Tilia cordata Mill. is a valuable tree species enriching the ecological values of the coniferous dominated boreal forests in northerly Europe. Following the historical decline, spreading of Tilia sp. is challenged by the elevated inbreeding and habitat fragmentation. We aimed to identify the main factors affecting the genetic potential of Tilia cordata for natural expansion by studying the geographical distribution of genetic diversity of Tilia cordata in semi-boreal forests of Lithuania. We used 14 genomic microsatellite markers to genotype 543 individuals from 23 wild growing populations of Tilia cordata in Lithuania. We found that Tilia cordata retained high levels of genetic diversity (population Fis = 0 to 0.15, Ho = 0.53 to 0.69, He = 0.56 to 0.75). AMOVA, Bayesian clustering and Monmonier’s barrier detection indicate weak but significant differentiation among the populations (Fst = 0.037***) into geographically interpretable clusters of (a) western Lithuania with high genetic heterogeneity but low genetic diversity, bottleneck effects, (b) peaking values of genetic diversity of Tilia cordata on rich and most soils of midland lowland, and (c) the most differentiated populations on poor soils of the coolest north-eastern highland possessing the highest rare alle frequency but elevated inbreeding and bottleneck effects, presumably, due to sub-structuring. We conclude that the genepool of Tilia cordata in Lithuania contains (a) the autochthonous populations of high genetic diversity representing the pre-historical genepools, that can be promoted, and (b) the escapes from urban sources of low diversity, that must be contained.
Exploring vegetation distribution spatial patterns facilitates understanding how biodiversity addresses the potential threat of future climate variability, especially for highly diverse and threatened tropical plant communities, but few empirical studies have been performed over various environmental scales. In this study, we used species-based and phylogeny-based methods to analyze the α- and β-diversity pattern variation in Dacrydium pectinatum communities and its key drivers along elevation and geographical gradients across three national nature reserves in Bawangling, Diaoluoshan and Jianfengling. Our study indicates that the species and phylogenetic α-diversity patterns presented consistent decreasing with elevation, with the peak occurring at low elevations. Environmental filtering caused by decreases in limiting factors, such as temperature, precipitation, soil organic matter, soil phosphorus, and light, is the main reason for the decline in diversity at high elevations, whereas low-elevation areas are affected by various factors, such as environmental filtering and similarity limitations. Species and phylogenetic β-diversity changes are closely related to environmental filtering and dispersal limitation, but the latter is key in community assembly at the heterogeneous spatial scale. In conclusion, combining species-based and phylogeny-based methods to explore the biogeographic patterns of tropical plant communities helps provide convincing evidence and confirms that the relative contributions of niche and neutral theory in the assembly process vary along environmental gradients. Though the D. pectinatum community constitute a floristically integrated unit, the genetic relationships between species are relatively far, and co-evolution to promote species coexistence is difficult when faced with habitat pressure. Hence, we believe that species coexistence in tropical plant communities requires mild environmental conditions, and low temperatures, precipitation, soil nutrients and light will aggravate environmental filtering and species competition. We also recommend strengthening the construction and management of nature reserves and the exploration of biodiversity formation mechanisms, which are crucial for biodiversity conservation in endangered tropical plant communities.
Understanding genetic variation and structure, adaptive genetic variation and its relationship with environmental factors is of great significance to understand how plants adapt to climate change and design effective conservation and management strategies. The objective of this study was to (I) investigate the genetic diversity and structure by AFLP markers in 36 populations of R. aureum from northeast China, (Ⅱ) reveal the relative contribution of geographical and environmental impacts on the distribution and genetic diﬀerentiation of R. aureum; (Ⅲ) identify outlier loci under selection and evaluate the association between outlier loci and environmental factors and (Ⅳ) exactly calculate development trend of population of R. aureum，as it is confronted with severe climate change and to provide information for designing eﬀective conservation and management strategies. We found high genetic variation (I = 0.584) and diﬀerentiation among populations (ΦST = 0.711) and moderate levels of genetic diversity within populations of R. aureum. A significant relationship between genetic distance and environmental distance was identified, which suggested that the differentiation of diﬀerent populations was the caused by environmental factors. Using BayeScan and Dfdist, 42 outlier loci identified and most of the outlier loci are associated with climate or relief factors, suggesting that these loci are linked to genes that are involved in the adaptability of R. aureum to environment. Species distribution models (SDM) showed that climate warming will cause a significant reduction of suitable area for R. aureum especially under the RCP 85 scenario. Our results help to understand the potential response of R. auruem to climatic changes, and provide new perspectives for R. auruem resource management and conservation strategies.
How and why species range size varies along spatial gradients is fundamental yet controversial topics in biogeography. To advance our understanding on these questions and to provide insight into biological conservation, we assessed the elevational variations in vascular plants range size for different life form and biogeographical affinities, and explored the main drivers underlying above variations in the longest valley in China's Himalayas---the Gyirong Valley. Elevational range sizes of vascular plants were documented by 96 sampling plots along 12 elevational bands of 300-m ranging from 1800 to 5400 m above sea level. We assessed the elevational variations in range size by averaging the range size of all species within each elevational band. We then related range size to climate, disturbance, competition factors and the mid-domain effect, and explored the relative importance of aforementioned factors in explaining the range size variations using the Random Forest model. Total 545 vascular plants were documented by our sampling plots along the elevational gradient. Out of 545 plants, 158, 387, 337 and 112 were woody, herbaceous, temperate and tropical species respectively. Range size of each groups of vascular plants shown uniform increasing trends along the elevational gradient which are in accordance with the prediction of Rapoport's rule. Climate was the main driver for the increasing trends of vascular plants range size in the Gyirong Valley. Climate variability hypothesis and mean climate condition hypothesis were both supported to jointly explain such climate-range size relationship. Our results reinforce previous notion that Rapoport's rule applies to where the influence of climate is most pronounced, and call for close attention to the impact of climate change in order to prevent range contraction and even extinction under global warming.
The mechanisms of forest seed dispersal and regeneration of various altered forest ecosystems are complemented by the action of carnivores. The objective of this study was to evaluate the role of endozoochoric and diploendozoochoric mammals in the dispersal, scarification, and germination of seeds in two different forest ecosystems: temperate forest (TF) and dry tropical forest (DTF). A direct search and scat collection were carried out to determine dispersing agents and the abundance and richness of seeds in the Protected Natural Area, Sierra Fría, Aguascalientes, Mexico. Viability was evaluated by means of X-rays and a germination test using an optical densitometry. In addition, thickness measurements and observations were made on the surfaces of the testas by a scanning electron microscopy. In the TF, four plant species were dispersed, mainly Arctostaphylos pungens (P < 0.05), by four mammals, where the gray fox dispersed the highest average (66.8 ± 68.2; P < 0.05) and diploendozoochory was detected in bobcat scats associated with rabbit hair (Sylvilagus floridanus). The DTF presented higher abundance and richness of species, where Myrtillocactus geometrizans had the highest abundance (2680 ± 4423) and the coati (P < 0.05) dispersed the highest number of seeds (8639 ± 12203). In both types of forest, endozoochory and diploendozoochory did not affect the viability, the thickness of the testas, or the germination of any species of seeds. These results suggest that dispersing carnivores adapt to the abundance and richness of seeds in the forests they inhabit, thus developing an important ecological function by dispersing, scarifying and promoting the selective germination of seeds with thick testas in TF and thin testas in DTF.
Diapause is an adaptive dormancy strategy by which arthropods endure extended periods of adverse climatic conditions. Seasonal variation in larval diapause initiation and duration in Ostrinia furnacalis influences adult mating generation number (voltinism) across different local environments. The degree of mating period overlap between sympatric voltine ecotypes influence hybridization level, but impacts on O. furnacalis population genetic structure and evolution of divergent adaptive phenotypes remains uncertain. Genetic differentiation was estimated between voltine ecotypes collected from 8 locations. Mitochondrial haplotypes were significantly different between historically allopatric univoltine and bivoltine locations. Haplotypes from sympatric locations were clustered more-closely to bivoltine locations, but influenced by local demographics. Additionally, analyses of single nucleotide polymorphism (SNP) genotypes implicate voltinism, as opposed to geographic distance, as contributing to low, but significant levels of variation among voltine ecotypes. Regardless, only 11 of 257 SNP loci were predicted to be under selection, suggesting population genetic homogenization except at loci proximal to factors putatively responsible for locally adaptive or voltinism-specific traits. These findings provide evidence that divergent voltine ecotypes may be maintained in allopatric and sympatric areas despite relatively high rates of nuclear gene flow, yet influence of voltinism on maintenance of observed haplotype divergence remains unresolved.
The koala, Phascolarctos cinereus, is an iconic Australian wildlife species, but faces rapid decline in South-East Queensland (SEQLD). For conservation planning, estimating koala populations is crucial. Systematic surveys are the most common approach to estimate koala populations, but such surveys are restricted to small geographic areas, they are costly and conducted infrequently. Public interest and participation in the collection of koala sightings is increasing in popularity, but such data is generally not used for population estimation. We used incidental sightings of koalas reported by members of the public from 1997-2013 in SEQLD to estimate the yearly spatio-temporal koala sightings density. For this, a spatio-temporal point process model was developed accounting for observed koala density, spatio-temporal detection bias and clustering. The density of koalas varied throughout the study period due to the heterogeneous nature of koala habitat in SEQLD, with density estimates ranging between 0.005 to 8.9 koalas per km2. The percentage of land areas with very low sightings densities (0-0.25 koalas per km2) remained similar throughout the study period representing in average (SD) 68.3% (0.06) of the total study area. However, land areas with more koalas per km2 showed larger annual variations, with koala mean (SD) densities of 0.25-0.5, 0.5-1, 1-2, 2-5 and > 5 koalas per km2 representing 16.8% (0.21), 13.8% (0.25), 0.7% (0.20), 0.3% (0.13), and 0.2% (0.1) of the study area in South-East Queensland, respectively.We did find that clustering of koala sightings was not prominently different between the mating and non-mating seasons of koalas. While acknowledging the limitations associated sightings data, we developed a statistical model that addressed the spatio-temporal bias associated with observed koala sightings and provided long-term relative koala density estimates for one of the largest koala populations of Australia.
1. Species are not genetically homogeneous, as the genetic structure among populations is related to the degree of isolation amongst them, such as isolation-by-distance, isolation-by-barrier and isolation-by-environment. 2. To decipher the isolation processes that drive population structuring in Jenynsia lineata we analyzed 221 sequences of the mitochondrial cytochrome c oxidase I gene (COI), which came from 19 localities. Jenynsia lineata is a small viviparous fish that inhabits a wide range of habitats in South America. Then, we examined the influence of the three most common types of isolation to explain the genetic variation found in this species. 3. Our results revealed a marked structuration, with three groups: i) La Plata/Desaguadero Rivers (sampling sites across Argentina, Uruguay, and Southern Brazil), ii) Central Argentina, and iii) Northern Argentina. A distance-based redundancy analysis including the explanatory variables geographical distances, altitude, latitude, basin, was able to explain up to 65% of the genetic structure. A variance partitioning analysis showed that the two most important variables underlying the structuration in J. lineata were altitude (isolation-by-environment) and type of basin (isolation-by-barrier). 4. Our results show that in this species, the processes of population diversification are complex and are not limited to a single mechanism. Population-structuring may lead to population reproductive isolation and ultimately to speciation. 5. This study demonstrated that the process of diversification of populations is complex and is not limited to a single mechanism. The processes that play a prominent role in this study could explain the high rate of diversity that characterizes freshwater fish species. And these processes in turn are the basis for possible speciation events.
Population size is a central parameter for conservation, however monitoring abundance is often problematic for threatened marine species. Despite substantial investment in research, many marine species remain data-poor resulting in uncertain population forecasts and restricting the evaluation of past and present conservation actions. Such is the case for the white shark (Carcharodon carcharias), a highly mobile apex predator for whom population monitoring is a conservation priority following substantial declines recorded through the 20th century. Here, we estimate the effective number of breeders that successfully contribute offspring in one reproductive cycle (Nb) providing a snapshot of recent reproductive effort in an east-Australian New Zealand population of white shark. Nb was estimated over four consecutive age cohorts (2010, 2011, 2012, 2013) using two genetic estimators (linkage-disequilibrium; LD and sibship assignment; SA) based on genetic data derived from two types of genetic markers (single-nucleotide-polymorphisms; SNPs and microsatellite loci). While estimates of Nb using different marker types produced comparable estimates, microsatellite loci were the least precise. The LD and SA estimates of Nb within cohorts using SNPs were comparable, for example the 2013 age-cohort Nb(SA) was 289 (95%CI 200-461) and Nb(LD) was 208.5 (95%CI 116.4-712.7). We show that over the time period studied Nb was stable and ranged between 206.1(±45.9) and 252.0(±46.7) per year using a combined estimate of Nb(SA+LD) from SNP loci, and a simulation approach showed that in this population effective population size (Ne) per generation can be expected to be larger than Nb per reproductive cycle. This study demonstrates how breeding population size can be monitored over time to provide insight into the effectiveness of recovery and conservation measures for the white shark, where the methods described here may be applicable to other data-poor species of conservation concern.
The evolutionary origins and hybridization patterns of Canis species in North America has been hotly debated for the past 30 years. Disentangling ancestry and timing of hybridization in Great Lakes wolves, eastern Canadian wolves, red wolves, and eastern coyotes is most often partitioned into a 2-species model that assigns all ancestry to grey wolves and/or coyotes, and a 3-species model that includes a third, North American evolved eastern wolf genome. The proposed models address recent or sometimes late Holocene hybridization events but have largely ignored Pleistocene era opportunities for hybridization that may have impacted the current mixed genomes in eastern Canada and the United States. Here, we re-analyze contemporary and ancient mitochondrial DNA genomes with Bayesian phylogenetic analyses to more accurately estimate divergence dates among lineages. We combine that with a review of the literature on Late Pleistocene Canis distributions to illuminate opportunities for ancient hybridization events between extinct Beringian grey wolves (C. lupus) and extinct large wolf-like coyotes (C. latrans orcutti) that we propose as a potentially unrecognized source of introgressed genomic variation within contemporary Canis genomes. These events speak to the potential origins of contemporary genomes and provide a new perspective on Canis ancestry, but do not influence/negate current conservation priorities of dwindling wolf populations with unique genomic signatures and key ecologically critical roles.
1. The Cormack-Jolly-Seber (CJS) model and its extensions have been widely applied to the study of animal survival rates in open populations. The model assumes that individuals within the population of interest have independent fates. It is, however, highly unlikely that a pair of animals which have formed a long-term pairing have dissociated fates. 2. We examine a model extension which allows animals who have formed a pair-bond to have correlated survival and recapture fates. Using the proposed extension to generate data, we conduct a simulation study exploring the impact that correlated fate data has on inference from the CJS model. We compute Monte Carlo estimates for the bias, range, and standard errors of the parameters of the CJS model for data with varying degrees of survival correlation between mates. Furthermore, we study the likelihood ratio test of gender effects within the CJS model by simulating densities of the deviance. Finally, we estimate the variance inflation factor for CJS models that incorporate sex-specific heterogeneity. 3. Our study shows that correlated fates between mated animals may result in underestimated standard errors for parsimonious models, significantly deflated likelihood ratio test statistics, and underestimated values of the variance inflation factor for models taking sex-specific effects into account. 4. Underestimated standard errors can result in lowered coverage of confidence intervals. Moreover, deflated test statistics will provide overly conservative test results. Finally, underestimated variance inflation factors can lead researchers to make incorrect conclusions about the level of extra-binomial variation present in their data.
1. Landscape change is a key driver of biodiversity declines due to habitat loss and fragmentation, but spatially shifting resources can also facilitate range expansion and invasion. Invasive populations are reproductively successful, and landscape change may buoy this success. 2. We show how modelling the spatial structure of reproductive success can elucidate the mechanisms of range shifts and sustained invasions for mammalian species with attendant young. We use an example of white-tailed deer (deer; Odocoileus virginianus) expansion in the Nearctic boreal forest, a North American phenomenon implicated in severe declines of threatened woodland caribou (Rangifer tarandus). 3. We hypothesized that deer reproductive success is linked to forage subsidies provided by extensive landscape change via resource extraction. We measured deer occurrence using data from 62 camera-traps in northern Alberta, Canada, over three years. We weighed support for multiple competing hypotheses about deer reproductive success using multi-state occupancy models and generalized linear models in an AIC-based model selection framework. 4. Spatial patterns of reproductive success were best explained by features associated with petroleum exploration and extraction, which offer early seral vegetation resource subsidies. Effect sizes of anthropogenic features eclipsed natural heterogeneity by two orders of magnitude. We conclude that deer populations are likely buffered from overwinter mortality by landscape change, wherein early seral forage subsidies support high springtime reproductive success to offset or exceed winter losses. 5. Synthesis and Applications. Modelling spatial structuring in reproductive success can become a key goal of remote camera-based global networks, yielding ecological insights into mechanisms of invasion and range shifts to inform effective decision-making for global biodiversity conservation.
Food habits are important factors for wild nonhuman primates’ environment adaptation. White-headed langurs (Trachypithecus leucocephalus) are endemic to the limestone forest and face to the habitat fragmentation, which have to adjust the food habits to adapt the special environment. In this study, we compared the dietary data for white-headed langurs living in Chongzuo White-headed Langur National Nature Reserve over two separate study periods to evaluate interannual variations in diet. Our results indicated that young leaves were the preferred major food for the langur. The plant parts consumption pattern was similar between the two separate study periods. The consumption of young leaves was varied with the availability of young leaves, whereas the consumption of mature leaves was negative correlated with the young leaf’s availability. The consumption of plant species and diet diversity varied in the two separate study periods, which were higher in 2013 than 2016. In both 2013 and 2016, the diet diversity varied with the consumption of mature leaves, but negative correlated with the consumption and availability of young leaves. Dietary interannual variation probably linked to the phenology variations, or probably mean that the white-headed langurs has a flexible ecological adaptation coping with habitat fragmentation.
The structure of Apteryx’s eggshell has generated much debate over the decades because it does not fit well with most allometric predictions. Apteryx eggshells are unusually thin and have been reported to be 60% less porous than expected. It has been suggested that these adaptations are compensations for a very long incubation period. Most studies so far have been carried out in what has been reported as Apteryx australis, and using infertile eggs or eggs laid in captivity. However, A. australis once comprised all kiwi with brown plumage, now separated into three distinct species: Brown Kiwi (A.mantelli), Rowi (A.rowi), and Tokoeka (A.australis). These three species use different habitats and live at different latitudes and altitudes. In addition, captive eggs are much smaller than wild laid eggs. These confounding factors make necessary to revise the assumptions made for Apteryx in the past. In this study, we analysed the physical characteristics of the Apteryx eggshells making a comparison between the three species of brown coloured kiwi and for some of the analysis we included some specimens of Roroa (A. haastii, Great Spotted Kiwi). We found that shell characteristics are different between the different species studied. The pore area of Apteryx eggshells was higher than previously suggested, and the water vapour conductance was much closer to what is expected for an egg that size. We found several new features such as triangular mineral particles composing the cuticle, only reported for a cretaceous Theropod, and the presence of plugs and caps on the eggshell pores. We suggest that the characteristics of the eggshells of the different species relate to the mating system of each species in addition to environmental variables, particularly pluviosity. We also suggest that the erosion of the cuticle during incubation is an adaptation to a long incubation period in a burrow.
Understanding trade-offs in wild populations is difficult, but important if we are to understand the evolution of life histories and the impact of ecological variables upon them. Markers that reflect physiological state and predict future survival would be of considerable benefit to unravelling such trade-offs and could provide insight into individual variation in senescence. However, currently used markers often yield inconsistent results. One underutilised measure is haematocrit, the proportional of blood comprising of erythrocytes, which relates to the blood’s oxygen-carrying capacity and viscosity, and to individual endurance. Haematocrit has been shown to decline with age in cross-sectional studies (which may be confounded by selective appearance/disappearance). However, few studies have tested whether haematocrit declines within-individuals or whether low haematocrit impacts survival in wild taxa. Using longitudinal data from the Seychelles warbler (Acrocephalus sechellensis), we demonstrated that haematocrit increases with age in young individuals (<1.5 years) but decreases with age in older individuals (1.5–13 years). In breeders, haematocrit was higher in males than females and varied relative to breeding stage. High haematocrit was associated with lower survival in young individuals, but not older individuals. Thus, while we did not find support for haematocrit as a marker of senescence, high haematocrit is indicative of poor condition in younger individuals. Possible explanations are that these individuals were experiencing dehydration and/or high endurance demands prior to capture, which warrants further investigation. Our study demonstrates that haematocrit can be an informative metric for life-history studies investigating trade-offs between survival, longevity and reproduction.
Understanding the processes that enable species coexistence has important implications for assessing how ecological systems will respond to global change. Morphology and functional similarity increase the potential for competition, and therefore, co-occurring morphologically similar but genetically unique species are a good model system for testing coexistence mechanisms. We used DNA metabarcoding and High Throughput Sequencing to characterise for first time the trophic ecology of two recently-described cryptic bat species with parapatric ranges, Myotis escalerai and Myotis crypticus. We collected faecal samples from allopatric and sympatric regions and locations to describe the diet both taxonomically and functionally and compare prey consumption with prey availability. The two bat species had similar diets characterised by high arthropod diversity, particularly Lepidoptera, Diptera and Araneae, and a high proportion of prey that is not volant at night, which points to extensive use of gleaning. Diet overlap at the prey-item level was lower in locally sympatric than allopatric locations, supporting trophic shift under fine-scale sympatry. Furthermore, locally sympatric samples of M. escalerai had a marginally lower proportion of not nocturnally volant prey, suggesting that the shift in diet may be driven by a change in foraging mode. Our findings suggest that fine-scale coexistence mechanisms can have implications for maintaining broad-scale diversity patterns. This study highlights the importance of including both allopatric and sympatric populations and choosing meaningful spatial scales for detecting ecological patterns. We conclude that a combination of high taxonomic resolution with a functional approach helps identify patterns of niche shift.
The Himalayan red panda (Ailurus fulgens) is of special interest in evolutionary studies due to its taxonomic uniqueness. Globally, Nepal represents the Westernmost edge of the red panda distribution. Fewer studies of red panda have been carried out which hinders the implementation of effective conservation actions of the species. We aim to determine important habitat features influencing the distribution of red panda and recommend possible habitat corridors. We conducted an extensive field survey and analyzed red panda presence data, key food resources (bamboo), and bioclimatic variables to build a Maxent habitat model and determine habitat requirements of the red panda. Himalayan red pandas were confined between the range of 2600 m - 3,600 m, with most records between 3250 m - 3400 m on the north and west-facing slopes. The potentially suitable habitat of the red panda in Western Nepal is estimated to be about 3,222 km2 with a relative abundance of 3.34 signs/km. Important habitat attributes for red panda occurrence include aspects, canopy cover, bamboo cover, and distance to water. Combining species habitat requirements and disturbance factors (human footprint), we suggested five potential biological corridors in Western Nepal. Western Nepal has suitable habitat attributes for the red panda distributions. Ecological variables such as canopy cover, bamboo cover, distance to the water, and aspects are important attributes for red panda occurrence in Western Nepal alike Central Nepal. We suggested five potential corridors in Western Nepal; however, due to a lack of detailed knowledge on corridors and connectivity, a comprehensive field-based assessment is required to validate it scientifically. Keywords: Biological Corridor; Distribution; Habitat requirements; Red panda
Arachnids are the most abundant land predators. Despite the importance of their functional roles as predators and the of necessity to understand their diet for conservation and nutrient fluxes, the trophic ecology of many arachnid species is not fully understood. In the case of the wandering spider, Phoneutria boliviensis F. O. Pickard-Cambridge, 1897, only selected field and laboratory observational studies about their diet exist. By using a DNA metabarcoding approach, we compared the prey found in the gut content of males and females from three distant Colombian populations of P. boliviensis. By DNA metabarcoding of the cytochrome c oxidase subunit I (COI), we detected and identiﬁed 234 prey records belonging to 96 operational taxonomic units (OTUs), as prey for this wandering predator. Our results broaden the known diet of P. boliviensis with at least 75 prey taxa not previously registered in fieldwork or laboratory experimental trials. These results suggest that P. boliviensis feeds predominantly on invertebrates (Diptera, Lepidoptera, Coleoptera and Orthoptera) and opportunistically on small squamates. Intersex and interpopulation differences are observed. Assuming that prey preference does not vary between populations, these differences are likely associated with a higher local prey availability. Finally, we suggest that DNA metabarcoding can be used for evaluating subtle differences in the diet of distinct populations of P. boliviensis, particularly when predation records in the field cannot be established or quantified using direct observation