%% This BibTeX bibliography file was created using BibDesk.
%% http://bibdesk.sourceforge.net/
%% Created for alexei at 2015-09-03 10:20:16 +0200
%% Saved with string encoding Unicode (UTF-8)
@article{HeledDrummond2015,
Abstract = {Here we introduce a general class of multiple calibration birth-death tree priors for use in Bayesian phylogenetic inference. All tree priors in this class separate ancestral node heights into a set of "calibrated nodes" and "uncalibrated nodes" such that the marginal distribution of the calibrated nodes is user-specified whereas the density ratio of the birth-death prior is retained for trees with equal values for the calibrated nodes. We describe two formulations, one in which the calibration information informs the prior on ranked tree topologies, through the (conditional) prior, and the other which factorizes the prior on divergence times and ranked topologies, thus allowing uniform, or any arbitrary prior distribution on ranked topologies. Although the first of these formulations has some attractive properties, the algorithm we present for computing its prior density is computationally intensive. However, the second formulation is always faster and computationally efficient for up to six calibrations. We demonstrate the utility of the new class of multiple-calibration tree priors using both small simulations and a real-world analysis and compare the results to existing schemes. The two new calibrated tree priors described in this article offer greater flexibility and control of prior specification in calibrated time-tree inference and divergence time dating, and will remove the need for indirect approaches to the assessment of the combined effect of calibration densities and tree priors in Bayesian phylogenetic inference.},
Author = {Heled, Joseph and Drummond, Alexei J.},
Date-Added = {2015-09-03 08:08:11 +0000},
Date-Modified = {2015-09-03 08:16:55 +0000},
Doi = {10.1093/sysbio/syu089},
Journal = {Syst Biol},
Journal-Full = {Systematic biology},
Keywords = {BEAST; Bayesian inference; Yule prior; birth--death tree prior; fossil calibrations; multiple calibrations},
Mesh = {Algorithms; Animals; Anura; Bayes Theorem; Calibration; Classification; Computer Simulation; Phylogeny; Time; Typhaceae},
Month = {May},
Number = {3},
Pages = {369-83},
Pmc = {PMC4395842},
Pmid = {25398445},
Pst = {ppublish},
Title = {Calibrated birth-death phylogenetic time-tree priors for bayesian inference},
Volume = {64},
Year = {2015},
Bdsk-Url-1 = {http://dx.doi.org/10.1093/sysbio/syu089}}
@article{Etienne:2012by,
Abstract = {The branching times of molecular phylogenies allow us to infer speciation and extinction dynamics even when fossils are absent. Troublingly, phylogenetic approaches usually return estimates of zero extinction, conflicting with fossil evidence. Phylogenies and fossils do agree, however, that there are often limits to diversity. Here, we present a general approach to evaluate the likelihood of a phylogeny under a model that accommodates diversity-dependence and extinction. We find, by likelihood maximization, that extinction is estimated most precisely if the rate of increase in the number of lineages in the phylogeny saturates towards the present or first decreases and then increases. We demonstrate the utility and limits of our approach by applying it to the phylogenies for two cases where a fossil record exists (Cetacea and Cenozoic macroperforate planktonic foraminifera) and to three radiations lacking fossil evidence (Dendroica, Plethodon and Heliconius). We propose that the diversity-dependence model with extinction be used as the standard model for macro-evolutionary dynamics because of its biological realism and flexibility.},
Author = {Etienne, Rampal S and Haegeman, Bart and Stadler, Tanja and Aze, Tracy and Pearson, Paul N and Purvis, Andy and Phillimore, Albert B},
Date-Added = {2015-08-26 14:56:34 +0000},
Date-Modified = {2015-08-26 14:56:34 +0000},
Doi = {10.1098/rspb.2011.1439},
Journal = {Proc Biol Sci},
Journal-Full = {Proceedings. Biological sciences / The Royal Society},
Mesh = {Animals; Evolution, Molecular; Extinction, Biological; Foraminifera; Fossils; Genetic Variation; Lepidoptera; Models, Genetic; Passeriformes; Phylogeny; Urodela},
Month = {Apr},
Number = {1732},
Pages = {1300-9},
Pmc = {PMC3282358},
Pmid = {21993508},
Pst = {ppublish},
Title = {Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record},
Volume = {279},
Year = {2012},
Bdsk-Url-1 = {http://dx.doi.org/10.1098/rspb.2011.1439}}
@book{Yang2014,
Annote = {LDR 01410cam 22003737i 4500
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100 1 $aYang, Ziheng,$eauthor.
245 10 $aMolecular evolution :$ba statistical approach /$cZiheng Yang.
250 $aFirst edition.
264 1 $aOxford, United Kingdom ;$aNew York, NY, United States of America :$bOxford University Press,$c2014.
300 $axv, 492 pages :$billustrations ;$c26 cm
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504 $aIncludes bibliographical references (pages 450-487) and index.
650 0 $aMolecular evolution$xMathematical models.
650 0 $aMolecular evolution$xStatistical methods.
650 0 $aPhylogeny$xMolecular aspects.
955 $apc20 2013-11-29
},
Author = {Yang, Ziheng},
Call-Number = {QH371.3.M37},
Date-Added = {2015-08-26 12:27:27 +0000},
Date-Modified = {2015-08-26 12:28:44 +0000},
Dewey-Call-Number = {572.8/38},
Edition = {First edition},
Genre = {Molecular evolution},
Isbn = {9780199602612 (pbk.)},
Library-Id = {2013956540},
Publisher = {Oxford University Press},
Title = {Molecular evolution: a statistical approach},
Year = {2014}}
@article{Slater2015,
Abstract = {A long-standing hypothesis in adaptive radiation theory is that ecological opportunity constrains rates of phenotypic evolution, generating a burst of morphological disparity early in clade history. Empirical support for the early burst model is rare in comparative data, however. One possible reason for this lack of support is that most phylogenetic tests have focused on extant clades, neglecting information from fossil taxa. Here, I test for the expected signature of adaptive radiation using the outstanding 40-My fossil record of North American canids. Models implying time- and diversity-dependent rates of morphological evolution are strongly rejected for two ecologically important traits, body size and grinding area of the molar teeth. Instead, Ornstein-Uhlenbeck processes implying repeated, and sometimes rapid, attraction to distinct dietary adaptive peaks receive substantial support. Diversity-dependent rates of morphological evolution seem uncommon in clades, such as canids, that exhibit a pattern of replicated adaptive radiation. Instead, these clades might best be thought of as deterministic radiations in constrained Simpsonian subzones of a major adaptive zone. Support for adaptive peak models may be diagnostic of subzonal radiations. It remains to be seen whether early burst or ecological opportunity models can explain broader adaptive radiations, such as the evolution of higher taxa.},
Author = {Slater, Graham J},
Date-Added = {2015-08-26 12:20:49 +0000},
Date-Modified = {2015-08-26 12:21:08 +0000},
Doi = {10.1073/pnas.1403666111},
Journal = {Proc Natl Acad Sci U S A},
Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
Keywords = {Canidae; adaptive radiation; macroevolution; phylogenetics; rates},
Mesh = {Adaptation, Biological; Animals; Bayes Theorem; Biological Evolution; Calibration; Canidae; Diet; Fossils; Genetic Variation; Quantitative Trait, Heritable; Time Factors},
Month = {Apr},
Number = {16},
Pages = {4897-902},
Pmc = {PMC4413353},
Pmid = {25901311},
Pst = {ppublish},
Title = {Iterative adaptive radiations of fossil canids show no evidence for diversity-dependent trait evolution},
Volume = {112},
Year = {2015},
Bdsk-Url-1 = {http://dx.doi.org/10.1073/pnas.1403666111}}
@article{WagnerMarcot2013,
Abstract = {1. Observed patterns in the fossil record reflect not just macroevolutionary dynamics, but preservation patterns. Sampling rates themselves vary not simply over time or among major taxonomic groups, but within time intervals over geography and environment, and among species within clades. Large databases of presences of taxa in fossil-bearing collections allow us to quantify variation in per-collection sampling rates among species within a clade. We do this separately not just for different time/stratigraphic intervals, but also for different geographic or ecologic units within time/stratigraphic intervals. We then re-assess per-million-year sampling rates given the distributions of per-collection sampling rates.
2. We use simple distribution models (geometric and lognormal) to assess general models of per-locality sampling rate distributions given occurrences among appropriate fossiliferous localities. We break these down not simply by time period, but by general biogeographic units in order to accommodate variation over space as well as among species.
3. We apply these methods to occurrence data for Meso-Cenozoic mammals drawn from the Paleobiology Database and the New and Old Worlds fossil mammal database. We find that all models of distributed rates do vastly better than the best uniform sampling rates and that the lognormal in particular does an excellent job of summarizing sampling rates. We also show that the lognormal distributions vary fairly substantially among biogeographic units of the same age.
4. As an example of the utility of these rates, we assess the most likely divergence times for basal (Eocene-Oligocene) carnivoramorphan mammals from North America and Eurasia using both stratigraphic and morphological data. The results allow for unsampled taxa or unsampled portions of sampled lineages to be in either continent and also allow for the variation in sampling rates among species. We contrast five models using stratigraphic likelihoods in different ways to summarize how they might affect macroevolutionary inferences.},
Address = {111 RIVER ST, HOBOKEN 07030-5774, NJ USA},
Author = {Wagner, Peter J. and Marcot, Jonathan D.},
Date-Added = {2015-08-26 11:28:14 +0000},
Date-Modified = {2015-08-26 11:28:34 +0000},
Doi = {10.1111/2041-210X.12088},
Issn = {2041-210X},
Journal = {Methods Ecol. Evol.},
Keywords = {NORTH-AMERICAN MAMMALS; MAXIMUM-LIKELIHOOD; TAXONOMIC DIVERSITY; DIVERGENCE TIMES; RECORD; DIVERSIFICATION; PATTERNS; EVOLUTION; PRESERVATION; HYPOTHESES},
Month = {August},
Number = {8},
Pages = {703--713},
Publisher = {WILEY-BLACKWELL},
Times-Cited = {7},
Title = {Modelling distributions of fossil sampling rates over time, space and taxa: assessment and implications for macroevolutionary studies},
Volume = {4},
Wok-Uid = {WOS:000322891200002},
Year = {2013},
Bdsk-Url-1 = {http://ws.isiknowledge.com/cps/openurl/service?url_ver=Z39.88-2004&rft_id=info:ut/WOS:000322891200002}}
@article{huelsenbeck1997maximum,
Author = {Huelsenbeck, John P and Rannala, Bruce},
Date-Added = {2015-08-26 11:23:28 +0000},
Date-Modified = {2015-08-26 11:23:28 +0000},
Journal = {Paleobiology},
Pages = {174--180},
Publisher = {JSTOR},
Title = {Maximum likelihood estimation of phylogeny using stratigraphic data},
Year = {1997}}
@article{BromhamPenny2003,
Abstract = {The discovery of the molecular clock--a relatively constant rate of molecular evolution--provided an insight into the mechanisms of molecular evolution, and created one of the most useful new tools in biology. The unexpected constancy of rate was explained by assuming that most changes to genes are effectively neutral. Theory predicts several sources of variation in the rate of molecular evolution. However, even an approximate clock allows time estimates of events in evolutionary history, which provides a method for testing a wide range of biological hypotheses ranging from the origins of the animal kingdom to the emergence of new viral epidemics.},
Author = {Bromham, Lindell and Penny, David},
Date-Added = {2015-08-26 09:43:42 +0000},
Date-Modified = {2015-08-26 09:43:52 +0000},
Doi = {10.1038/nrg1020},
Journal = {Nat Rev Genet},
Journal-Full = {Nature reviews. Genetics},
Mesh = {Animals; Communicable Diseases, Emerging; DNA; Disease Outbreaks; Evolution, Molecular; Genetics, Population; History, Ancient; Humans; Models, Genetic; Mutation; Population Density; Proteins; Selection, Genetic; Time Factors},
Month = {Mar},
Number = {3},
Pages = {216-24},
Pmid = {12610526},
Pst = {ppublish},
Title = {The modern molecular clock},
Volume = {4},
Year = {2003},
Bdsk-Url-1 = {http://dx.doi.org/10.1038/nrg1020}}
@article{Benton2000,
Abstract = {Does the fossil record present a true picture of the history of life, or should it be viewed with caution? Raup argued that plots of the diversification of life were an illustration of bias: the older the rocks, the less we know. The debate was partially resolved by the observation that different data sets gave similar patterns of rising diversity through time. Here we show that new assessment methods, in which the order of fossils in the rocks (stratigraphy) is compared with the order inherent in evolutionary trees (phylogeny), provide a more convincing analytical tool: stratigraphy and phylogeny offer independent data on history. Assessments of congruence between stratigraphy and phylogeny for a sample of 1,000 published phylogenies show no evidence of diminution of quality backwards in time. Ancient rocks clearly preserve less information, on average, than more recent rocks. However, if scaled to the stratigraphic level of the stage and the taxonomic level of the family, the past 540 million years of the fossil record provide uniformly good documentation of the life of the past.},
Author = {Benton, M J and Wills, M A and Hitchin, R},
Date-Added = {2015-08-26 09:07:13 +0000},
Date-Modified = {2015-08-26 09:07:25 +0000},
Doi = {10.1038/35000558},
Journal = {Nature},
Journal-Full = {Nature},
Mesh = {Animals; Fossils; Geological Phenomena; Geology; Phylogeny; Time},
Month = {Feb},
Number = {6769},
Pages = {534-7},
Pmid = {10676959},
Pst = {ppublish},
Title = {Quality of the fossil record through time},
Volume = {403},
Year = {2000},
Bdsk-Url-1 = {http://dx.doi.org/10.1038/35000558}}
@article{Donoghue2007,
Abstract = {A great tradition in macroevolution and systematics has been the ritual squabbling between palaeontologists and molecular biologists. But, because both sides were talking past each other, they could never agree. Practitioners in both fields should play to their strengths and work together: palaeontologists can provide minimum constraints on branching points in the Tree of Life with considerable precision, and estimate the extent of unrecorded prehistory. Molecular tree analysts have remarkable modelling tools in their armoury to convert multiple minimum age constraints into meaningful dated trees. As we discuss here, work should now focus on establishing reasonable, dated trees that satisfy rigorous assessment of the available fossils and careful consideration of molecular tree methods: rocks and clocks together are an unbeatable combination. Reliably dated trees provide, for the first time, the opportunity to explore wider questions in macroevolution.},
Author = {Donoghue, Philip C J and Benton, Michael J},
Date-Added = {2015-08-26 09:06:56 +0000},
Date-Modified = {2015-08-26 09:08:58 +0000},
Doi = {10.1016/j.tree.2007.05.005},
Journal = {Trends Ecol Evol},
Journal-Full = {Trends in ecology \& evolution},
Mesh = {Animals; Biological Clocks; Biological Evolution; Calibration; Fossils; Humans; Molecular Biology; Time Factors},
Month = {Aug},
Number = {8},
Pages = {424-31},
Pmid = {17573149},
Pst = {ppublish},
Title = {Rocks and clocks: calibrating the Tree of Life using fossils and molecules},
Volume = {22},
Year = {2007},
Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.tree.2007.05.005}}
@article{BentonAyala2003,
Abstract = {The relative merits of molecular and paleontological dates of major branching points in the tree of life are currently debated. In some cases, molecular date estimates are up to twice as old as paleontological dates. However, although it is true that paleontological dates are often too young (missing fossils), molecular dates are often too old (statistical bias). Intense study of the dating of major splits in the tree of mammals has shown rapprochement as fossil dates become older and molecular dates become younger.},
Author = {Benton, Michael J and Ayala, Francisco J},
Date-Added = {2015-08-26 09:04:51 +0000},
Date-Modified = {2015-08-26 09:36:16 +0000},
Doi = {10.1126/science.1077795},
Journal = {Science},
Journal-Full = {Science (New York, N.Y.)},
Mesh = {Amino Acid Sequence; Animals; Base Sequence; Biological Evolution; Birds; Classification; DNA; Evolution, Molecular; Fossils; Invertebrates; Mammals; Paleontology; Phylogeny; Plants; Polymorphism, Genetic; Proteins; RNA; Time; Vertebrates},
Month = {Jun},
Number = {5626},
Pages = {1698-700},
Pmid = {12805535},
Pst = {ppublish},
Title = {Dating the tree of life},
Volume = {300},
Year = {2003},
Bdsk-Url-1 = {http://dx.doi.org/10.1126/science.1077795}}
@article{Benton2007,
Abstract = {The role of fossils in dating the tree of life has been misunderstood. Fossils can provide good "minimum" age estimates for branches in the tree, but "maximum" constraints on those ages are poorer. Current debates about which are the "best" fossil dates for calibration move to consideration of the most appropriate constraints on the ages of tree nodes. Because fossil-based dates are constraints, and because molecular evolution is not perfectly clock-like, analysts should use more rather than fewer dates, but there has to be a balance between many genes and few dates versus many dates and few genes. We provide "hard" minimum and "soft" maximum age constraints for 30 divergences among key genome model organisms; these should contribute to better understanding of the dating of the animal tree of life.},
Author = {Benton, Michael J and Donoghue, Philip C J},
Date-Added = {2015-08-26 08:59:14 +0000},
Date-Modified = {2015-08-26 08:59:58 +0000},
Doi = {10.1093/molbev/msl150},
Journal = {Mol Biol Evol},
Journal-Full = {Molecular biology and evolution},
Mesh = {Animals; Biological Evolution; Chronology as Topic; Evolution, Molecular; Fossils; Humans; Paleontology; Phylogeny},
Month = {Jan},
Number = {1},
Pages = {26-53},
Pmid = {17047029},
Pst = {ppublish},
Title = {Paleontological evidence to date the tree of life},
Volume = {24},
Year = {2007},
Bdsk-Url-1 = {http://dx.doi.org/10.1093/molbev/msl150}}
@book{Yang:2006yu,
Address = {Oxford},
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082 04 $a572.838015118$222
100 1 $aYang, Ziheng.
245 10 $aComputational molecular evolution /$cZiheng Yang.
260 $aOxford :$bOxford University Press,$c2006.
300 $axvi, 357 p. :$bill. ;$c24 cm.
440 0 $aOxford series in ecology and evolution
504 $aIncludes bibliographical references (p. [319]-352) and index.
650 0 $aMolecular evolution$xMathematical models.
650 0 $aMolecular evolution$xData processing.
856 41 $3Table of contents only$uhttp://www.loc.gov/catdir/toc/fy0711/2007271492.html
856 42 $3Contributor biographical information$uhttp://www.loc.gov/catdir/enhancements/fy0726/2007271492-b.html
856 42 $3Publisher description$uhttp://www.loc.gov/catdir/enhancements/fy0726/2007271492-d.html
},
Author = {Yang, Ziheng},
Call-Number = {QH371.3.M37},
Date-Added = {2015-08-11 13:32:48 +0000},
Date-Modified = {2015-08-11 13:32:48 +0000},
Dewey-Call-Number = {572.838015118},
Genre = {Molecular evolution},
Isbn = {0198566999},
Library-Id = {2007271492},
Publisher = {Oxford University Press},
Title = {Computational molecular evolution},
Url = {http://www.loc.gov/catdir/toc/fy0711/2007271492.html},
Year = {2006},
Bdsk-Url-1 = {http://www.loc.gov/catdir/toc/fy0711/2007271492.html}}
@book{Felsenstein2004,
Address = {Sunderland, MA},
Author = {Felsenstein, J.},
Date-Added = {2015-08-11 13:31:15 +0000},
Date-Modified = {2015-08-11 13:31:15 +0000},
Publisher = {Sinauer Associates, Inc.},
Title = {Inferring Phylogenies},
Year = {2004}}
@article{yang:1994ma,
Author = {Yang, Ziheng},
Date-Added = {2015-08-05 16:14:53 +0000},
Date-Modified = {2015-08-05 16:14:53 +0000},
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{gray2013evolutionary,
Author = {Gray, Rebecca R and Tanaka, Yasuhito and Takebe, Yutaka and Magiorkinis, Gkikas and Buskell, Zelma and Seeff, Leonard and Alter, Harvey J and Pybus, Oliver G},
Date-Added = {2015-07-29 14:00:24 +0000},
Date-Modified = {2015-07-29 14:00:24 +0000},
Journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
Number = {1626},
Pages = {20130168},
Publisher = {The Royal Society},
Title = {Evolutionary analysis of hepatitis C virus gene sequences from 1953},
Volume = {368},
Year = {2013}}
@article{meyer2014mitochondrial,
Author = {Meyer, Matthias and Fu, Qiaomei and Aximu-Petri, Ayinuer and Glocke, Isabelle and Nickel, Birgit and Arsuaga, Juan-Luis and Mart{\'\i}nez, Ignacio and Gracia, Ana and de Castro, Jos{\'e} Mar{\'\i}a Berm{\'u}dez and Carbonell, Eudald and others},
Date-Added = {2015-07-29 13:08:55 +0000},
Date-Modified = {2015-07-29 13:08:55 +0000},
Journal = {Nature},
Number = {7483},
Pages = {403--406},
Publisher = {Nature Publishing Group},
Title = {A mitochondrial genome sequence of a hominin from Sima de los Huesos},
Volume = {505},
Year = {2014}}
@article{shapiro2011bayesian,
Author = {Shapiro, Beth and Ho, Simon YW and Drummond, Alexei J. and Suchard, Marc A and Pybus, Oliver G and Rambaut, Andrew},
Date-Added = {2015-07-29 12:53:23 +0000},
Date-Modified = {2015-07-29 13:02:09 +0000},
Journal = {Molecular biology and evolution},
Number = {2},
Pages = {879--887},
Publisher = {SMBE},
Title = {A Bayesian phylogenetic method to estimate unknown sequence ages},
Volume = {28},
Year = {2011}}
@phdthesis{drummond2002computational,
Author = {Drummond, Alexei J.},
Date-Added = {2015-07-29 12:52:36 +0000},
Date-Modified = {2015-07-29 13:02:56 +0000},
School = {ResearchSpace@ Auckland},
Title = {Computational Statistical Inference for Molecular Evolution and Population Genetics},
Year = {2002}}
@article{tavare2002using,
Author = {Tavar{\'e}, Simon and Marshall, Charles R and Will, Oliver and Soligo, Christophe and Martin, Robert D},
Date-Added = {2015-07-28 15:57:27 +0000},
Date-Modified = {2015-07-28 15:57:27 +0000},
Journal = {Nature},
Number = {6882},
Pages = {726--729},
Publisher = {Nature Publishing Group},
Title = {Using the fossil record to estimate the age of the last common ancestor of extant primates},
Volume = {416},
Year = {2002}}
@article{gavryushkina2015bayesian,
Author = {Gavryushkina, Alexandra and Heath, Tracy A. and Ksepka, Daniel T. and Stadler, Tanja and Welch, David and Drummond, Alexei J.},
Date-Added = {2015-07-28 15:55:07 +0000},
Date-Modified = {2015-08-05 15:55:17 +0000},
Journal = {arXiv preprint arXiv:1506.04797},
Title = {Bayesian total evidence dating reveals the recent crown radiation of penguins},
Year = {2015}}
@article{Lambert2010,
Author = {Lambert, Amaury and others},
Journal = {The Annals of Probability},
Number = {1},
Pages = {348--395},
Publisher = {Institute of Mathematical Statistics},
Title = {The contour of splitting trees is a {L}{\'e}vy process},
Volume = {38},
Year = {2010}}
@article{Alfaro2009,
Author = {Alfaro, Michael E and Santini, Francesco and Brock, Chad and Alamillo, Hugo and Dornburg, Alex and Rabosky, Daniel L and Carnevale, Giorgio and Harmon, Luke J},
Journal = {Proceedings of the National Academy of Sciences, USA},
Number = {32},
Pages = {13410--13414},
Publisher = {National Acad Sciences},
Title = {Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates},
Volume = {106},
Year = {2009}}
@article{Maddison2007,
Author = {Maddison, Wayne P and Midford, Peter E and Otto, Sarah P},
Journal = {Systematic Biology},
Number = {5},
Pages = {701--710},
Publisher = {Oxford University Press},
Title = {Estimating a binary character's effect on speciation and extinction},
Volume = {56},
Year = {2007}}
@article{drummond2010,
Author = {Drummond, Alexei J. and Suchard, Marc A.},
Date-Added = {2015-04-21 22:40:37 +0000},
Date-Modified = {2015-09-03 08:20:13 +0000},
Issn = {1741-7007},
Journal = {BMC Biology},
Number = {1},
Pages = {114},
Publisher = {BioMed Central Ltd},
Title = {{Bayesian random local clocks, or one rate to rule them all}},
Volume = {8},
Year = {2010}}
@article{Shankarappa1999,
Author = {R. Shankarappa and J.B. Margolick and S.J. Gange and A.G. Rodrigo and D. Upchurch and H. Farzadegan and P. Gupta and C.R. Rinaldo and G.H. Learn and X. He and X.L. Huang and J.I. Mullins},
Date-Added = {2014-05-23 02:26:26 +0000},
Date-Modified = {2014-05-23 02:26:26 +0000},
Journal = {Journal Virology},
Notes = {cr},
Pages = {10489--10502},
Title = {Consistent viral evolutionary changes associated with the disease progression of human immunodeficiency virus type 1 infection},
Volume = {73},
Year = {1999}}
@article{Lewis2001,
Abstract = {Evolutionary biologists have adopted simple likelihood models for purposes of estimating ancestral states and evaluating character independence on specified phylogenies; however, for purposes of estimating phylogenies by using discrete morphological data, maximum parsimony remains the only option. This paper explores the possibility of using standard, well-behaved Markov models for estimating morphological phylogenies (including branch lengths) under the likelihood criterion. An important modification of standard Markov models involves making the likelihood conditional on characters being variable, because constant characters are absent in morphological data sets. Without this modification, branch lengths are often overestimated, resulting in potentially serious biases in tree topology selection. Several new avenues of research are opened by an explicitly model-based approach to phylogenetic analysis of discrete morphological data, including combined-data likelihood analyses (morphology + sequence data), likelihood ratio tests, and Bayesian analyses.},
Author = {Lewis, P. O.},
Date = {2001},
Date-Added = {2014-05-23 02:21:19 +0000},
Date-Modified = {2015-08-05 16:16:23 +0000},
Journal = {Systematic Biology},
Journal-Full = {Systematic Biology},
Mesh = {Biometry; Likelihood Functions; Markov Chains; Models, Genetic; Phylogeny},
Number = {6},
Pages = {913-25},
Pmid = {12116640},
Pst = {ppublish},
Title = {A likelihood approach to estimating phylogeny from discrete morphological character data},
Volume = {50},
Year = {2001}}
@article{Heled2012,
Abstract = {The use of fossil evidence to calibrate divergence time estimation has a long history. More recently, Bayesian Markov chain Monte Carlo has become the dominant method of divergence time estimation, and fossil evidence has been reinterpreted as the specification of prior distributions on the divergence times of calibration nodes. These so-called "soft calibrations" have become widely used but the statistical properties of calibrated tree priors in a Bayesian setting hashave not been carefully investigated. Here, we clarify that calibration densities, such as those defined in BEAST 1.5, do not represent the marginal prior distribution of the calibration node. We illustrate this with a number of analytical results on small trees. We also describe an alternative construction for a calibrated Yule prior on trees that allows direct specification of the marginal prior distribution of the calibrated divergence time, with or without the restriction of monophyly. This method requires the computation of the Yule prior conditional on the height of the divergence being calibrated. Unfortunately, a practical solution for multiple calibrations remains elusive. Our results suggest that direct estimation of the prior induced by specifying multiple calibration densities should be a prerequisite of any divergence time dating analysis.},
Author = {Heled, Joseph and Drummond, Alexei J.},
Date-Added = {2014-05-15 21:54:36 +0000},
Date-Modified = {2015-09-03 08:17:01 +0000},
Doi = {10.1093/sysbio/syr087},
Journal = {Systematic Biology},
Journal-Full = {Systematic Biology},
Mesh = {Animals; Bayes Theorem; Calibration; Classification; Computer Simulation; Evolution, Molecular; Fossils; Markov Chains; Marsupialia; Models, Genetic; Monte Carlo Method; Papio; Phylogeny},
Month = {Jan},
Number = {1},
Pages = {138-49},
Pmc = {PMC3243734},
Pmid = {21856631},
Pst = {ppublish},
Title = {Calibrated tree priors for relaxed phylogenetics and divergence time estimation},
Volume = {61},
Year = {2012},
Bdsk-Url-1 = {http://dx.doi.org/10.1093/sysbio/syr087}}
@article{Hastings1970,
Author = {W.K. Hastings},
Date-Added = {2014-05-15 21:37:54 +0000},
Date-Modified = {2014-05-15 21:37:54 +0000},
Journal = {Biometrika},
Pages = {97--109},
Title = {{Monte Carlo} sampling methods using {Markov} chains and their applications},
Volume = {57},
Year = {1970}}
@article{Metropolis1953,
Author = {N. Metropolis and A.W. Rosenbluth and M.N. Rosenbluth and A.H. Teller and E. Teller},
Date-Added = {2014-05-15 21:37:38 +0000},
Date-Modified = {2014-05-15 21:37:38 +0000},
Journal = {Journal of Chemistry and Physics},
Pages = {1087--1092},
Title = {Equations of state calculations by fast computing machines},
Volume = {21},
Year = {1953}}
@article{Beast17,
Abstract = {Computational evolutionary biology, statistical phylogenetics and coalescent-based population genetics are becoming increasingly central to the analysis and understanding of molecular sequence data. We present the Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package version 1.7, which implements a family of Markov chain Monte Carlo (MCMC) algorithms for Bayesian phylogenetic inference, divergence time dating, coalescent analysis, phylogeography and related molecular evolutionary analyses. This package includes an enhanced graphical user interface program called Bayesian Evolutionary Analysis Utility (BEAUti) that enables access to advanced models for molecular sequence and phenotypic trait evolution that were previously available to developers only. The package also provides new tools for visualizing and summarizing multispecies coalescent and phylogeographic analyses. BEAUti and BEAST 1.7 are open source under the GNU lesser general public license and available at http://beast-mcmc.googlecode.com and http://beast.bio.ed.ac.uk.},
Author = {Drummond, Alexei J and Suchard, Marc A and Xie, Dong and Rambaut, Andrew},
Date-Added = {2014-05-15 21:34:18 +0000},
Date-Modified = {2014-05-15 21:34:37 +0000},
Doi = {10.1093/molbev/mss075},
Journal = {Molecular Biology and Evolution},
Journal-Full = {Molecular Biology and Evolution},
Mesh = {Animals; Base Sequence; Bayes Theorem; Computational Biology; DNA, Mitochondrial; Finches; Molecular Sequence Data; Phenotype; Phylogeny; Software; User-Computer Interface},
Month = {Aug},
Number = {8},
Pages = {1969-73},
Pmc = {PMC3408070},
Pmid = {22367748},
Pst = {ppublish},
Title = {{B}ayesian phylogenetics with {BEAUti} and the {BEAST} 1.7},
Volume = {29},
Year = {2012},
Bdsk-Url-1 = {http://dx.doi.org/10.1093/molbev/mss075}}
@article{PhyloBayes3,
Abstract = {MOTIVATION: A variety of probabilistic models describing the evolution of DNA or protein sequences have been proposed for phylogenetic reconstruction or for molecular dating. However, there still lacks a common implementation allowing one to freely combine these independent features, so as to test their ability to jointly improve phylogenetic and dating accuracy.
RESULTS: We propose a software package, PhyloBayes 3, which can be used for conducting Bayesian phylogenetic reconstruction and molecular dating analyses, using a large variety of amino acid replacement and nucleotide substitution models, including empirical mixtures or non-parametric models, as well as alternative clock relaxation processes.},
Author = {Lartillot, Nicolas and Lepage, Thomas and Blanquart, Samuel},
Date-Added = {2014-05-15 21:30:04 +0000},
Date-Modified = {2014-05-15 21:31:33 +0000},
Doi = {10.1093/bioinformatics/btp368},
Journal = {Bioinformatics},
Journal-Full = {Bioinformatics (Oxford, England)},
Mesh = {Animals; Bayes Theorem; Computational Biology; Databases, Nucleic Acid; Phylogeny; Predictive Value of Tests; Reproducibility of Results; Software; Time Factors},
Month = {Sep},
Number = {17},
Pages = {2286-8},
Pmid = {19535536},
Pst = {ppublish},
Title = {{PhyloBayes} 3: A {B}ayesian software package for phylogenetic reconstruction and molecular dating},
Volume = {25},
Year = {2009},
Bdsk-Url-1 = {http://dx.doi.org/10.1093/bioinformatics/btp368}}
@article{MrBayes,
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.},
Author = {Huelsenbeck, J P and Ronquist, F},
Date-Added = {2014-05-15 21:23:19 +0000},
Date-Modified = {2014-05-15 21:24:18 +0000},
Journal = {Bioinformatics},
Journal-Full = {Bioinformatics (Oxford, England)},
Mesh = {Algorithms; Bayes Theorem; Computational Biology; Markov Chains; Phylogeny; Software},
Month = {Aug},
Number = {8},
Pages = {754-5},
Pmid = {11524383},
Pst = {ppublish},
Title = {{MRBAYES}: {B}ayesian inference of phylogenetic trees},
Volume = {17},
Year = {2001}}
@article{Mau1999,
Abstract = {We derive a Markov chain to sample from the posterior distribution for a phylogenetic tree given sequence information from the corresponding set of organisms, a stochastic model for these data, and a prior distribution on the space of trees. A transformation of the tree into a canonical cophenetic matrix form suggests a simple and effective proposal distribution for selecting candidate trees close to the current tree in the chain. We illustrate the algorithm with restriction site data on 9 plant species, then extend to DNA sequences from 32 species of fish. The algorithm mixes well in both examples from random starting trees, generating reproducible estimates and credible sets for the path of evolution.},
Author = {Mau, B and Newton, M A and Larget, B},
Date-Added = {2014-05-15 21:23:13 +0000},
Date-Modified = {2014-05-15 21:24:51 +0000},
Journal = {Biometrics},
Journal-Full = {Biometrics},
Mesh = {Algorithms; Animals; Bayes Theorem; Biometry; DNA; Markov Chains; Monte Carlo Method; Perches; Phylogeny; Plants; Stochastic Processes},
Month = {Mar},
Number = {1},
Pages = {1-12},
Pmid = {11318142},
Pst = {ppublish},
Title = {{B}ayesian phylogenetic inference via {Markov chain Monte Carlo} methods},
Volume = {55},
Year = {1999}}
@article{Yang1997,
Abstract = {An improved Bayesian method is presented for estimating phylogenetic trees using DNA sequence data. The birth-death process with species sampling is used to specify the prior distribution of phylogenies and ancestral speciation times, and the posterior probabilities of phylogenies are used to estimate the maximum posterior probability (MAP) tree. Monte Carlo integration is used to integrate over the ancestral speciation times for particular trees. A Markov Chain Monte Carlo method is used to generate the set of trees with the highest posterior probabilities. Methods are described for an empirical Bayesian analysis, in which estimates of the speciation and extinction rates are used in calculating the posterior probabilities, and a hierarchical Bayesian analysis, in which these parameters are removed from the model by an additional integration. The Markov Chain Monte Carlo method avoids the requirement of our earlier method for calculating MAP trees to sum over all possible topologies (which limited the number of taxa in an analysis to about five). The methods are applied to analyze DNA sequences for nine species of primates, and the MAP tree, which is identical to a maximum-likelihood estimate of topology, has a probability of approximately 95%.},
Author = {Yang, Z and Rannala, B},
Date-Added = {2014-05-15 21:23:10 +0000},
Date-Modified = {2014-05-15 21:25:01 +0000},
Journal = {Molecular Biology and Evolution},
Journal-Full = {Molecular Biology and Evolution},
Mesh = {Algorithms; Animals; Bayes Theorem; DNA, Mitochondrial; Monte Carlo Method; Phylogeny; Primates; Sequence Analysis},
Month = {Jul},
Number = {7},
Pages = {717-24},
Pmid = {9214744},
Pst = {ppublish},
Title = {{B}ayesian phylogenetic inference using {DNA} sequences: A {Markov chain Monte Carlo} method},
Volume = {14},
Year = {1997}}
@article{Huelsenbeck2001,
Abstract = {As a discipline, phylogenetics is becoming transformed by a flood of molecular data. These data allow broad questions to be asked about the history of life, but also present difficult statistical and computational problems. Bayesian inference of phylogeny brings a new perspective to a number of outstanding issues in evolutionary biology, including the analysis of large phylogenetic trees and complex evolutionary models and the detection of the footprint of natural selection in DNA sequences.},
Author = {Huelsenbeck, J P and Ronquist, F and Nielsen, R and Bollback, J P},
Date-Added = {2014-05-15 21:21:10 +0000},
Date-Modified = {2014-05-15 21:21:26 +0000},
Doi = {10.1126/science.1065889},
Journal = {Science},
Journal-Full = {Science (New York, N.Y.)},
Mesh = {Algorithms; Animals; Base Sequence; Bayes Theorem; Biological Evolution; Computer Simulation; DNA; Evolution, Molecular; Hemagglutinins, Viral; Insects; Likelihood Functions; Markov Chains; Models, Biological; Monte Carlo Method; Orthomyxoviridae; Phylogeny; Plants; Probability; Selection, Genetic; Software},
Month = {Dec},
Number = {5550},
Pages = {2310-4},
Pmid = {11743192},
Pst = {ppublish},
Title = {{B}ayesian inference of phylogeny and its impact on evolutionary biology},
Volume = {294},
Year = {2001},
Bdsk-Url-1 = {http://dx.doi.org/10.1126/science.1065889}}
@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.},
Author = {Pybus, O G and Charleston, M A and Gupta, S and Rambaut, A and Holmes, E C and Harvey, P H},
Date-Added = {2014-05-10 05:20:01 +0000},
Date-Modified = {2014-05-10 05:20:08 +0000},
Doi = {10.1126/science.1058321},
Journal = {Science},
Journal-Full = {Science (New York, N.Y.)},
Mesh = {Endemic Diseases; Genes, Viral; Hepacivirus; Hepatitis C; Humans; Likelihood Functions; Models, Biological; Molecular Epidemiology; Phylogeny; Population Dynamics; Prevalence; Substance Abuse, Intravenous},
Month = {Jun},
Number = {5525},
Pages = {2323-2325},
Pmid = {11423661},
Pst = {ppublish},
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{Drummond2003,
Author = {Drummond, A.J. and Pybus, O.G. and Rambaut, A. and Forsberg, R. and Rodrigo, A.G.},
Date-Added = {2014-05-10 05:18:08 +0000},
Date-Modified = {2014-05-10 05:18:08 +0000},
Journal = {Trends in Ecology \& Evolution},
Pages = {481--488},
Title = {Measurably evolving populations},
Volume = {18},
Year = {2003}}
@article{Drummond2006,
Abstract = {In phylogenetics, the unrooted model of phylogeny and the strict molecular clock model are two extremes of a continuum. Despite their dominance in phylogenetic inference, it is evident that both are biologically unrealistic and that the real evolutionary process lies between these two extremes. Fortunately, intermediate models employing relaxed molecular clocks have been described. These models open the gate to a new field of "relaxed phylogenetics." Here we introduce a new approach to performing relaxed phylogenetic analysis. We describe how it can be used to estimate phylogenies and divergence times in the face of uncertainty in evolutionary rates and calibration times. Our approach also provides a means for measuring the clocklikeness of datasets and comparing this measure between different genes and phylogenies. We find no significant rate autocorrelation among branches in three large datasets, suggesting that autocorrelated models are not necessarily suitable for these data. In addition, we place these datasets on the continuum of clocklikeness between a strict molecular clock and the alternative unrooted extreme. Finally, we present analyses of 102 bacterial, 106 yeast, 61 plant, 99 metazoan, and 500 primate alignments. From these we conclude that our method is phylogenetically more accurate and precise than the traditional unrooted model while adding the ability to infer a timescale to evolution.},
Author = {Drummond, Alexei J. and Ho, Simon Y. W. and Phillips, Matthew J. and Rambaut, Andrew},
Date-Added = {2014-05-10 05:06:20 +0000},
Date-Modified = {2015-08-05 15:48:31 +0000},
Doi = {10.1371/journal.pbio.0040088},
Journal = {PLoS Biology},
Journal-Full = {PLoS biology},
Mesh = {Animals; Bacteria; Bayes Theorem; Computer Simulation; Dengue Virus; Evolution; Fishes; Fungi; Genetic Variation; Influenza A virus; Insects; Markov Chains; Marsupialia; Models, Biological; Monte Carlo Method; Phylogeny; Plants; Primates; Time Factors},
Month = {May},
Number = {5},
Pages = {e88},
Pmc = {PMC1395354},
Pmid = {16683862},
Pst = {ppublish},
Title = {Relaxed phylogenetics and dating with confidence},
Volume = {4},
Year = {2006},
Bdsk-Url-1 = {http://dx.doi.org/10.1371/journal.pbio.0040088}}
@article{Thorne1998,
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, Jeffrey L. and Kishino, Hirohisa and Painter, I. S.},
Da = {19990119},
Date-Added = {2014-05-10 05:05:53 +0000},
Date-Modified = {2015-08-06 14:17:12 +0000},
Dcom = {19990119},
Edat = {1998/12/29},
Gr = {P01-GM45344/GM/United States NIGMS},
Issn = {0737-4038 (Print)},
Jid = {8501455},
Journal = {Molecular Biology and Evolution},
Jt = {Molecular Biology and Evolution},
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}}
@article{Rannala2007,
Author = {Rannala, Bruce and Yang, Ziheng},
Date-Added = {2014-05-10 05:04:49 +0000},
Date-Modified = {2014-05-10 05:04:49 +0000},
Journal = {Systematic Biology},
Number = {3},
Owner = {dpm},
Pages = {453--466},
Publisher = {Taylor \& Francis},
Timestamp = {2008.12.03},
Title = {Inferring Speciation Times under an Episodic Molecular Clock},
Volume = {56},
Year = {2007},
Bdsk-Url-1 = {http://www.informaworld.com/10.1080/10635150701420643}}
@article{Sanderson1997,
Author = {Sanderson, M.J.},
Date-Added = {2014-05-10 05:04:32 +0000},
Date-Modified = {2014-05-10 05:04:32 +0000},
Journal = {Molecular Biology and Evolution},
Pages = {1218--1231},
Title = {A nonparametric approach to estimating divergence times in the absence of rate consistency},
Volume = {14},
Year = {1997}}
@article{volz2013inferring,
Author = {Volz, Erik M and Frost, Simon DW},
Date-Added = {2014-05-10 04:59:36 +0000},
Date-Modified = {2014-05-10 04:59:36 +0000},
Journal = {PLoS Computational Biology},
Number = {12},
Pages = {e1003397},
Publisher = {Public Library of Science},
Title = {Inferring the Source of Transmission with Phylogenetic Data},
Volume = {9},
Year = {2013}}
@article{Stadler2010,
Author = {Stadler, Tanja},
Journal = {Journal of Theoretical Biology},
Number = {3},
Pages = {396-404},
Title = {Sampling-through-time in birth-death trees},
Volume = {267},
Year = {2010}}
@article{Stadler2011,
Author = {Stadler, Tanja and Kouyos, Roger D. and von Wyl, Viktor and Yerly, Sabine and B\"{o}ni, J\"{u}rg and B\"{u}rgisser, Philippe and Klimkait, Thomas and Joos, Beda and Rieder, Philip and Xie, Dong and G\"{u}nthard, Huldrych F. and Drummond, Alexei and Bonhoeffer, Sebastian and the Swiss HIV Cohort Study},
Journal = {Molecular Biology and Evolution},
Pages = {347-357},
Publisher = {SMBE},
Title = {Estimating the basic reproductive number from viral sequence data},
Volume = {29},
Year = {2011}}
@article{StadKuhn12,
Author = {Stadler, Tanja and K\"{u}nert, Denise and Bonhoeffer, Sebastian and Drummond, Alexei J.},
Doi = {10.1073/pnas.1207965110},
Eprint = {http://www.pnas.org/content/early/2012/12/13/1207965110.full.pdf+html},
Journal = {Proceedings of the National Academy of Sciences, USA},
Pages = {228--33},
Title = {Birth-death skyline plot reveals temporal changes of epidemic spread in {HIV} and hepatitis {C} virus ({HCV})},
Url = {http://www.pnas.org/content/early/2012/12/13/1207965110.abstract},
Volume = {110},
Year = {2013},
Bdsk-Url-1 = {http://www.pnas.org/content/early/2012/12/13/1207965110.abstract},
Bdsk-Url-2 = {http://dx.doi.org/10.1073/pnas.1207965110}}
@article{WilsBald,
Author = {Wilson, Ian J. and Balding, David J.},
Journal = {Genetics},
Number = {1},
Pages = {499-510},
Title = {Genealogical Inference From Microsatellite Data},
Volume = {150},
Year = {1998}}
@article{Gavr2013,
Author = {Gavryushkina, Alexandra and Welch, David and Drummond, Alexei J.},
Date-Modified = {2015-07-29 13:04:22 +0000},
Journal = {Algorithms for Molecular Biology},
Pages = {26},
Title = {Recursive algorithms for phylogenetic tree counting},
Volume = {8},
Year = {2013}}
@article{Green1995,
Author = {Green, Peter J.},
Date-Modified = {2014-05-15 21:24:38 +0000},
Journal = {Biometrica},
Number = {4},
Pages = {771--732},
Title = {Reversible jump {Markov chain Monte Carlo} computation and {B}ayesian model determination},
Volume = {82},
Year = {1995}}
@article{Beast2,
Author = {Bouckaert, Remco and Heled, Joseph and K\"{u}nert, Denise and Vaughan, Tim G. and Wu, Cheih-Hsi and Xie, Dong and Suchard, Marc A and Rambaut, Andrew and Drummond, Alexei J},
Journal = {PLoS Computational Biology},
Number = {4},
Pages = {e1003537},
Title = {{BEAST2}: A software platform for {B}ayesian evolutionary analysis},
Volume = {10},
Year = {2014}}
@article{Heath2014,
Author = {Heath, Tracy A. and Huelsenbeck, John P. and Stadler, Tanja},
Doi = {doi: 10.1073/pnas.1319091111},
Journal = {Proceedings of the National Academy of Sciences, USA},
Pages = {E2957--E2966},
Title = {The fossilized birth--death process for coherent calibration of divergence-time estimates},
Url = {http://arxiv.org/abs/1310.2968},
Volume = {111},
Year = {2014},
Bdsk-Url-1 = {http://arxiv.org/abs/1310.2968}}
@article{Ronq2012,
Author = {Ronquist, Fredrik and Klopfstein, Seraina and Vilhelmsen, Lars and Schulmeister, Susanne and Murray, Debra L and Rasnitsyn, Alexander P},
Journal = {Systematic Biology},
Pages = {973-999},
Title = {A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the {H}ymenoptera},
Volume = {61},
Year = {2012}}
@article{Silv2014,
Author = {Silvestro, Daniele and Schnitzler, Jan and Liow, Lee Hsiang and Antonelli, Alexandre and Salamin, Nicolas},
Doi = {doi: 10.1093/sysbio/syu006},
Journal = {Systematic Biology},
Number = {3},
Pages = {349--367},
Title = {{B}ayesian Estimation of Speciation and Extinction from Incomplete Fossil Occurrence Data},
Volume = {63},
Year = {2014},
Bdsk-Url-1 = {http://dx.doi.org/10.1093/sysbio/syu006}}
@article{Hue2005,
Author = {Hu\'{e}, St\'{e}phone and Pillay, Deenan and Clewley, Jonathan P. and Pybus, Oliver G.},
Journal = {Proceedings of the National Academy of Sciences, USA},
Number = {12},
Pages = {4425-4429},
Title = {Genetic analysis reveals the complex structure of {HIV}-1 transmission within defined risk groups},
Volume = {102},
Year = {2005}}
@article{Kuhnert2014,
Author = {K\"{u}nert, Denise and Stadler, Tanja and Vaughan, Timothy G and Drummond, Alexei J},
Journal = {Journal of The Royal Society Interface},
Number = {94},
Pages = {20131106},
Title = {Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth-death {SIR} model},
Volume = {11},
Year = {2014}}
@article{Gren2004,
Author = {Grenfell, Bryan T and Pybus, Oliver G and Gog, Julia R and Wood, James L N and Daly, Janet M and Mumford, Jenny A. and Holmes, Edward C},
Journal = {Science},
Pages = {327-32},
Title = {Unifying the epidemiological and evolutionary dynamics of pathogens},
Volume = {303},
Year = {2004}}
@article{Ypma13,
Author = {Ypma, Rolf J.F. and van Ballegooijen, W. Marijn and Wallinga, Jacco},
Doi = {10.1534/genetics.113.154856},
Journal = {Genetics},
Pages = {1055-1062},
Title = {Relating phylogenetic trees to transmission trees of infectious disease outbreaks},
Volume = {195},
Year = {2013},
Bdsk-Url-1 = {http://dx.doi.org/10.1534/genetics.113.154856}}
@article{Larget,
Author = {Larget, Bret},
Journal = {Systematic Biology},
Number = {4},
Pages = {501-511},
Title = {The Estimation of Tree Posterior Probabilities Using Conditional Clade Probability Distributions},
Volume = {62},
Year = {2013}}
@article{Vrancken2014,
Author = {Vrancken, Bram and Rambaut, Andrew and Suchard, Marc A. and Drummond, Alexei and Baele, Guy and Derdelinckx, Inge and Wijngaerden, Eric Van and Vandamme, Anne-Mieke and Laethem, Kristel Van},
Doi = {10.1371/journal.pcbi.1003505},
Journal = {PLoS Computational Biology},
Number = {4},
Pages = {e1003505},
Title = {The Genealogical Population Dynamics of {HIV}-1 in a Large Transmission Chain: Bridging within and among Host Evolutionary Rates},
Volume = {10},
Year = {2014},
Bdsk-Url-1 = {http://dx.doi.org/10.1371/journal.pcbi.1003505}}
@article{Lewis2005,
Author = {Lewis, Paul O. and Holder, Mark T. and Holsinger, Kent E.},
Doi = {doi: 10.1080/10635150590924208},
Journal = {Systematic Biology},
Number = {2},
Pages = {241--253},
Title = {Polytomies and {B}ayesian Phylogenetic Inference},
Volume = {54},
Year = {2005},
Bdsk-Url-1 = {http://dx.doi.org/10.1080/10635150590924208}}
@article{MrBayes32,
Author = {Ronquist, Fredrik and Teslenko, Maxim and van der Mark, Paul and Ayres, Daniel L and Darling, Aaron and H\"{o}hna, Sebastian and Larget, Bret and Liu, Liang and Suchard, Marc A. and Huelsenbeck, John P.},
Date-Modified = {2014-05-15 21:24:23 +0000},
Journal = {Systematic Biology},
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