共查询到20条相似文献，搜索用时 15 毫秒
1.
Pedro Tarroso Guillermo Velo‐Antón Sílvia B. Carvalho 《Molecular ecology resources》2015,15(2):349-357
phylin is a package for the r programming environment which offers different methods to spatially interpolate genetic information from phylogeographic data. These interpolations can be used to predict the spatial occurrence of different lineages within a phylogeny using a modified method of kriging, which allows the usage of a genetic distance matrix to derive a model of spatial dependence. phylin improves the available methods to generate interpolated surfaces from a phylogenetic trees by assessing the autocorrelation structure of the genetic information, interpolating the genetic data based on a statistical model, estimating the uncertainty of the predictions and identifying lineage occurrence and contact zones probability without projection of pairwise genetic distances into mid‐points between sample locations. The package also includes methods to plot interpolation surfaces and provide summary tables from the generated data and models. We provide an example of the usefulness of this tool by inferring the spatial occurrence of distinct historical evolutionary lineages of the Lataste's viper (Vipera latastei Boscá, 1878) in the Iberian Peninsula and identifying potential contact areas. The maps of phylogenetic patterns obtained with these methods provide a spatial context to test hypotheses related to processes underlying the geographic distribution of genetic diversity and to inform conservation planning. 相似文献
2.
McRae BH 《Evolution; international journal of organic evolution》2006,60(8):1551-1561
Despite growing interest in the effects of landscape heterogeneity on genetic structuring, few tools are available to incorporate data on landscape composition into population genetic studies. Analyses of isolation by distance have typically either assumed spatial homogeneity for convenience or applied theoretically unjustified distance metrics to compensate for heterogeneity. Here I propose the isolation-by-resistance (IBR) model as an alternative for predicting equilibrium genetic structuring in complex landscapes. The model predicts a positive relationship between genetic differentiation and the resistance distance, a distance metric that exploits precise relationships between random walk times and effective resistances in electronic networks. As a predictor of genetic differentiation, the resistance distance is both more theoretically justified and more robust to spatial heterogeneity than Euclidean or least cost path-based distance measures. Moreover, the metric can be applied with a wide range of data inputs, including coarse-scale range maps, simple maps of habitat and nonhabitat within a species' range, or complex spatial datasets with habitats and barriers of differing qualities. The IBR model thus provides a flexible and efficient tool to account for habitat heterogeneity in studies of isolation by distance, improve understanding of how landscape characteristics affect genetic structuring, and predict genetic and evolutionary consequences of landscape change. 相似文献
3.
Katherine A. Zeller Tyler G. Creech Katie L. Millette Rachel S. Crowhurst Robert A. Long Helene H. Wagner Niko Balkenhol Erin L. Landguth 《Ecology and evolution》2016,6(12):4115-4128
Mantel‐based tests have been the primary analytical methods for understanding how landscape features influence observed spatial genetic structure. Simulation studies examining Mantel‐based approaches have highlighted major challenges associated with the use of such tests and fueled debate on when the Mantel test is appropriate for landscape genetics studies. We aim to provide some clarity in this debate using spatially explicit, individual‐based, genetic simulations to examine the effects of the following on the performance of Mantel‐based methods: (1) landscape configuration, (2) spatial genetic nonequilibrium, (3) nonlinear relationships between genetic and cost distances, and (4) correlation among cost distances derived from competing resistance models. Under most conditions, Mantel‐based methods performed poorly. Causal modeling identified the true model only 22% of the time. Using relative support and simple Mantel r values boosted performance to approximately 50%. Across all methods, performance increased when landscapes were more fragmented, spatial genetic equilibrium was reached, and the relationship between cost distance and genetic distance was linearized. Performance depended on cost distance correlations among resistance models rather than cell‐wise resistance correlations. Given these results, we suggest that the use of Mantel tests with linearized relationships is appropriate for discriminating among resistance models that have cost distance correlations <0.85 with each other for causal modeling, or <0.95 for relative support or simple Mantel r. Because most alternative parameterizations of resistance for the same landscape variable will result in highly correlated cost distances, the use of Mantel test‐based methods to fine‐tune resistance values will often not be effective. 相似文献
4.
Nicolas Duforet‐Frebourg Michael G.B. Blum 《Evolution; international journal of organic evolution》2014,68(4):1110-1123
Patterns of isolation‐by‐distance (IBD) arise when population differentiation increases with increasing geographic distances. Patterns of IBD are usually caused by local spatial dispersal, which explains why differences of allele frequencies between populations accumulate with distance. However, spatial variations of demographic parameters such as migration rate or population density can generate nonstationary patterns of IBD where the rate at which genetic differentiation accumulates varies across space. To characterize nonstationary patterns of IBD, we infer local genetic differentiation based on Bayesian kriging. Local genetic differentiation for a sampled population is defined as the average genetic differentiation between the sampled population and fictive neighboring populations. To avoid defining populations in advance, the method can also be applied at the scale of individuals making it relevant for landscape genetics. Inference of local genetic differentiation relies on a matrix of pairwise similarity or dissimilarity between populations or individuals such as matrices of between pairs of populations. Simulation studies show that maps of local genetic differentiation can reveal barriers to gene flow but also other patterns such as continuous variations of gene flow across habitat. The potential of the method is illustrated with two datasets: single nucleotide polymorphisms from human Swedish populations and dominant markers for alpine plant species. 相似文献
5.
Dai Suzuki Tsutomu Hikida 《Journal of Zoological Systematics and Evolutionary Research》2011,49(2):141-147
The phylogeography of the Japanese pond turtle, Mauremys japonica (Temminck and Schlegel, 1835), which is an endemic species in Japan, was studied by analyzing the variation in two mitochondrial DNA sequences, the cytochrome b gene and the control region. These analyses suggest that M. japonica comprises two major groups. The first one was found in the more eastern region, eastern Honshu Island and Shikoku Island, while the second was found in a western region, Kyushu Island and the Chugoku District (the westernmost part of Honshu Island). The boundary between the two groups is located in the Chugoku District. The nucleotide and haplotype diversities were very low, and these low diversities seem to have been caused by a bottleneck in the last glacial age. These results suggest that this species survived the last glacial period in two refugia, one in the central part of Honshu Island and the other one in Kyushu Island. Subsequently, population expansion took place in the postglacial period, and the groups from the two refugia extended their distribution ranges to the present boundary in the Chugoku District which represents a secondary contact zone. 相似文献
6.
PHILIPP TRÉNEL MICHAEL M. HANSEN† SIGNE NORMAND FINN BORCHSENIUS 《Molecular ecology》2008,17(15):3528-3540
Knowledge of the role of landscapes in shaping genetic connectivity and divergence is essential for understanding patterns of biogeography and diversity. This is particularly relevant for the Andes region, a major biodiversity hotspot of relatively recent origin. We examined the phylogeography and landscape genetics of the Andean wax palm Ceroxylon echinulatum (Arecaceae) that occurs in two narrow bands of montane forests on each side of the Andes in Ecuador and northeastern Peru. First, we tested the hypothesis of C. echinulatum being a geographic cline species crossing the Andes in the Amotape–Huancabamba zone (AHZ) of southern Ecuador/northern Peru, as indicated by observations on fruit morphology. Second, we assessed the timeframe of cross-Andean divergence, and third, we investigated the impact of contemporary and historical landscape features on observed spatio-genetic patterns. Individual-based Bayesian clustering (BC) identified a northeastern, southeastern, southwestern, and northwestern cluster, with areas of genetic discontinuity coinciding with the Andes and the Giron–Paute deflection. F -statistics derived from BC suggested an east-to-west dispersal history. Population-based analyses revealed strong genetic structuring at both small and large geographic scales. Interpopulation relationships and Mantel tests strongly supported the cline model with cross-Andean dispersal in the AHZ. Along the cline, gene flow measured as F ST was mainly limited by distance, with less but significant impact of climatic friction. Coalescent analysis revealed that cross-Andean divergence took place during the Quaternary. Significant historical isolation ( R ST > F ST ) was found in the southwestern population. The current study illustrates a joint effect of founder dynamics, divergence by distance and historical isolation on patterns of Andean diversity and distribution. 相似文献
7.
Aritz Ruiz‐Gonzalez Samuel A. Cushman María José Madeira Ettore Randi Benjamín J. Gómez‐Moliner 《Molecular ecology》2015,24(20):5110-5129
Landscape genetics provides a valuable framework to understand how landscape features influence gene flow and to disentangle the factors that lead to discrete and/or clinal population structure. Here, we attempt to differentiate between these processes in a forest‐dwelling small carnivore [European pine marten (Martes martes)]. Specifically, we used complementary analytical approaches to quantify the spatially explicit genetic structure and diversity and analyse patterns of gene flow for 140 individuals genotyped at 15 microsatellite loci. We first used spatially explicit and nonspatial Bayesian clustering algorithms to partition the sample into discrete clusters and evaluate hypotheses of ‘isolation by barriers’ (IBB). We further characterized the relationships between genetic distance and geographical (‘isolation by distance’, IBD) and ecological distances (‘isolation by resistance’, IBR) obtained from optimized landscape models. Using a reciprocal causal modelling approach, we competed the IBD, IBR and IBB hypotheses with each other to unravel factors driving population genetic structure. Additionally, we further assessed spatially explicit indices of genetic diversity using sGD across potentially overlapping genetic neighbourhoods that matched the inferred population structure. Our results revealed a complex spatial genetic cline that appears to be driven jointly by IBD and partial barriers to gene flow (IBB) associated with poor habitat and interspecific competition. Habitat loss and fragmentation, in synergy with past overharvesting and possible interspecific competition with sympatric stone marten (Martes foina), are likely the main factors responsible for the spatial genetic structure we observed. These results emphasize the need for a more thorough evaluation of discrete and clinal hypotheses governing gene flow in landscape genetic studies, and the potential influence of different limiting factors affecting genetic structure at different spatial scales. 相似文献
8.
Amphibians are often considered excellent environmental indicator species. Natural and man‐made landscape features are known to form effective genetic barriers to amphibian populations; however, amphibians with different characteristics may have different species–landscape interaction patterns. We conducted a comparative landscape genetic analysis of two closely related syntopic frog species from central China, Pelophylax nigromaculatus (PN) and Fejervarya limnocharis (FL). These two species differ in several key life history traits; PN has a larger body size and larger clutch size, and reaches sexual maturity later than FL. Microsatellite DNA data were collected and analyzed using conventional (FST, isolation by distance (IBD), AMOVA) and recently developed (Bayesian assignment test, isolation by resistance) landscape genetic methods. As predicted, a higher level of population structure in FL (FST′ = 0.401) than in PN (FST′ = 0.354) was detected, in addition to FL displaying strong IBD patterns (r = .861) unlike PN (r = .073). A general north–south break in FL populations was detected, consistent with the IBD pattern, while PN exhibited clustering of northern‐ and southern‐most populations, suggestive of altered dispersal patterns. Species‐specific resistant landscape features were also identified, with roads and land cover the main cause of resistance to FL, and elevation the main influence on PN. These different species–landscape interactions can be explained mostly by their life history traits, revealing that closely related and ecologically similar species have different responses to the same landscape features. Comparative landscape genetic studies are important in detecting such differences and refining generalizations about amphibians in monitoring environmental changes. 相似文献
9.
Phenotypically cryptic lineages comprise an important yet understudied part of biodiversity; in particular, we have much to learn about how these lineages are formed and maintained. To better understand the evolutionary significance of such lineages, we studied a hybrid zone between two morphologically cryptic phylogeographic lineages in the rainforest lizard, Lampropholis coggeri. Analyzing a multilocus genetic dataset through cline inference, individual-based methods and population measures of disequilibrium and using simulations to explore our genetic results in context of theoretical expectations, we inferred the processes maintaining this hybrid zone. We find that these lineages meet in a hybrid zone that is narrow (≈400 m) relative to inferred dispersal rate. Further, the hybrid zone exhibits substantial genetic disequilibrium and sharply coincident and largely concordant clines. Based on our knowledge about the region's biogeography, the species' natural history, and our simulation results, we suggest that strong selection against hybrids structures this system. As all clines show a relatively narrow range of introgression, we posit that this hybrid zone might not yet be in equilibrium. Nonetheless, our results clearly show that phylogeographic lineages can evolve substantial reproductive isolation without concomitant morphological diversification, suggesting that such lineages can constitute a significant component of evolutionary diversity. 相似文献
10.
The North American deserts were impacted by both Neogene plate tectonics and Quaternary climatic fluctuations, yet it remains unclear how these events influenced speciation in this region. We tested published hypotheses regarding the timing and mode of speciation, population structure, and demographic history of the Mojave Fringe‐toed Lizard (Uma scoparia), a sand dune specialist endemic to the Mojave Desert of California and Arizona. We sampled 109 individual lizards representing 22 insular dune localities, obtained DNA sequences for 14 nuclear loci, and found that U. scoparia has low genetic diversity relative to the U. notata species complex, comparable to that of chimpanzees and southern elephant seals. Analyses of genotypes using Bayesian clustering algorithms did not identify discrete populations within U. scoparia. Using isolation‐with‐migration (IM) models and a novel coalescent‐based hypothesis testing approach, we estimated that U. scoparia diverged from U. notata in the Pleistocene epoch. The likelihood ratio test and the Akaike Information Criterion consistently rejected nested speciation models that included parameters for migration and population growth of U. scoparia. We reject the Neogene vicariance hypothesis for the speciation of U. scoparia and define this species as a single evolutionarily significant unit for conservation purposes. 相似文献
11.
Tropical montane taxa are often locally adapted to very specific climatic conditions, contributing to their lower dispersal potential across complex landscapes. Climate and landscape features in montane regions affect population genetic structure in predictable ways, yet few empirical studies quantify the effects of both factors in shaping genetic structure of montane-adapted taxa. Here, we considered temporal and spatial variability in climate to explain contemporary genetic differentiation between populations of the montane salamander, Pseudoeurycea leprosa. Specifically, we used ecological niche modelling (ENM) and measured spatial connectivity and gene flow (using both mtDNA and microsatellite markers) across extant populations of P. leprosa in the Trans-Mexican Volcanic Belt (TVB). Our results indicate significant spatial and genetic isolation among populations, but we cannot distinguish between isolation by distance over time or current landscape barriers as mechanisms shaping population genetic divergences. Combining ecological niche modelling, spatial connectivity analyses, and historical and contemporary genetic signatures from different classes of genetic markers allows for inference of historical evolutionary processes and predictions of the impacts future climate change will have on the genetic diversity of montane taxa with low dispersal rates. Pseudoeurycea leprosa is one montane species among many endemic to this region and thus is a case study for the continued persistence of spatially and genetically isolated populations in the highly biodiverse TVB of central Mexico. 相似文献
12.
ASUKA NODA YUKI MITSUI HIROAKI SETOGUCHI 《Biological journal of the Linnean Society. Linnean Society of London》2011,102(1):51-66
Lake Biwa is an ancient freshwater lake that was formed approximately 4 Mya and harbours many coastal plants that commonly inhabit the seashore. We used chloroplast DNA haplotype analysis using two spacer sequences and simple sequence repeat (SSR) analysis using eight nuclear microsatellite markers to detect genomic signatures indicating long‐term isolation of inland populations of Calystegia soldanella in Lake Biwa from coastal populations. We used 348 samples from 63 populations for haplotype analysis and 478 samples from 27 populations for SSR analysis covering the inland and coastal distribution of the species. We detected seven haplotypes, and the distribution pattern of these haplotypes was geographically highly structured between Lake Biwa and the coast. Nuclear SSR analysis also supported genetic differentiation between Lake Biwa and coastal populations (analyses of molecular variance, 43%), and the grouping of Lake Biwa and coastal populations by a Neighbour‐joining tree. In addition, genetic diversity of the inland populations (mean HE = 0.153) was significantly lower than that of coastal populations (mean HE = 0.328). These results suggested that inland populations at Lake Biwa have been isolated from coastal populations for a very long time. The inland populations most likely experienced a bottleneck effect, resulting in sufficient in situ genetic divergence to clearly distinguish them from coastal populations. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 51–66. 相似文献
13.
S. Corrigan C. Huveneers T. S. Schwartz R. G. Harcourt L. B. Beheregaray 《Journal of fish biology》2008,73(7):1662-1675
This study reports on evidence for reproductive isolation among Orectolobus ornatus and Orectolobus halei, two previously cryptic and recently redescribed species of wobbegong shark (Orectolobiformes: Orectolobidae) from the east coast of Australia. The evidence is based on disparity in size at sexual maturity, diagnostic nuclear and mitochondrial DNA variants, and marked phylogenetic divergence. Plots of total length (LT) and maturity for the two species were non‐overlapping and illustrative of statistically significant size dimorphism. Genetic analyses and phylogenetic reconstruction did not provide indication of hybridization between O. ornatus and O. halei. In fact, sequence divergence between them was higher than in comparisons with another congeneric and largely co‐distributed wobbegong species (Orectolobus maculatus). The assumption of a molecular clock revealed that the two species have evolved in isolation for c. 3·9 million years. These results challenge a paradigm often mentioned in the biodiversity literature that most cryptic species are the product of recent speciation events and will contribute to the development of effective management strategies for wobbegong sharks. 相似文献
14.
Colin Bran Alexander Macfarlane Libby Natola Mike W. Brown Theresa M. Burg 《Ecology and evolution》2016,6(22):8304-8317
Using a combination of mitochondrial and z‐linked sequences, microsatellite data, and spatio‐geographic modeling, we examined historical and contemporary factors influencing the population genetic structure of the purple finch (Haemorhous purpureus). Mitochondrial DNA data show the presence of two distinct groups corresponding to the two subspecies, H. p. purpureus and H. p. californicus. The two subspecies likely survived in separate refugia during the last glacial maximum, one on the Pacific Coast and one east of the Rocky Mountains, and now remain distinct lineages with little evidence of gene flow between them. Southwestern British Columbia is a notable exception, as subspecies mixing between central British Columbia and Vancouver Island populations suggests a possible contact zone in this region. Z‐linked data support two mitochondrial groups; however, Coastal Oregon and central British Columbia sites show evidence of mixing. Contemporary population structure based on microsatellite data identified at least six genetic clusters: three H. p. purpureus clusters, two H. p. californicus clusters, and one mixed cluster, which likely resulted from high site fidelity and isolation by distance, combined with sexual selection on morphological characters reinforcing subspecies differences. 相似文献
15.
&#x;ukasz Kajtoch Daniel Kubisz Jerzy M. Gutowski Wies&#x;aw Babik 《Insect Conservation and Diversity》2014,7(1):41-54
- The distribution of steppe‐like habitats and, consequently, species dependent on these habitats in Eurasia is currently highly fragmented beyond the zone of continental climate, as a result of unfavourable climatic conditions and anthropogenic transformation of the environment. This patchy distribution may pose a threat for persistence of steppic species, especially in central Europe. To develop conservation strategies, it is essential to collect information on genetic structure of the species occupying this kind of habitats.
- We investigated the genetic structure and diversity of central and eastern Coraebus elatus (F.) populations using sequences of mtDNA and an anonymous fragment of the nuclear genome. Both markers exhibited similar pattern, indicating the presence of four or five highly differentiated evolutionary units (2.1–3.2% sequence divergence in mtDNA and 0.7–2.1% in the nuclear marker) encompassing populations from the Caucasus, the Azov Sea coasts, central Europe with the Balkans (with further substructuring) and probably western Europe. These clusters should be considered evolutionary significant units for the conservation biology of this species, and may form the basis for a future taxonomic revision.
- Pattern of C. elatus diversity suggests that this species presently occupies not only continental ‘warm‐stage’ refugia formerly described in Pontic and Pannonian areas but also cryptic steppic ‘warm‐stage’ refugia in north‐central Europe.
- In line with other studies on steppic beetles, our data strongly suggest that such species are strongly structured genetically, with very limited genetic variation within populations, which may have very serious consequences for their persistence in the future.
16.
A major aim of landscape genetics is to understand how landscapes resist gene flow and thereby influence population genetic structure. An empirical understanding of this process provides a wealth of information that can be used to guide conservation and management of species in fragmented landscapes and also to predict how landscape change may affect population viability. Statistical approaches to infer the true model among competing alternatives are based on the strength of the relationship between pairwise genetic distances and landscape distances among sampled individuals in a population. A variety of methods have been devised to quantify individual genetic distances, but no study has yet compared their relative performance when used for model selection in landscape genetics. In this study, we used population genetic simulations to assess the accuracy of 16 individual‐based genetic distance metrics under varying sample sizes and degree of population genetic structure. We found most metrics performed well when sample size and genetic structure was high. However, it was much more challenging to infer the true model when sample size and genetic structure was low. Under these conditions, we found genetic distance metrics based on principal components analysis were the most accurate (although several other metrics performed similarly), but only when they were derived from multiple principal components axes (the optimal number varied depending on the degree of population genetic structure). Our results provide guidance for which genetic distance metrics maximize model selection accuracy and thereby better inform conservation and management decisions based upon landscape genetic analysis. 相似文献
17.
Hypotheses to explain phylogeographic structure traditionally invoke geographic features, but often fail to provide a general explanation for spatial patterns of genetic variation. Organisms' intrinsic characteristics might play more important roles than landscape features in determining phylogeographic structure. We developed a novel comparative approach to explore the role of ecological and life‐history variables in determining spatial genetic variation and tested it on frog communities in Panama. We quantified spatial genetic variation within 31 anuran species based on mitochondrial DNA sequences, for which hierarchical approximate Bayesian computation analyses rejected simultaneous divergence over a common landscape. Regressing ecological variables, on genetic divergence allowed us to test the importance of individual variables revealing that body size, current landscape resistance, geographic range, biogeographic origin and reproductive mode were significant predictors of spatial genetic variation. Our results support the idea that phylogeographic structure represents the outcome of an interaction between organisms and their environment, and suggest a conceptual integration we refer to as trait‐based phylogeography. 相似文献
18.
Gabriela Parra‐Olea Juan Carlos Windfield Kelly R. Zamudio 《Journal of Biogeography》2012,39(2):353-370
Aim Our goal was to reconstruct the phylogenetic history and historical demography of highly divergent populations of the endemic plethodontid salamander Pseudoeurycea leprosa, to elucidate the timing and mechanisms of divergence in the Trans‐Volcanic Belt of Mexico. Location The Trans‐Volcanic Belt (TVB) of central Mexico, including the states of Mexico, Morelos, Puebla, Tlaxcala and Veracruz. Methods We sequenced the cytochrome b mitochondrial DNA gene for 281 individuals from 26 populations and nine mountain ranges in the TVB, and used Bayesian phylogenetic reconstruction and Markov chain Monte Carlo coalescent methods to infer historical demographic parameters and divergences among populations in each mountain system. Results We found deep genetic divergences between eastern and central TVB mountain systems despite their recent volcanic origin. Populations of P. leprosa show a pattern of refugial populations in the north‐eastern and eastern limits of the species’ distribution, and genetic evidence of rapid population expansion in mountain ranges of the central TVB. The oldest divergences among populations date to c. 3.8 Ma, and the most recent divergences in the central TVB are Pleistocene in age (c. 0.7 Ma). Main conclusions Given the timing and order of population diversification in P. leprosa, we conclude that early isolation in multiple habitat refuges in north‐eastern and eastern mountain ranges played an important role in structuring population diversity in the TVB, followed by population expansion and genetic divergence of the central range populations. The dynamic climatic and volcanic changes in this landscape generally coincide with the history of intra‐specific diversification in P. leprosa. Climate‐driven changes in habitat distribution in an actively changing volcanic landscape have shaped divergences in the TVB and very likely contributed to the high levels of speciation and endemism in this biodiverse region. 相似文献
19.
With advances in sequencing technology, research in the field of landscape genetics can now be conducted at unprecedented spatial and genomic scales. This has been especially evident when using sequence data to visualize patterns of genetic differentiation across a landscape due to demographic history, including changes in migration. Two recent model‐based visualization methods that can highlight unusual patterns of genetic differentiation across a landscape, SpaceMix and EEMS, are increasingly used. While SpaceMix's model can infer long‐distance migration, EEMS’ model is more sensitive to short‐distance changes in genetic differentiation, and it is unclear how these differences may affect their results in various situations. Here, we compare SpaceMix and EEMS side by side using landscape genetics simulations representing different migration scenarios. While both methods excel when patterns of simulated migration closely match their underlying models, they can produce either un‐intuitive or misleading results when the simulated migration patterns match their models less well, and this may be difficult to assess in empirical data sets. We also introduce unbundled principal components (un‐PC), a fast, model‐free method to visualize patterns of genetic differentiation by combining principal components analysis (PCA), which is already used in many landscape genetics studies, with the locations of sampled individuals. Un‐PC has characteristics of both SpaceMix and EEMS and works well with simulated and empirical data. Finally, we introduce msLandscape, a collection of tools that streamline the creation of customizable landscape‐scale simulations using the popular coalescent simulator ms and conversion of the simulated data for use with un‐PC, SpaceMix and EEMS. 相似文献
20.
Mariana M. Vasconcellos Guarino R. Colli Jesse N. Weber Edgardo M. Ortiz Miguel T. Rodrigues David C. Cannatella 《Molecular ecology》2019,28(7):1748-1764
Although the impact of Pleistocene glacial cycles on the diversification of the tropical biota was once dismissed, increasing evidence suggests that Pleistocene climatic fluctuations greatly affected the distribution and population divergence of tropical organisms. Landscape genomic analyses coupled with paleoclimatic distribution models provide a powerful way to understand the consequences of past climate changes on the present‐day tropical biota. Using genome‐wide SNP data and mitochondrial DNA, combined with projections of the species distribution across the late Quaternary until the present, we evaluate the effect of paleoclimatic shifts on the genetic structure and population differentiation of Hypsiboas lundii, a treefrog endemic to the South American Cerrado savanna. Our results show a recent and strong genetic divergence in H. lundii across the Cerrado landscape, yielding four genetic clusters that do not seem congruent with any current physical barrier to gene flow. Isolation by distance (IBD) explains some of the population differentiation, but we also find strong support for past climate changes promoting range shifts and structuring populations even in the presence of IBD. Post‐Pleistocene population persistence in four main areas of historical stable climate in the Cerrado seems to have played a major role establishing the present genetic structure of this treefrog. This pattern is consistent with a model of reduced gene flow in areas with high climatic instability promoting isolation of populations, defined here as “isolation by instability,” highlighting the effects of Pleistocene climatic fluctuations structuring populations in tropical savannas. 相似文献