @article{Fredricks1996, Author = {Fredricks, D.N. and Relman, D.A.}, Journal = {Clinical Microbiology Reviews}, Notes = {id}, Pages = {18--33}, Title = {Sequence-based identification of microbial pathogens: a reconsideration of Koch 's postulates}, Volume = {9}, Year = {1996}} @article{Friedman2001, Author = {Friedman, R. and Hughes, A.L.}, Journal = {Genome Research}, Notes = {tetralogy}, Pages = {1842--1847}, Title = {Pattern and timing of gene duplication in animal genomes}, Volume = {11}, Year = {2001}} @techreport{Fronk????, Author = {Fronk, E.M.}, Notes = {networks}, Title = {Model selection for DAGs via RJMCMC for the discrete and mixed case}, Year = {????}} @techreport{Fronk????a, Author = {Fronk, E.M. and Giudici, P.}, Notes = {networks}, Title = {Markov chain Monte Carlo model selection for DAG models}, Year = {????}} @article{Frost2005, Author = {Frost, S.D.W. and Wrin, T. and Smith, D.M. and Kosakovsky-Pond, S.L. and Liu, Y. and Paxinos, E. and Chappey, C. and Galovich, J. and Beauchaine, J. and Petropoulos, C.J. and Little, S.J. and Richman, D.D.}, Journal = {Proceedings of the National Academy of Sciences, USA}, Pages = {18514--18519}, Title = {Neutralizing antibody responses drive the evolution of human immunodeficiency virus type 1 envelope during recent HIV infection}, Volume = {102}, Year = {2005}} @article{Frye1995, Author = {Frye, M.S. and Hedges, S.B.}, Journal = {Molecular Biology and Evolution}, Pages = {168--176}, Title = {Monophyly of the order Rodentia inferred from mitochondrial DNA sequences of the genes for 12S ribosomal RNA, 16S ribosomal RNA and transfer RNA valine}, Volume = {12}, Year = {1995}} @article{Fryxell1996, Author = {Fryxell, K.J.}, Journal = {Trends in Genetics}, Notes = {gene families}, Pages = {364--369}, Title = {The coevolution of gene family trees}, Volume = {12}, Year = {1996}} @article{fu1994, Author = {Fu, YX}, Journal = {Genetics}, Number = {2}, Pages = {685}, Publisher = {Genetics Soc America}, Title = {{A phylogenetic estimator of effective population size or mutation rate}}, Volume = {136}, Year = {1994}} @article{Fuchs1998, Author = {Fuchs, B.M. and Wallner, G. and Beisker, W. and Schwippl, I. and Ludwig, W. and Amann, R.}, Journal = {Applied and Environmental Microbiology}, Notes = {urosenor}, Pages = {4973--4982}, Title = {Flow cytometric analysis of the in situ accessibility of Escherichia coli 16S rRNA for fluorescently labeled oligonucleotide probes}, Volume = {64}, Year = {1998}} @article{Fullerton2001, Author = {Fullerton, S.M. and Carvalho, A.B. and Clark, A.G.}, Journal = {Molecular Biology and Evolution}, Notes = {cg}, Pages = {1139--1142}, Title = {Local rates of recombination are positively correlated with GC content in the human genome}, Volume = {18}, Year = {2001}} @article{Furnival1974, Author = {Furnival, G.M. and Wilson, R.W.}, Journal = {Technometrics}, Pages = {499--511}, Title = {Regressions by Leaps and Bounds}, Volume = {16}, Year = {1974}} @article{Gabrielsson2000, Author = {Gabrielsson, J. and Jusko, W.J. and Alari, L.}, Journal = {Biopharmaceutics \& Drug Disposition}, Notes = {chang}, Pages = {41--52}, Title = {Modeling of dose-response-time data: four examples of estimating the turnover parameters and generating kinetic functions from response profiles}, Volume = {21}, Year = {2000}} @article{Ganapathy, Author = {Ganapathy, G. and Ramachandran, V. and Warnow, T.}, Notes = {HGT}, Title = {Better hill-climbing searches for parsimony}} @article{Ganeshan1997, Author = {Ganeshan, S. and Dickover, R.E. and Korber, B.T. and Bryson, Y.J. and Wolinsky, S.M.}, Journal = jv, Notes = {cr}, Pages = {663--677}, Title = {Human Immunodeficiency virus type 1 genetic evolution in children with different rates of development of disease}, Volume = {71}, Year = {1997}} @article{Garcia-Vallve2000, Author = {Garcia-Vallve, S. and Romeu, A. and Palau, J.}, Journal = {Genome Research}, Notes = {HGT}, Pages = {1719--1725}, Title = {Horizontal gene transfer in bacterial and archeal complete genomes}, Volume = {10}, Year = {2000}} @book{Gardiner2004, Address = {Berlin}, Author = {Gardiner, C. W}, Edition = {3rd ed}, Genre = {Stochastic processes}, Isbn = {3540208828 (acid-free paper)}, Library-Id = {2004043676}, Publisher = {Springer-Verlag}, Title = {Handbook of stochastic methods for physics, chemistry, and the natural sciences}, Year = {2004}} @article{Gasch2000, Author = {Gasch, A.P. and Spellman, P.T. and Kao, C.M. and Carmel-Harel, O. and Eisen, M.B. and Storz, G. and Botstein, D. and Brown, P.O.}, Journal = {Molecular Biology of the Cell}, Notes = {Yeast expression}, Pages = {4241--4257}, Title = {Genome expression programs in the response of yeast cells to environmental changes}, Volume = {11}, Year = {2000}} @article{Gaschen2002, Author = {Gaschen, B. and Taylor, J. and Yusim, K. and Foley, B. and Gao, F. and Lang, D. and Novitsky, V. and Haynes, B. and Hahn, B.H. and Bhattacharya, T. and Korber, B.}, Journal = {Science}, Pages = {2354--2360}, Title = {Diversity considerations in HIV-1 vaccine selection}, Volume = {296}, Year = {2002}} @article{Gatesy1999, Author = {Gatesy, J. and Milinkovitch, M. and Waddell, V. and Stanhope, M.}, Journal = {Systematic Biology}, Pages = {6--20}, Title = {Stability of cladistic relationships between Cetacea and higher-level Artiodactyl taxa}, Volume = {48}, Year = {1999}} @article{Gau2001, Author = {Gau, J.J. and Lan, E.H and Dunn, B. and Ho, C.M. and Woo, J.C.}, Journal = {Biosensors and Bioelectronics}, Notes = {urosensor}, Pages = {745--755}, Title = {A MEMS based amperometric detector for E. coli bacteria using self-assembled monolayers}, Volume = {16}, Year = {2001}} @article{Gaveau1996, Author = {Gaveau, B. and Moreau, M. and T{\'o}th, J.}, Date-Added = {2008-03-28 16:47:22 +1300}, Date-Modified = {2008-03-28 16:49:18 +1300}, Journal = {Lett. Math. Phys.}, Pages = {285-292}, Title = {Decay of the metastable state: different predictions between discrete and continuous models}, Volume = {37}, Year = {1996}} @article{Gebo1999, Author = {Gebo, K.A. and Chaisson, R.E. and Folkerner, J.G. and Barlett, J.G. and Moore, R.D.}, Journal = {AIDS}, Pages = {963--969}, Title = {Costs of HIV medical care in the era of highly active antiretroviral therapy}, Volume = {13}, Year = {1999}} @article{Gelfand1990, Author = {Gelfand, A.E. and Hills, S.E. and Racine-Poon, A. and Smith, A.F.M.}, Journal = {Journal of the American Statistical Association}, Pages = {972--985}, Title = {Illustration of Bayesian inference in normal data models using Gibbs sampling}, Volume = {85}, Year = {1990}} @article{Gelfand1990a, Author = {Gelfand, A.E. and Smith, A.F.M.}, Journal = {Journal of the American Statistical Association}, Pages = {398--409}, Title = {Sampling-based approaches to calculating marginal densities}, Volume = {85}, Year = {1990}} @book{Gelman2004, Address = {New York, NY}, Author = {Gelman, A. and Carlin, J.B. and Stern, H.S. and Rubin, D.B.}, Edition = {Second}, Publisher = {Chapman \& Hall/CRC}, Title = {Bayesian Data Analysis}, Year = {2004}} @book{Gelman1995, Address = {New York}, Author = {Gelman, A. and Carlin, J.B. and Stern, H.S. and Rubin, D.B.}, Publisher = {Chapman and Hall/CRC}, Title = {Bayesian Data Analysis}, Year = {1995}} @article{Gelman1996, Author = {Gelman, A. and Meng, X. and Stern, H.}, Journal = {Statistica Sinica}, Pages = {733--807}, Title = {Posterior predictive assessment of model fitness via realized discrepancies (with discussion)}, Volume = {6}, Year = {1996}} @article{Gelman2005, Author = {Gelman, A. and Meng, X.-L.}, Journal = {Statistical Sciences}, Pages = {163--185}, Title = {Simulating normalizing constants: from importance sampling to bridge sampling and path sampling}, Volume = {13}, Year = {2005}} @incollection{Gelman1996a, Address = {Oxford}, Author = {Gelman, A. and Roberts, G. O. and Gilks, W. R.}, Booktitle = {Bayesian Statistics}, Date-Modified = {2014-07-06 02:39:33 +0000}, Editor = {Bernardo, J. M. and Berger, J. O. and Dawid, A. P. and Smith, A. F. M.}, Pages = {599--608}, Publisher = {Oxford University Press}, Title = {Efficient Metropolis jumping rules}, Volume = {5}, Year = {1996}} @incollection{Gelman1992, Address = {Oxford, UK}, Author = {Gelman, A. and Rubin, D. B.}, Booktitle = {Bayesian Statistics 4}, Date-Modified = {2014-07-06 03:04:54 +0000}, Editor = {Bernardo, J. and Berger, J. O. and Dawid, J. O. and Smith, A. F. M.}, Pages = {625--631}, Publisher = {Oxford University Press}, Title = {A single series from the Gibbs sampler provides a false sense of security}, Year = {1992}} @article{Gelman1992a, Author = {Gelman, A. and Rubin, D.B.}, Journal = {Statistical Science}, Pages = {457--511}, Title = {Inference from iterative simulation using multiple sequences}, Volume = {7}, Year = {1992}} @article{Geman1984, Author = {Geman, S. and Geman, D.}, Journal = {IEEE Transactions on Pattern Analysis and Machine intelligence}, Pages = {721--741}, Title = {Stochastic relaxation, Gibbs distribution, and the Bayesian restoration of images}, Volume = {6}, Year = {1984}} @article{George1993, Author = {George, E.L. and McCulloch, R.E.}, Journal = {Journal of the American Statistical Association}, Pages = {881--889}, Title = {Variable selection via Gibbs sampling}, Volume = {88}, Year = {1993}} @article{Gerlach2000, Author = {Gerlach, R. and Carter, C. and Kohn, R.}, Journal = {Journal of the American Statistical Association}, Notes = {karen}, Pages = {819--828}, Title = {Efficient Bayesian inference for dynamic mixture models}, Volume = {95}, Year = {2000}} @incollection{Geweke1992, Address = {Oxford, UK}, Author = {Geweke, J.}, Booktitle = {Bayesian Statistics 4}, Date-Modified = {2014-07-06 02:39:16 +0000}, Editor = {Bernardo, J. and Berger, J. O. and Dawid, J. O. and Smith, A. F. M.}, Pages = {169--193}, Publisher = {Oxford University Press}, Title = {Evaluating the accuracy of sampling-based approaches to the calculation of posterior moments}, Year = {1992}} @techreport{Geweke2001, Author = {Geweke, J.}, Title = {Getting it right: checking for errors in Bayesian models and posterior simulators}, Year = {2001}} @techreport{Gewerke2001, Author = {Gewerke, J.}, Title = {Getting it right: checking for errors in Bayesian models and posterior simulators}, Year = {2001}} @article{Ghosh1995, Author = {Ghosh, M and Carlin, B.P. and Srivatava, M.S.}, Journal = {Test}, Notes = {calibration}, Pages = {333--369}, Title = {Probability matching priors for linear calibration}, Volume = {4}, Year = {1995}} @article{Gibbs2001, Author = {Gibbs, M.J. and Armstrong, J.S. and Gibbs, A.J.}, Journal = {Science}, Pages = {1842--1845}, Title = {Recombination in the hemagglutinin gene of the 1918 Spanish Flu}, Volume = {293}, Year = {2001}} @article{Gibson2000, Author = {Gibson, T.J. and Spring, J.}, Notes = {tetralogy}, Publisher = {Biochemical Society}, Title = {Evidence in favour of ancient octaploidy in the vertebrate genome}, Year = {2000}} @book{Gilks1996, Address = {New York}, Author = {Gilks, W.R. and Richardson, S. and Spiegelhalter, D.J.}, Publisher = {Chapman and Hall}, Title = {Markov Chain Monte Carlo in Practice}, Year = {1996}} @article{Gillespie1977, Author = {Gillespie, D.T.}, Date-Added = {2008-04-13 16:45:54 +1200}, Date-Modified = {2008-04-13 16:49:19 +1200}, Journal = {The Journal of Physical Chemistry}, Number = {25}, Pages = {2340-2361}, Title = {Exact Stochastic Simulation of Coupled Chemical Reactions}, Volume = {81}, Year = {1977}} @incollection{Giovannoni1996, Address = {Cambridge, UK}, Author = {Giovannoni, S.J. and Rapp{\'e}, M. and Gordon, D. and Urbach, E. and Suzuki, M. and Field, K.G.}, Booktitle = {Evolution of Microbial Life}, Editor = {Roberts, D.M. and Sharp, P. and Alderson, G. and Collins, M.A.}, Pages = {63--85}, Publisher = {Cambridge University Press}, Title = {Ribosomal RNA and the evolultion of bacterial diversity}, Year = {1996}} @article{Goffe1994, Author = {Goffe, W.L. and Ferrier, G.D. and Rogers, J.}, Journal = {Journal of Econometrics}, Pages = {65--100}, Title = {Global optimization of statistical functions with simulated annealing}, Volume = {60}, Year = {1994}} @article{Gogarten2002, Author = {Gogarten, J.P. and Doolittle, W.F. and Lawrence, J.G.}, Journal = {Molecular Biology and Evolution}, Notes = {HGT}, Pages = {2226--2238}, Title = {Prokaryotic evolution in light of gene transfer}, Volume = {19}, Year = {2002}} @book{Goldberg1989, Author = {Goldberg, D.}, Publisher = {Wesley}, Title = {Genetic Algorithms in Search, Optimization, and Machine Learning}, Year = {1989}} @article{Goldman1998, Author = {Goldman, N.}, Journal = {Proceedings of the Royal Society of London. Series B: Biological Science}, Pages = {1779--1786}, Title = {Phylogenetic information and experimental design in molecular systematics}, Volume = {265}, Year = {1998}} @article{Goldman1998a, Author = {Goldman, N.}, Journal = {BioEssays}, Notes = {alignment}, Pages = {287--290}, Title = {Effects of sequence alignment procedures on estimates of phylogeny}, Volume = {20}, Year = {1998}} @article{Goldman1993, Author = {Goldman, N.}, Journal = {Journal of Molecular Evolution}, Pages = {182--198}, Title = {Statistical tests of models of DNA substitution}, Volume = {36}, Year = {1993}} @article{Goldman1993a, Author = {Goldman, N.}, Journal = {Journal of Molecular Evolution}, Pages = {650--661}, Title = {Simple diagnostic statistical tests of models for DNA substitution}, Volume = {37}, Year = {1993}} @article{Goldman2002, Author = {Goldman, N. and Whelan, S.}, Journal = {Molecular Biology and Evolution}, Pages = {1821--1831}, Title = {A novel use of equilibrium frequencies in models of sequence evolution}, Volume = {19}, Year = {2002}} @article{Goldman1994, Author = {Goldman, N. and Yang, Z.}, Journal = {Molecular Biology and Evolution}, Pages = {725--736}, Title = {A codon-based model of nucleotide substitution for protein-coding DNA sequences}, Volume = {11}, Year = {1994}} @article{Golenberg1993, Author = {Golenberg, E.M. and Clegg, M.T. and Durbin, M.L and Doebley, J. and Ma, D.P.}, Journal = {Molecular Phylogenetic and Evolution}, Pages = {52--64}, Title = {Evolution of a noncoding region of the chloroplast genome}, Volume = {2}, Year = {1993}} @article{Gonnet1993, Author = {Gonnet, G.H. and Cohen, M.A. and Brenner, S.A.}, Journal = {Journal of Molecular Biology}, Notes = {Zipfian; alignment; indel}, Pages = {1065--1082}, Title = {Empirical and structural models for insertion and deletions in the divergent evolution of proteins}, Volume = {229}, Year = {1993}} @article{Goodnight1979, Author = {Goodnight, J.H.}, Journal = {American Statistician}, Pages = {149--158}, Title = {A tutorial on the SWEEP operator}, Volume = {33}, Year = {1979}} @article{Goonesekere2004, Author = {Goonesekere, N.C.W. and Lee, B.}, Journal = {Nucleic Acids Research}, Notes = {indel}, Pages = {2838--2843}, Title = {Frequency of gaps observed in a structurally aligned protein pair database suggests a simple penalty function}, Volume = {32}, Year = {2004}} @article{Goulder1997, Author = {Goulder, P.W. and Sewell, A.K. and Lalloo, D.G. and Price, D.A. and Whelan, J.A. and Evans, J. and Taylor, G.P. and Luzzi, G. and Giangrande, P. and Phillips, R.E. and McMichael, A.J.}, Journal = jem, Notes = {cr}, Pages = {1423--1433}, Title = {Patterns of immunodomiance in HIV-1 specific cytotoxic T lymphocyte responsed in two human histocompatability leukocyte antigens (HLA) identical siblings with HLA-A*0201 are influenced by epitope mutation}, Volume = {185}, Year = {1997}} @article{Grabar2004, Author = {Grabar, S. and Kousignian, I. and Sobel, A. and Bras, P. 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We first derive a formula for a stochastic differential equation model (canonical model) of a population with logistic growth with environmental and demographic stochasticities. We then study an approximate maximum likelihood (AML) estimate of three parameters (intrinsic growth rate r, carrying capacity K, and environmental stochasticity sigma(2)(e)) from a time series of population size. The AML estimate of r has a significant bias, but by adopting the Monte Carlo method, we can remove the bias very effectively (bias-corrected estimate). We can also determine the confidence interval of the parameter based on the Monte Carlo method. If the length of the time series is moderately long (with 40-50 data points), parameter estimation with the Monte Carlo sampling bias correction has a relatively small variance. However, if the time series is short (less than or equal to 10 data points), the estimate has a large variance and is not reliable. If we know the intrinsic growth rate r, however, the estimate of K and sigma(2)(e)and the mean extinction time T are reliable even if only a short time series is available. We illustrate the method using data for a freshwater fish, Japanese crucian carp (Carassius auratus subsp.) in Lake Biwa, in which the growth rate and environmental noise of crucian carp are estimated using fishery records.}, Address = {Department of Biology, Kyushu University, Fukuoka, 812-8581, Japan. [email protected]}, Au = {Hakoyama, H and Iwasa, Y}, Author = {Hakoyama, H and Iwasa, Y}, Ci = {Copyright 2000 Academic Press.}, Da = {20000717}, Date-Added = {2008-04-13 17:32:20 +1200}, Date-Modified = {2008-04-13 17:39:02 +1200}, Dcom = {20000717}, Doi = {10.1006/jtbi.2000.2019}, Edat = {2000/05/19 09:00}, Issn = {0022-5193 (Print)}, Jid = {0376342}, Journal = {J Theor Biol}, Jt = {Journal of theoretical biology}, Language = {eng}, Lr = {20061115}, Mh = {Animals; *Carps; *Computer Simulation; Ecology; Logistic Models; *Population Dynamics; Sensitivity and Specificity; Time Factors; Water Pollution, Chemical}, Mhda = {2000/07/25 11:00}, Number = {3}, Own = {NLM}, Pages = {337--359}, Pii = {S0022-5193(00)92019-8}, Pl = {ENGLAND}, Pmid = {10816359}, Pst = {ppublish}, Pt = {Journal article; Research Support, Non-U.S. Gov't}, Pubm = {Print}, Sb = {IM}, So = {J Theor Biol. 2000 Jun 7;204(3):337-59.}, Stat = {MEDLINE}, Title = {Extinction risk of a density-dependent population estimated from a time series of population size.}, Volume = {204}, Year = {2000}, Bdsk-Url-1 = {http://dx.doi.org/10.1006/jtbi.2000.2019}} @book{Haldane1932, Address = {London}, Author = {Haldane, J. B. S}, Call-Number = {QH366}, Date-Added = {2008-03-28 17:08:09 +1300}, Date-Modified = {2008-03-28 17:08:21 +1300}, Dewey-Call-Number = {575.01}, Genre = {Evolution (Biology)}, Library-Id = {32033284}, Publisher = {Longmans, Green and co.}, Title = {The causes of evolution}, Year = {1932}} @article{Hall2002, Author = {Hall, M.A. Leverstein-van and Box, A.T.A. and Blok, H.E.M. and Pauuw, A. and Fluit, A.C. and Verhoef, J.}, Journal = {The Journal of Infectious Diseases}, Pages = {49--56}, Title = {Evidence of extensive interspecies transfer of integron-mediated antimicrobial resistance genes among multidrug-resistant Enterobacteriaceae in a clinical setting}, Volume = {186}, Year = {2002}} @article{Hamada2003, Author = {Hamada, H. and Pohl, A. and Spiegelman, C. and Wendelberger, J.}, Journal = {Journal of Quality Technology}, Notes = {calibration}, Pages = {194--205}, Title = {A Bayesian approach to calibration intervals and properly calibrated tolerance intervals}, Volume = {35}, Year = {2003}} @article{Hamilton2003, Author = {Hamilton, M.B. and Braverman, J.M. and Soria-Hernanz, D.F.}, Journal = {Molecular Biology and Evolution}, Pages = {1710--1721}, Title = {Patterns and relative rates of nucleotide and insertion/deletion evolution in six chloroplast intergenic regions in New World species of the Lecythidaceae}, Volume = {20}, Year = {2003}} @techreport{Han2001, Author = {Han, C. and Carlin, B.P.}, Title = {MCMC methods for computing Bayes factors: a compartive review}, Year = {2001}} @article{Handt1998, Author = {Handt, O. and Meyer, S. and von Haeseler, A.}, Journal = {Nucleic Acids Research}, Pages = {126--129}, Title = {Compilation of human mtDNA control region sequences}, Volume = {26}, Year = {1998}} @article{Hanson2001, Author = {Hanson, K.M.}, Journal = {Proceedings of SPIE}, Title = {Markov chain Monte Carlo posterior sampling with the Hamiltonian method}, Year = {2001}} @article{Harding1971, Author = {Harding, E.F.}, Journal = {Advances in Applied Probability}, Notes = {tree shape}, Pages = {44--77}, Title = {The probabilities of rooted tree-shapes generated by random bifurcation}, Volume = {3}, Year = {1971}} @techreport{Hartemink????, Author = {Hartemink, A.J. and Gifford, D.K. and Jaakkola, T.S. and Young, R.A.}, Notes = {networks}, Title = {Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks}, Year = {????}} @article{Hartley2005, Author = {Hartley, O. and Klasse, P.J. and Sattentau, Q.J. and Moore, J.P.}, Journal = {AIDS Research and Human Retroviruses}, Pages = {171--189}, Title = {V3: HIV's Switch-Hitter}, Volume = {21}, Year = {2005}} @article{Harville1976, Author = {Harville, D.}, Journal = {Annals of Statistics}, Pages = {384--395}, Title = {Extension of the Gauss-Markov theorem to include the estimation of random effects}, Volume = {4}, Year = {1976}} @article{Hasegawa1992, Author = {Hasegawa, M. and Cao, Y. and Adachi, J. and Yano, T.}, Journal = {Nature}, Pages = {595}, Title = {Rodent polyphyly}, Volume = {355}, Year = {1992}} @article{Hasegawa1985, Author = {Hasegawa, M. and Kishino, H. and Yano, T.}, Journal = {Journal of Molecular Evolution}, Pages = {160--174}, Title = {Dating the human-ape splitting by a molecular clock of mitochondrial DNA}, Volume = {22}, Year = {1985}} @article{Hasegawa1993, Author = {Hasegawa, M. and Rienzo, A.D. and Kocher, T.D. and Wilson, A. C.}, Date-Modified = {2014-07-06 03:41:21 +0000}, Journal = {Journal of Molecular Evolution}, Pages = {347--354}, Title = {Toward a more accurate time scale for the human mitochondrial DNA tree}, Volume = {37}, Year = {1993}} @book{Hastie2001, Author = {Hastie, T. and Tibshirani, R. and Friedman, J.H.}, Publisher = {Springer}, Title = {The Elements of Statistical Learning}, Year = {2001}} @article{Hastings1970, Author = {Hastings, W.K.}, Journal = {Biometrika}, Pages = {97--109}, Title = {Monte Carlo sampling methods using Markov chains and their applications}, Volume = {57}, Year = {1970}} @article{Hayasaka1988, Author = {Hayasaka, K. and Gojobori, K.T. and Horai, S.}, Journal = {Molecular Biology and Evolution}, Pages = {626--644}, Title = {Molecular phylogeny and evolution of primate mitochondrial DNA}, Volume = {5}, Year = {1988}} @article{He2007, Abstract = {Seasonal oscillations in birth rates are ubiquitous in human populations. These oscillations might play an important role in infectious disease dynamics because they induce seasonal variation in the number of susceptible individuals that enter populations. We incorporate seasonality of birth rate into the standard, deterministic susceptible-infectious-recovered (SIR) and susceptible-exposed-infectious-recovered (SEIR) epidemic models and identify parameter regions in which birth seasonality can be expected to have observable epidemiological effects. The SIR and SEIR models yield similar results if the infectious period in the SIR model is compared with the infected period (the sum of the latent and infectious periods) in the SEIR model. For extremely transmissible pathogens, large amplitude birth seasonality can induce resonant oscillations in disease incidence, bifurcations to stable multi-year epidemic cycles, and hysteresis. Typical childhood infectious diseases are not sufficiently transmissible for their asymptotic dynamics to be likely to exhibit such behaviour. However, we show that fold and period-doubling bifurcations generically occur within regions of parameter space where transients are phase-locked onto cycles resembling the limit cycles beyond the bifurcations, and that these phase-locking regions extend to arbitrarily small amplitude of seasonality of birth rates. Consequently, significant epidemiological effects of birth seasonality may occur in practice in the form of transient dynamics that are sustained by demographic stochasticity.}, Address = {Department of Mathematics and Statistics, McMaster University, Hamilton, Ont., Canada L8S 4K1. [email protected]}, Au = {He, D and Earn, DJ}, Author = {He, Daihai and Earn, David J D}, Da = {20070813}, Date-Added = {2008-04-13 17:20:00 +1200}, Date-Modified = {2008-04-13 17:23:48 +1200}, Dcom = {20071120}, Dep = {20070507}, Doi = {10.1016/j.tpb.2007.04.004}, Edat = {2007/06/26 09:00}, Issn = {0040-5809 (Print)}, Jid = {0256422}, Journal = {Theor Popul Biol}, Jt = {Theoretical population biology}, Language = {eng}, Mh = {*Birth Rate; Canada/epidemiology; Communicable Diseases/*epidemiology; Disease Progression; Disease Susceptibility; Humans; Models, Statistical; *Seasons; Sentinel Surveillance}, Mhda = {2007/12/06 09:00}, Number = {2}, Own = {NLM}, Pages = {274--291}, Pii = {S0040-5809(07)00041-X}, Pl = {United States}, Pmid = {17588629}, Pst = {ppublish}, Pt = {Journal article}, Pubm = {Print-Electronic}, Sb = {IM}, So = {Theor Popul Biol. 2007 Sep;72(2):274-91. Epub 2007 May 7.}, Stat = {MEDLINE}, Title = {Epidemiological effects of seasonal oscillations in birth rates.}, Volume = {72}, Year = {2007}, Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.tpb.2007.04.004}} @article{Heckman2000, Author = {Heckman, N.E. and Ramsay, J.O.}, Journal = {Canadian Journal of Statistics}, Notes = {expression}, Pages = {241--258}, Title = {Penalized regression with model-based penalties}, Volume = {28}, Year = {2000}} @article{Hedges1990, Author = {Hedges, S.B. and Moberg, K.D. and Maxson, L.R.}, Journal = {Molecular Biology and Evolution}, Notes = {alignment; rRNA}, Pages = {607--633}, Title = {Tetrapod phylogeny inferred from 18S and 28S ribosomal RNA sequences and a review of the evidence for Amniote relationships}, Volume = {7}, Year = {1990}} @article{Heiberger1978, Author = {Heiberger, R. M.}, Date-Modified = {2014-07-06 02:40:44 +0000}, Journal = {Applied Statistics}, Pages = {199--206}, Title = {Algorithm AS 127. 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Garcia and Ferreros, I. and del Amo, J. and de Olalla, P. Garcia and Hoyos, S. Perez and Muga, R. and del Romero, J. and Guerrero, R. and I, I. 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This linkage is useful because, while the dynamical and population genetic theories have developed independently, the biological processes they describe are completely interrelated. Parameters of the dynamical models are important determinants of evolutionary processes such as natural selection and genetic drift. We develop analytical methods, based on coupled differential equations and Markov chain theory, to predict the accumulation of genetic diversity within the viral population as a function of dynamical parameters. These methods are first applied to the standard model of viral dynamics and then generalized to consider the infection of multiple host cell types by the viral population. Each cell type is characterized by specific parameter values. Inclusion of multiple cell types increases the likelihood of persistent infection and can increase the amount of genetic diversity within the viral population. However, the overall rate of gene sequence evolution may actually be reduced.}, Address = {Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045, USA. [email protected]}, Au = {Kelly, JK and Williamson, S and Orive, ME and Smith, MS and Holt, RD}, Author = {Kelly, John K and Williamson, Scott and Orive, Maria E and Smith, Marilyn S and Holt, Robert D}, Da = {20030711}, Date-Added = {2008-04-13 17:03:57 +1200}, Date-Modified = {2008-04-13 17:04:30 +1200}, Dcom = {20031009}, Dep = {20030612}, Edat = {2003/07/12 05:00}, Gr = {1 R01 GM60792-01A1/GM/United States NIGMS}, Issn = {0003-0147 (Print)}, Jid = {2984688R}, Journal = {Am Nat}, Jt = {The American naturalist}, Language = {eng}, Lr = {20071114}, Mh = {Evolution; *Genetics, Population; Markov Chains; *Models, Biological; Variation (Genetics); Virus Diseases/*genetics}, Mhda = {2003/10/10 05:00}, Number = {1}, Own = {NLM}, Pages = {14--28}, Pii = {AN020270}, Pl = {United States}, Pmid = {12856234}, Pst = {ppublish}, Pt = {Journal article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, P.H.S.}, Pubm = {Print-Electronic}, Sb = {IM}, So = {Am Nat. 2003 Jul;162(1):14-28. Epub 2003 Jun 12.}, Stat = {MEDLINE}, Title = {Linking dynamical and population genetic models of persistent viral infection.}, Volume = {162}, Year = {2003}} @article{Kemal2003, Author = {Kemal, K.S. and Foley, B. and Burger, H. and Anastos, K. and Minkoff, H. and Kitchen, C. and Philpott, S.M. and Gao, W. and Robison, E. and Holman, S. and Dehner, C. and Beck, S. and Meyer, W.A. and Landay, A. and Kovacs, A. and Bremer, J. and Weiser, B.}, Journal = {Proceedings of the National Academy of Sciences, USA}, Pages = {12972--12977}, Title = {HIV-1 in genital tract and plasma of women: compartmentalization of viral sequences, coreceptor usage and glycosylation}, Volume = {100}, Year = {2003}} @article{Kerr2001, Author = {Kerr, M.K. and Churchill, G.A.}, Journal = {Proceedings of the National Academies of Science, USA}, Notes = {yeast expression}, Pages = {8961--8965}, Title = {Bootstrapping cluster analysis: assessing the reliability of conclusions from microarray experiments}, Volume = {98}, Year = {2001}} @article{Kijak2002, Author = {Kijak, G.H. and Simon, V. and Balfe, P. and Vanderhoeven, J. and Pampuro, S.E. and Zala, C. and Ochoa, C. and Cahn, P. and Markowitz, M. and Salomon, H.}, Journal = {Journal of Virology}, Pages = {7000-7009}, Title = {Origin of human immunodeficiency virus type 1 quasispecies emerging after antiretroviral treatment interruption in patients with therapeutic failure}, Volume = {76}, Year = {2002}} @article{Killian2001, Author = {Killian, J.K. and Buckley, T.R. and Stewart, N. and Munday, B.L. and Jirtle, R.L.}, Journal = {Mammalian Genetics}, Keywords = {hierarchical}, Pages = {513--517}, Title = {Marsupials and Eutherians reunited: genetic evidence for the Theria hypothesis of mammalian evolution}, Volume = {12}, Year = {2001}} @article{Kim2000, Author = {Kim, C.B. and Amemiya, C. and Bailey, W. and Kawasaki, K. and Mezey, J. and Miller, W. and Minoshima, S. and Shimizu, N. and Wagner, G. and Ruddle, F.}, Journal = {PNAS}, Notes = {hox phylogeny, tetralogy}, Pages = {1655--1660}, Title = {Hox cluster genomics in the horn shark, Heterodontus francisci}, Volume = {97}, Year = {2000}} @article{Kimura1980, Author = {Kimura, M.}, Journal = {Journal of Molecular Evolution}, Pages = {111--120}, Title = {A simple model for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences}, Volume = {16}, Year = {1980}} @article{King1975, Author = {King, M. C. and Wilson, A. C.}, Date-Modified = {2014-07-06 03:42:51 +0000}, Journal = {Science}, Notes = {107--116}, Title = {Evolution at two levels in humans and chimpanzees}, Volume = {188}, Year = {1975}} @article{Kingman2000, Author = {Kingman, J.F.C.}, Journal = {Genetics}, Pages = {1461--1463}, Title = {Origins of the coalescent: 1974-1982}, Volume = {156}, Year = {2000}} @article{Kirkpatrick1993, Author = {Kirkpatrick, M. and Slatkin, M.}, Journal = {Evolution}, Notes = {tree shape}, Pages = {1171--1181}, Title = {Searching for evolutionary patterns in the shape of a phylogenetic tree}, Volume = {47}, Year = {1993}} @article{Kirkpatrick1983, Author = {Kirkpatrick, S. and Gelatt, C.D. and Wecci, M.P.}, Journal = {Science}, Pages = {671--680}, Title = {Optimization by simulated annealing}, Volume = {220}, Year = {1983}} @article{Kitchen2004, Author = {Kitchen, C. M. R. and Philpott, S. and Burger, H. and Weiser, B. and Suchard, M. A.}, Date-Modified = {2014-07-06 02:34:27 +0000}, Journal = {Journal of Virology}, Pages = {11296--11302}, Title = {Bayesian analysis of viral evolution: shared patterns in HIV-1 coreceptor utilization during antiretroviral therapy}, Volume = {78}, Year = {2004}} @article{Kitcheninpress, Author = {Kitchen, C. M. R. and Suchard, M. A. and Liu, J. and Hoh, R. and Kuritzkes, D. and Deeks, S. G.}, Date-Modified = {2014-07-06 02:33:43 +0000}, Journal = {AIDS Research and Human Retroviruses}, Title = {Continued evolution in \textit{gp41} after interruption of enfuviritide in patients with advanced HIV disease}, Year = {in press}} @article{Kjems1991, Author = {Kjems, J. and Brown, M. and Chang, D. and Sharp, S.}, Journal = {Proceedings of the National Academy of Sciences, USA}, Pages = {683-687}, Title = {Structural analysis of the interaction between the human immunodeficiency virus Rev protein and the Rev response element}, Volume = {88}, Year = {1991}} @article{Klevytska2002, Author = {Klevytska, A.M. and Miracna, M.R. and Guay, L. and Becker-Pergola, G. and Furtado, M. and Zhang, L. and Jackson, J.B. and Eshleman, S.H.}, Journal = {AIDS Research and Human Retroviruses}, Pages = {791--796}, Title = {Analysis of length variation in the V1-V2 region of \textit{env} in nonsubtype B HIV type 1 from Uganda}, Volume = {18}, Year = {2002}} @article{Kluge1989, Author = {Kluge, A.G.}, Journal = {Systematic Zoology}, Pages = {7--25}, Title = {A concern for evidence and a phylogenetic hypothesis of relationships among \textit{Epicates} (Boidae, Serpentes)}, Volume = {38}, Year = {1989}} @article{Knorr-Held2002, Author = {Knorr-Held, L. and Rue, H.}, Journal = {Scandinavian Journal of Statistics}, Pages = {597-614}, Title = {On block updating in Markov random field models for disease mapping}, Volume = {29}, Year = {2002}} @article{Kolzsch2007, Abstract = {1. During the last centuries, the breeding range of the great snipe Gallinago media has declined dramatically in the western part of its distribution. To examine present population dynamics in the Scandinavian mountains, we collected and analysed a 19-year time series of counts of great snipe males at leks in central Norway, 1987-2005. 2. The population showed large annual fluctuations in the number of males displaying at lek sites (range 45-90 males at the peak of the mating season), but no overall trend. 3. We detected presence of direct density-dependent mechanisms regulating this population. Inclusion of the density-dependent term in a Ricker-type model significantly improved the fit with observed data (evaluated with Parametric Bootstrap Likelihood Ratio tests and Akaike's Information Criterion for small sample size). 4. An analysis of (a number of a priori likely) environmental covariates suggests that the population dynamics were affected by conditions influencing reproduction and survival of offspring during the summer, but not by conditions influencing survival at the wintering grounds in Africa. This is in contrast to many altricial birds breeding in the northern hemisphere, and supports the idea that population dynamics of migratory nidifugous birds are more influenced by conditions during reproduction. 5. Inclusion of these external factors into our model improved the detectability of density dependence. This illustrates that allowing for external effects may increase statistical power of density dependence tests and thus be of particular importance in relatively short time series. 6. In our best model of the population dynamics, two likely density-independent offspring survival covariates explained 47.3% of the variance in great snipe numbers (predation pressure estimated by willow grouse reproductive success and food availability estimated by the amount of precipitation in June), whereas density dependence explained 35.5%. Demographic stochasticity and unidentified environmental stochasticity may account for the remaining 17.2%.}, Address = {Department of Physics, AGNLD, University of Potsdam, Am Neuen Palais 10, 14469 Potsdam, Germany. [email protected]}, Au = {Kolzsch, A and Saether, SA and Gustafsson, H and Fiske, P and Hoglund, J and Kalas, JA}, Author = {Kolzsch, Andrea and Saether, Stein Are and Gustafsson, Henrik and Fiske, Peder and Hoglund, Jacob and Kalas, John Atle}, Da = {20070622}, Date-Added = {2008-04-13 17:20:00 +1200}, Date-Modified = {2008-04-13 17:24:54 +1200}, Dcom = {20070925}, Doi = {10.1111/j.1365-2656.2007.01246.x}, Edat = {2007/06/23 09:00}, Issn = {0021-8790 (Print)}, Jid = {0376574}, Journal = {J Anim Ecol}, Jt = {The Journal of animal ecology}, Language = {eng}, Mh = {Animal Migration/*physiology; Animals; *Breeding; Charadriiformes/growth \& development/*physiology; Environment; Female; Male; Norway; Population Density; Population Dynamics; *Predatory Behavior; Seasons; Sex Ratio; Stochastic Processes}, Mhda = {2007/09/26 09:00}, Number = {4}, Own = {NLM}, Pages = {740--749}, Pii = {JAE1246}, Pl = {England}, Pmid = {17584380}, Pst = {ppublish}, Pt = {Journal article; Research Support, Non-U.S. Gov't}, Pubm = {Print}, Sb = {IM}, So = {J Anim Ecol. 2007 Jul;76(4):740-9.}, Stat = {MEDLINE}, Title = {Population fluctuations and regulation in great snipe: a time-series analysis.}, Volume = {76}, Year = {2007}, Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.1365-2656.2007.01246.x}} @article{Kong2003, Author = {Kong, A. and McCullagh, P. and Meng, X.-L. and Nicolae, D. and Tan, Z.}, Journal = {Journal of the Royal Statistical Society, Series B}, Pages = {585-618}, Title = {A theory of statistical models for Monte Carlo integration}, Volume = {65}, Year = {2003}} @article{Koonin2001, Author = {Koonin, E.V. and Makarova, K.S. and Aravind, L.}, Journal = {Annual Review of Microbiology}, Notes = {HGT}, Pages = {709--742}, Title = {Horizontal gene transfer in prokaryotes: quantification and classification}, Volume = {55}, Year = {2001}} @incollection{Korber1998, Address = {Los Alamos, NM}, Author = {Korber, B.T. and Foley, B.T. and Kuiken, C.L. and Pillai, S.K. and Sodroski, J.G.}, Booktitle = {Human Retroviruses and AIDS 1998}, Editor = {Korber, B. and Kuiken, C. and Foley, B. and Hahn, B. and McCutchan, F. and Mellors, J. and Sodroski, J.}, Pages = {102--111}, Publisher = {Theoretical Biology and Biophysics Group, Los Alamos National Laboratory}, Title = {Numbering positions in HIV relative to HXB2}, Year = {1998}} @article{Korber2001, Author = {Korber, B. and Gaschen, B. and Yusim, K. and Thakallapally, R. and Kesmir, C. and Detours, V.}, Journal = {British Medical Bulletin}, Pages = {19--42}, Title = {Evolutionary and immunological implications of contemporary HIV-1 variation}, Volume = {58}, Year = {2001}} @article{Korber1998a, Author = {Korber, B.T. and Theiler, J. and Wolinsky, S.}, Journal = sc, Notes = {cr}, Pages = {1868--1871}, Title = {Limitations of a Molecular clock to the considerations of the origin of HIV-1}, Volume = {280}, Year = {1998}} @article{Koski2001, Author = {Koski, L.B. and Golding, G.B.}, Journal = {Journal of Molecular Evolution}, Pages = {587--599}, Title = {The closest BLAST hit is often not the nearest neighbor}, Volume = {52}, Year = {2001}} @article{Koski2001a, Author = {Koski, L.B. and Morton, R.A. and Golding, G.B.}, Journal = {Molecular Biology and Evolution}, Notes = {HGT}, Pages = {404--412}, Title = {Codon bias and base composition are poor indicators of horizontally transferred genes}, Volume = {18}, Year = {2001}} @article{Kotsopoulou2000, Author = {Kotsopoulou, E. and Kim, V.N. and Kingsman, A.J. and Kingsman, S.M. and Mitrophanous, K.A.}, Journal = {Journal of Virology}, Pages = {4839--4852}, Title = {A Rev-independent human immunodeficiency virus type 1 (HIV-1)-based vector that exploits a codon-optimized HIV-1 gag-pol gene}, Volume = {74}, Year = {2000}} @article{Kramers1940, Author = {Kramers, H.A.}, Date-Added = {2008-03-28 16:39:47 +1300}, Date-Modified = {2008-03-28 16:40:33 +1300}, Journal = {Physica}, Number = {4}, Pages = {284-304}, Title = {Brownian motion in a field of force and the diffusion model of chemical reactions}, Volume = {7}, Year = {1940}} @article{Kroes1999, Author = {Kroes, I. and Lepp, P.W. and Relman, D.A.}, Journal = {PNAS}, Pages = {14547--14552}, Title = {Bacterial diversity within the human subgingival crevice}, Volume = {96}, Year = {1999}} @article{Krone1997, Author = {Krone, S.M. and Neuhauser, C.}, Journal = {Theoretical Population Biology}, Pages = {210--237}, Title = {Ancestral processes with selection}, Volume = {51}, Year = {1997}} @article{Kuhner1994, Author = {Kuhner, M. K. and Felsenstein, J.}, Date-Modified = {2014-07-06 01:58:23 +0000}, Journal = {Molecular Biology and Evolution}, Pages = {459--468}, Title = {A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates}, Volume = {11}, Year = {1994}} @article{Kuhner1998, Author = {Kuhner, M. K. and Yamato, J. and Felsenstein, J.}, Date-Modified = {2014-07-06 01:57:54 +0000}, Journal = {Genetics}, Pages = {429--434}, Title = {Maximum likelihood estimation of population growth rates based on the coalescent}, Volume = {149}, Year = {1998}} @article{kuhner2000, Author = {Kuhner, M. K. and Yamato, J. and Felsenstein, J.}, Date-Modified = {2014-07-06 01:35:36 +0000}, Journal = {Genetics}, Number = {3}, Pages = {1393}, Publisher = {Genetics Soc America}, Title = {{Maximum likelihood estimation of recombination rates from population data}}, Volume = {156}, Year = {2000}} @article{Kuhner1995, Author = {Kuhner, M. K. and Yamato, J. and Felsenstein, J.}, Date-Modified = {2014-07-06 01:58:04 +0000}, Journal = {Genetics}, Pages = {1421--1430}, Title = {Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling}, Volume = {140}, Year = {1995}} @article{Kuo1998, Author = {Kuo, L. and Mallick, B.}, Journal = {Sankhya B}, Notes = {model selection}, Pages = {65--81}, Title = {Variable selection for regression models}, Volume = {60}, Year = {1998}} @techreport{Kuo1998a, Author = {Kuo, L. and Mallick, B.}, Notes = {model selection}, Title = {Variable selection for regression models}, Year = {1998}} @article{Kuwata1997, Author = {Kuwata, T. and Miyazaki, Y. and Igarashi, T. and Takehisa, J. and Hayami, M.}, Journal = {Journal of Virology}, Pages = {7088--7091}, Title = {The rapid spread of recombinants during a natural in vitro infection with two human immunodeficiency virus type 1 strains}, Volume = {71}, Year = {1997}} @article{Ladoukakis2001, Author = {Ladoukakis, E.D. and Zouros, E.}, Journal = {Molecular Biology and Evolution}, Pages = {1168--1175}, Title = {Direct evidence for homologous recombination in Mussel (\textit{Mytilus galloprovincialis}) mitochondrial DNA}, Volume = {18}, Year = {2001}} @article{Ladoukakis2001a, Author = {Ladoukakis, E.D. and Zouros, E.}, Journal = {Molecular Biology and Evolution}, Pages = {2127--2131}, Title = {Recombination in animal mitochondrial DNA: evidence from published sequences}, Volume = {18}, Year = {2001}} @article{Lahn1997, Author = {Lahn, B.T. and Page, D.C.}, Journal = {Science}, Pages = {675--680}, Title = {Functional coherence of the human Y chromosome}, Volume = {278}, Year = {1997}} @article{Lai1992, Author = {Lai, M.M.C.}, Journal = {Microbiol Review}, Pages = {61-79}, Title = {RNA recombination in animal and plan viruses}, Volume = {56}, Year = {1992}} @article{Laird1978, Author = {Laird, N.}, Journal = {Journal of the American Statistical Association}, Pages = {805--811}, Title = {Nonparametric maximum likelihood estimation of a mixture distribution}, Volume = {73}, Year = {1978}} @article{Laird1982, Author = {Laird, N.M. and Ware, J.H.}, Journal = {Biometrics}, Pages = {963--974}, Title = {Random-effects models for longitudinal data}, Volume = {38}, Year = {1982}} @article{Lake1998, Author = {Lake, J.A.}, Journal = {Molecular Biology and Evolution}, Pages = {1224--1231}, Title = {Optimally recovering rate variation information from genomes and sequences: pattern filtering}, Volume = {15}, Year = {1998}} @article{Lake1994, Author = {Lake, J.A.}, Journal = {PNAS, USA}, Pages = {1455--1459}, Title = {Reconstructing evolutionary trees from DNA and protein sequences: paralinear distances}, Volume = {91}, Year = {1994}} @article{Lake1991, Author = {Lake, J.A.}, Journal = {Molecular Biology and Evolution}, Notes = {alignment}, Pages = {378--385}, Title = {The order of sequence alignment can bias the selection of tree topology}, Volume = {8}, Year = {1991}} @article{Lake1988, Author = {Lake, J.A.}, Journal = {Nature}, Pages = {184--186}, Title = {Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences}, Volume = {331}, Year = {1988}} @article{Lake1987, Author = {Lake, J.A.}, Journal = {Molecular Biology and Evolution}, Pages = {167--191}, Title = {A rate-independent technique for analysis of nucleic acid sequences: evolutionary parsimony}, Volume = {4}, Year = {1987}} @incollection{Lake1996, Address = {Cambridge, UK}, Author = {Lake, J.A. and Rivera, M.C.}, Booktitle = {Evolution of Microbial Life}, Editor = {Roberts, D.M. and Sharp, P. and Alderson, G. and Collins, M.A.}, Pages = {87--108}, Publisher = {Cambridge University Press}, Title = {The prokaryotic ancestry of eukaryotes}, Year = {1996}} @article{Lambert2006, Abstract = {We link two-allele population models by Haldane and Fisher with Kimura's diffusion approximations of the Wright-Fisher model, by considering continuous-state branching (CB) processes which are either independent (model I) or conditioned to have constant sum (model II). Recent works by the author allow us to further include logistic density-dependence (model III), which is ubiquitous in ecology. In all models, each allele (mutant or resident) is then characterized by a triple demographic trait: intrinsic growth rate r, reproduction variance sigma and competition sensitivity c. Generally, the fixation probability u of the mutant depends on its initial proportion p, the total initial population size z, and the six demographic traits. Under weak selection, we can linearize u in all models thanks to the same master formula u = p + p(1-p )g(r)s(r) + g(sigma)s(sigma) + g(c)s(c) + o(s(r), s(sigma) s(c)), where s(r) = r' - r, s(sigma) = sigma - sigma' and s(c) = c - c' are selection coefficients, and g(r), g(sigma), g(c) are invasibility coefficients (' refers to the mutant traits), which are positive and do not depend on p. In particular, increased reproduction variance is always deleterious. We prove that in all three models g(sigma) = 1/sigma and g(r) = z/sigma for small initial population sizes z. In model II, g(r) = z/sigma for all z, and we display invasion isoclines of the 'mean vs variance' type. A slight departure from the isocline is shown to be more beneficial to alleles with low u than with high r. In model III, g(c) increases with z like ln(z)/c, and g(r)(Z) converges to a finite limit L > K/sigma, where K = r/c is the carrying capacity. For r > 0 the growth invasibility is above z/sigma when z < K, and below z/sigma when z > K, showing that classical models I and II underestimate the fixation probabilities in growing populations, and overestimate them in declining populations. (c) 2006 Elsevier Inc. All rights reserved.}, Author = {Lambert, A}, Date-Added = {2008-03-28 15:44:55 +1300}, Date-Modified = {2008-03-28 15:45:00 +1300}, Doi = {DOI 10.1016/j.tpb.2006.01.002}, Journal = {Theoretical Population Biology}, Keywords = {continuous-state branching process; diffusion theory; fixation probability; demographic stochasticity; mutant allele; mean-variance trade-off; weak selection}, Pages = {419-441}, Timescited = {0}, Title = {Probability of fixation under weak selection: A branching process unifying approach}, Volume = {69}, Year = {2006}, Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.tpb.2006.01.002}} @article{Lambert2005, Abstract = {In order to model random density-dependence in population dynamics, we construct the random analogue of the well-known logistic process in the branching process' framework. This density-dependence corresponds to intraspecific competition pressure, which is ubiquitous in ecology, and translates mathematically into a quadratic death rate. The logistic branching process, or LB-process, can thus be seen as (the mass of) a fragmentation process (corresponding to the branching mechanism) combined with constant coagulation rate (the death rate is proportional to the number of possible coalescing pairs). In the continuous state-space setting, the LB-process is a time-changed (in Lamperti's fashion) Ornstein-Uhlenbeck type process. We obtain similar results for both constructions: when natural deaths do not occur, the LB-process converges to a specified distribution; otherwise, it goes extinct a.s. In the latter case, we provide the expectation and the Laplace transform of the absorption time, as a functional of the solution of a Riccati differential equation. We also show that the quadratic regulatory term allows the LB-process to start at infinity, despite the fact that births occur infinitely often as the initial state goes to \&INFIN;. This result can be viewed as an extension of the pure-death process starting from infinity associated to Kingman's coalescent, when some independent fragmentation is added.}, Author = {Lambert, A}, Date-Added = {2008-03-28 15:43:33 +1300}, Date-Modified = {2008-03-28 15:44:07 +1300}, Journal = {Annals of Applied Probability}, Keywords = {stochastic logistic; size-dependent branching process; continuous-state branching process; population dynamics; logistic process; density dependence; Ornstein-Uhlenbeck type process; Riccati differential equation; fragmentation-coalescence process}, Pages = {1506-1535}, Timescited = {0}, Title = {The branching process with logistic growth}, Volume = {15}, Year = {2005}} @article{Lanave2000, Author = {Lanave, C. and Liuni, S. and Licciulli, F. and Attimonelli, M.}, Journal = {Nucleic Acids Research}, Pages = {153--154}, Title = {Update of AMmtDB: a databsae of multi-aligned Metazoa mitochondrial DNA sequences}, Volume = {28}, Year = {2000}} @article{Lanave1984, Author = {Lanave, C. and Preparata, G. and Saccone, C. and Serio, G.}, Journal = {Journal of Molecular Evolution}, Pages = {86--93}, Title = {A new method for calculating evolutionary substitution rates}, Volume = {20}, Year = {1984}} @article{Lanciotti1997, Author = {Lanciotti, R.S. and Gubler, D.J. and Trent, D.W.}, Journal = {Journal of General Virology}, Notes = {molecular clock}, Pages = {2279--2286}, Title = {Molecular evolution and phylogeny of dengue-4 viruses}, Volume = {78}, Year = {1997}} @article{Lande1993, Abstract = {Stochastic factors affecting the demography of a single population are analyzed to determine the relative risks of extinction from demographic stochasticity, environmental stochasticity, and random catastrophes. Relative risks are assessed by comparing asymptotic scaling relationships describing how the average time to extinction, T, increases with the carrying capacity of a population, K, under each stochastic factor alone. Stochastic factors are added to a simple model of exponential growth up to K. A critical parameter affecting the extinction dynamics is r, the long-run growth rate of a population below K, including stochastic factors. If r is positive, with demographic stochasticity T increases asymptotically as a nearly exponential function of K, and with either environmental stochasticity or random catastrophes T increases asymptotically as a power of K. If r is negative, under any stochastic demographic factor, T increases asymptotically with the logarithm of K. Thus, for sufficiently large populations, the risk of extinction from demographic stochasticity is less important than that from either environmental stochasticity or random catastrophes. The relative risks of extinction from environmental stochasticity and random catastrophes depend on the mean and environmental variance of population growth rate, and the magnitude and frequency of catastrophes. Contrary to previous assertions in the literature, a population of modest size subject to environmental stochasticity or random catastrophes can persist for a long time, if r is substantially positive.}, Author = {Lande, R}, Date-Added = {2008-03-28 15:41:38 +1300}, Date-Modified = {2008-05-23 11:10:25 +1200}, Journal = {American Naturalist}, Pages = {911-927}, Timescited = {0}, Title = {Risks of Population Extinction from Demographic and Environmental Stochasticity and Random Catastrophes}, Volume = {142}, Year = {1993}} @article{Lang2004, Author = {Lang, S. and Brezger, A.}, Journal = {Journal of Computational and Graphical Statistics}, Pages = {183--212}, Title = {Bayesian P-splines}, Volume = {13}, Year = {2004}} @book{Lange2003, Address = {New York}, Author = {Lange, K.}, Publisher = {Springer}, Series = {Springer Texts in Statistics}, Title = {Applied Probability}, Year = {2003}} @book{Lange1999, Address = {New York}, Author = {Lange, K.}, Publisher = {Springer}, Title = {Numerical Analysis for Statisticians}, Year = {1999}} @book{Lange1997, Address = {New York}, Author = {Lange, K.}, Publisher = {Springer}, Title = {Mathematical and Statistical Methods for Genetic Analysis}, Year = {1997}} @article{Lapointe1992, Author = {Lapointe, F.J. and Legendre, P.}, Journal = {Systematic Biology}, Pages = {158--171}, Title = {A statistical framework to test the consensus among additive trees (cladograms)}, Volume = {41}, Year = {1992}} @article{Larder1995, Author = {Larder, B.}, Journal = aidshr, Notes = {cr}, Pages = {S28--S33}, Title = {Viral Resistance and the selection of anti-retroviral mutants}, Volume = {10}, Year = {1995}} @article{Larget1999, Author = {Larget, B. and Simon, D.L.}, Journal = {Molecular Biology and Evolution}, Pages = {750--759}, Title = {Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees}, Volume = {16}, Year = {1999}} @article{Laroche1999, Author = {Laroche, J. and Bousquet, J.}, Journal = {Molecular 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and discrimination}, Volume = {20}, Year = {1992}} @article{Lawrence1993, Author = {Lawrence, C.E. and Altschul, S.F. and Boguski, M.S. and Liu, J.S. and Neuwald, A.F. and Wootton, J.C.}, Journal = {Science}, Notes = {alignment}, Pages = {208--214}, Title = {Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment}, Volume = {262}, Year = {1993}} @article{Lawrence1999, Author = {Lawrence, J.G.}, Journal = {Current Opinions in Microbiology}, Notes = {HGT}, Pages = {519--523}, Title = {Gene transfer, speciation and the evolution of bacterial genomes}, Volume = {2}, Year = {1999}} @article{Lawrence2003, Author = {Lawrence, J. and Mayers, D.L. and Hullsiek, K.H. and Collins, G. and Abrams, D.I. and Reisler, R.B. and Crane, L.R. and Schmetter, B.S. and Dionne, T.J. and Saldanha, J.M. and Jones, M.C. and Baxter, J.D and of the Terry Beirn Community Programs for Clinical Research on AIDS, 064 Study Team}, Journal = {New England Journal of Medicine}, Pages = 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Techniques which can be used to estimate the magnitude of this stochastic effect are of clear importance. In this study, we assess and compare the use of two moment closure approximations to estimate the variability seen about the average behavior of stochastic models for the recurrent epidemics seen in childhood diseases. The performance of the approximations are assessed using analytic techniques available for the simplest epidemiological model and using numerical simulations in more complex settings. We also present epidemiologically important extensions of previous work, considering variability in the SEIR model and in situations for which there is seasonal variation in disease transmission. Important implications of stochastic effects for the dynamics of childhood diseases are highlighted, including serious deficiencies of deterministic descriptions of dynamical behavior.}, Address = {Program in Theoretical Biology, Institute for Advanced Study, Einstein Drive, Princeton, NJ 08540, USA. [email protected]}, Au = {Lloyd, AL}, Author = {Lloyd, Alun L}, Da = {20031203}, Date-Added = {2008-04-13 17:32:20 +1200}, Date-Modified = {2008-04-13 17:34:46 +1200}, Dcom = {20040310}, Edat = {2003/12/04 05:00}, Issn = {0040-5809 (Print)}, Jid = {0256422}, Journal = {Theor Popul Biol}, Jt = {Theoretical population biology}, Language = {eng}, Lr = {20061115}, Mh = {Demography; *Disease Outbreaks; Humans; *Models, Theoretical; *Population Dynamics; Recurrence; Seasons; Stochastic Processes}, Mhda = {2004/03/11 05:00}, Number = {1}, Own = {NLM}, Pages = {49--65}, Pii = {S0040580903001175}, Pl = {United States}, Pmid = {14642344}, Pst = {ppublish}, Pt = {Journal article; Research Support, Non-U.S. Gov't}, Pubm = {Print}, Sb = {IM}, So = {Theor Popul Biol. 2004 Feb;65(1):49-65.}, Stat = {MEDLINE}, Title = {Estimating variability in models for recurrent epidemics: assessing the use of moment closure techniques.}, Volume = {65}, Year = {2004}} @article{Loftsgaarden1965, Author = {Loftsgaarden, D.O. and Quesenberry, C.P.}, Journal = {The Annals of Mathematical Statistics}, Pages = {1049--1051}, Title = {A nonparametric estimate of a multivariate density function}, Volume = {36}, Year = {1965}} @article{Lopes2004, Author = {Lopes, H.F. and West, M.}, Journal = {Statistica Sinica}, Pages = {41--67}, Title = {Bayesian model assessment in factor analysis}, Volume = {14}, Year = {2004}} @article{Lopez1999, Author = {Lopez, F.A. and Manglicmot, J. and Schmidt, T.M. and Yeh, C. and Smith, H.V.}, Journal = {The Journal of Infectious Diseases}, Notes = {id}, Pages = {670--676}, Title = {Molecular characterization of \textit{Cylospora}-like organisms from baboons}, Volume = {179}, Year = {1999}} @article{loreille2001, Author = {Loreille, O. and Orlando, L. and Patou-Mathis, M. and Philippe, M. and Taberlet, P. and H{\"a}nni, C.}, Date-Modified = {2012-05-20 11:53:04 +1200}, Journal = {Current Biology}, Number = {3}, Pages = {200--203}, Publisher = {Elsevier}, Title = {{Ancient DNA analysis reveals divergence of the cave bear, Ursus spelaeus, and brown bear, Ursus arctos, lineages}}, Volume = {11}, Year = {2001}} @article{Lotka1920, Author = {Lotka, A.J.}, Date-Added = {2008-03-28 16:14:48 +1300}, Date-Modified = {2008-03-28 16:16:12 +1300}, Journal = {J. 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D. and Peeb, V.}, Date-Modified = {2014-07-06 05:57:27 +0000}, Journal = {Nature}, Pages = {937--940}, Title = {Major fungal lineages are derived from lichen symbiotic ancestors}, Volume = {411}, Year = {2001}} @article{Lutzoni2000, Author = {Lutzoni, F. and Wagner, P. and Reeb, V. and Zoller, S.}, Journal = {Systematic Biology}, Notes = {alignment}, Pages = {628--651}, Title = {Integrating ambiguously aligned regions of DNA sequences in phylogentic analyses without violating positional homology}, Volume = {49}, Year = {2000}} @article{Lyons2000, Author = {Lyons, T.J. and Gasch, A.P. and Gaither, L.A. and Botstein, D. and Brown, P.O. and Eide, D.J.}, Journal = {Proceedings of the National Academies of Science, USA}, Notes = {yeast expression}, Pages = {7957--7962}, Title = {Genome-wide characterization of the Zap1p zinc-responsive regulon in yeast}, Volume = {97}, Year = {2000}} @article{Macaulay1999, Author = {Macaulay, V. and Richards, M. and Sykes, B.}, Journal = {Proceedings of the Royal Society of London, B}, Pages = {2037--2039}, Title = {Mitochondrial DNA recombination -- no need to panic}, Volume = {266}, Year = {1999}} @article{MacEachern1998, Author = {MacEachern, S.N. and Muller, P.}, Journal = {Journal of Computational and Graphical Statistics}, Pages = {223--238}, Title = {Estimating mixture of Dirichlet process models}, Volume = {7}, Year = {1998}} @article{MacNab2003, Author = {MacNab, Y.C.}, Journal = {Biometrics}, Notes = {spatial}, Pages = {305--316}, Title = {Hierarchical Bayesian modeling of spatially correlated health service outcomes and utilization rates}, Volume = {59}, Year = {2003}} @article{Maddison1997, Author = {Maddison, W. 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The differential equations for the low-order cumulant functions (i.e., mean, variance, and skewness) of the single birth model are reviewed, and the corresponding equations for the multiple birth model are derived. Accurate approximate solutions for the cumulant functions are obtained using moment closure methods for two families of model parameterizations, one for badger and the other for fox population growth. For both model families, the equilibrium size distribution may be approximated well using the Normal approximation, and even more accurately using the saddlepoint approximation. It is shown that in comparison with the corresponding single birth model, the multiple birth mechanism increases the skewness and the variance of the equilibrium distribution, but slightly reduces its mean. Moreover, the type of density-dependent population control is shown to influence the sign of the skewness and the size of the variance.}, Address = {Department of Statistics, Texas A\&M University, 3143 TAMU, College Station, TX 77843-3143, USA. [email protected]}, Au = {Matis, JH and Kiffe, TR}, Author = {Matis, James H and Kiffe, Thomas R}, Da = {20031203}, Date-Added = {2008-03-28 15:35:36 +1300}, Date-Modified = {2008-03-28 15:42:42 +1300}, Dcom = {20040310}, Edat = {2003/12/04 05:00}, Issn = {0040-5809 (Print)}, Jid = {0256422}, Journal = {Theor Popul Biol}, Jt = {Theoretical population biology}, Keywords = {stochastic logistic}, Language = {eng}, Mh = {*Animal Migration; Animals; Carnivora; Foxes; Litter Size; Multiple Birth Offspring/*statistics \& numerical data; *Population Growth; *Stochastic Processes}, Mhda = {2004/03/11 05:00}, Number = {1}, Own = {NLM}, Pages = {89--104}, Pii = {S0040580903001151}, Pl = {United States}, Pmid = {14642347}, Pst = {ppublish}, Pt = {Journal article}, Pubm = {Print}, Sb = {IM}, So = {Theor Popul Biol. 2004 Feb;65(1):89-104.}, Stat = {MEDLINE}, Title = {On stochastic logistic population growth models with immigration and multiple births.}, Volume = {65}, Year = {2004}} @article{Matis2003, Author = {Matis, James H and Kiffe, Thomas R and Renshaw, E and Hassan, J}, Date-Added = {2008-03-28 16:28:44 +1300}, Date-Modified = {2008-03-28 16:30:52 +1300}, Journal = {Ecological Modelling}, Pages = {239-248}, Title = {A simple saddlepoint approximation for the equilibrium distribution of the stochastic logistic model of population growth}, Volume = {161}, Year = {2003}} @article{Matseninpress, Author = {Matsen, F.A.}, Journal = {Systematic Biology}, Title = {A geometric approach to tree shape statistics}, Year = {in press}} @techreport{Matsen2006, Author = {Matsen, F.A.}, Institution = {University of Canterbury}, Title = {Optimization over a class of tree shape statistics}, Year = {2006}} @article{Mau1997, Author = {Mau, B. and Newton, M.A.}, Journal = {Journal of Computational and Graphical Statistics}, Pages = {122--131}, Title = {Phylogenetic inference for binary data on dendograms using Markov chain Monte Carlo}, Volume = {6}, Year = {1997}} 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The coefficient of variation in the extinction time V is found to have a maximum value when the death and birth rates are close in value. For large habitat size K we find that Vmax is of order K1/4 / M1/2, which is much larger than unity so long as M is small compared to K1/2. We also present a study of the SLP using the moment closure approximation (MCA), and discuss the successes and failures of this method. Regarding the former, the MCA yields a steady-state distribution for the population when the death rate is low. Although not correct for the SLP model, the first three moments of this distribution coincide with those calculated exactly for an adjusted SLP in which extinction is forbidden. These exact calculations also pinpoint the breakdown of the MCA as the death rate is increased.}, Address = {Department of Physics and Astronomy, Arizona State University, P.O. Box 871504, Tempe, AZ 85287, USA. 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Van and Vandamme, A.}, Date-Modified = {2014-07-06 02:35:36 +0000}, Journal = {Molecular Biology and Evolution}, Pages = {1986--1996}, Title = {Analysis of the evolutionary relationships of HIV-1 and SIVcpz sequences using Bayesian inference: implications for the origins of HIV-1}, Volume = {20}, Year = {2003}} @article{Parsons2007, Abstract = {We extend the one-locus two allele Moran model of fixation in a haploid population to the case where the total size of the population is not fixed. The model is defined as a two-dimensional birth-and-death process for allele number. Changes in allele number occur through density-independent death events and birth events whose per capita rate decreases linearly with the total population density. Uniquely for models of this type, the latter is determined by these same birth-and-death events. This provides a framework for investigating both the effects of fluctuation in total population number through demographic stochasticity, and deterministic density-dependent changes in mean density, on allele fixation. We analyze this model using a combination of asymptotic analytic approximations supported by numerics. We find that for advantageous mutants demographic stochasticity of the resident population does not affect the fixation probability, but that deterministic changes in total density do. In contrast, for deleterious mutants, the fixation probability increases with increasing resident population fluctuation size, but is relatively insensitive to initial density. These phenomena cannot be described by simply using a harmonic mean effective population size.}, Address = {Department of Mathematics, University of Toronto, 40 St. George Street, Toronto, Ont., Canada M5S 2E4. [email protected]}, Au = {Parsons, TL and Quince, C}, Author = {Parsons, Todd L and Quince, Christopher}, Da = {20070612}, Date-Added = {2008-04-13 17:20:00 +1200}, Date-Modified = {2008-04-13 17:26:36 +1200}, Dcom = {20071218}, Dep = {20061215}, Doi = {10.1016/j.tpb.2006.11.004}, Edat = {2007/01/24 09:00}, Issn = {0040-5809 (Print)}, Jid = {0256422}, Journal = {Theor Popul Biol}, Jt = {Theoretical population biology}, Language = {eng}, Mh = {Alleles; Genetics, Population/*methods; *Haploidy; Logistic Models; Markov Chains; *Models, Genetic; Mutation/genetics; Population Density; *Stochastic Processes}, Mhda = {2007/12/19 09:00}, Number = {1}, Own = {NLM}, Pages = {121--135}, Pii = {S0040-5809(06)00163-8}, Pl = {United States}, Pmid = {17239910}, Pst = {ppublish}, Pt = {Journal article; Research Support, Non-U.S. Gov't}, Pubm = {Print-Electronic}, Sb = {IM}, So = {Theor Popul Biol. 2007 Aug;72(1):121-35. Epub 2006 Dec 15.}, Stat = {MEDLINE}, Title = {Fixation in haploid populations exhibiting density dependence I: The non-neutral case.}, Volume = {72}, Year = {2007}, Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.tpb.2006.11.004}} @article{Patel2001, Author = {Patel, M. and Dorman, K.S. and Zhang, Y.H. and Huang, B.L. and Arnold, A.P. and Sinsheimer, J.S. and Vilain, E. and McCabe, E.R.B.}, Journal = {American Journal of Human Genetics}, Pages = {275--280}, Title = {Priamte DAX1, SRY and SOX9: evolutionary stratification of sex determination pathway}, Volume = {68}, Year = {2001}} @article{Pathak1992, Author = {Pathak, V. and Temin, H.}, Journal = {Journal of Virology}, Pages = {3093--3100}, Title = {5-azacytidine and RNA secondary structure increase the retrovirus mutation rate}, Volume = {66}, Year = {1992}} @article{Peleg2003, Author = {Peleg, O. and Trifonov, E.N. and Bolshoy, A.}, Journal = {Nucleic Acids Research}, Pages = {4192-4200}, Title = {Hidden messages in the nef gene of human immunodeficiency virus type 1 suggest a novel RNA secondary structure}, Volume = {31}, Year = {2003}} @article{Penny1986, Author = {Penny, D. and Hendy, M.D.}, Journal = {Molecular Biology and Evolution}, Pages = {403--417}, Title = {Estimating the reliability of evolutionary trees}, Volume = {3}, Year = {1986}} @article{Perez-Hoyos2003, Author = {Perez-Hoyos, S. and del Amo J, J. and Muga, R. and del Romero, J. and de Olalla, P. 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G. and Rambaut, A. and Harvey, P. H.}, Date-Modified = {2013-02-13 01:22:22 +0000}, Journal = {Genetics}, Pages = {1429--1437}, Title = {An integrated framework for the inference of viral population history from reconstructed genealogies}, Volume = {155}, Year = {2000}} @article{Pybus2001, Abstract = {Hepatitis C virus (HCV) is a leading worldwide cause of liver disease. Here, we use a new model of HCV spread to investigate the epidemic behavior of the virus and to estimate its basic reproductive number from gene sequence data. We find significant differences in epidemic behavior among HCV subtypes and suggest that these differences are largely the result of subtype-specific transmission patterns. Our model builds a bridge between the disciplines of population genetics and mathematical epidemiology by using pathogen gene sequences to infer the population dynamic history of an infectious disease.}, Au = {Pybus, OG and Charleston, MA and Gupta, S and Rambaut, A and Holmes, EC and Harvey, PH}, Author = {Pybus, O G and Charleston, M A and Gupta, S and Rambaut, A and Holmes, E C and Harvey, P H}, Da = {20010625}, Date-Added = {2008-04-13 17:01:59 +1200}, Date-Modified = {2014-07-03 23:04:27 +0000}, Dcom = {20010712}, Doi = {10.1126/science.1058321}, Edat = {2001/06/26 10:00}, Issn = {0036-8075 (Print)}, Jid = {0404511}, Journal = {Science}, Jt = {Science (New York, N.Y.)}, Language = {eng}, Lr = {20070319}, Mh = {Endemic Diseases; Epidemiology, Molecular; Genes, Viral; Hepacivirus/classification/genetics/*physiology; Hepatitis C/*epidemiology/transmission/*virology; Humans; Likelihood Functions; Models, Biological; Phylogeny; Population Dynamics; Prevalence; Substance Abuse, Intravenous/complications}, Mhda = {2001/07/13 10:01}, Number = {5525}, Own = {NLM}, Pages = {2323--2325}, Pii = {292/5525/2323}, Pl = {United States}, Pmid = {11423661}, Pst = {ppublish}, Pt = {Journal article; Research Support, Non-U.S. Gov't}, Pubm = {Print}, Sb = {IM}, So = {Science. 2001 Jun 22;292(5525):2323-5.}, Stat = {MEDLINE}, Title = {The epidemic behavior of the hepatitis C virus.}, Volume = {292}, Year = {2001}, Bdsk-Url-1 = {http://dx.doi.org/10.1126/science.1058321}} @article{Qian2001, Author = {Qian, B. and Goldstein, R.A.}, Journal = {Proteins}, Notes = {indel}, Pages = {102--104}, Title = {Distribution of indel lengths}, Volume = {45}, Year = {2001}} @other{Queiroz2007, Author = {de Queiroz, Alan and Gatesy, John}, Issn = {0169-5347}, Month = jan, Number = {1}, Owner = {dpm}, Pages = {34--41}, Refid = {S0169-5347(06)00332-6 DOI - 10.1016/j.tree.2006.10.002}, Timestamp = {2009.01.25}, Title = {The supermatrix approach to systematics}, Url = {http://linkinghub.elsevier.com/retrieve/pii/S0169534706003326}, Volume = {22}, Year = {2007}, Bdsk-Url-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0169534706003326}} @article{Racine-Poon1988, Author = {Racine-Poon, A.}, Journal = {Journal of the American Statistical Assocation}, Notes = {calibration}, Pages = {650--656}, Title = {A Bayesian approach to nonlinear calibration problems}, Volume = {83}, Year = {1988}} @article{Racine-Poon1991, Author = {Racine-Poon, A. and Weihs, C. and Smith, A.F.M.}, Journal = {Biometrics}, Notes = {calibration,serial dilution}, Pages = {1235--1246}, Title = {Estimation of relative potency with sequential dilution errors in radioimmunoassay}, Volume = {47}, Year = {1991}} @incollection{Raftery1996, Address = {New York, NY}, Author = {Raftery, A. E. and Lewis, S. M.}, Booktitle = {Markov Chain Monte Carlo in Practice}, Date-Modified = {2014-12-04 01:11:07 +0000}, Editor = {Gilks, W.R. and Richardson, S. and Spiegelhalter, D.J.}, Pages = {115--130}, Publisher = {Chapman \& Hall}, Title = {Implementing MCMC}, Year = {1996}} @techreport{Raftery2006, Author = {Raftery, A. E. and Newton, M. 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The results confirm the theoretical superiority of the likelihood method. 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There are, however, a growing number of examples in which large Bayesian posterior clade probabilities are associated with very short branch lengths and low values for non-Bayesian measures of support such as nonparametric bootstrapping. For the four-taxon case when the true tree is the star phylogeny, Bayesian analyses become increasingly unpredictable in their preference for one of the three possible resolved tree topologies as data set size increases. This leads to the prediction that hard (or near-hard) polytomies in nature will cause unpredictable behavior in Bayesian analyses, with arbitrary resolutions of the polytomy receiving very high posterior probabilities in some cases. We present a simple solution to this problem involving a reversible-jump Markov chain Monte Carlo (MCMC) algorithm that allows exploration of all of tree space, including unresolved tree topologies with one or more polytomies. The reversible-jump MCMC approach allows prior distributions to place some weight on less-resolved tree topologies, which eliminates misleadingly high posteriors associated with arbitrary resolutions of hard polytomies. Fortunately, assigning some prior probability to polytomous tree topologies does not appear to come with a significant cost in terms of the ability to assess the level of support for edges that do exist in the true tree. Methods are discussed for applying arbitrary prior distributions to tree topologies of varying resolution, and an empirical example showing evidence of polytomies is analyzed and discussed.}, Au = {Lewis, PO and Holder, MT and Holsinger, KE}, Author = {Lewis, Paul O and Holder, Mark T and Holsinger, Kent E}, Da = {20050713}, Date-Added = {2008-11-28 18:55:33 -0800}, Date-Modified = {2014-07-06 00:37:13 +0000}, Dcom = {20050818}, Doi = {10.1080/10635150590924208}, Edat = {2005/07/14 09:00}, Issn = {1063-5157 (Print)}, Jid = {9302532}, Journal = {Syst Biol}, Jt = {Systematic biology}, Language = {eng}, Lr = {20061115}, Mh = {Algae, Green/genetics; *Bayes Theorem; Classification/*methods; *Data Interpretation, Statistical; Markov Chains; Monte Carlo Method; *Phylogeny; Reproducibility of Results}, Mhda = {2005/08/19 09:00}, Number = {2}, Own = {NLM}, Pages = {241--253}, Pii = {X8576658LP734021}, Pl = {England}, Pmid = {16012095}, Pst = {ppublish}, Pt = {Comparative Study; Journal Article; Research Support, U.S. Gov't, Non-P.H.S.}, Pubm = {Print}, Sb = {IM}, So = {Syst Biol. 2005 Apr;54(2):241-53.}, Stat = {MEDLINE}, Title = {Polytomies and Bayesian phylogenetic inference.}, Volume = {54}, Year = {2005}, Bdsk-Url-1 = {http://dx.doi.org/10.1080/10635150590924208}} @article{Thorne:1998lh, Abstract = {A simple model for the evolution of the rate of molecular evolution is presented. With a Bayesian approach, this model can serve as the basis for estimating dates of important evolutionary events even in the absence of the assumption of constant rates among evolutionary lineages. The method can be used in conjunction with any of the widely used models for nucleotide substitution or amino acid replacement. It is illustrated by analyzing a data set of rbcL protein sequences.}, Address = {Statistics Department, North Carolina State University, Raleigh 27695-8203, USA. [email protected]}, Au = {Thorne, JL and Kishino, H and Painter, IS}, Author = {Thorne, J L and Kishino, H and Painter, I S}, Da = {19990119}, Date-Added = {2008-11-28 18:43:28 -0800}, Date-Modified = {2008-11-28 18:43:28 -0800}, Dcom = {19990119}, Edat = {1998/12/29}, Gr = {P01-GM45344/GM/United States NIGMS}, Issn = {0737-4038 (Print)}, Jid = {8501455}, Journal = {Mol Biol Evol}, Jt = {Molecular biology and evolution}, Language = {eng}, Lr = {20071114}, Mh = {Algorithms; *Evolution; *Evolution, Molecular; *Models, Genetic; Models, Statistical; *Phylogeny; Plant Proteins/genetics; Plants/*classification/*genetics; *Ribulose-Bisphosphate Carboxylase; *Time}, Mhda = {1998/12/29 00:01}, Number = {12}, Own = {NLM}, Pages = {1647--1657}, Pl = {UNITED STATES}, Pmid = {9866200}, Pst = {ppublish}, Pt = {Journal Article; Research Support, U.S. Gov't, P.H.S.}, Pubm = {Print}, Rn = {0 (Plant Proteins); EC 4.1.1.39 (RbcL protein, plastid); EC 4.1.1.39 (Ribulose-Bisphosphate Carboxylase)}, Sb = {IM; S}, So = {Mol Biol Evol. 1998 Dec;15(12):1647-57.}, Stat = {MEDLINE}, Title = {Estimating the rate of evolution of the rate of molecular evolution.}, Volume = {15}, Year = {1998 Dec}} @article{Kishino:2001ec, Abstract = {Rates of molecular evolution vary over time and, hence, among lineages. In contrast, widely used methods for estimating divergence times from molecular sequence data assume constancy of rates. Therefore, methods for estimation of divergence times that incorporate rate variation are attractive. Improvements on a previously proposed Bayesian technique for divergence time estimation are described. New parameterization more effectively captures the phylogenetic structure of rate evolution on a tree. Fossil information and other evidence can now be included in Bayesian analyses in the form of constraints on divergence times. Simulation results demonstrate that the accuracy of divergence time estimation is substantially enhanced when constraints are included.}, Address = {Laboratory of Biometrics, Graduate School of Agriculture and Life Sciences, University of Tokyo, Tokyo, Japan. [email protected]}, Au = {Kishino, H and Thorne, JL and Bruno, WJ}, Author = {Kishino, H and Thorne, J L and Bruno, W J}, Da = {20010314}, Date-Added = {2008-11-28 18:43:16 -0800}, Date-Modified = {2008-11-28 18:43:16 -0800}, Dcom = {20010614}, Edat = {2001/03/07 10:00}, Gr = {GM45344/GM/United States NIGMS}, Issn = {0737-4038 (Print)}, Jid = {8501455}, Journal = {Mol Biol Evol}, Jt = {Molecular biology and evolution}, Language = {eng}, Lr = {20071114}, Mh = {Bayes Theorem; *Evolution; Fossils; *Models, Genetic; Probability}, Mhda = {2001/06/15 10:01}, Number = {3}, Own = {NLM}, Pages = {352--361}, Pl = {United States}, Pmid = {11230536}, Pst = {ppublish}, Pt = {Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, P.H.S.}, Pubm = {Print}, Sb = {IM}, So = {Mol Biol Evol. 2001 Mar;18(3):352-61.}, Stat = {MEDLINE}, Title = {Performance of a divergence time estimation method under a probabilistic model of rate evolution.}, Volume = {18}, Year = {2001 Mar}} @article{Thorne:2002ff, Abstract = {Bayesian methods for estimating evolutionary divergence times are extended to multigene data sets, and a technique is described for detecting correlated changes in evolutionary rates among genes. Simulations are employed to explore the effect of multigene data on divergence time estimation, and the methodology is illustrated with a previously published data set representing diverse plant taxa. The fact that evolutionary rates and times are confounded when sequence data are compared is emphasized and the importance of fossil information for disentangling rates and times is stressed.}, Au = {Thorne, JL and Kishino, H}, Author = {Thorne, Jeffrey L and Kishino, Hirohisa}, Da = {20021024}, Date-Added = {2008-11-28 18:43:05 -0800}, Date-Modified = {2014-07-06 00:40:45 +0000}, Dcom = {20030513}, Doi = {10.1080/10635150290102456}, Edat = {2002/10/25 04:00}, Issn = {1063-5157 (Print)}, Jid = {9302532}, Journal = {Syst Biol}, Jt = {Systematic biology}, Language = {eng}, Lr = {20061115}, Mh = {Algorithms; Bayes Theorem; *Evolution; Evolution, Molecular; Markov Chains; *Models, Genetic; Monte Carlo Method; *Phylogeny; Plants/genetics; Time Factors}, Mhda = {2003/05/14 05:00}, Number = {5}, Own = {NLM}, Pages = {689--702}, Pl = {England}, Pmid = {12396584}, Pst = {ppublish}, Pt = {Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.}, Pubm = {Print}, Sb = {IM}, So = {Syst Biol. 2002 Oct;51(5):689-702.}, Stat = {MEDLINE}, Title = {Divergence time and evolutionary rate estimation with multilocus data.}, Volume = {51}, Year = {2002 Oct}, Bdsk-Url-1 = {http://dx.doi.org/10.1080/10635150290102456}} @article{beerli1999, Author = {Beerli, Peter and Felsenstein, J.}, Date-Modified = {2014-12-04 01:05:53 +0000}, Journal = {Genetics}, Number = {2}, Pages = {763}, Publisher = {Genetics Soc America}, Title = {{Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach}}, Volume = {152}, Year = {1999}} @article{Beerli:2001fe, Abstract = {A maximum likelihood estimator based on the coalescent for unequal migration rates and different subpopulation sizes is developed. The method uses a Markov chain Monte Carlo approach to investigate possible genealogies with branch lengths and with migration events. Properties of the new method are shown by using simulated data from a four-population n-island model and a source-sink population model. Our estimation method as coded in migrate is tested against genetree; both programs deliver a very similar likelihood surface. The algorithm converges to the estimates fairly quickly, even when the Markov chain is started from unfavorable parameters. The method was used to estimate gene flow in the Nile valley by using mtDNA data from three human populations.}, Au = {Beerli, P and Felsenstein, J}, Author = {Beerli, Peter and Felsenstein, J.}, Da = {20010411}, Date-Added = {2008-11-28 18:40:20 -0800}, Date-Modified = {2014-12-04 01:05:47 +0000}, Dcom = {20010510}, Dep = {20010403}, Doi = {10.1073/pnas.081068098}, Edat = {2001/04/05 10:00}, Gr = {R01 GM 01989/GM/United States NIGMS; R01 GM 51929/GM/United States NIGMS}, Issn = {0027-8424 (Print)}, Jid = {7505876}, Journal = {Proc Natl Acad Sci U S A}, Jt = {Proceedings of the National Academy of Sciences of the United States of America}, Language = {eng}, Lr = {20071114}, Mh = {*Genetics, Population; Humans; Likelihood Functions; Markov Chains; Monte Carlo Method; *Population Density; *Transients and Migrants}, Mhda = {2001/05/22 10:01}, Number = {8}, Own = {NLM}, Pages = {4563--4568}, Phst = {2001/04/03 {$[$}aheadofprint{$]$}}, Pii = {081068098}, Pl = {United States}, Pmc = {PMC31874}, Pmid = {11287657}, Pst = {ppublish}, Pt = {Journal Article; Research Support, U.S. Gov't, Non-P.H.S.; Research Support, U.S. Gov't, P.H.S.}, Pubm = {Print-Electronic}, Sb = {IM}, So = {Proc Natl Acad Sci U S A. 2001 Apr 10;98(8):4563-8. Epub 2001 Apr 3.}, Stat = {MEDLINE}, Title = {Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach.}, Volume = {98}, Year = {2001}, Bdsk-Url-1 = {http://dx.doi.org/10.1073/pnas.081068098}} @article{Beerli:2006pi, Abstract = {Comparison of the performance and accuracy of different inference methods, such as maximum likelihood (ML) and Bayesian inference, is difficult because the inference methods are implemented in different programs, often written by different authors. Both methods were implemented in the program MIGRATE, that estimates population genetic parameters, such as population sizes and migration rates, using coalescence theory. Both inference methods use the same Markov chain Monte Carlo algorithm and differ from each other in only two aspects: parameter proposal distribution and maximization of the likelihood function. Using simulated datasets, the Bayesian method generally fares better than the ML approach in accuracy and coverage, although for some values the two approaches are equal in performance. MOTIVATION: The Markov chain Monte Carlo-based ML framework can fail on sparse data and can deliver non-conservative support intervals. A Bayesian framework with appropriate prior distribution is able to remedy some of these problems. RESULTS: The program MIGRATE was extended to allow not only for ML(-) maximum likelihood estimation of population genetics parameters but also for using a Bayesian framework. Comparisons between the Bayesian approach and the ML approach are facilitated because both modes estimate the same parameters under the same population model and assumptions.}, Au = {Beerli, P}, Author = {Beerli, Peter}, Da = {20060201}, Date-Added = {2008-11-28 18:40:12 -0800}, Date-Modified = {2014-07-06 00:40:01 +0000}, Dcom = {20060307}, Dep = {20051129}, Doi = {10.1093/bioinformatics/bti803}, Edat = {2005/12/01 09:00}, Issn = {1367-4803 (Print)}, Jid = {9808944}, Journal = {Bioinformatics}, Jt = {Bioinformatics (Oxford, England)}, Language = {eng}, Lr = {20061115}, Mh = {*Bayes Theorem; Chromosome Mapping/*methods; Computer Simulation; Evolution; Genetics, Population/*methods; *Likelihood Functions; *Models, Genetic; *Models, Statistical; Phylogeny; *Software}, Mhda = {2006/03/08 09:00}, Month = {Feb}, Number = {3}, Own = {NLM}, Pages = {341--345}, Phst = {2005/11/29 {$[$}aheadofprint{$]$}}, Pii = {bti803}, Pl = {England}, Pmid = {16317072}, Pst = {ppublish}, Pt = {Comparative Study; Evaluation Studies; Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.}, Pubm = {Print-Electronic}, Sb = {IM}, So = {Bioinformatics. 2006 Feb 1;22(3):341-5. Epub 2005 Nov 29.}, Stat = {MEDLINE}, Title = {Comparison of Bayesian and maximum-likelihood inference of population genetic parameters.}, Volume = {22}, Year = {2006}, Bdsk-Url-1 = {http://dx.doi.org/10.1093/bioinformatics/bti803}} @article{Yang:2007xr, Abstract = {PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML). The programs may be used to compare and test phylogenetic trees, but their main strengths lie in the rich repertoire of evolutionary models implemented, which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses. Uses of the programs include estimation of synonymous and nonsynonymous rates (d(N) and d(S)) between two protein-coding DNA sequences, inference of positive Darwinian selection through phylogenetic comparison of protein-coding genes, reconstruction of ancestral genes and proteins for molecular restoration studies of extinct life forms, combined analysis of heterogeneous data sets from multiple gene loci, and estimation of species divergence times incorporating uncertainties in fossil calibrations. This note discusses some of the major applications of the package, which includes example data sets to demonstrate their use. The package is written in ANSI C, and runs under Windows, Mac OSX, and UNIX systems. It is available at -- (http://abacus.gene.ucl.ac.uk/software/paml.html).}, Address = {Department of Biology, Galton Laboratory, University College London, London, UK. [email protected]}, Au = {Yang, Z}, Author = {Yang, Ziheng}, Da = {20070803}, Date-Added = {2008-11-28 18:38:46 -0800}, Date-Modified = {2008-11-28 18:38:46 -0800}, Dcom = {20071029}, Dep = {20070504}, Doi = {10.1093/molbev/msm088}, Edat = {2007/05/08 09:00}, Issn = {0737-4038 (Print)}, Jid = {8501455}, Journal = {Mol Biol Evol}, Jt = {Molecular biology and evolution}, Language = {eng}, Mh = {Animals; Computer Simulation; *Likelihood Functions; Models, Genetic; *Phylogeny; Selection (Genetics); Software; Species Specificity; Variation (Genetics)}, Mhda = {2007/10/30 09:00}, Number = {8}, Own = {NLM}, Pages = {1586--1591}, Phst = {2007/05/04 {$[$}aheadofprint{$]$}}, Pii = {msm088}, Pl = {United States}, Pmid = {17483113}, Pst = {ppublish}, Pt = {Journal Article; Research Support, Non-U.S. Gov't}, Pubm = {Print-Electronic}, Sb = {IM}, So = {Mol Biol Evol. 2007 Aug;24(8):1586-91. Epub 2007 May 4.}, Stat = {MEDLINE}, Title = {PAML 4: phylogenetic analysis by maximum likelihood.}, Volume = {24}, Year = {2007 Aug}, Bdsk-Url-1 = {http://dx.doi.org/10.1093/molbev/msm088}} @article{Huelsenbeck:2001oz, Abstract = {SUMMARY: The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo. AVAILABILITY: MRBAYES, including the source code, documentation, sample data files, and an executable, is available at http://brahms.biology.rochester.edu/software.html.}, Address = {Department of Biology, University of Rochester, Rochester, NY 14627, USA. [email protected]}, Au = {Huelsenbeck, JP and Ronquist, F}, Author = {Huelsenbeck, J P and Ronquist, F}, Da = {20010828}, Date-Added = {2008-11-28 18:37:14 -0800}, Date-Modified = {2008-11-28 18:37:14 -0800}, Dcom = {20011204}, Edat = {2001/08/29 10:00}, Issn = {1367-4803 (Print)}, Jid = {9808944}, Journal = {Bioinformatics}, Jt = {Bioinformatics (Oxford, England)}, Language = {eng}, Lr = {20061115}, Mh = {Algorithms; *Bayes Theorem; Computational Biology; Markov Chains; *Phylogeny; *Software}, Mhda = {2002/01/05 10:01}, Number = {8}, Own = {NLM}, Pages = {754--755}, Pl = {England}, Pmid = {11524383}, Pst = {ppublish}, Pt = {Journal Article; Research Support, U.S. Gov't, Non-P.H.S.}, Pubm = {Print}, Sb = {IM}, So = {Bioinformatics. 2001 Aug;17(8):754-5.}, Stat = {MEDLINE}, Title = {{MrBayes}: Bayesian inference of phylogenetic trees.}, Volume = {17}, Year = {2001 Aug}} @article{Ronquist2003, Au = {Ronquist, F and Huelsenbeck, JP}, Author = {Ronquist, Fredrik and Huelsenbeck, John P}, Da = {20030812}, Date-Added = {2008-11-28 18:37:11 -0800}, Date-Modified = {2014-07-05 08:50:12 +0000}, Dcom = {20040428}, Edat = {2003/08/13 05:00}, Issn = {1367-4803 (Print)}, Jid = {9808944}, Journal = {Bioinformatics}, Jt = {Bioinformatics (Oxford, England)}, Language = {eng}, Lr = {20061115}, Mh = {*Algorithms; Bayes Theorem; *Evolution, Molecular; Gene Expression Profiling/*methods; *Models, Genetic; *Models, Statistical; *Phylogeny; Sequence Alignment/*methods; Sequence Homology; Software; Stochastic Processes}, Mhda = {2004/04/29 05:00}, Month = {8}, Number = {12}, Own = {NLM}, Pages = {1572--1574}, Pl = {England}, Pmid = {12912839}, Pst = {ppublish}, Pt = {Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.}, Pubm = {Print}, Sb = {IM}, So = {Bioinformatics. 2003 Aug 12;19(12):1572-4.}, Stat = {MEDLINE}, Title = {{MrBayes 3}: Bayesian phylogenetic inference under mixed models.}, Volume = {19}, Year = {2003}} @article{Drummond:2001yf, Abstract = {It is frequently true that molecular sequences do not evolve in a strictly clocklike manner. Instead, substitution rate may vary for a number of reasons, including changes in selection pressure and effective population size, as well as changes in mean generation time. Here we present two new methods for estimating stepwise changes in substitution rates when serially sampled molecular sequences are available. These methods are based on multiple rates with dated tips (MRDT) models and allow different rates to be estimated for different intervals of time. These intervals may correspond to the sampling intervals or to a priori--defined intervals that are not coincident with the times the serial samples are obtained. Two methods for obtaining estimates of multiple rates are described. The first is an extension of the phylogeny-based maximum-likelihood estimation procedure introduced by Rambaut. The second is a new parameterization of the pairwise distance least-squares procedure used by Drummond and Rodrigo. The utility of these methods is demonstrated on a genealogy of HIV sequences obtained at five different sampling times from a single patient over a period of 34 months.}, Au = {Drummond, A and Forsberg, R and Rodrigo, AG}, Author = {Drummond, A. J. and Forsberg, R. and Rodrigo, A. G.}, Da = {20010622}, Date-Added = {2008-11-28 10:43:42 -0800}, Date-Modified = {2014-07-06 00:56:50 +0000}, Dcom = {20010927}, Edat = {2001/06/23 10:00}, Gr = {GM59174/GM/United States NIGMS}, Issn = {0737-4038 (Print)}, Jid = {8501455}, Journal = {Mol Biol Evol}, Jt = {Molecular biology and evolution}, Language = {eng}, Lr = {20071114}, Mh = {Anti-HIV Agents/therapeutic use; *Evolution, Molecular; Genes, env; *Genetic Techniques; HIV Infections/drug therapy/virology; HIV-1/drug effects/genetics/isolation \& purification; Humans; Least-Squares Analysis; Likelihood Functions; *Models, Genetic; Time Factors; Zidovudine/therapeutic use}, Mhda = {2001/09/28 10:01}, Number = {7}, Own = {NLM}, Pages = {1365--1371}, Pl = {United States}, Pmid = {11420374}, Pst = {ppublish}, Pt = {Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, P.H.S.}, Pubm = {Print}, Rn = {0 (Anti-HIV Agents); 30516-87-1 (Zidovudine)}, Sb = {IM}, So = {Mol Biol Evol. 2001 Jul;18(7):1365-71.}, Stat = {MEDLINE}, Title = {The inference of stepwise changes in substitution rates using serial sequence samples.}, Volume = {18}, Year = {2001}} @article{Drummond:2001sf, Abstract = {Phylogenetic Analysis Library (PAL) is a collection of Java classes for use in molecular evolution and phylogenetics. PAL provides a modular environment for the rapid construction of both special-purpose and general analysis programs. PAL version 1.1 consists of 145 public classes or interfaces in 13 packages, including classes for models of character evolution, maximum-likelihood estimation, and the coalescent, with a total of more than 27000 lines of code. The PAL project is set up as a collaborative project to facilitate contributions from other researchers. AVAILIABILTY: The program is free and is available at http://www.pal-project.org. It requires Java 1.1 or later. PAL is licensed under the GNU General Public License.}, Address = {School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland, New Zealand. [email protected]}, Au = {Drummond, A and Strimmer, K}, Author = {Drummond, A. J. and Strimmer, K}, Da = {20010712}, Date-Added = {2008-11-28 10:43:39 -0800}, Date-Modified = {2014-07-06 00:49:52 +0000}, Dcom = {20011204}, Edat = {2001/07/13 10:00}, Gr = {GM59174/GM/United States NIGMS}, Issn = {1367-4803 (Print)}, Jid = {9808944}, Journal = {Bioinformatics}, Jt = {Bioinformatics (Oxford, England)}, Language = {eng}, Lr = {20071114}, Mh = {Computational Biology; *Evolution, Molecular; Likelihood Functions; *Phylogeny; *Software}, Mhda = {2002/01/05 10:01}, Number = {7}, Own = {NLM}, Pages = {662--663}, Pl = {England}, Pmid = {11448888}, Pst = {ppublish}, Pt = {Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, P.H.S.}, Pubm = {Print}, Sb = {IM}, So = {Bioinformatics. 2001 Jul;17(7):662-3.}, Stat = {MEDLINE}, Title = {PAL: an object-oriented programming library for molecular evolution and phylogenetics.}, Volume = {17}, Year = {2001}} @article{Biek:2003hb, Abstract = {Within the large body of research on retroviruses, the distribution and evolution of endemic retroviruses in natural host populations have so far received little attention. In this study, the epidemiology, genetic diversity, and molecular evolution of feline immunodeficiency virus specific to cougars (FIVpco) was examined using blood samples collected over several years from a free-ranging cougar population in the western United States. The virus prevalence was 58% in this population (n = 52) and increased significantly with host age. Based on phylogenetic analysis of fragments of envelope (env) and polymerase (pol) genes, two genetically distinct lineages of FIVpco were found to cooccur in the population but not in the same individuals. Within each of the virus lineages, geographically nearby isolates formed monophyletic clusters of closely related viruses. Sequence diversity for env within a host rarely exceeded 1%, and the evolution of this gene was dominated by purifying selection. For both pol and env, our data indicate mean rates of molecular evolution of 1 to 3% per 10 years. These results support the premise that FIVpco is well adapted to its cougar host and provide a basis for comparing lentivirus evolution in endemic and epidemic infections in natural hosts.}, Address = {Wildlife Biology Program, University of Montana, Missoula, Montana 59812, USA.}, Au = {Biek, R and Rodrigo, AG and Holley, D and Drummond, A and Anderson CR, Jr and Ross, HA and Poss, M}, Author = {Biek, Roman and Rodrigo, Allen G and Holley, David and Drummond, Alexei J. and Anderson, Charles R Jr and Ross, Howard A and Poss, Mary}, Da = {20030813}, Date-Added = {2008-11-28 10:43:18 -0800}, Date-Modified = {2014-07-06 00:52:12 +0000}, Dcom = {20030924}, Edat = {2003/08/14 05:00}, Issn = {0022-538X (Print)}, Jid = {0113724}, Journal = {J Virol}, Jt = {Journal of virology}, Language = {eng}, Lr = {20061115}, Mh = {Animals; Antibodies, Viral/blood; Base Sequence; Carnivora/*virology; DNA, Viral/genetics; Epidemiology, Molecular; Evolution, Molecular; Female; Genes, env; Genes, pol; Immunodeficiency Virus, Feline/*genetics/immunology/isolation \& purification; Lentivirus Infections/epidemiology/immunology/veterinary/virology; Male; Molecular Sequence Data; Phylogeny; United States/epidemiology; Variation (Genetics)}, Mhda = {2003/09/25 05:00}, Number = {17}, Own = {NLM}, Pages = {9578--9589}, Pl = {United States}, Pmc = {PMC187433}, Pmid = {12915571}, Pst = {ppublish}, Pt = {Journal Article; Research Support, Non-U.S. Gov't}, Pubm = {Print}, Rn = {0 (Antibodies, Viral); 0 (DNA, Viral)}, Sb = {IM}, So = {J Virol. 2003 Sep;77(17):9578-89.}, Stat = {MEDLINE}, Title = {Epidemiology, genetic diversity, and evolution of endemic feline immunodeficiency virus in a population of wild cougars.}, Volume = {77}, Year = {2003 Sep}} @article{Rodrigo:2003jt, Abstract = {The estimation of evolutionary rates from serially sampled sequences has recently been the focus of several studies. In this paper, we extend these analyzes to allow the estimation of a joint rate of substitution, omega, from several evolving populations from which serial samples are drawn. In the case of viruses evolving in different hosts, therapy may halt replication and therefore the accumulation of substitutions in the population. In such cases, it may be that only a proportion, p, of subjects are nonresponders who have viral populations that continue to evolve. We develop two likelihood-based procedures to jointly estimate p and omega, and empirical Bayes' tests of whether an individual should be classified as a responder or nonresponder. An example data set comprising HIV-1 partial envelope sequences from six patients on highly active antiretroviral therapy is analyzed.}, Address = {Computational and Evolutionary Biology Laboratory, School of Biological Sciences, University of Auckland, Auckland, New Zealand. [email protected]}, Au = {Rodrigo, AG and Goode, M and Forsberg, R and Ross, HA and Drummond, A}, Author = {Rodrigo, Allen G and Goode, Matthew and Forsberg, Roald and Ross, Howard A and Drummond, Alexei J.}, Da = {20031222}, Date-Added = {2008-11-28 10:43:09 -0800}, Date-Modified = {2014-07-06 00:50:37 +0000}, Dcom = {20041109}, Dep = {20030829}, Doi = {10.1093/molbev/msg215}, Edat = {2003/09/02 05:00}, Gr = {R01 GM59174/GM/United States NIGMS; R01-GM60729/GM/United States NIGMS}, Issn = {0737-4038 (Print)}, Jid = {8501455}, Journal = {Mol Biol Evol}, Jt = {Molecular biology and evolution}, Language = {eng}, Lr = {20071114}, Mh = {Algorithms; Antiretroviral Therapy, Highly Active/statistics \& numerical data; Bayes Theorem; *Evolution, Molecular; HIV-1/genetics; Humans; Likelihood Functions; Models, Genetic; Phylogeny}, Mhda = {2004/11/13 09:00}, Number = {12}, Own = {NLM}, Pages = {2010--2018}, Phst = {2003/08/29 {$[$}aheadofprint{$]$}}, Pii = {msg215}, Pl = {United States}, Pmid = {12949147}, Pst = {ppublish}, Pt = {Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, P.H.S.}, Pubm = {Print-Electronic}, Sb = {IM}, So = {Mol Biol Evol. 2003 Dec;20(12):2010-8. Epub 2003 Aug 29.}, Stat = {MEDLINE}, Title = {Inferring evolutionary rates using serially sampled sequences from several populations.}, Volume = {20}, Year = {2003 Dec}, Bdsk-Url-1 = {http://dx.doi.org/10.1093/molbev/msg215}} @article{Bunce:2003pi, Abstract = {The ratite moa (Aves; Dinornithiformes) were massive graviportal browsers weighing up to 250 kg (ref. 1) that dominated the New Zealand biota until their extinction approximately 500 yr ago. Despite an extensive Quaternary fossil record, moa taxonomy remains problematic and currently 11 species are recognized. Three Dinornis species were found throughout New Zealand and differed markedly in size (1-2 m height at back) and mass (from approximately 34 to 242 kg). Surprisingly, ancient mitochondrial DNA sequences show that the three species were genetically indistinguishable within each island, but formed separate North and South Island clades. Here we show, using the first sex-linked nuclear sequences from an extinct species, that on each island the three morphological forms actually represent just one species, whose size varied markedly according to sex and habitat. The largest females in this example of extreme reversed sexual size dimorphism were about 280% the weight and 150% the height of the largest males, which is unprecedented among birds and terrestrial mammals. The combination of molecular and palaeontological data highlights the difficulties of analysing extinct groups, even those with detailed fossil records.}, Au = {Bunce, M and Worthy, TH and Ford, T and Hoppitt, W and Willerslev, E and Drummond, A and Cooper, A}, Author = {Bunce, Michael and Worthy, Trevor H and Ford, Tom and Hoppitt, Will and Willerslev, Eske and Drummond, Alexei J. and Cooper, Alan}, Da = {20030911}, Date-Added = {2008-11-28 10:43:07 -0800}, Date-Modified = {2014-07-06 00:51:29 +0000}, Dcom = {20030924}, Doi = {10.1038/nature01871}, Edat = {2003/09/12 05:00}, Issn = {1476-4687 (Electronic)}, Jid = {0410462}, Journal = {Nature}, Jt = {Nature}, Language = {eng}, Lr = {20061115}, Mh = {Animals; *Body Constitution; Body Weight; Bone and Bones/anatomy \& histology; DNA, Mitochondrial/genetics; *Ecosystem; Evolution; Female; *Fossils; Geography; Male; Molecular Sequence Data; New Zealand; Palaeognathae/*anatomy \& histology/classification/genetics; Phylogeny; *Sex Characteristics; Sex Determination (Analysis); Time Factors}, Mhda = {2003/09/25 05:00}, Number = {6954}, Own = {NLM}, Pages = {172--175}, Phst = {2003/03/06 {$[$}received{$]$}; 2003/06/23 {$[$}accepted{$]$}}, Pii = {nature01871}, Pl = {England}, Pmid = {12968178}, Pst = {ppublish}, Pt = {Journal Article; Research Support, Non-U.S. Gov't}, Pubm = {Print}, Rn = {0 (DNA, Mitochondrial)}, Sb = {IM}, Si = {GENBANK/AY326127; GENBANK/AY326128; GENBANK/AY326129; GENBANK/AY326130; GENBANK/AY326131; GENBANK/AY326132; GENBANK/AY326133; GENBANK/AY326134; GENBANK/AY326135; GENBANK/AY326136; GENBANK/AY326137; GENBANK/AY326138; GENBANK/AY326139; GENBANK/AY326140; GENBANK/AY326141; GENBANK/AY326142; GENBANK/AY326143; GENBANK/AY326144; GENBANK/AY326145; GENBANK/AY326146; GENBANK/AY326147; GENBANK/AY326148; GENBANK/AY326149; GENBANK/AY326150; GENBANK/AY326151; GENBANK/AY326152; GENBANK/AY326153; GENBANK/AY326154; GENBANK/AY326155; GENBANK/AY326156; GENBANK/AY326157; GENBANK/AY326158; GENBANK/AY326159; GENBANK/AY326160; GENBANK/AY326161; GENBANK/AY326162; GENBANK/AY326163; GENBANK/AY326164; GENBANK/AY326165; GENBANK/AY326166; GENBANK/AY326167; GENBANK/AY326168; GENBANK/AY326169; GENBANK/AY326170; GENBANK/AY326171; GENBANK/AY326172; GENBANK/AY326173; GENBANK/AY326174; GENBANK/AY326175; GENBANK/AY326176; GENBANK/AY326177; GENBANK/AY326178; GENBANK/AY326179; GENBANK/AY326180; GENBANK/AY326181; GENBANK/AY326182; GENBANK/AY326183; GENBANK/AY326184; GENBANK/AY326185; GENBANK/AY326186; GENBANK/AY326187; GENBANK/AY326188; GENBANK/AY326189; GENBANK/AY326190; GENBANK/AY326191; GENBANK/AY326192; GENBANK/AY326193}, So = {Nature. 2003 Sep 11;425(6954):172-5.}, Stat = {MEDLINE}, Title = {Extreme reversed sexual size dimorphism in the extinct New Zealand moa Dinornis.}, Volume = {425}, Year = {2003}, Bdsk-Url-1 = {http://dx.doi.org/10.1038/nature01871}} @article{Drummond2003inference, Abstract = {The processes of mutation and nucleotide substitution contribute to the observed variability in virulence, transmission and persistence of viral pathogens. Since most viruses evolve many times faster than their human hosts, we are in the unusual position of being able to measure these processes directly by comparing viral genes that have been isolated and sequenced at different points in time. The analysis of such data requires the use of specific statistical methods that take into account the shared ancestry of the sequences and the randomness inherent in the process of nucleotide substitution. In this paper we describe the various statistical methods for estimating evolutionary rates, which can be classified into three general approaches: linear regression, maximum likelihood, and Bayesian inference. We discuss the advantages and shortcomings of each approach and illustrate their use through the analysis of two example viruses; human immunodeficiency virus type 1 and dengue virus serotype 4. Reliable estimates of viral substitution rates have many important applications in population genetics and phylogenetics, including dating evolutionary events and divergence times, estimating demographic parameters such as population size and generation time, and investigating the effect of natural selection on molecular evolution.}, Au = {Drummond, A. and Pybus, O. G. and Rambaut, A.}, Author = {Drummond, Alexei J. and Pybus, Oliver G and Rambaut, Andrew}, Da = {20040108}, Date-Added = {2008-11-28 10:43:05 -0800}, Date-Modified = {2014-08-02 22:08:22 +0000}, Dcom = {20040122}, Edat = {2004/01/09 05:00}, Issn = {0065-308X (Print)}, Jid = {0370435}, Journal = {Adv Parasitol}, Jt = {Advances in parasitology}, Lr = {20061115}, Mh = {Base Sequence; *Evolution, Molecular; *Genes, Viral; Humans; Models, Statistical; Viruses/*genetics}, Mhda = {2004/01/24 05:00}, Own = {NLM}, Pages = {331--358}, Pl = {England}, Pmid = {14711090}, Pst = {ppublish}, Pt = {Journal Article; Research Support, Non-U.S. Gov't; Review}, Pubm = {Print}, Rf = {62}, Sb = {IM}, So = {Adv Parasitol. 2003;54:331-58.}, Stat = {MEDLINE}, Title = {Inference of viral evolutionary rates from molecular sequences.}, Volume = {54}, Year = {2003}} @article{Hon:2006ph, Abstract = {Infectious bursal disease virus (IBDV) is a birnavirus causing immunosuppressive disease in chickens. Emergence of the very virulent form of IBDV (vvIBDV) in the late 1980s dramatically changed the epidemiology of the disease. In this study, we investigated the phylogenetic origins of its genome segments and estimated the time of emergence of their most recent common ancestors. Moreover, with recently developed coalescence techniques, we reconstructed the past population dynamics of vvIBDV and timed the onset of its expansion to the late 1980s. Our analysis suggests that genome segment A of vvIBDV emerged at least 20 years before its expansion, which argues against the hypothesis that mutation of genome segment A is the major contributing factor in the emergence and expansion of vvIBDV. Alternatively, the phylogeny of genome segment B suggests a possible reassortment event estimated to have taken place around the mid-1980s, which seems to coincide with its expansion within approximately 5 years. We therefore hypothesize that the reassortment of genome segment B initiated vvIBDV expansion in the late 1980s, possibly by enhancing the virulence of the virus synergistically with its existing genome segment A. This report reveals the possible mechanisms leading to the emergence and expansion of vvIBDV, which would certainly provide insights into the scope of surveillance and prevention efforts regarding the disease.}, Address = {Department of Zoology, The University of Hong Kong, China.}, Au = {Hon, CC and Lam, TY and Drummond, A and Rambaut, A and Lee, YF and Yip, CW and Zeng, F and Lam, PY and Ng, PT and Leung, FC}, Author = {Hon, Chung-Chau and Lam, Tsan-Yuk and Drummond, Alexei J. and Rambaut, Andrew and Lee, Yiu-Fai and Yip, Chi-Wai and Zeng, Fanya and Lam, Pui-Yi and Ng, Patrick T W and Leung, Frederick C C}, Da = {20060816}, Date-Added = {2008-11-28 10:42:26 -0800}, Date-Modified = {2014-07-06 00:49:38 +0000}, Dcom = {20060925}, Doi = {10.1128/JVI.00585-06}, Edat = {2006/08/17 09:00}, Issn = {0022-538X (Print)}, Jid = {0113724}, Journal = {J Virol}, Jt = {Journal of virology}, Language = {eng}, Mh = {Animals; Birnaviridae Infections/epidemiology/*veterinary/virology; Chickens; Evolution, Molecular; *Genome, Viral; Infectious bursal disease virus/classification/*genetics/*pathogenicity; *Phylogeny; Poultry Diseases/epidemiology/virology; Reassortant Viruses/classification/*genetics/*pathogenicity; Time Factors; Virulence}, Mhda = {2006/09/26 09:00}, Number = {17}, Own = {NLM}, Pages = {8503--8509}, Pii = {80/17/8503}, Pl = {United States}, Pmc = {PMC1563883}, Pmid = {16912300}, Pst = {ppublish}, Pt = {Journal Article}, Pubm = {Print}, Sb = {IM}, So = {J Virol. 2006 Sep;80(17):8503-9.}, Stat = {MEDLINE}, Title = {Phylogenetic analysis reveals a correlation between the expansion of very virulent infectious bursal disease virus and reassortment of its genome segment B.}, Volume = {80}, Year = {2006 Sep}, Bdsk-Url-1 = {http://dx.doi.org/10.1128/JVI.00585-06}} @article{Lambert:2002gd, Abstract = {Well-preserved subfossil bones of Adelie penguins, Pygoscelis adeliae, underlie existing and abandoned nesting colonies in Antarctica. These bones, dating back to more than 7000 years before the present, harbor some of the best-preserved ancient DNA yet discovered. From 96 radiocarbon-aged bones, we report large numbers of mitochondrial haplotypes, some of which appear to be extinct, given the 380 living birds sampled. We demonstrate DNA sequence evolution through time and estimate the rate of evolution of the hypervariable region I using a Markov chain Monte Carlo integration and a least-squares regression analysis. Our calculated rates of evolution are approximately two to seven times higher than previous indirect phylogenetic estimates.}, Au = {Lambert, DM and Ritchie, PA and Millar, CD and Holland, B and Drummond, AJ and Baroni, C}, Author = {Lambert, D M and Ritchie, P A and Millar, C D and Holland, B and Drummond, A J and Baroni, C}, Cin = {Science. 2002 Mar 22;295(5563):2197. PMID: 11910085}, Da = {20020322}, Date-Added = {2008-11-28 10:41:19 -0800}, Date-Modified = {2014-07-03 23:04:46 +0000}, Dcom = {20020404}, Doi = {10.1126/science.1068105}, Edat = {2002/03/23 10:00}, Issn = {1095-9203 (Electronic)}, Jid = {0404511}, Journal = {Science}, Jt = {Science (New York, N.Y.)}, Language = {eng}, Lr = {20070319}, Mh = {Animals; Antarctic Regions; Birds/*genetics; Bone and Bones/metabolism; Calibration; Carbon Radioisotopes; DNA, Mitochondrial/*genetics/isolation \& purification; Ecosystem; *Evolution, Molecular; Fossils; Haplotypes/genetics; Least-Squares Analysis; Markov Chains; Monte Carlo Method; Phylogeny; Polymerase Chain Reaction; Time Factors}, Mhda = {2002/04/18 10:01}, Number = {5563}, Own = {NLM}, Pages = {2270--2273}, Pii = {295/5563/2270}, Pl = {United States}, Pmid = {11910113}, Pst = {ppublish}, Pt = {Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, P.H.S.}, Pubm = {Print}, Rn = {0 (Carbon Radioisotopes); 0 (DNA, Mitochondrial)}, Sb = {IM}, So = {Science. 2002 Mar 22;295(5563):2270-3.}, Stat = {MEDLINE}, Title = {Rates of evolution in ancient DNA from Adelie penguins.}, Volume = {295}, Year = {2002}, Bdsk-Url-1 = {http://dx.doi.org/10.1126/science.1068105}} @article{Pybus:2003la, Abstract = {Hepatitis C virus (HCV) is a leading cause of liver cancer and cirrhosis, and Egypt has possibly the highest HCV prevalence worldwide. In this article we use a newly developed Bayesian inference framework to estimate the transmission dynamics of HCV in Egypt from sampled viral gene sequences, and to predict the public health impact of the virus. Our results indicate that the effective number of HCV infections in Egypt underwent rapid exponential growth between 1930 and 1955. The timing and speed of this spread provides quantitative genetic evidence that the Egyptian HCV epidemic was initiated and propagated by extensive antischistosomiasis injection campaigns. Although our results show that HCV transmission has since decreased, we conclude that HCV is likely to remain prevalent in Egypt for several decades. Our combined population genetic and epidemiological analysis provides detailed estimates of historical changes in Egyptian HCV prevalence. Because our results are consistent with a demographic scenario specified a priori, they also provide an objective test of inference methods based on the coalescent process.}, Au = {Pybus, OG and Drummond, AJ and Nakano, T and Robertson, BH and Rambaut, A}, Author = {Pybus, O G and Drummond, A J and Nakano, T and Robertson, B H and Rambaut, A}, Da = {20030319}, Date-Added = {2008-11-28 10:41:16 -0800}, Date-Modified = {2014-07-04 01:56:39 +0000}, Dcom = {20031023}, Edat = {2003/03/20 04:00}, Issn = {0737-4038 (Print)}, Jid = {8501455}, Journal = {Mol Biol Evol}, Jt = {Molecular biology and evolution}, Language = {eng}, Lr = {20061115}, Mh = {Bayes Theorem; Demography; Egypt/epidemiology; Hepacivirus/*genetics/pathogenicity; Hepatitis C/*epidemiology/*transmission; Humans; Iatrogenic Disease/epidemiology; Models, Genetic; Mutagenesis; Prevalence}, Mhda = {2003/10/24 05:00}, Month = {3}, Number = {3}, Own = {NLM}, Pages = {381--387}, Pl = {United States}, Pmid = {12644558}, Pst = {ppublish}, Pt = {Journal Article; Research Support, Non-U.S. Gov't}, Pubm = {Print}, Sb = {IM}, So = {Mol Biol Evol. 2003 Mar;20(3):381-7.}, Stat = {MEDLINE}, Title = {The epidemiology and iatrogenic transmission of hepatitis C virus in Egypt: a Bayesian coalescent approach.}, Volume = {20}, Year = {2003}} @article{Strugnell:2004ek, Au = {Strugnell, J and Norman, M and Drummond, AJ and Cooper, A}, Author = {Strugnell, Jan and Norman, Mark and Drummond, Alexei J and Cooper, Alan}, Da = {20040415}, Date-Added = {2008-11-28 10:41:13 -0800}, Date-Modified = {2008-11-28 10:41:13 -0800}, Dcom = {20040608}, Doi = {10.1016/j.cub.2004.03.048}, Edat = {2004/04/16 05:00}, Issn = {0960-9822 (Print)}, Jid = {9107782}, Journal = {Curr Biol}, Jt = {Current biology : CB}, Language = {eng}, Lr = {20061115}, Mh = {*Adaptation, Physiological; Animals; Base Sequence; Bayes Theorem; Environment; Likelihood Functions; Models, Genetic; Molecular Sequence Data; Octopodiformes/embryology/*genetics/physiology; *Phylogeny; Sequence Analysis, DNA; Time Factors}, Mhda = {2004/06/21 10:00}, Number = {8}, Own = {NLM}, Pages = {R300-1}, Pii = {S0960982204002258}, Pl = {England}, Pmid = {15084297}, Pst = {ppublish}, Pt = {Comparative Study; Letter}, Pubm = {Print}, Sb = {IM}, So = {Curr Biol. 2004 Apr 20;14(8):R300-1.}, Stat = {MEDLINE}, Title = {Neotenous origins for pelagic octopuses.}, Volume = {14}, Year = {2004 Apr 20}, Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.cub.2004.03.048}} @article{Cooper:2004qq, Abstract = {Mitochondrial DNA sequences recovered from eight Neandertal specimens cannot be detected in either early fossil Europeans or in modern populations. This indicates that, if Neandertals made any genetic contribution at all to modern humans, it must have been limited, though the extent of the contribution cannot be resolved at present.}, Address = {Henry Wellcome Ancient Biomolecules Centre and Department of Zoology, University of Oxford, Oxford OX1 3PS, UK.}, Au = {Cooper, A and Drummond, AJ and Willerslev, E}, Author = {Cooper, Alan and Drummond, Alexei J and Willerslev, Eske}, Ci = {Copyright 2004 Elsevier Ltd.}, Da = {20040608}, Date-Added = {2008-11-28 10:41:09 -0800}, Date-Modified = {2008-11-28 10:41:09 -0800}, Dcom = {20040902}, Doi = {10.1016/j.cub.2004.05.037}, Edat = {2004/06/09 05:00}, Issn = {0960-9822 (Print)}, Jid = {9107782}, Journal = {Curr Biol}, Jt = {Current biology : CB}, Language = {eng}, Lr = {20051116}, Mh = {Animals; DNA, Mitochondrial/*genetics; *Fossils; Hominidae/*genetics; Humans; *Models, Genetic; Time Factors}, Mhda = {2004/09/03 05:00}, Number = {11}, Own = {NLM}, Pages = {R431-3}, Pii = {S0960982204003641}, Pl = {England}, Pmid = {15182692}, Pst = {ppublish}, Pt = {Journal Article; Review}, Pubm = {Print}, Rf = {17}, Rn = {0 (DNA, Mitochondrial)}, Sb = {IM}, So = {Curr Biol. 2004 Jun 8;14(11):R431-3.}, Stat = {MEDLINE}, Title = {Ancient DNA: would the real Neandertal please stand up?}, Volume = {14}, Year = {2004 Jun 8}, Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.cub.2004.05.037}} @article{Lemey:2004uo, Abstract = {HIV-1 group O originated through cross-species transmission of SIV from chimpanzees to humans and has established a relatively low prevalence in Central Africa. Here, we infer the population genetics and epidemic history of HIV-1 group O from viral gene sequence data and evaluate the effect of variable evolutionary rates and recombination on our estimates. First, model selection tools were used to specify suitable evolutionary and coalescent models for HIV group O. Second, divergence times and population genetic parameters were estimated in a Bayesian framework using Markov chain Monte Carlo sampling, under both strict and relaxed molecular clock methods. Our results date the origin of the group O radiation to around 1920 (1890-1940), a time frame similar to that estimated for HIV-1 group M. However, group O infections, which remain almost wholly restricted to Cameroon, show a slower rate of exponential growth during the twentieth century, explaining their lower current prevalence. To explore the effect of recombination, the Bayesian framework is extended to incorporate multiple unlinked loci. Although recombination can bias estimates of the time to the most recent common ancestor, this effect does not appear to be important for HIV-1 group O. In addition, we show that evolutionary rate estimates for different HIV genes accurately reflect differential selective constraints along the HIV genome.}, Address = {Rega Institute for Medical Research, KULeuven, B-3000 Leuven, Belgium. [email protected]}, Au = {Lemey, P and Pybus, OG and Rambaut, A and Drummond, AJ and Robertson, DL and Roques, P and Worobey, M and Vandamme, AM}, Author = {Lemey, Philippe and Pybus, Oliver G and Rambaut, Andrew and Drummond, Alexei J and Robertson, David L and Roques, Pierre and Worobey, Michael and Vandamme, Anne-Mieke}, Da = {20040728}, Date-Added = {2008-11-28 10:41:08 -0800}, Date-Modified = {2008-11-28 10:41:08 -0800}, Dcom = {20050224}, Doi = {10.1534/genetics.104.026666}, Edat = {2004/07/29 05:00}, Issn = {0016-6731 (Print)}, Jid = {0374636}, Journal = {Genetics}, Jt = {Genetics}, Language = {eng}, Lr = {20061115}, Mh = {Bayes Theorem; Cameroon; *Evolution, Molecular; *Genetics, Population; *Genome, Viral; HIV-1/*genetics; Humans; Likelihood Functions; *Models, Genetic; Phylogeny; Recombination, Genetic/genetics; Species Specificity; Viral Proteins/genetics}, Mhda = {2005/02/25 09:00}, Number = {3}, Own = {NLM}, Pages = {1059--1068}, Pii = {167/3/1059}, Pl = {United States}, Pmc = {PMC1470933}, Pmid = {15280223}, Pst = {ppublish}, Pt = {Comparative Study; Journal Article; Research Support, Non-U.S. Gov't}, Pubm = {Print}, Rn = {0 (Viral Proteins)}, Sb = {IM}, So = {Genetics. 2004 Jul;167(3):1059-68.}, Stat = {MEDLINE}, Title = {The molecular population genetics of HIV-1 group O.}, Volume = {167}, Year = {2004 Jul}, Bdsk-Url-1 = {http://dx.doi.org/10.1534/genetics.104.026666}} @article{leonard2002, Author = {Leonard, J.A. and Wayne, R.K. and Wheeler, J. and Valadez, R. and Guillen, S. and Vila, C.}, Journal = {Science}, Number = {5598}, Pages = {1613}, Publisher = {AAAS}, Title = {{Ancient DNA evidence for Old World origin of New World dogs}}, Volume = {298}, Year = {2002}} @article{Shapiro:2004xe, Abstract = {The widespread extinctions of large mammals at the end of the Pleistocene epoch have often been attributed to the depredations of humans; here we present genetic evidence that questions this assumption. We used ancient DNA and Bayesian techniques to reconstruct a detailed genetic history of bison throughout the late Pleistocene and Holocene epochs. Our analyses depict a large diverse population living throughout Beringia until around 37,000 years before the present, when the population's genetic diversity began to decline dramatically. The timing of this decline correlates with environmental changes associated with the onset of the last glacial cycle, whereas archaeological evidence does not support the presence of large populations of humans in Eastern Beringia until more than 15,000 years later.}, Au = {Shapiro, B and Drummond, AJ and Rambaut, A and Wilson, MC and Matheus, PE and Sher, AV and Pybus, OG and Gilbert, MT and Barnes, I and Binladen, J and Willerslev, E and Hansen, AJ and Baryshnikov, GF and Burns, JA and Davydov, S and Driver, JC and Froese, DG and Harington, CR and Keddie, G and Kosintsev, P and Kunz, ML and Martin, LD and Stephenson, RO and Storer, J and Tedford, R and Zimov, S and Cooper, A}, Author = {Shapiro, Beth and Drummond, Alexei J and Rambaut, Andrew and Wilson, Michael C and Matheus, Paul E and Sher, Andrei V and Pybus, Oliver G and Gilbert, M Thomas P and Barnes, Ian and Binladen, Jonas and Willerslev, Eske and Hansen, Anders J and Baryshnikov, Gennady F and Burns, James A and Davydov, Sergei and Driver, Jonathan C and Froese, Duane G and Harington, C Richard and Keddie, Grant and Kosintsev, Pavel and Kunz, Michael L and Martin, Larry D and Stephenson, Robert O and Storer, John and Tedford, Richard and Zimov, Sergei and Cooper, Alan}, Cin = {Science. 2004 Nov 26;306(5701):1454. PMID: 15567821}, Da = {20041129}, Date-Added = {2008-11-28 10:41:06 -0800}, Date-Modified = {2014-07-06 00:40:24 +0000}, Dcom = {20041221}, Doi = {10.1126/science.1101074}, Edat = {2004/11/30 09:00}, Issn = {1095-9203 (Electronic)}, Jid = {0404511}, Journal = {Science}, Jt = {Science (New York, N.Y.)}, Language = {eng}, Lr = {20070319}, Mh = {Alaska; Animals; Bayes Theorem; *Bison/classification/genetics; Canada; China; *Climate; DNA, Mitochondrial/genetics; Environment; *Fossils; Genetics, Population; Human Activities; Humans; North America; Phylogeny; Population Dynamics; Sequence Analysis, DNA; Time; Variation (Genetics)}, Mhda = {2004/12/22 09:00}, Number = {5701}, Own = {NLM}, Pages = {1561--1565}, Pii = {306/5701/1561}, Pl = {United States}, Pmid = {15567864}, Pst = {ppublish}, Pt = {Journal Article; Research Support, Non-U.S. Gov't}, Pubm = {Print}, Rn = {0 (DNA, Mitochondrial)}, Sb = {IM}, So = {Science. 2004 Nov 26;306(5701):1561-5.}, Stat = {MEDLINE}, Title = {Rise and fall of the Beringian steppe bison.}, Volume = {306}, Year = {2004}, Bdsk-Url-1 = {http://dx.doi.org/10.1126/science.1101074}} @article{Ho:2005rw, Abstract = {In recent years, a number of phylogenetic methods have been developed for estimating molecular rates and divergence dates under models that relax the molecular clock constraint by allowing rate change throughout the tree. These methods are being used with increasing frequency, but there have been few studies into their accuracy. We tested the accuracy of several relaxed-clock methods (penalized likelihood and Bayesian inference using various models of rate change) using nucleotide sequences simulated on a nine-taxon tree. When the sequences evolved with a constant rate, the methods were able to infer rates accurately, but estimates were more precise when a molecular clock was assumed. When the sequences evolved under a model of auto-correlated rate change, rates were accurately estimated using penalized likelihood and by Bayesian inference using lognormal and exponential models of rate change, while other models did not perform as well. When the sequences evolved under a model of uncorrelated rate change, only Bayesian inference using an exponential rate model performed well. Collectively, the results provide a strong recommendation for using the exponential model of rate change if a conservative approach to divergence time estimation is required. A case study is presented in which we use a simulation-based approach to examine the hypothesis of elevated rates in the Cambrian period, and it is found that these high rate estimates might be an artifact of the rate estimation method. If this bias is present, then the ages of metazoan divergences would be systematically underestimated. The results of this study have implications for studies of molecular rates and divergence dates.}, Address = {Henry Wellcome Ancient Biomolecules Centre, Oxford, United Kingdom. [email protected]}, Au = {Ho, SY and Phillips, MJ and Drummond, AJ and Cooper, A}, Author = {Ho, Simon Y W and Phillips, Matthew J and Drummond, Alexei J and Cooper, Alan}, Da = {20050413}, Date-Added = {2008-11-28 10:41:04 -0800}, Date-Modified = {2008-11-28 10:41:04 -0800}, Dcom = {20050830}, Dep = {20050309}, Doi = {10.1093/molbev/msi125}, Edat = {2005/03/11 09:00}, Gr = {United Kingdom Wellcome Trust}, Issn = {0737-4038 (Print)}, Jid = {8501455}, Journal = {Mol Biol Evol}, Jt = {Molecular biology and evolution}, Language = {eng}, Lr = {20070813}, Mh = {*Algorithms; Animals; Bayes Theorem; *Evolution, Molecular; Invertebrates/*genetics/*radiation effects; Likelihood Functions; Markov Chains; *Models, Genetic; Phylogeny; Time Factors}, Mhda = {2005/09/01 09:00}, Number = {5}, Own = {NLM}, Pages = {1355--1363}, Phst = {2005/03/09 {$[$}aheadofprint{$]$}}, Pii = {msi125}, Pl = {United States}, Pmid = {15758207}, Pst = {ppublish}, Pt = {Journal Article; Research Support, Non-U.S. Gov't}, Pubm = {Print-Electronic}, Sb = {IM}, So = {Mol Biol Evol. 2005 May;22(5):1355-63. Epub 2005 Mar 9.}, Stat = {MEDLINE}, Title = {Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation.}, Volume = {22}, Year = {2005 May}, Bdsk-Url-1 = {http://dx.doi.org/10.1093/molbev/msi125}} @article{Ho:2005rc, Abstract = {Studies of molecular evolutionary rates have yielded a wide range of rate estimates for various genes and taxa. Recent studies based on population-level and pedigree data have produced remarkably high estimates of mutation rate, which strongly contrast with substitution rates inferred in phylogenetic (species-level) studies. Using Bayesian analysis with a relaxed-clock model, we estimated rates for three groups of mitochondrial data: avian protein-coding genes, primate protein-coding genes, and primate d-loop sequences. In all three cases, we found a measurable transition between the high, short-term (< 1-2 Myr) mutation rate and the low, long-term substitution rate. The relationship between the age of the calibration and the rate of change can be described by a vertically translated exponential decay curve, which may be used for correcting molecular date estimates. The phylogenetic substitution rates in mitochondria are approximately 0.5% per million years for avian protein-coding sequences and 1.5% per million years for primate protein-coding and d-loop sequences. Further analyses showed that purifying selection offers the most convincing explanation for the observed relationship between the estimated rate and the depth of the calibration. We rule out the possibility that it is a spurious result arising from sequence errors, and find it unlikely that the apparent decline in rates over time is caused by mutational saturation. Using a rate curve estimated from the d-loop data, several dates for last common ancestors were calculated: modern humans and Neandertals (354 ka; 222-705 ka), Neandertals (108 ka; 70-156 ka), and modern humans (76 ka; 47-110 ka). If the rate curve for a particular taxonomic group can be accurately estimated, it can be a useful tool for correcting divergence date estimates by taking the rate decay into account. Our results show that it is invalid to extrapolate molecular rates of change across different evolutionary timescales, which has important consequences for studies of populations, domestication, conservation genetics, and human evolution.}, Address = {Henry Wellcome Ancient Biomolecules Centre, Department of Zoology, University of Oxford, Oxford, United Kingdom. [email protected]}, Au = {Ho, SY and Phillips, MJ and Cooper, A and Drummond, AJ}, Author = {Ho, Simon Y W and Phillips, Matthew J and Cooper, Alan and Drummond, Alexei J}, Da = {20050606}, Date-Added = {2008-11-28 10:41:03 -0800}, Date-Modified = {2008-11-28 10:41:03 -0800}, Dcom = {20051214}, Dep = {20050406}, Doi = {10.1093/molbev/msi145}, Edat = {2005/04/09 09:00}, Gr = {United Kingdom Wellcome Trust}, Issn = {0737-4038 (Print)}, Jid = {8501455}, Journal = {Mol Biol Evol}, Jt = {Molecular biology and evolution}, Language = {eng}, Lr = {20070813}, Mh = {Animals; Bayes Theorem; Birds/genetics; DNA, Mitochondrial/*genetics; *Evolution, Molecular; *Genetics, Population; Hominidae/genetics; Humans/genetics; Mutation; *Phylogeny; Primates/genetics; Species Specificity; Time Factors; Variation (Genetics)}, Mhda = {2005/12/15 09:00}, Number = {7}, Own = {NLM}, Pages = {1561--1568}, Phst = {2005/04/06 {$[$}aheadofprint{$]$}}, Pii = {msi145}, Pl = {United States}, Pmid = {15814826}, Pst = {ppublish}, Pt = {Journal Article; Research Support, Non-U.S. Gov't}, Pubm = {Print-Electronic}, Rn = {0 (DNA, Mitochondrial)}, Sb = {IM}, So = {Mol Biol Evol. 2005 Jul;22(7):1561-8. Epub 2005 Apr 6.}, Stat = {MEDLINE}, Title = {Time dependency of molecular rate estimates and systematic overestimation of recent divergence times.}, Volume = {22}, Year = {2005 Jul}, Bdsk-Url-1 = {http://dx.doi.org/10.1093/molbev/msi145}} @article{Strugnell:2005qr, Address = {Molecular Evolution, Department of Zoology, South Parks Road, Oxford OX1 3PS, UK. [email protected]}, Au = {Strugnell, J and Norman, M and Jackson, J and Drummond, AJ and Cooper, A}, Author = {Strugnell, Jan and Norman, Mark and Jackson, Jennifer and Drummond, Alexei J and Cooper, Alan}, Da = {20051014}, Date-Added = {2008-11-28 10:41:02 -0800}, Date-Modified = {2008-11-28 10:41:02 -0800}, Dcom = {20051223}, Dep = {20050602}, Doi = {10.1016/j.ympev.2005.03.020}, Edat = {2005/06/07 09:00}, Issn = {1055-7903 (Print)}, Jid = {9304400}, Journal = {Mol Phylogenet Evol}, Jt = {Molecular phylogenetics and evolution}, Language = {eng}, Lr = {20061115}, Mh = {Animals; Bayes Theorem; Cephalopoda/*classification/*genetics; *Evolution, Molecular; *Genes; *Phylogeny}, Mhda = {2005/12/24 09:00}, Number = {2}, Own = {NLM}, Pages = {426--441}, Phst = {2004/12/09 {$[$}received{$]$}; 2005/03/03 {$[$}revised{$]$}; 2005/03/15 {$[$}accepted{$]$}; 2005/06/02 {$[$}aheadofprint{$]$}}, Pii = {S1055-7903(05)00094-1}, Pl = {United States}, Pmid = {15935706}, Pst = {ppublish}, Pt = {Journal Article; Research Support, Non-U.S. Gov't}, Pubm = {Print-Electronic}, Sb = {IM}, So = {Mol Phylogenet Evol. 2005 Nov;37(2):426-41. Epub 2005 Jun 2.}, Stat = {MEDLINE}, Title = {Molecular phylogeny of coleoid cephalopods (Mollusca: Cephalopoda) using a multigene approach; the effect of data partitioning on resolving phylogenies in a Bayesian framework.}, Volume = {37}, Year = {2005 Nov}, Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.ympev.2005.03.020}} @article{Forsberg:2005qd, Address = {Bioinformatics Research Center, Department of Genetics and Ecology, University of Aarhus, Arhus, Denmark. [email protected]}, Au = {Forsberg, R and Drummond, AJ and Hein, J}, Author = {Forsberg, Roald and Drummond, Alexei J and Hein, Jotun}, Da = {20050815}, Date-Added = {2008-11-28 10:40:57 -0800}, Date-Modified = {2008-11-28 10:40:57 -0800}, Dcom = {20060612}, Dep = {20050616}, Doi = {10.1186/1471-2156-6-35}, Edat = {2005/06/18 09:00}, Gr = {1-R01-GM60729-01/GM/United States NIGMS}, Issn = {1471-2156 (Electronic)}, Jid = {100966978}, Journal = {BMC Genet}, Jt = {BMC genetics}, Language = {eng}, Lr = {20071114}, Mh = {Animals; DNA, Mitochondrial/genetics; *Evolution; Humans; *Models, Genetic; *Mutation; Pedigree; Probability; Time}, Mhda = {2006/06/13 09:00}, Own = {NLM}, Pages = {35}, Phst = {2004/10/19 {$[$}received{$]$}; 2005/06/16 {$[$}accepted{$]$}; 2005/06/16 {$[$}aheadofprint{$]$}}, Pii = {1471-2156-6-35}, Pl = {England}, Pmc = {PMC1185533}, Pmid = {15960847}, Pst = {epublish}, Pt = {Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, P.H.S.}, Pubm = {Electronic}, Rn = {0 (DNA, Mitochondrial)}, Sb = {IM}, So = {BMC Genet. 2005 Jun 16;6:35.}, Stat = {MEDLINE}, Title = {Tree measures and the number of segregating sites in time-structured population samples.}, Volume = {6}, Year = {2005}, Bdsk-Url-1 = {http://dx.doi.org/10.1186/1471-2156-6-35}} @article{Shapiro:2006hl, Abstract = {Although phylogenetic inference of protein-coding sequences continues to dominate the literature, few analyses incorporate evolutionary models that consider the genetic code. This problem is exacerbated by the exclusion of codon-based models from commonly employed model selection techniques, presumably due to the computational cost associated with codon models. We investigated an efficient alternative to standard nucleotide substitution models, in which codon position (CP) is incorporated into the model. We determined the most appropriate model for alignments of 177 RNA virus genes and 106 yeast genes, using 11 substitution models including one codon model and four CP models. The majority of analyzed gene alignments are best described by CP substitution models, rather than by standard nucleotide models, and without the computational cost of full codon models. These results have significant implications for phylogenetic inference of coding sequences as they make it clear that substitution models incorporating CPs not only are a computationally realistic alternative to standard models but may also frequently be statistically superior.}, Au = {Shapiro, B and Rambaut, A and Drummond, AJ}, Author = {Shapiro, Beth and Rambaut, Andrew and Drummond, Alexei J}, Da = {20051205}, Date-Added = {2008-11-28 10:40:55 -0800}, Date-Modified = {2008-11-28 10:40:55 -0800}, Dcom = {20060810}, Dep = {20050921}, Doi = {10.1093/molbev/msj021}, Edat = {2005/09/24 09:00}, Gr = {United Kingdom Wellcome Trust}, Issn = {0737-4038 (Print)}, Jid = {8501455}, Journal = {Mol Biol Evol}, Jt = {Molecular biology and evolution}, Language = {eng}, Lr = {20070813}, Mh = {Classification/*methods; Codon/genetics; *Models, Genetic; *Phylogeny; Proteins/*genetics; RNA Viruses/genetics; Sequence Alignment/methods; Yeasts/genetics}, Mhda = {2006/08/11 09:00}, Number = {1}, Own = {NLM}, Pages = {7--9}, Phst = {2005/09/21 {$[$}aheadofprint{$]$}}, Pii = {msj021}, Pl = {United States}, Pmid = {16177232}, Pst = {ppublish}, Pt = {Comparative Study; Letter; Research Support, Non-U.S. Gov't}, Pubm = {Print-Electronic}, Rn = {0 (Codon); 0 (Proteins)}, Sb = {IM}, So = {Mol Biol Evol. 2006 Jan;23(1):7-9. Epub 2005 Sep 21.}, Stat = {MEDLINE}, Title = {Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences.}, Volume = {23}, Year = {2006}, Bdsk-Url-1 = {http://dx.doi.org/10.1093/molbev/msj021}} @article{Biek:2006db, Address = {Wildlife Biology Program, University of Montana, Missoula, MT 59812, USA. [email protected]}, Au = {Biek, R and Drummond, AJ and Poss, M}, Author = {Biek, Roman and Drummond, Alexei J and Poss, Mary}, Da = {20060127}, Date-Added = {2008-11-28 10:40:54 -0800}, Date-Modified = {2008-11-28 10:40:54 -0800}, Dcom = {20060203}, Doi = {10.1126/science.1121360}, Edat = {2006/01/28 09:00}, Issn = {1095-9203 (Electronic)}, Jid = {0404511}, Journal = {Science}, Jt = {Science (New York, N.Y.)}, Language = {eng}, Lr = {20070319}, Mh = {Alberta/epidemiology; Animals; Bayes Theorem; British Columbia/epidemiology; Ecosystem; *Evolution, Molecular; Genes, env; Genes, pol; Geography; Immunodeficiency Virus, Feline/*classification/*genetics; Lentivirus Infections/epidemiology/*veterinary/virology; Microsatellite Repeats; Molecular Sequence Data; Montana/epidemiology; Phylogeny; Population Dynamics; *Puma/genetics/virology; Time Factors; Wyoming/epidemiology}, Mhda = {2006/02/04 09:00}, Number = {5760}, Own = {NLM}, Pages = {538--541}, Pii = {311/5760/538}, Pl = {United States}, Pmid = {16439664}, Pst = {ppublish}, Pt = {Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.}, Pubm = {Print}, Sb = {IM}, Si = {GENBANK/DQ106985; GENBANK/DQ106986; GENBANK/DQ106987; GENBANK/DQ106988; GENBANK/DQ106989; GENBANK/DQ106990; GENBANK/DQ106991; GENBANK/DQ106992; GENBANK/DQ106993; GENBANK/DQ106994; GENBANK/DQ106995; GENBANK/DQ106996; GENBANK/DQ106997; GENBANK/DQ106998; GENBANK/DQ106999; GENBANK/DQ107000; GENBANK/DQ107001; GENBANK/DQ107002; GENBANK/DQ107003; GENBANK/DQ107004; GENBANK/DQ107005; GENBANK/DQ107006; GENBANK/DQ107007; GENBANK/DQ107008; GENBANK/DQ107009; GENBANK/DQ107010; GENBANK/DQ107011; GENBANK/DQ107012; GENBANK/DQ107013; GENBANK/DQ107014; GENBANK/DQ107015; GENBANK/DQ107016; GENBANK/DQ107017; GENBANK/DQ107018; GENBANK/DQ107019; GENBANK/DQ107020; GENBANK/DQ107021; GENBANK/DQ107022; GENBANK/DQ107023; GENBANK/DQ107024; GENBANK/DQ107025; GENBANK/DQ107026; GENBANK/DQ107027; GENBANK/DQ107028; GENBANK/DQ107029; GENBANK/DQ107030; GENBANK/DQ107031; GENBANK/DQ107032; GENBANK/DQ107033; GENBANK/DQ107034; GENBANK/DQ107035; GENBANK/DQ107036; GENBANK/DQ107037; GENBANK/DQ107038; GENBANK/DQ107039; GENBANK/DQ107040; GENBANK/DQ107041; GENBANK/DQ107042; GENBANK/DQ107043; GENBANK/DQ107044; GENBANK/DQ107045; GENBANK/DQ107046; GENBANK/DQ107047; GENBANK/DQ107048; GENBANK/DQ107049; GENBANK/DQ107050; GENBANK/DQ107051; GENBANK/DQ107052; GENBANK/DQ107053; GENBANK/DQ107054; GENBANK/DQ107055; GENBANK/DQ107056; GENBANK/DQ107057; GENBANK/DQ107058; GENBANK/DQ107059; GENBANK/DQ107060; GENBANK/DQ107061; GENBANK/DQ107062; GENBANK/DQ107063; GENBANK/DQ107064; GENBANK/DQ107065; GENBANK/DQ107066; GENBANK/DQ107067; GENBANK/DQ107068; GENBANK/DQ107069; GENBANK/DQ107070; GENBANK/DQ107071; GENBANK/DQ107072; GENBANK/DQ107073; GENBANK/DQ107074; GENBANK/DQ107075; GENBANK/DQ107076; GENBANK/DQ107077; GENBANK/DQ107078; GENBANK/DQ107079; GENBANK/DQ107080; GENBANK/DQ107081; GENBANK/DQ107082; GENBANK/DQ107083; GENBANK/DQ107084; GENBANK/DQ107085; GENBANK/DQ107086; GENBANK/DQ107087; GENBANK/DQ107088; GENBANK/DQ107089; GENBANK/DQ107090; GENBANK/DQ107091; GENBANK/DQ107092; GENBANK/DQ107093; GENBANK/DQ107094; GENBANK/DQ107095; GENBANK/DQ107096; GENBANK/DQ107097; GENBANK/DQ107098; GENBANK/DQ107099; GENBANK/DQ107100; GENBANK/DQ107101; GENBANK/DQ107102; GENBANK/DQ107103; GENBANK/DQ107104; GENBANK/DQ107105; GENBANK/DQ107106; GENBANK/DQ107107; GENBANK/DQ107108; GENBANK/DQ107109; GENBANK/DQ107110; GENBANK/DQ107111; GENBANK/DQ107112; GENBANK/DQ107113; GENBANK/DQ107114; GENBANK/DQ107115; GENBANK/DQ107116; GENBANK/DQ107117; GENBANK/DQ107118; GENBANK/DQ107119; GENBANK/DQ107120; GENBANK/DQ107121; GENBANK/DQ107122; GENBANK/DQ107123; GENBANK/DQ107124; GENBANK/DQ107125; GENBANK/DQ107126; GENBANK/DQ107127; GENBANK/DQ107128; GENBANK/DQ107129; GENBANK/DQ107130; GENBANK/DQ107131; GENBANK/DQ107132; GENBANK/DQ107133; GENBANK/DQ107134; GENBANK/DQ107135; GENBANK/DQ107136; GENBANK/DQ107137; GENBANK/DQ107138; GENBANK/DQ107139; GENBANK/DQ107140; GENBANK/DQ107141; GENBANK/DQ107142; GENBANK/DQ107143; GENBANK/DQ107144; GENBANK/DQ107145; GENBANK/DQ107146; GENBANK/DQ107147; GENBANK/DQ107148; GENBANK/DQ107149; GENBANK/DQ107150; GENBANK/DQ107151; GENBANK/DQ107152; GENBANK/DQ107153; GENBANK/DQ107154; GENBANK/DQ107155; GENBANK/DQ107156; GENBANK/DQ107157; GENBANK/DQ107158; GENBANK/DQ107159; GENBANK/DQ107160}, So = {Science. 2006 Jan 27;311(5760):538-41.}, Stat = {MEDLINE}, Title = {A virus reveals population structure and recent demographic history of its carnivore host.}, Volume = {311}, Year = {2006 Jan 27}, Bdsk-Url-1 = {http://dx.doi.org/10.1126/science.1121360}} @article{Edwards:2006fp, Abstract = {BACKGROUND: Genetic diversity of the human immunodeficiency virus type 1 (HIV-1) population within an individual is lost during transmission to a new host. The demography of transmission is an important determinant of evolutionary dynamics, particularly the relative impact of natural selection and genetic drift immediately following HIV-1 infection. Despite this, the magnitude of this population bottleneck is unclear. RESULTS: We use coalescent methods to quantify the bottleneck in a single case of homosexual transmission and find that over 99% of the env and gag diversity present in the donor is lost. This was consistent with the diversity present at seroconversion in nine other horizontally infected individuals. Furthermore, we estimated viral diversity at birth in 27 infants infected through vertical transmission and found there to be no difference between the two modes of transmission. CONCLUSION: Assuming the bottleneck at transmission is selectively neutral, such a severe reduction in genetic diversity has important implications for adaptation in HIV-1, since beneficial mutations have a reduced chance of transmission.}, Address = {Nuffield Department of Clinical Medicine, University of Oxford, The Peter Medawar Building for Pathogen Research, Oxford, OX1 3SY, UK. [email protected]}, Au = {Edwards, C T and Holmes, E C and Wilson, D J and Viscidi, R P and Abrams, E J and Phillips, R E and Drummond, A J}, Author = {Edwards, Charles T T and Holmes, Edward C and Wilson, Daniel J and Viscidi, Raphael P and Abrams, Elaine J and Phillips, Rodney E and Drummond, Alexei J}, Da = {20060424}, Date-Added = {2008-11-28 10:40:53 -0800}, Date-Modified = {2014-07-06 03:57:25 +0000}, Dcom = {20060721}, Dep = {20060323}, Doi = {10.1186/1471-2148-6-28}, Edat = {2006/03/25 09:00}, Gr = {United Kingdom Wellcome Trust}, Issn = {1471-2148 (Electronic)}, Jid = {100966975}, Journal = {BMC Evol Biol}, Jt = {BMC evolutionary biology}, Language = {eng}, Lr = {20070813}, Mh = {Bayes Theorem; *Disease Transmission, Horizontal; Disease Transmission, Vertical; *Evolution, Molecular; Female; HIV Core Protein p24/genetics; HIV Envelope Protein gp120/genetics; HIV Infections/*transmission/*virology; HIV-1/*genetics; Homosexuality; Humans; Infant, Newborn; Male; Models, Biological; Phylogeny; Time Factors; Variation (Genetics)/*genetics}, Mhda = {2006/07/22 09:00}, Own = {NLM}, Pages = {28}, Phst = {2005/10/04 {$[$}received{$]$}; 2006/03/23 {$[$}accepted{$]$}; 2006/03/23 {$[$}aheadofprint{$]$}}, Pii = {1471-2148-6-28}, Pl = {England}, Pmc = {PMC1444934}, Pmid = {16556318}, Pst = {epublish}, Pt = {Journal Article; Research Support, Non-U.S. Gov't}, Pubm = {Electronic}, Rn = {0 (HIV Core Protein p24); 0 (HIV Envelope Protein gp120)}, Sb = {IM}, So = {BMC Evol Biol. 2006 Mar 23;6:28.}, Stat = {MEDLINE}, Title = {Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1.}, Volume = {6}, Year = {2006}, Bdsk-Url-1 = {http://dx.doi.org/10.1186/1471-2148-6-28}} @article{Edwards:2006eu, Abstract = {The evolution of the human immunodeficiency virus (HIV-1) during chronic infection involves the rapid, continuous turnover of genetic diversity. However, the role of natural selection, relative to random genetic drift, in governing this process is unclear. We tested a stochastic model of genetic drift using partial envelope sequences sampled longitudinally in 28 infected children. In each case the Bayesian posterior (empirical) distribution of coalescent genealogies was estimated using Markov chain Monte Carlo methods. Posterior predictive simulation was then used to generate a null distribution of genealogies assuming neutrality, with the null and empirical distributions compared using four genealogy-based summary statistics sensitive to nonneutral evolution. Because both null and empirical distributions were generated within a coalescent framework, we were able to explicitly account for the confounding influence of demography. From the distribution of corrected P-values across patients, we conclude that empirical genealogies are more asymmetric than expected if evolution is driven by mutation and genetic drift only, with an excess of low-frequency polymorphisms in the population. This indicates that although drift may still play an important role, natural selection has a strong influence on the evolution of HIV-1 envelope. A negative relationship between effective population size and substitution rate indicates that as the efficacy of selection increases, a smaller proportion of mutations approach fixation in the population. This suggests the presence of deleterious mutations. We therefore conclude that intrahost HIV-1 evolution in envelope is dominated by purifying selection against low-frequency deleterious mutations that do not reach fixation.}, Address = {Nuffield Department of Clinical Medicine, University of Oxford, UK, and Department of Pediatrics, The Johns Hopkins Hospital, Baltimore, MD 21287, USA. [email protected]}, Au = {Edwards, CT and Holmes, EC and Pybus, OG and Wilson, DJ and Viscidi, RP and Abrams, EJ and Phillips, RE and Drummond, AJ}, Author = {Edwards, C T T and Holmes, E C and Pybus, O G and Wilson, D J and Viscidi, R P and Abrams, E J and Phillips, R E and Drummond, A J}, Da = {20061123}, Date-Added = {2008-11-28 10:40:46 -0800}, Date-Modified = {2008-11-28 10:40:46 -0800}, Dcom = {20070131}, Dep = {20060901}, Doi = {10.1534/genetics.105.052019}, Edat = {2006/09/05 09:00}, Gr = {United Kingdom Wellcome Trust}, Issn = {0016-6731 (Print)}, Jid = {0374636}, Journal = {Genetics}, Jt = {Genetics}, Language = {eng}, Lr = {20070813}, Mh = {Base Sequence; Bayes Theorem; Child; Chronic Disease; Computer Simulation; *Evolution, Molecular; Gene Products, env/*genetics; Genes, Viral; *Genetic Drift; HIV Infections/genetics; *HIV-1; Humans; Molecular Sequence Data; Monte Carlo Method; Mutation; Polymorphism, Genetic; *Selection (Genetics); Stochastic Processes}, Mhda = {2007/02/01 09:00}, Number = {3}, Own = {NLM}, Pages = {1441--1453}, Phst = {2006/09/01 {$[$}aheadofprint{$]$}}, Pii = {genetics.105.052019}, Pl = {United States}, Pmc = {PMC1667091}, Pmid = {16951087}, Pst = {ppublish}, Pt = {Comparative Study; Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, P.H.S.}, Pubm = {Print-Electronic}, Rn = {0 (Gene Products, env)}, Sb = {IM}, Si = {GENBANK/AY823998; GENBANK/AY823999; GENBANK/AY824000; GENBANK/AY824001; GENBANK/AY824002; GENBANK/AY824003; GENBANK/AY824004; GENBANK/AY824005; GENBANK/AY824006; GENBANK/AY824007; GENBANK/AY824008; GENBANK/AY824009; GENBANK/AY824010; GENBANK/AY824011; GENBANK/AY824012; GENBANK/AY824013; GENBANK/AY824014; GENBANK/AY824015; GENBANK/AY824016; GENBANK/AY824017; GENBANK/AY824018; GENBANK/AY824019; GENBANK/AY824020; GENBANK/AY824021; GENBANK/AY824022; GENBANK/AY824023; GENBANK/AY824024; GENBANK/AY824025; GENBANK/AY824026; GENBANK/AY824027; GENBANK/AY824028; GENBANK/AY824029; GENBANK/AY824030; GENBANK/AY824031; GENBANK/AY824032; GENBANK/AY824033; GENBANK/AY824034; GENBANK/AY824035; GENBANK/AY824036; GENBANK/AY824037; GENBANK/AY824038; GENBANK/AY824039; GENBANK/AY824040; GENBANK/AY824041; GENBANK/AY824042; GENBANK/AY824043; GENBANK/AY824044; 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GENBANK/AY824829; GENBANK/AY824830; GENBANK/AY824831; GENBANK/AY824832; GENBANK/AY824833; GENBANK/AY824834; GENBANK/AY824835; GENBANK/AY824836; GENBANK/AY824837; GENBANK/AY824838; GENBANK/AY824839; GENBANK/AY824840; GENBANK/AY824841; GENBANK/AY824842; GENBANK/AY824843; GENBANK/AY824844; GENBANK/AY824845; GENBANK/AY824846; GENBANK/AY824847; GENBANK/AY824848; GENBANK/AY824849; GENBANK/AY824850; GENBANK/AY824851; GENBANK/AY824852; GENBANK/AY824853; GENBANK/AY824854; GENBANK/AY824855; GENBANK/AY824856; GENBANK/AY824857; GENBANK/AY824858; GENBANK/AY824859; GENBANK/AY824860; GENBANK/AY824861; GENBANK/AY824862; GENBANK/AY824863; GENBANK/AY824864; GENBANK/AY824865; GENBANK/AY824866; GENBANK/AY824867; GENBANK/AY824868; GENBANK/AY824869; GENBANK/AY824870; GENBANK/AY824871; GENBANK/AY824872; GENBANK/AY824873; GENBANK/AY824874; GENBANK/AY824875; GENBANK/AY824876; GENBANK/AY824877; GENBANK/AY824878; GENBANK/AY824879; GENBANK/AY824880; GENBANK/AY824881; GENBANK/AY824882; GENBANK/AY824883; GENBANK/AY824884; GENBANK/AY824885; GENBANK/AY824886; GENBANK/AY824887; GENBANK/AY824888; GENBANK/AY824889; GENBANK/AY824890; GENBANK/AY824891; GENBANK/AY824892; GENBANK/AY824893; GENBANK/AY824894; GENBANK/AY824895; GENBANK/AY824896; GENBANK/AY824897; GENBANK/AY824898; GENBANK/AY824899; GENBANK/AY824900; GENBANK/AY824901; GENBANK/AY824902; GENBANK/AY824903; GENBANK/AY824904; GENBANK/AY824905; GENBANK/AY824906; GENBANK/AY824907; GENBANK/AY824908; GENBANK/AY824909; GENBANK/AY824910; GENBANK/AY824911; GENBANK/AY824912; GENBANK/AY824913; GENBANK/AY824914; GENBANK/AY824915; GENBANK/AY824916; GENBANK/AY824917; GENBANK/AY824918; GENBANK/AY824919; GENBANK/AY824920; GENBANK/AY824921; GENBANK/AY824922; GENBANK/AY824923; GENBANK/AY824924; GENBANK/AY824925; GENBANK/AY824926; GENBANK/AY824927; GENBANK/AY824928; GENBANK/AY824929; GENBANK/AY824930; GENBANK/AY824931; GENBANK/AY824932; GENBANK/AY824933; GENBANK/AY824934; GENBANK/AY824935; GENBANK/AY824936; GENBANK/AY824937; GENBANK/AY824938; GENBANK/AY824939; GENBANK/AY824940; GENBANK/AY824941; GENBANK/AY824942; GENBANK/AY824943; GENBANK/AY824944; GENBANK/AY824945; GENBANK/AY824946}, So = {Genetics. 2006 Nov;174(3):1441-53. Epub 2006 Sep 1.}, Stat = {MEDLINE}, Title = {Evolution of the human immunodeficiency virus envelope gene is dominated by purifying selection.}, Volume = {174}, Year = {2006 Nov}, Bdsk-Url-1 = {http://dx.doi.org/10.1534/genetics.105.052019}} @article{Pybus:2007fv, Abstract = {Populations of RNA viruses are often characterized by abundant genetic variation. However, the relative fitness of these mutations is largely unknown, although this information is central to our understanding of viral emergence, immune evasion, and drug resistance. Here we develop a phylogenetic method, based on the distribution of nonsynonymous and synonymous changes, to assess the relative fitness of polymorphisms in the structural genes of 143 RNA viruses. This reveals that a substantial proportion of the amino acid variation observed in natural populations of RNA viruses comprises transient deleterious mutations that are later purged by purifying selection, potentially limiting virus adaptability. We also demonstrate, for the first time, the existence of a relationship between amino acid variability and the phylogenetic distribution of polymorphisms. From this relationship, we propose an empirical threshold for the maximum viable deleterious mutation load in RNA viruses.}, Address = {Department of Zoology, University of Oxford, Oxford, United Kingdom. [email protected]}, Au = {Pybus, OG and Rambaut, A and Belshaw, R and Freckleton, RP and Drummond, AJ and Holmes, EC}, Author = {Pybus, Oliver G and Rambaut, Andrew and Belshaw, Robert and Freckleton, Robert P and Drummond, Alexei J and Holmes, Edward C}, Da = {20070301}, Date-Added = {2008-11-28 10:40:45 -0800}, Date-Modified = {2008-11-28 10:40:45 -0800}, Dcom = {20070823}, Dep = {20070111}, Doi = {10.1093/molbev/msm001}, Edat = {2007/01/16 09:00}, Issn = {0737-4038 (Print)}, Jid = {8501455}, Journal = {Mol Biol Evol}, Jt = {Molecular biology and evolution}, Language = {eng}, Mh = {Amino Acid Sequence; Computational Biology; *Evolution, Molecular; Likelihood Functions; Models, Genetic; Mutation/*genetics; *Phylogeny; *Polymorphism, Genetic; RNA Viruses/*genetics; Selection (Genetics)}, Mhda = {2007/08/24 09:00}, Number = {3}, Own = {NLM}, Pages = {845--852}, Phst = {2007/01/11 {$[$}aheadofprint{$]$}}, Pii = {msm001}, Pl = {United States}, Pmid = {17218639}, Pst = {ppublish}, Pt = {Comparative Study; Journal Article; Research Support, Non-U.S. Gov't}, Pubm = {Print-Electronic}, Sb = {IM}, So = {Mol Biol Evol. 2007 Mar;24(3):845-52. Epub 2007 Jan 11.}, Stat = {MEDLINE}, Title = {Phylogenetic evidence for deleterious mutation load in RNA viruses and its contribution to viral evolution.}, Volume = {24}, Year = {2007 Mar}, Bdsk-Url-1 = {http://dx.doi.org/10.1093/molbev/msm001}} @article{Lemey:2007yg, Address = {Department of Zoology, University of Oxford, Oxford, United Kingdom. [email protected]}, Au = {Lemey, P and Kosakovsky Pond, SL and Drummond, AJ and Pybus, OG and Shapiro, B and Barroso, H and Taveira, N and Rambaut, A}, Author = {Lemey, Philippe and Kosakovsky Pond, Sergei L and Drummond, Alexei J and Pybus, Oliver G and Shapiro, Beth and Barroso, Helena and Taveira, Nuno and Rambaut, Andrew}, Da = {20070521}, Date-Added = {2008-11-28 10:40:43 -0800}, Date-Modified = {2008-11-28 10:40:43 -0800}, Dcom = {20070619}, Dep = {20070102}, Doi = {10.1371/journal.pcbi.0030029}, Edat = {2007/02/20 09:00}, Gr = {AI36214/AI/United States NIAID; AI43638/AI/United States NIAID; AI47745/AI/United States NIAID; AI57167/AI/United States NIAID; United Kingdom Wellcome Trust}, Issn = {1553-7358 (Electronic)}, Jid = {101238922}, Journal = {PLoS Comput Biol}, Jt = {PLoS computational biology}, Language = {eng}, Lr = {20071114}, Mh = {Amino Acid Sequence; Amino Acid Substitution/*genetics; Codon/genetics; Computer Simulation; DNA Mutational Analysis/methods; Disease Progression; *Evolution, Molecular; Genetic Predisposition to Disease/genetics; HIV Infections/*genetics; Humans; *Models, Genetic; Molecular Sequence Data; Variation (Genetics)/genetics; Viral Envelope Proteins/*genetics; Virus Activation/*genetics; Virus Replication/*genetics}, Mhda = {2007/06/20 09:00}, Number = {2}, Own = {NLM}, Pages = {e29}, Phst = {2006/09/05 {$[$}received{$]$}; 2006/12/29 {$[$}accepted{$]$}; 2007/01/02 {$[$}aheadofprint{$]$}}, Pii = {06-PLCB-RA-0364R2}, Pl = {United States}, Pmc = {PMC1797821}, Pmid = {17305421}, Pst = {ppublish}, Pt = {Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't}, Pubm = {Print-Electronic}, Rn = {0 (Codon); 0 (Viral Envelope Proteins)}, Sb = {IM}, Si = {GENBANK/DQ787116; GENBANK/DQ787117; GENBANK/DQ787118; GENBANK/DQ787119; GENBANK/DQ787120; GENBANK/DQ787121}, So = {PLoS Comput Biol. 2007 Feb 16;3(2):e29. Epub 2007 Jan 2.}, Stat = {MEDLINE}, Title = {Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics.}, Volume = {3}, Year = {2007 Feb 16}, Bdsk-Url-1 = {http://dx.doi.org/10.1371/journal.pcbi.0030029}} @article{Ho:2007zl, Address = {Department of Zoology, University of Oxford, Oxford, United Kingdom. [email protected]}, Au = {Ho, SY and Shapiro, B and Phillips, MJ and Cooper, A and Drummond, AJ}, Author = {Ho, Simon Y W and Shapiro, Beth and Phillips, Matthew J and Cooper, Alan and Drummond, Alexei J}, Da = {20070612}, Date-Added = {2008-11-28 10:40:40 -0800}, Date-Modified = {2008-11-28 10:40:40 -0800}, Dcom = {20070913}, Doi = {10.1080/10635150701435401}, Edat = {2007/06/15 09:00}, Issn = {1063-5157 (Print)}, Jid = {9302532}, Journal = {Syst Biol}, Jt = {Systematic biology}, Language = {eng}, Mh = {Animals; Bison/classification; Computational Biology/*methods; *Evolution, Molecular; Humans; Time Factors}, Mhda = {2007/09/14 09:00}, Number = {3}, Own = {NLM}, Pages = {515--522}, Pii = {779485199}, Pl = {England}, Pmid = {17562475}, Pst = {ppublish}, Pt = {Journal Article; Research Support, Non-U.S. Gov't}, Pubm = {Print}, Sb = {IM}, So = {Syst Biol. 2007 Jun;56(3):515-22.}, Stat = {MEDLINE}, Title = {Evidence for time dependency of molecular rate estimates.}, Volume = {56}, Year = {2007 Jun}, Bdsk-Url-1 = {http://dx.doi.org/10.1080/10635150701435401}} @article{Holmes:2007rm, Abstract = {Despite the wealth of data describing the ecological factors that underpin viral emergence, little is known about the evolutionary processes that allow viruses to jump species barriers and establish productive infections in new hosts. Understanding the evolutionary basis to virus emergence is therefore a key research goal and many of the debates in this area can be considered within the rigorous theoretical framework established by evolutionary genetics. In particular, the respective roles played by natural selection and genetic drift in shaping genetic diversity are also of fundamental importance for understanding the nature of viral emergence. Herein, we discuss whether there are evolutionary rules to viral emergence, and especially whether certain types of virus, or those that infect a particular type of host species, are more likely to emerge than others. We stress the complex interplay between rates of viral evolution and the ability to recognize cell receptors from phylogenetically divergent host species. We also emphasize the current lack of convincing data as to whether viral emergence requires adaptation to the new host species during the early stages of infection, or whether it is largely a chance process involving the transmission of a viral strain with the necessary genetic characteristics.}, Address = {Center for Infectious Disease Dynamics, Department of Biology, Mueller Laboratory, The Pennsylvania State University, University Park, PA 16802, USA. [email protected]}, Au = {Holmes, EC and Drummond, AJ}, Author = {Holmes, E C and Drummond, A J}, Da = {20070912}, Date-Added = {2008-11-28 10:40:34 -0800}, Date-Modified = {2008-11-28 10:40:34 -0800}, Dcom = {20070927}, Edat = {2007/09/13 09:00}, Gr = {United Kingdom Wellcome Trust}, Issn = {0070-217X (Print)}, Jid = {0110513}, Journal = {Curr Top Microbiol Immunol}, Jt = {Current topics in microbiology and immunology}, Language = {eng}, Mh = {Adaptation, Physiological; Animals; Communicable Diseases, Emerging/transmission/*veterinary/virology; *Evolution, Molecular; Humans; Recombination, Genetic; Species Specificity; Viral Physiology; Virus Diseases/*transmission/*veterinary/virology; Viruses/*genetics; *Zoonoses}, Mhda = {2007/09/28 09:00}, Own = {NLM}, Pages = {51--66}, Pl = {Germany}, Pmid = {17848060}, Pst = {ppublish}, Pt = {Journal Article; Research Support, Non-U.S. Gov't; Review}, Pubm = {Print}, Rf = {53}, Sb = {IM}, So = {Curr Top Microbiol Immunol. 2007;315:51-66.}, Stat = {MEDLINE}, Title = {The evolutionary genetics of viral emergence.}, Volume = {315}, Year = {2007}} @article{Rambaut:2008rz, Abstract = {DNA sequences extracted from ancient remains are increasingly used to generate large population data sets, often spanning tens of thousands of years of population history. Bayesian coalescent methods such as those implemented in the software package BEAST can be used to estimate the demographic history of these populations, sometimes resulting in complex scenarios of fluctuations in population size, which can be correlated with the timing of environmental events, such as glaciations. Recently, however, Axelsson et al. (2008) claimed that many of these complex demographic trends are likely to be the result of post-mortem DNA damage, a problem that they investigate by removing all sites involving transitions from ancient sequences prior to analysis. When this solution is applied to a previously published data set of Pleistocene bison, they show that the demographic signal of population expansion and decline disappears. While some apparently segregating mutations in ancient sequences may be due to post-mortem damage, we argue that discarding the data will result in loss of power to detect patterns of population change. Instead, to accommodate this problem, we implement a model in which sequences are the result of a joint process of molecular evolution and post-mortem DNA damage within a probabilistic inference framework. Through simulation, we demonstrate the ability of this model to accurately recover evolutionary parameters, demographic history and DNA damage rates. When this model is applied to the bison data set, we find that the rate of DNA damage is significant but low, and that the reconstruction of population size history is nearly identical to previously published estimates.}, Address = {Institute of Evolutionary Biology, University of Edinburgh, King's Buildings, Edinburgh, EH9 3JT, UK.}, Author = {Rambaut, A and Ho, S. Y. W. and Drummond, A. J. and Shapiro, B}, Da = {20081112}, Date-Added = {2008-11-28 10:40:27 -0800}, Date-Modified = {2014-07-06 00:54:27 +0000}, Dep = {20081111}, Doi = {10.1093/molbev/msn256}, Edat = {2008/11/13 09:00}, Issn = {1537-1719 (Electronic)}, Jid = {8501455}, Journal = {Mol Biol Evol}, Jt = {Molecular biology and evolution}, Language = {ENG}, Mhda = {2008/11/13 09:00}, Own = {NLM}, Pii = {msn256}, Pmid = {19001634}, Pst = {aheadofprint}, Pt = {JOURNAL ARTICLE}, Pubm = {Print-Electronic}, So = {Mol Biol Evol. 2008 Nov 11.}, Stat = {Publisher}, Title = {Accommodating the effect of ancient DNA damage on inferences of demographic histories.}, Year = {2008 Nov 11}, Bdsk-Url-1 = {http://dx.doi.org/10.1093/molbev/msn256}} @article{Atkinson:2008nr, Abstract = {Past population size can be estimated from modern genetic diversity using coalescent theory. Estimates of ancestral human population dynamics in sub-Saharan Africa can tell us about the timing and nature of our first steps towards colonizing the globe. Here, we combine Bayesian coalescent inference with a dataset of 224 complete human mitochondrial DNA (mtDNA) sequences to estimate effective population size through time for each of the four major African mtDNA haplogroups (L0-L3). We find evidence of three distinct demographic histories underlying the four haplogroups. Haplogroups L0 and L1 both show slow, steady exponential growth from 156 to 213kyr ago. By contrast, haplogroups L2 and L3 show evidence of substantial growth beginning 12-20 and 61-86kyr ago, respectively. These later expansions may be associated with contemporaneous environmental and/or cultural changes. The timing of the L3 expansion-8-12kyr prior to the emergence of the first non-African mtDNA lineages-together with high L3 diversity in eastern Africa, strongly supports the proposal that the human exodus from Africa and subsequent colonization of the globe was prefaced by a major expansion within Africa, perhaps driven by some form of cultural innovation.}, Address = {Institute of Cognitive and Evolutionary Anthropology, University of Oxford, 64 Banbury Road, Oxford OX2 6PN, UK.}, Author = {Atkinson, Q. D. and Gray, R. D. and Drummond, A. J.}, Da = {20081001}, Date-Added = {2008-11-28 10:40:25 -0800}, Date-Modified = {2014-07-06 00:53:55 +0000}, Dep = {20080930}, Doi = {10.1098/rspb.2008.0785}, Edat = {2008/10/02 09:00}, Issn = {0962-8452 (Print)}, Jid = {101245157}, Journal = {Proc Biol Sci}, Jt = {Proceedings. Biological sciences / The Royal Society}, Language = {ENG}, Mhda = {2008/10/02 09:00}, Own = {NLM}, Pii = {Q322007083Q68417}, Pmid = {18826938}, Pst = {aheadofprint}, Pt = {JOURNAL ARTICLE}, Pubm = {Print-Electronic}, So = {Proc Biol Sci. 2008 Sep 30.}, Stat = {Publisher}, Title = {Bayesian coalescent inference of major human mitochondrial DNA haplogroup expansions in Africa.}, Year = {2008 Sep 30}, Bdsk-Url-1 = {http://dx.doi.org/10.1098/rspb.2008.0785}} @article{Atkinson:2008qv, Abstract = {The relative timing and size of regional human population growth following our expansion from Africa remain unknown. Human mitochondrial DNA (mtDNA) diversity carries a legacy of our population history. Given a set of sequences, we can use coalescent theory to estimate past population size through time and draw inferences about human population history. However, recent work has challenged the validity of using mtDNA diversity to infer species population sizes. Here we use Bayesian coalescent inference methods, together with a global data set of 357 human mtDNA coding-region sequences, to infer human population sizes through time across 8 major geographic regions. Our estimates of relative population sizes show remarkable concordance with the contemporary regional distribution of humans across Africa, Eurasia, and the Americas, indicating that mtDNA diversity is a good predictor of population size in humans. Plots of population size through time show slow growth in sub-Saharan Africa beginning 143-193 kya, followed by a rapid expansion into Eurasia after the emergence of the first non-African mtDNA lineages 50-70 kya. Outside Africa, the earliest and fastest growth is inferred in Southern Asia approximately 52 kya, followed by a succession of growth phases in Northern and Central Asia (approximately 49 kya), Australia (approximately 48 kya), Europe (approximately 42 kya), the Middle East and North Africa (approximately 40 kya), New Guinea (approximately 39 kya), the Americas (approximately 18 kya), and a second expansion in Europe (approximately 10-15 kya). Comparisons of relative regional population sizes through time suggest that between approximately 45 and 20 kya most of humanity lived in Southern Asia. These findings not only support the use of mtDNA data for estimating human population size but also provide a unique picture of human prehistory and demonstrate the importance of Southern Asia to our recent evolutionary past.}, Address = {Institute of Cognitive and Evolutionary Anthropology, University of Oxford, 58A Banbury Rd, Oxford, OX2 6QS, United Kingdom. [email protected]}, Au = {Atkinson, QD and Gray, RD and Drummond, AJ}, Author = {Atkinson, Quentin D and Gray, Russell D and Drummond, Alexei J}, Da = {20080206}, Date-Added = {2008-11-28 10:40:24 -0800}, Date-Modified = {2008-11-28 10:40:24 -0800}, Dcom = {20080519}, Dep = {20071218}, Doi = {10.1093/molbev/msm277}, Edat = {2007/12/21 09:00}, Issn = {1537-1719 (Electronic)}, Jid = {8501455}, Journal = {Mol Biol Evol}, Jt = {Molecular biology and evolution}, Language = {eng}, Mh = {Asia; Bayes Theorem; DNA, Mitochondrial/*genetics; *Genetics, Population; Humans; *Population Density; *Variation (Genetics)}, Mhda = {2008/05/20 09:00}, Number = {2}, Own = {NLM}, Pages = {468--474}, Phst = {2007/12/18 {$[$}aheadofprint{$]$}; 2008/01/03 {$[$}aheadofprint{$]$}}, Pii = {msm277}, Pl = {United States}, Pmid = {18093996}, Pst = {ppublish}, Pt = {Journal Article; Research Support, Non-U.S. Gov't}, Pubm = {Print-Electronic}, Rn = {0 (DNA, Mitochondrial)}, Sb = {IM}, So = {Mol Biol Evol. 2008 Feb;25(2):468-74. Epub 2007 Dec 18.}, Stat = {MEDLINE}, Title = {mtDNA variation predicts population size in humans and reveals a major Southern Asian chapter in human prehistory.}, Volume = {25}, Year = {2008 Feb}, Bdsk-Url-1 = {http://dx.doi.org/10.1093/molbev/msm277}} @article{Hon:2008xy, Abstract = {Bats have been identified as the natural reservoir of severe acute respiratory syndrome (SARS)-like and SARS coronaviruses (SLCoV and SCoV). However, previous studies suggested that none of the currently sampled bat SLCoVs is the descendant of the direct ancestor of SCoV, based on their relatively distant phylogenetic relationship. In this study, evidence of the recombinant origin of the genome of a bat SLCoV is demonstrated. We identified a potential recombination breakpoint immediately after the consensus intergenic sequence between open reading frame 1 and the S coding region, suggesting the replication intermediates may participate in the recombination event, as previously speculated for other CoVs. Phylogenetic analysis of its parental regions suggests the presence of an uncharacterized SLCoV lineage that is phylogenetically closer to SCoVs than any of the currently sampled bat SLCoVs. Using various Bayesian molecular-clock models, interspecies transfer of this SLCoV lineage from bats to the amplifying host (e.g., civets) was estimated to have happened a median of 4.08 years before the SARS outbreak. Based on this relatively short window period, we speculate that this uncharacterized SLCoV lineage may contain the direct ancestor of SCoV. This study sheds light on the possible host bat species of the direct ancestor of SCoV, providing valuable information on the scope and focus of surveillance for the origin of SCoV.}, Address = {5N-12, Kadoorie Biological Science Building, The University of Hong Kong, Hong Kong, China.}, Au = {Hon, CC and Lam, TY and Shi, ZL and Drummond, AJ and Yip, CW and Zeng, F and Lam, PY and Leung, FC}, Author = {Hon, Chung-Chau and Lam, Tsan-Yuk and Shi, Zheng-Li and Drummond, Alexei J and Yip, Chi-Wai and Zeng, Fanya and Lam, Pui-Yi and Leung, Frederick Chi-Ching}, Da = {20080131}, Date-Added = {2008-11-28 10:40:24 -0800}, Date-Modified = {2008-11-28 10:40:24 -0800}, Dcom = {20080305}, Dep = {20071205}, Doi = {10.1128/JVI.01926-07}, Edat = {2007/12/07 09:00}, Issn = {1098-5514 (Electronic)}, Jid = {0113724}, Journal = {J Virol}, Jt = {Journal of virology}, Language = {eng}, Mh = {Animals; Base Sequence; Bayes Theorem; Chiroptera/*virology; Genome, Viral/*genetics; *Models, Genetic; Molecular Sequence Data; Phylogeny; Recombination, Genetic; SARS Virus/*classification/*genetics/isolation \& purification}, Mhda = {2008/03/06 09:00}, Number = {4}, Own = {NLM}, Pages = {1819--1826}, Phst = {2007/12/05 {$[$}aheadofprint{$]$}}, Pii = {JVI.01926-07}, Pl = {United States}, Pmc = {PMC2258724}, Pmid = {18057240}, Pst = {ppublish}, Pt = {Journal Article; Research Support, Non-U.S. Gov't}, Pubm = {Print-Electronic}, Sb = {IM}, So = {J Virol. 2008 Feb;82(4):1819-26. Epub 2007 Dec 5.}, Stat = {MEDLINE}, Title = {Evidence of the recombinant origin of a bat severe acute respiratory syndrome (SARS)-like coronavirus and its implications on the direct ancestor of SARS coronavirus.}, Volume = {82}, Year = {2008 Feb}, Bdsk-Url-1 = {http://dx.doi.org/10.1128/JVI.01926-07}} @article{treeviz, Author = {Hillis, D.M. and Heath, T.A. and St John, K.}, Journal = {Systematic Biology}, Number = {3}, Pages = {471-82}, Title = {Analysis and Visualization of Tree Space}, Volume = {54}, Year = {2005}} @incollection{bryant2003, Added-At = {2009-01-28T01:17:14.000+0100}, Address = {Providence, RI}, Author = {Bryant, David}, Biburl = {http://www.bibsonomy.org/bibtex/221aa009b601dcdb642893c96da9b98ef/compevol}, Booktitle = {Bioconsensus ({P}iscataway, {NJ}, 2000/2001)}, Date-Added = {2009-01-28 12:07:05 +1300}, Date-Modified = {2009-01-28 13:04:38 +1300}, Interhash = {084b5b31a5f89e171dc2a85942abd28b}, Intrahash = {21aa009b601dcdb642893c96da9b98ef}, Keywords = {from:davidjamesbryant}, Mrclass = {92B10 (05C05 91B12 92D15)}, Mrnumber = {MR1982426 (2004f:92002)}, Pages = {163--183}, Publisher = {Amer. Math. Soc.}, Series = {DIMACS Ser. Discrete Math. Theoret. Comput. Sci.}, Title = {A classification of consensus methods for phylogenetics}, Volume = 61, Year = 2003} @article{SplitsTree, Author = {Huson, D. H. and Bryant, D.}, Doi = {10.1093/molbev/msj030}, Journal = {Mol. Biol. Evol.}, Number = {2}, Pages = {254--267}, Title = {Application of Phylogenetic Networks in Evolutionary Studies}, Volume = {23}, Year = {2006}, Bdsk-Url-1 = {http://dx.doi.org/10.1093/molbev/msj030}} @article{jackman1999, Author = {Jackman, T. and Larson, A. and Queiroz, K. De and Losos, J.}, Journal = {Systematic Biology}, Number = {2}, Pages = {254-285}, Title = {Phylogenetic relationships and tempo of early diversification in Anolis lizards}, Volume = {48}, Year = {1999}} @article{wiens2008, Author = {Wiens, John J. and Moen, Daniel S.}, Doi = {DOI: 10.3724/SP.J.1002.2008.08040}, Journal = {Journal of Systematics and Evolution}, Number = {3}, Pages = {307－314}, Title = {Missing data and the accuracy of Bayesian phylogenetics}, Volume = {46}, Year = {2008}, Bdsk-Url-1 = {http://dx.doi.org/10.3724/SP.J.1002.2008.08040}} @article{rosenbergSK2003, Author = {Rosenberg, M. S. and Subramanian, S and Kumar, S}, Date-Modified = {2014-12-04 01:13:04 +0000}, Journal = {Mol Biol Evol}, Number = {6}, Pages = {988-93}, Title = {Patterns of transitional mutation biases within and among mammalian genomes}, Volume = {20}, Year = {2003}} @article{yangY1999, Author = {Yang, Z. and Yoder, A.D.}, Issue = {3}, Journal = {Journal of Molecular Evolution}, Pages = {274-283}, Title = {Estimation of the transition/transversion rate bias and species sampling}, Volume = {48}, Year = {1999}} @book{TAOC, Author = {Knuth, Donald}, Publisher = {Addison-Wesley}, Title = {The Art of Computer Programming. Vol. 2: Seminumerical algorithms}, Year = {1997}} @article{MatsumotoN1998, Author = {Matsumoto, M. and Nishimura, T.}, Journal = {ACM Transactions on Modeling and Computer Simulation}, Month = {January}, Number = {1}, Pages = {3--30}, Title = {Mersenne Twister: A 623-Dimensionally Equidistributed Uniform Pseudo-Random Number Generator}, Volume = {8}, Year = {1998}} @article{BaeleEtAl2012, Author = {Baele, G. and Lemey, P. and Bedford, T. and Rambaut, A. and Suchard, M. A. and Alekseyenko, A. V.}, Journal = {Mol. Biol. Evol.}, Number = {9}, Pages = {2157-2167}, Title = {Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty}, Volume = {29}, Year = {2012}} @article{Steel2005, Author = {Steel, M.}, Journal = {Trends in Genetics}, Number = {6}, Pages = {307-309}, Title = {Should phylogenetic models be trying to 'fit an elephant'?}, Volume = {21}, Year = {2005}} @article{SNAPP, Author = {Bryant, David and Bouckaert, Remco R. and Felsenstein, Joseph and Rosenberg, Noah and RoyChoudhury, Arindam}, Date-Modified = {2014-07-06 03:46:27 +0000}, Journal = {Mol. Biol. Evol.}, Number = {8}, Pages = {1917-1932}, Title = {Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis}, Volume = {29}, Year = {2012}} @article{CIR, Author = {Cox, J.C. and Ingersoll, J.E. and Ross, S.A.}, Journal = {Econometrica}, Pages = {385--407}, Title = {A Theory of the Term Structure of Interest Rates}, Volume = {53}, Year = {1985}} @incollection{Raftery2007, Author = {Raftery, A. E. and Newton, M. A. and Satagopan, J and Krivitsky, P}, Booktitle = {Bayesian Statistics}, Date-Modified = {2014-12-04 01:11:27 +0000}, Editor = {Bernardo JM, Bayarri MJ, Berger JO}, Pages = {1--45}, Publisher = {Oxford: Oxford University Press}, Title = {Estimating the integrated likelihood via posterior simulation using the harmonic mean identity}, Year = {2007}} @article{Xie2011, Author = {Xie, W and Lewis, PO and Fan, Y and Kuo, L and Chen, MH}, Journal = {Syst Biol}, Pages = {150--160}, Title = {Improving marginal likelihood estimation for Bayesian phylogenetic model selection}, Volume = {60}, Year = {2011}} @article{densitree, Author = {Bouckaert, Remco R.}, Doi = {10.1093/bioinformatics/btq110}, Journal = {Bioinformatics}, Number = {10}, Pages = {1372-1373}, Title = {DensiTree: making sense of sets of phylogenetic trees}, Volume = {26}, Year = {2010}, Bdsk-Url-1 = {http://dx.doi.org/10.1093/bioinformatics/btq110}} @article{Bouckaert2012, Author = {Bouckaert, Remco R. and Lemey, Philippe and Dunn, Michael and Greenhill, Simon J. and Alekseyenko, Alexander V. and Drummond, Alexei J. and Gray, Russell D. and Suchard, Marc A. and Atkinson, Quentin D.}, Date-Modified = {2014-07-06 00:50:24 +0000}, Doi = {DOI: 10.1126/science.1219669}, Journal = {Science}, Number = {6097}, Pages = {957-960}, Title = {Mapping the Origins and Expansion of the Indo-European Language Family}, Volume = {337}, Year = {2012}, Bdsk-Url-1 = {http://dx.doi.org/10.1126/science.1219669}} @article{Heled2013, Author = {Heled, Joseph and Bouckaert, Remco R}, Journal = {BMC evolutionary biology}, Number = {1}, Pages = {221}, Publisher = {BioMed Central Ltd}, Title = {Looking for trees in the forest: summary tree from posterior samples}, Volume = {13}, Year = {2013}} @article{RGTSNAPP, Author = {Bouckaert, Remco R. and Bryant, David}, Date-Modified = {2014-07-05 10:31:14 +0000}, Journal = {Available from BEAST 2 wiki}, Title = {A rough guide to SNAPP}, Year = {2012}} @article{beagle2, Author = {Ayres, D and Darling, A and Zwickl, D and Beerli, P and Holder, M and Lewis, P and Huelsenbeck, J. P. and Ronquist, F and Swofford, D. L. and Cummings, M. P. and Rambaut, A and Suchard, M. A.}, Date-Modified = {2014-07-06 02:04:20 +0000}, Journal = {Syst Biol}, Pages = {170-173}, Title = {BEAGLE: a common application programming inferface and high-performance computing library for statistical phylogenetics}, Volume = {61}, Year = {2012}} @article{finches, Author = {Sato, A. and O'hUigin, C. and Figueroa, F. and Grant, P. R. and Grant, B. R. and Tichy, H. and Klein, J.}, Journal = {Proc. Natl. Acad. Sci}, Pages = {5101--5106}, Title = {Phylogeny of Darwin's finches as revealed by mtDNA sequences}, Volume = {96}, Year = {1999}} @article{RBmodel, Author = {Bouckaert, Remco R. and Alvarado-Mora, M\'onica and Rebello Pinho, Jo\~ao}, Date-Modified = {2014-07-06 03:46:34 +0000}, Journal = {Antiviral therapy}, Title = {Evolutionary rates and HBV: issues of rate estimation with Bayesian molecular methods}, Year = {2013}} @article{clustal, Author = {Larkin, M.A. and Blackshields, G. and Brown, N.P. and Chenna, R. and McGettigan, P.A. and McWilliam, H. and Valentin, F. and Wallace, I.M. and Wilm, A. and Lopez, R. and Thompson, J.D. and Gibson, T.J. and Higgins, D.G.}, Journal = {Bioinformatics}, Pages = {2947-2948}, Title = {Clustal W and Clustal X version 2.0}, Volume = {23}, Year = {2007}} @article{deSilva2012inf, Abstract = {Using sequence data to infer population dynamics is playing an increasing role in the analysis of outbreaks. The most common methods in use, based on coalescent inference, have been widely used but not extensively tested against simulated epidemics. Here, we use simulated data to test the ability of both parametric and non-parametric methods for inference of effective population size (coded in the popular BEAST package) to reconstruct epidemic dynamics. We consider a range of simulations centred on scenarios considered plausible for pandemic influenza, but our conclusions are generic for any exponentially growing epidemic. We highlight systematic biases in non-parametric effective population size estimation. The most prominent such bias leads to the false inference of slowing of epidemic spread in the recent past even when the real epidemic is growing exponentially. We suggest some sampling strategies that could reduce (but not eliminate) some of the biases. Parametric methods can correct for these biases if the infected population size is large. We also explore how some poor sampling strategies (e.g. that over-represent epidemiologically linked clusters of cases) could dramatically exacerbate bias in an uncontrolled manner. Finally, we present a simple diagnostic indicator, based on coalescent density and which can easily be applied to reconstructed phylogenies, that identifies time-periods for which effective population size estimates are less likely to be biased. We illustrate this with an application to the 2009 H1N1 pandemic. }, Author = {de Silva, E. and Ferguson, N.M. and Fraser, C.}, Journal = {J R Soc Interface}, Number = {73}, Pages = {1797-808}, Title = {Inferring pandemic growth rates from sequence data}, Volume = {9}, Year = {2012}} @article{suchardRed2006, Author = {Suchard, M A and Redelings, B D}, Date-Modified = {2013-02-13 03:45:18 +0000}, Journal = {Bioinformatics}, Number = {16}, Pages = {2047-2048}, Title = {BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny}, Volume = {22}, Year = {2006}} @article{RedelingsSuchard2005, Author = {Redelings, B. D. and Suchard, M. A.}, Date-Modified = {2014-07-06 02:06:20 +0000}, Journal = {Systematic Biology}, Number = {3}, Pages = {401-418}, Title = {Joint Bayesian Estimation of Alignment and Phylogeny}, Volume = {54}, Year = {2005}} @article{Notredame2000205, Author = {Notredame, C{\'e}dric and Higgins, Desmond G and Heringa, Jaap}, Doi = {10.1006/jmbi.2000.4042}, Issn = {0022-2836}, Journal = {Journal of Molecular Biology}, Keywords = {multiple sequence alignment}, Number = {1}, Pages = {205 - 217}, Title = {T-coffee: a novel method for fast and accurate multiple sequence alignment}, Url = {http://www.sciencedirect.com/science/article/pii/S0022283600940427}, Volume = {302}, Year = {2000}, Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S0022283600940427}, Bdsk-Url-2 = {http://dx.doi.org/10.1006/jmbi.2000.4042}} @book{mcmcHandBook, Author = {Brooks, Steve and Gelman, Andrew and Jones, Galin L. and Meng, Xiao-Li}, Publisher = {Chapman \& Hall/CRC.}, Title = {Handbook of Markov Chain Monte Carlo}, Year = {2010}} @article{Hailer20042012, Abstract = {Recent studies have shown that the polar bear matriline (mitochondrial DNA) evolved from a brown bear lineage since the late Pleistocene, potentially indicating rapid speciation and adaption to arctic conditions. Here, we present a high-resolution data set from multiple independent loci across the nuclear genomes of a broad sample of polar, brown, and black bears. Bayesian coalescent analyses place polar bears outside the brown bear clade and date the divergence much earlier, in the middle Pleistocene, about 600 (338 to 934) thousand years ago. This provides more time for polar bear evolution and confirms previous suggestions that polar bears carry introgressed brown bear mitochondrial DNA due to past hybridization. Our results highlight that multilocus genomic analyses are crucial for an accurate understanding of evolutionary history.}, Author = {Hailer, Frank and Kutschera, Verena E. and Hallstr{\"o}m, Bj{\"o}rn M. and Klassert, Denise and Fain, Steven R. and Leonard, Jennifer A. and Arnason, Ulfur and Janke, Axel}, Doi = {10.1126/science.1216424}, Eprint = {http://www.sciencemag.org/content/336/6079/344.full.pdf}, Journal = {Science}, Number = {6079}, Pages = {344-347}, Title = {Nuclear Genomic Sequences Reveal that Polar Bears Are an Old and Distinct Bear Lineage}, Url = {http://www.sciencemag.org/content/336/6079/344.abstract}, Volume = {336}, Year = {2012}, Bdsk-Url-1 = {http://www.sciencemag.org/content/336/6079/344.abstract}, Bdsk-Url-2 = {http://dx.doi.org/10.1126/science.1216424}} @article{Molina17052011, Abstract = {Asian rice, Oryza sativa, is one of world's oldest and most important crop species. Rice is believed to have been domesticated ∼9,000 y ago, although debate on its origin remains contentious. A single-origin model suggests that two main subspecies of Asian rice, indica and japonica, were domesticated from the wild rice O. rufipogon. In contrast, the multiple independent domestication model proposes that these two major rice types were domesticated separately and in different parts of the species range of wild rice. This latter view has gained much support from the observation of strong genetic differentiation between indica and japonica as well as several phylogenetic studies of rice domestication. We reexamine the evolutionary history of domesticated rice by resequencing 630 gene fragments on chromosomes 8, 10, and 12 from a diverse set of wild and domesticated rice accessions. Using patterns of SNPs, we identify 20 putative selective sweeps on these chromosomes in cultivated rice. Demographic modeling based on these SNP data and a diffusion-based approach provide the strongest support for a single domestication origin of rice. Bayesian phylogenetic analyses implementing the multispecies coalescent and using previously published phylogenetic sequence datasets also point to a single origin of Asian domesticated rice. Finally, we date the origin of domestication at ∼8,200--13,500 y ago, depending on the molecular clock estimate that is used, which is consistent with known archaeological data that suggests rice was first cultivated at around this time in the Yangtze Valley of China.}, Author = {Molina, Jeanmaire and Sikora, Martin and Garud, Nandita and Flowers, Jonathan M. and Rubinstein, Samara and Reynolds, Andy and Huang, Pu and Jackson, Scott and Schaal, Barbara A. and Bustamante, Carlos D. and Boyko, Adam R. and Purugganan, Michael D.}, Doi = {10.1073/pnas.1104686108}, Eprint = {http://www.pnas.org/content/108/20/8351.full.pdf+html}, Journal = {Proceedings of the National Academy of Sciences}, Number = {20}, Pages = {8351-8356}, Title = {Molecular evidence for a single evolutionary origin of domesticated rice}, Url = {http://www.pnas.org/content/108/20/8351.abstract}, Volume = {108}, Year = {2011}, Bdsk-Url-1 = {http://www.pnas.org/content/108/20/8351.abstract}, Bdsk-Url-2 = {http://dx.doi.org/10.1073/pnas.1104686108}} @article{StarBeastApp2010, Author = {Leach{\'e}, Adam D. and Fujita, Matthew K.}, Date-Modified = {2014-07-07 01:27:07 +0000}, Journal = {Proc R Soc B}, Pages = {3071-3077}, Title = {Bayesian species delimitation in West African forest geckos (Hemidactylus fasciatus)}, Volume = {277}, Year = {2010}} @article{StarBeastApp2011, Author = {Dinc{\u a}, Vlad and Lukhtanov, Vladimir A and Talavera, Gerard and Vila, Roger}, Journal = {Nature Communications}, Number = {324}, Title = {Unexpected layers of cryptic diversity in wood white Leptidea butterflies}, Volume = {2}, Year = {2011}} @article{EVO:EVO1097, Author = {McCormack, John E. and Heled, Joseph and Delaney, Kathleen S. and Peterson, A. Townsend and Knowles, L. Lacey}, Date-Modified = {2014-07-04 01:47:17 +0000}, Doi = {10.1111/j.1558-5646.2010.01097.x}, Issn = {1558-5646}, Journal = {Evolution}, Keywords = {Aphelocoma, BEAST, divergence times, fossil calibration, gene tree, glaciations, mountain uplift, Pleistocene, species tree}, Number = {1}, Pages = {184--202}, Publisher = {Blackwell Publishing Inc}, Title = {Calibrating Divergence Times On Species Trees Versus Gene Trees: Implications For Speciation History Of Aphelocoma Jays}, Url = {http://dx.doi.org/10.1111/j.1558-5646.2010.01097.x}, Volume = {65}, Year = {2011}, Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.1558-5646.2010.01097.x}} @article{Chaves2011207, Author = {Chaves, Jaime A. and Smith, Thomas B.}, Date-Modified = {2014-07-05 08:48:09 +0000}, Doi = {10.1016/j.ympev.2011.04.007}, Issn = {1055-7903}, Journal = {Molecular Phylogenetics and Evolution}, Keywords = {Remote sensing}, Number = {2}, Pages = {207 - 218}, Title = {Evolutionary patterns of diversification in the Andean hummingbird genus Adelomyia}, Url = {http://www.sciencedirect.com/science/article/pii/S1055790311001916}, Volume = {60}, Year = {2011}, Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S1055790311001916}, Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.ympev.2011.04.007}} @article{DensiTreeApp2011, Author = {Levinson, Stephen C. and Greenhill, Simon J. and Gray, Russell D. and Dunn, Michael}, Doi = {doi:10.1515/lity.2011.034}, Journal = {Linguistic Typology}, Number = {2}, Pages = {509-534}, Title = {Universal typological dependencies should be detectable in the history of language families}, Volume = {15}, Yar = {2011}, Bdsk-Url-1 = {http://dx.doi.org/10.1515/lity.2011.034}} @article{PhyloGeoApp2013, Author = {He, Miao and Miyajima, Fabio and Roberts, Paul and Ellison, Louise and Pickard, Derek J and Martin, Melissa J and Connor, Thomas R and Harris, Simon R and Fairley, Derek and Bamford, Kathleen B and D'Arc, Stephanie and Brazier, Jon and Brown, Derek and Coia, John E and Douce, Gill and Gerding, Dale and Kim, Hee Jung and Koh, Tse Hsien and Kato, Haru and Senoh, Mitsutoshi and Louie, Tom and Michell, Stephen and Butt, Emma and Peacock, Sharon J and Brown, Nick M and Riley, Tom and Songer, Glen and Wilcox, Mark and Pirmohamed, Munir and Kuijper, Ed and Hawkey, Peter and Wren, Brendan W and Dougan, Gordon and Parkhill, Julian and Lawley, Trevor D}, Doi = {http://dx.doi.org/10.1038/ng.2478}, Journal = {Nature Genetics}, Number = {1}, Pages = {109--113}, Title = {Emergence and global spread of epidemic healthcare-associated Clostridium difficile}, Volume = {45}, Year = {2013}, Bdsk-Url-1 = {http://dx.doi.org/10.1038/ng.2478}} @article{Campos23032010, Abstract = {The causes of the late Pleistocene megafaunal extinctions are poorly understood. Different lines of evidence point to climate change, the arrival of humans, or a combination of these events as the trigger. Although many species went extinct, others, such as caribou and bison, survived to the present. The musk ox has an intermediate story: relatively abundant during the Pleistocene, it is now restricted to Greenland and the Arctic Archipelago. In this study, we use ancient DNA sequences, temporally unbiased summary statistics, and Bayesian analytical techniques to infer musk ox population dynamics throughout the late Pleistocene and Holocene. Our results reveal that musk ox genetic diversity was much higher during the Pleistocene than at present, and has undergone several expansions and contractions over the past 60,000 years. Northeast Siberia was of key importance, as it was the geographic origin of all samples studied and held a large diverse population until local extinction at ≈45,000 radiocarbon years before present (14C YBP). Subsequently, musk ox genetic diversity reincreased at ca. 30,000 14C YBP, recontracted at ca. 18,000 14C YBP, and finally recovered in the middle Holocene. The arrival of humans into relevant areas of the musk ox range did not affect their mitochondrial diversity, and both musk ox and humans expanded into Greenland concomitantly. Thus, their population dynamics are better explained by a nonanthropogenic cause (for example, environmental change), a hypothesis supported by historic observations on the sensitivity of the species to both climatic warming and fluctuations.}, Author = {Campos, Paula F. and Willerslev, Eske and Sher, Andrei and Orlando, Ludovic and Axelsson, Erik and Tikhonov, Alexei and Aaris-S{\o}rensen, Kim and Greenwood, Alex D. and Kahlke, Ralf-Dietrich and Kosintsev, Pavel and Krakhmalnaya, Tatiana and Kuznetsova, Tatyana and Lemey, Philippe and MacPhee, Ross and Norris, Christopher A. and Shepherd, Kieran and Suchard, Marc A. and Zazula, Grant D. and Shapiro, Beth and Gilbert, M. Thomas P.}, Doi = {10.1073/pnas.0907189107}, Eprint = {http://www.pnas.org/content/107/12/5675.full.pdf+html}, Journal = {Proceedings of the National Academy of Sciences}, Number = {12}, Pages = {5675-5680}, Title = {Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics}, Volume = {107}, Year = {2010}, Bdsk-Url-1 = {http://dx.doi.org/10.1073/pnas.0907189107}} @article{Faria2012453, Author = {Faria, Nuno R. and Suchard, Marc A. and Abecasis, Ana and Sousa, Jo{\~a}o D. and Ndembi, Nicaise and Bonfim, Idalina and Camacho, Ricardo J. and Vandamme, Anne-Mieke and Lemey, Philippe}, Doi = {10.1016/j.meegid.2011.04.028}, Issn = {1567-1348}, Journal = {Infection, Genetics and Evolution}, Keywords = {Cameroon}, Number = {2}, Pages = {453 - 460}, Title = {Phylodynamics of the HIV-1 CRF02\_AG clade in Cameroon}, Volume = {12}, Year = {2012}, Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.meegid.2011.04.028}} @article{monjane2011reconstructing, Author = {Monjane, Ad{\'e}rito L and Harkins, Gordon W and Martin, Darren P and Lemey, Philippe and Lefeuvre, Pierre and Shepherd, Dionne N and Oluwafemi, Sunday and Simuyandi, Michelo and Zinga, Innocent and Komba, Ephrem K and others}, Journal = {Journal of virology}, Number = {18}, Pages = {9623--9636}, Publisher = {Am Soc Microbiol}, Title = {Reconstructing the history of Maize streak virus strain A dispersal to reveal diversification hot spots and its origin in southern Africa}, Volume = {85}, Year = {2011}} @article{vijaykrishna2011long, Author = {Vijaykrishna, Dhanasekaran and Smith, Gavin JD and Pybus, Oliver G and Zhu, Huachen and Bhatt, Samir and Poon, Leo LM and Riley, Steven and Bahl, Justin and Ma, Siu K and Cheung, Chung L and others}, Journal = {Nature}, Number = {7348}, Pages = {519--522}, Publisher = {Nature Publishing Group}, Title = {Long-term evolution and transmission dynamics of swine influenza A virus}, Volume = {473}, Year = {2011}} @article{mutreja2011evidence, Author = {Mutreja, Ankur and Kim, Dong Wook and Thomson, Nicholas R and Connor, Thomas R and Lee, Je Hee and Kariuki, Samuel and Croucher, Nicholas J and Choi, Seon Young and Harris, Simon R and Lebens, Michael and others}, Journal = {Nature}, Number = {7365}, Pages = {462--465}, Publisher = {Nature Publishing Group}, Title = {Evidence for several waves of global transmission in the seventh cholera pandemic}, Volume = {477}, Year = {2011}} @article{pybus2012unifying, Author = {Pybus, O. G. and Suchard, M. A. and Lemey, P. and Bernardin, F. J. and Rambaut, A. and Crawford, F. W. and Gray, R. R. and Arinaminpathy, N. and Stramer, S. L. and Busch, M. 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P.}, Date-Modified = {2014-07-06 02:04:59 +0000}, Journal = {Science}, Number = {5862}, Pages = {473--476}, Publisher = {American Association for the Advancement of Science}, Title = {Alignment uncertainty and genomic analysis}, Volume = {319}, Year = {2008}} @article{moran1962statistical, Author = {Moran, Patrick Alfred Pierce and others}, Journal = {The statistical processes of evolutionary theory.}, Publisher = {Clarendon Press; Oxford University Press.}, Title = {The statistical processes of evolutionary theory.}, Year = {1962}} @inproceedings{moran1958random, Author = {Moran, Patrick Alfred Pierce}, Booktitle = {Mathematical Proceedings of the Cambridge Philosophical Society}, Date-Modified = {2013-08-10 08:12:44 +0000}, Organization = {Cambridge Univ Press}, Pages = {60--71}, Title = {Random processes in genetics}, Volume = {54}, Year = {1958}} @article{hogg2009probability, Author = {HOGG, Robert V and TANIS, Elliot}, Title = {Probability and statistical inference}, Year = {2009}} @book{mackay2003information, Author = {MacKay, David JC}, Publisher = {Cambridge university press}, Title = {Information theory, inference and learning algorithms}, Year = {2003}} @book{jaynes2003probability, Author = {Jaynes, Edwin T}, Publisher = {Cambridge university press}, Title = {Probability theory: The logic of science}, Year = {2003}} @article{camargo2012accuracy, Author = {Camargo, Arley and Avila, Luciano J and Morando, Mariana and Sites, Jack W}, Journal = {Systematic biology}, Number = {2}, Pages = {272--288}, Publisher = {Oxford University Press}, Title = {Accuracy and precision of species trees: effects of locus, individual, and base pair sampling on inference of species trees in lizards of the Liolaemus darwinii group (Squamata, Liolaemidae)}, Volume = {61}, Year = {2012}} @article{chung2011comparing, Author = {Chung, Yujin and An{\'e}, C{\'e}cile}, Journal = {Systematic biology}, Number = {3}, Pages = {261--275}, Publisher = {Oxford University Press}, Title = {Comparing two Bayesian methods for gene tree/species tree reconstruction: simulations with incomplete lineage sorting and horizontal gene transfer}, Volume = {60}, Year = {2011}} @article{yu2011coalescent, Author = {Yu, Yun and Than, Cuong and Degnan, James H and Nakhleh, Luay}, Journal = {Systematic Biology}, Number = {2}, Pages = {138--149}, Publisher = {Oxford University Press}, Title = {Coalescent histories on phylogenetic networks and detection of hybridization despite incomplete lineage sorting}, Volume = {60}, Year = {2011}} @article{smith2008rates, Author = {Smith, Stephen A and Donoghue, Michael J}, Journal = {Science}, Number = {5898}, Pages = {86--89}, Publisher = {American Association for the Advancement of Science}, Title = {Rates of molecular evolution are linked to life history in flowering plants}, Volume = {322}, Year = {2008}} @article{nagalingum2011recent, Author = {Nagalingum, NS and Marshall, CR and Quental, TB and Rai, HS and Little, DP and Mathews, S}, Journal = {Science}, Number = {6057}, Pages = {796--799}, Publisher = {American Association for the Advancement of Science}, Title = {Recent synchronous radiation of a living fossil}, Volume = {334}, Year = {2011}} @article{bahl2011ancient, Author = {Bahl, Justin and Lau, Maggie CY and Smith, Gavin JD and Vijaykrishna, Dhanasekaran and Cary, S Craig and Lacap, Donnabella C and Lee, Charles K and Papke, R Thane and Warren-Rhodes, Kimberley A and Wong, Fiona KY and others}, Journal = {Nature Communications}, Pages = {163}, Publisher = {Nature Publishing Group}, Title = {Ancient origins determine global biogeography of hot and cold desert cyanobacteria}, Volume = {2}, Year = {2011}} @article{boni2007exact, Author = {Boni, Maciej F and Posada, David and Feldman, Marcus W}, Journal = {Genetics}, Number = {2}, Pages = {1035--1047}, Publisher = {Genetics Soc America}, Title = {An exact nonparametric method for inferring mosaic structure in sequence triplets}, Volume = {176}, Year = {2007}} @article{currie2010horizontal, Author = {Currie, Thomas E and Greenhill, Simon J and Mace, Ruth and Currie, Thomas E and Greenhill, Simon J and Mace, Ruth}, Journal = {Philosophical Transactions of the Royal Society B: Biological Sciences}, Number = {1559}, Pages = {3903--3912}, Publisher = {The Royal Society}, Title = {Is horizontal transmission really a problem for phylogenetic comparative methods? A simulation study using continuous cultural traits}, Volume = {365}, Year = {2010}} @article{greenhill2010accurate, Author = {Greenhill, Simon J and Drummond, Alexei J and Gray, Russell D}, Journal = {PloS one}, Number = {3}, Pages = {e9573}, Publisher = {Public Library of Science}, Title = {How accurate and robust are the phylogenetic estimates of Austronesian language relationships?}, Volume = {5}, Year = {2010}} @article{atarhouch2006signature, Author = {Atarhouch, Touriya and R{\"u}ber, Lukas and Gonzalez, Elena G and Albert, Eva M and Rami, Mohamed and Dakkak, Allal and Zardoya, Rafael}, Journal = {Molecular Phylogenetics and Evolution}, Number = {2}, Pages = {373--383}, Publisher = {Elsevier}, Title = {Signature of an early genetic bottleneck in a population of Moroccan sardines (< i> Sardina pilchardus)}, Volume = {39}, Year = {2006}} @article{hoffman2011bayesian, Author = {Hoffman, JI and Grant, SM and Forcada, Jaume and Phillips, CD}, Journal = {Molecular Ecology}, Number = {19}, Pages = {3989--4008}, Publisher = {Wiley Online Library}, Title = {Bayesian inference of a historical bottleneck in a heavily exploited marine mammal}, Volume = {20}, Year = {2011}} @article{teixeira2012panmixia, Author = {Teixeira, Sara and Serr{\~a}o, Ester A and Arnaud-Haond, Sophie}, Journal = {PloS one}, Number = {6}, Pages = {e38521}, Publisher = {Public Library of Science}, Title = {Panmixia in a Fragmented and Unstable Environment: The Hydrothermal Shrimp Rimicaris exoculata Disperses Extensively along the Mid-Atlantic Ridge}, Volume = {7}, Year = {2012}} @article{finlay2007bayesian, Author = {Finlay, Emma K and Gaillard, C and Vahidi, SMF and Mirhoseini, SZ and Jianlin, H and Qi, XB and El-Barody, MAA and Baird, JF and Healy, BC and Bradley, Daniel G}, Journal = {Biology Letters}, Number = {4}, Pages = {449--452}, Publisher = {The Royal Society}, Title = {Bayesian inference of population expansions in domestic bovines}, Volume = {3}, Year = {2007}} 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and Evolution}, Publisher = {SMBE}, Title = {The influence of rate heterogeneity among sites on the time dependence of molecular rates}, Year = {2012}} @article{ho2011skyline, Author = {Ho, Simon YW and Shapiro, Beth}, Journal = {Molecular Ecology Resources}, Number = {3}, Pages = {423--434}, Publisher = {Wiley Online Library}, Title = {Skyline-plot methods for estimating demographic history from nucleotide sequences}, Volume = {11}, Year = {2011}} @article{mourier2012statistical, Author = {Mourier, Tobias and Ho, Simon YW and Gilbert, M Thomas P and Willerslev, Eske and Orlando, Ludovic}, Journal = {Molecular biology and evolution}, Number = {9}, Pages = {2241--2251}, Publisher = {SMBE}, Title = {Statistical guidelines for detecting past population shifts using ancient DNA}, Volume = {29}, Year = {2012}} @book{bolstad2011understanding, Author = {Bolstad, William M}, Publisher = {Wiley}, Title = {Understanding computational Bayesian statistics}, Volume = {644}, Year = {2011}} @article{roure2013impact, Author = {Roure, B{\'e}atrice and Baurain, Denis and Philippe, Herv{\'e}}, Journal = {Molecular biology and evolution}, Number = {1}, Pages = {197--214}, Publisher = {SMBE}, Title = {Impact of Missing Data on Phylogenies Inferred from Empirical Phylogenomic Data Sets}, Volume = {30}, Year = {2013}} @article{raftery1992practical, Author = {Raftery, Adrian E. and Lewis, Steven M}, Date-Modified = {2014-12-04 01:11:00 +0000}, Journal = {Statistical Science}, Number = {4}, Pages = {493--497}, Publisher = {JSTOR}, Title = {[Practical Markov Chain Monte Carlo]: Comment: One Long Run with Diagnostics: Implementation Strategies for Markov Chain Monte Carlo}, Volume = {7}, Year = {1992}} @article{heidelberger1983simulation, Author = {Heidelberger, Philip and Welch, Peter D}, Journal = {Operations Research}, Number = {6}, Pages = {1109--1144}, Publisher = {INFORMS}, Title = {Simulation run length control in the presence of an initial transient}, Volume = {31}, Year = 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Journal = {Molecular biology and evolution}, Number = {7}, Pages = {1253--1256}, Publisher = {SMBE}, Title = {jModelTest: phylogenetic model averaging}, Volume = {25}, Year = {2008}} @misc{rambaut2010path, Author = {Rambaut, A}, Publisher = {Edinburgh, UK: Institute of Evolutionary Biology, University of Edinburgh}, Title = {Path-O-Gen: Temporal Signal Investigation Tool. Version 1.3}, Year = {2010}} @article{yang1995maximum, Author = {Yang, Ziheng and Goldman, Nick and Friday, Adrian}, Journal = {Systematic Biology}, Number = {3}, Pages = {384--399}, Publisher = {Oxford University Press}, Title = {Maximum likelihood trees from DNA sequences: a peculiar statistical estimation problem}, Volume = {44}, Year = {1995}} @article{alekseyenko2008wagner, Author = {Alekseyenko, Alexander V and Lee, Christopher J and Suchard, Marc A}, Journal = {Systematic biology}, Number = {5}, Pages = {772--784}, Publisher = {Oxford University Press}, Title = {Wagner and Dollo: a stochastic duet by composing two parsimonious solos}, Volume = {57}, Year = {2008}} @article{nicholls2008dated, Author = {Nicholls, Geoff K and Gray, Russell D}, Journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)}, Number = {3}, Pages = {545--566}, Publisher = {Wiley Online Library}, Title = {Dated ancestral trees from binary trait data and their application to the diversification of languages}, Volume = {70}, Year = {2008}} @article{duffy2008rates, Author = {Duffy, Siobain and Shackelton, Laura A and Holmes, Edward C}, Journal = {Nature Reviews Genetics}, Number = {4}, Pages = {267--276}, Publisher = {Nature Publishing Group}, Title = {Rates of evolutionary change in viruses: patterns and determinants}, Volume = {9}, Year = {2008}} @inproceedings{amenta2002case, Author = {Amenta, Nina and Klingner, Jeff}, Booktitle = {Information Visualization, 2002. INFOVIS 2002. IEEE Symposium on}, Organization = {IEEE}, Pages = {71--74}, Title = {Case study: Visualizing sets of evolutionary trees}, Year = {2002}} @article{stockham2002statistically, Author = {Stockham, Cara and Wang, Li-San and Warnow, Tandy}, Journal = {Bioinformatics}, Number = {suppl 1}, Pages = {S285--S293}, Publisher = {Oxford Univ Press}, Title = {Statistically based postprocessing of phylogenetic analysis by clustering}, Volume = {18}, Year = {2002}} @article{graham2010survey, Author = {Graham, Martin and Kennedy, Jessie}, Journal = {Information Visualization}, Number = {4}, Pages = {235--252}, Publisher = {SAGE Publications}, Title = {A survey of multiple tree visualisation}, Volume = {9}, Year = {2010}} @article{procter2010visualization, Author = {Procter, James B and Thompson, Julie and Letunic, Ivica and Creevey, Chris and Jossinet, Fabrice and Barton, Geoffrey J}, Journal = {Nature methods}, Pages = {S16--S25}, Publisher = {Nature Publishing Group}, Title = {Visualization of multiple alignments, phylogenies and gene family evolution}, Volume = {7}, Year = {2010}} @book{rosenberg2009sequence, Author = {Rosenberg, Michael S.}, Date-Modified = {2014-12-04 01:12:55 +0000}, Publisher = {Univ of California Press}, Title = {Sequence alignment: methods, models, concepts, and strategies}, Year = {2009}} @book{durbin1998biological, Author = {Durbin, Richard and Eddy, Sean R and Krogh, Anders and Mitchison, Graeme}, Publisher = {Cambridge university press}, Title = {Biological sequence analysis: probabilistic models of proteins and nucleic acids}, Year = {1998}} @article{robinson1981comparison, Author = {Robinson, DF and Foulds, Leslie R}, Journal = {Mathematical Biosciences}, Number = {1}, Pages = {131--147}, Publisher = {Elsevier}, Title = {Comparison of phylogenetic trees}, Volume = {53}, Year = {1981}} @article{bryant2004neighbor, Author = {Bryant, David and Moulton, Vincent}, Journal = {Molecular biology and evolution}, Number = {2}, Pages = {255--265}, 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Author = {Berger, James O.}, Date-Modified = {2014-07-06 02:37:28 +0000}, Journal = {Bayesian Analysis}, Number = {3}, Pages = {385--402}, Publisher = {International Society for Bayesian Analysis}, Title = {The case for objective Bayesian analysis}, Volume = {1}, Year = {2006}} @article{goldstein2006subjective, Author = {Goldstein, Michael}, Journal = {Bayesian Analysis}, Number = {3}, Pages = {403--420}, Title = {Subjective Bayesian analysis: principles and practice}, Volume = {1}, Year = {2006}} @article{degnan2006discordance, Author = {Degnan, James H and Rosenberg, Noah A}, Journal = {PLoS genetics}, Number = {5}, Pages = {e68}, Publisher = {Public Library of Science}, Title = {Discordance of species trees with their most likely gene trees}, Volume = {2}, Year = {2006}} @article{kubatko2007inconsistency, Author = {Kubatko, Laura Salter and Degnan, James H}, Journal = {Systematic Biology}, Number = {1}, Pages = {17--24}, Publisher = {Oxford University Press}, Title = {Inconsistency 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