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opencc-zeroDec 2012View details →

Data from: Gene flow and demographic history of leopards (Panthera pardus) in the central Indian highlands

Gene flow is a critical ecological process that must be maintained in order to counteract the detrimental effects of genetic drift in sub-divided populations, with conservation benefits ranging from promoting the persistence of small populations to spreading adaptive traits in changing environments. We evaluated historical and contemporary gene flow and effective population sizes of leopards in a landscape in central India using non-invasive sampling. Despite the dramatic changes in land use patterns in this landscape through recent times, we did not detect any signs that the leopard populations have been through a genetic bottleneck and they appear to have maintained migration-drift equilibrium. We found that historical levels of gene flow (mean mh = 0.07) were significantly higher than contemporary levels (mean mc = 0.03) and populations with large effective population sizes (Satpura and Kanha Tiger Reserves) are the larger exporters of migrants at both time scales. The greatest decline in historical versus contemporary gene flow is between pairs of reserves that are currently not connected by forest corridors (i.e, Melghat-Pench mh-mc= 0.063; and Kanha-Satpura mh-mc= 0.054). We attribute this reduction in gene flow to accelerated fragmentation and habitat alteration in the landscape over the past few centuries, and suggest protection of forest corridors to maintain gene flow in this landscape.

opencc-zeroDec 2010View details →

Data from: Comparative genetic structure and demographic history in endemic Galápagos weevils

The challenge of maintaining genetic diversity within populations can be exacerbated for island endemics if they display population dynamics and behavioral attributes that expose them to genetic drift without the benefits of gene-flow. We assess patterns of genetic structure and demographic history in twenty seven populations of nine species of flightless endemic Galápagos weevils from nine of the islands and one winged introduced close relative. Analysis of mitochondrial DNA reveals significant population structure and moderately variable, though demographically stable, populations for lowland endemics (Fst= 0.094 to 0.541; π: 0.014 to 0.042; Mismatch p=0.003 to 0.026 and D (Tajima)=-0.601to1.203), in contrast to signals of past contractions and expansions in highland specialists on two islands (Mismatch p=0.003 to 0.026 and D (Tajima)=-0.601to1.203). We interpret this series of variable and highly structured population groups as a system of long-established independently founded island units, where structuring could be a signal of micro-allopatric differentiation due to patchy host plant distribution and poor dispersal abilities. We suggest that the severe reduction and subsequent increase of suitably moist habitat that accompanied past climatic variation could have contributed to the observed population fluctuations in highland specialists. We propose the future exploration of hybridization between the introduced and highland endemic species on Santa Cruz, especially given the expansion of the introduced species into the highlands, the sensitivity to past climatic variation detected in highland populations and the potentially threatened state of single-island endemics.

Data from: Range-wide multilocus phylogeography of the red fox reveals ancient continental divergence, minimal genomic exchange, and distinct demographic histories

Widely distributed taxa provide an opportunity to compare biogeographic responses to climatic fluctuations on multiple continents and to investigate speciation. We conducted the most geographically and genomically comprehensive study to date of the red fox (Vulpes vulpes), the world's most widely distributed wild terrestrial carnivore. Analyses of 697 bp of mitochondrial sequence in ~1000 individuals suggested an ancient Middle Eastern origin for all extant red foxes and a 400 kya (SD = 139 kya) origin of the primary North American (Nearctic) clade. Demographic analyses indicated a major expansion in Eurasia during the last glaciation (~50 kya), coinciding with a previously described secondary transfer of a single matriline (Holarctic) to North America. In contrast, North American matrilines (including the transferred portion of Holarctic clade) exhibited no signatures of expansion until the end of the Pleistocene (~12 kya). Analyses of 11 autosomal loci from a subset of foxes supported the colonization timeframe suggested by mtDNA (and the fossil record) but, in contrast, reflected no detectable secondary transfer, resulting in the most fundamental genomic division of red foxes at the Bering Strait. Endemic continental Y-chromosome clades further supported this pattern. Thus, intercontinental genomic exchange was overall very limited, consistent with long-term reproductive isolation since the initial colonization of North America. Based on continental divergence times in other carnivoran species pairs, our findings support a model of peripatric speciation and are consistent with the previous classification of the North American red fox as a distinct species, V. fulva.

Data from: Tropical specialist versus climate generalist: diversification and demographic history of sister species of Carlia skinks from northwestern Australia

Species endemic to the tropical regions are expected to be vulnerable to future climate change due in part to their relatively narrow climatic niches. In addition, these species are more likely to have responded strongly to past climatic change, and this can be explored through phylogeographic analyses. To test the hypothesis that tropical specialists are more sensitive to climate change than climate generalists, we generated and analyze sequence data from mtDNA and ~2500 exons to compare scales of historical persistence and population fluctuation in two sister species of Australian rainbow skinks: the tropical specialist Carlia johnstonei and the climate generalist C. triacantha. We expect the tropical specialist species to have deeper and finer-scale phylogeographic structure and stronger demographic fluctuations relative to the closely related climate generalist species, which should have had more stable populations through periods of harsh climate in the late Quaternary. Within C. johnstonei, we find that populations from the northern Kimberley islands are highly divergent from mainland populations. In C. triacantha, one major clade occurs across the deserts and into the mesic Top End, and another occurs primarily in the Kimberley with scattered records eastwards. Where their ranges overlap in the Kimberley, both mitochondrial and nuclear DNA suggest stronger phylogeographic structure and range expansion within the tropical specialist, whereas the climate generalist has minimal structuring and no evidence of recent past range expansion. These results are consistent with the hypothesis that tropical specialists are more sensitive to past climatic change.

Data from: Demographic history influences spatial patterns of genetic diversity in recently expanded coyote (Canis latrans) populations

Human-mediated range expansions have increased in recent decades and represent unique opportunities to evaluate genetic outcomes of establishing peripheral populations across broad expansion fronts. Over the past century, coyotes (Canis latrans) have undergone a pervasive range expansion and now inhabit every state in the continental United States. Coyote expansion into eastern North America was facilitated by anthropogenic landscape changes and followed two broad expansion fronts. The northern expansion extended through the Great Lakes region and southern Canada, where hybridization with remnant wolf populations was common. The southern and more recent expansion front occurred approximately 40 years later and across territory where gray wolves have been historically absent and remnant red wolves were extirpated in the 1970s. We conducted a genetic survey at 10 microsatellite loci of 482 coyotes originating from 11 eastern U.S. states to address how divergent demographic histories influence geographic patterns of genetic diversity. We found that population structure corresponded to a north-south divide, which is consistent with the two known expansion routes. Additionally, we observed extremely high genetic diversity, which is atypical of recently expanded populations and is likely the result of multiple complex demographic processes, in addition to hybridization with other Canis species. Finally, we considered the transition of allele frequencies across geographic space and suggest the mid-Atlantic states of North Carolina and Virginia as an emerging contact zone between these two distinct coyote expansion fronts.

Data from: Museum DNA reveals the demographic history of the endangered Seychelles warbler

The importance of evolutionary conservation – how understanding evolutionary forces can help guide conservation decisions – is widely recognized. However, the historical demography of many endangered species is unknown, despite the fact that this can have important implications for contemporary ecological processes and for extinction risk. Here, we reconstruct the population history of the Seychelles warbler (Acrocephalus sechellensis) – an ecological model species. By the 1960s, this species was on the brink of extinction, but its previous history is unknown. We used DNA samples from contemporary and museum specimens spanning 140 years to reconstruct bottleneck history. We found a 25% reduction in genetic diversity between museum and contemporary populations, and strong genetic structure. Simulations indicate that the Seychelles warbler was bottlenecked from a large population, with an ancestral Ne of several thousands falling to <50 within the last century. Such a rapid decline, due to anthropogenic factors, has important implications for extinction risk in the Seychelles warbler, and our results will inform conservation practices. Reconstructing the population history of this species also allows us to better understand patterns of genetic diversity, inbreeding and promiscuity in the contemporary populations. Our approaches can be applied across species to test ecological hypotheses and inform conservation.

Data from: Geographical barriers and climate influence demographic history in narrowleaf cottonwoods

Studies of genetic variation can clarify the role of geography and spatio-temporal variation of climate in shaping demography, particularly in temperate zone tree species with large latitudinal ranges. Here, we examined genetic variation in narrowleaf cottonwood, Populus angustifolia, a dominant riparian tree. Using multi-locus surveys of polymorphism in 363 individuals across the species' 1800 km latitudinal range, we found that, first, P. angustifolia has stronger neutral genetic structure than many forest trees (simple sequence repeat (SSR) FST=0.21), with major genetic groups corresponding to large apparent geographical barriers to gene flow. Second, using SSRs and putatively neutral sequenced loci, coalescent simulations indicated that populations diverged before the last glacial maximum (LGM), suggesting the presence of population structure before the LGM. Third, the LGM and subsequent warming appear to have had different influences on each of these distinct populations, with effective population size reduction in the southern extent of the range but major expansion in the north. These results are consistent with the hypothesis that climate and geographic barriers have jointly affected the demographic history of P. angustifolia, and point the importance of both factors as being instrumental in shaping genetic variation and structure in widespread forest trees.

opencc-zeroDec 2018View details →

Data from: Coalescent models characterize sources and demographic history of recent round goby colonization of Great Lakes and inland waters

The establishment and spread of aquatic invasive species is ecologically and economically harmful and a source of conservation concern internationally. Processes of species invasion have traditionally been inferred from observational data of species presence/absence and relative abundance. However, genetic-based approaches can provide valuable sources of inference. Restriction-site associated DNA sequencing was used to identify and genotype single nucleotide polymorphism (SNP) loci for Round Gobies (Neogobius melanostomus) (N=440) from 18 sampling locations in the Great Lakes and in three Michigan, USA drainages (Flint, Au Sable, and Cheboygan River basins). Sampled rivers differed in size, accessibility, and physical characteristics including man-made dispersal barriers. Population levels of genetic diversity and inter-population variance in SNP allele frequency were used in coalescence-based Approximate Bayesian Computation (ABC) to statistically compare models representing competing hypotheses regarding source population, post-colonization dispersal, and demographic history in the Great Lakes and inland waters. Results indicate different patterns of colonization across the three drainages. In the Flint River, models indicate a strong population bottleneck (< 3% of contemporary effective population size) and a single founding event from Saginaw Bay led to the colonization of inland river segments. In the Au Sable River, analyses could not distinguish potential source populations, but supported models indicated multiple introductions from one source population. In the Cheboygan River, supported models indicated that colonization likely proceeded from east (Lake Huron source) to west among inland locales sampled in the system. Despite the recent occupancy of Great Lakes and inland habitats, large numbers of loci analyzed in an ABC framework enable statistically supported identification of source populations and reconstruction of the direction of inland spread and demographic history following establishment. Information from analyses can direct management actions to limit the spread of invasive species from identified sources and most probable vectors into additional inland aquatic habitats.

Data from: Reconstructing the demographic history of orang-utans using approximate Bayesian computation

Investigating how different evolutionary forces have shaped patterns of DNA variation within and among species requires detailed knowledge of their demographic history. Orang-utans, whose distribution is currently restricted to the Southeast Asian islands of Borneo (Pongo pygmaeus) and Sumatra (Pongo abelii), have likely experienced a complex demographic history, influenced by recurrent changes in climate and sea levels, volcanic activities and anthropogenic pressures. Using the most extensive sample set of wild orang-utans to date, we employed an approximate Bayesian computation (ABC) approach to test the fit of 12 different demographic scenarios to the observed patterns of variation in autosomal, X-chromosomal, mitochondrial and Y-chromosomal markers. In the best-fitting model, Sumatran orang-utans exhibit a deep split of populations north and south of Lake Toba, probably caused by multiple eruptions of the Toba volcano. In addition, we found signals for a strong decline in all Sumatran populations ~24 ka, probably associated with hunting by human colonizers. In contrast, Bornean orang-utans experienced a severe bottleneck ~135 ka, followed by a population expansion and substructuring starting ~82 ka, which we link to an expansion from a glacial refugium. Therefore, we showed that orang-utans went through drastic changes in population size and connectedness, caused by the recurrent contraction and expansion of rainforest habitat during Pleistocene glaciations, and probably also by the impact of hunting by early humans. Our findings also emphasize the fact that important aspects of the evolutionary past of species with complex demographic histories might remain obscured when applying overly simplified models.

Data from: Demographic legacies of fire history in an African savanna

Fire is a key determinant of woody vegetation structure in savanna ecosystems, acting both independently and synergistically through interactions with herbivores. Fire influences biodiversity and ecological functioning, but quantifying its effects on woody structure is challenging at both species and community scales. Deeper insight into fire effects, and fire-herbivore interactions, can be gained through the examination of species-specific demographic and dynamic changes occurring across areas with different fire regimes in the presence of large herbivores. We used the Carnegie Airborne Observatory (an integrated LiDAR and imaging spectroscopy system) to map woody tree structure, species and dynamics over a four-year interval across two adjacent savanna landscapes with contrasting fire histories in Kruger National Park, South Africa. A history of higher fire frequency was associated with reduced woody canopy cover (17% vs. 23%) and an increased overall rate of treefall (27% vs. 18%). The landscape with a history of higher fire frequency displayed a shift in woody canopy height distribution from a unimodal curve to a bimodal pattern at the community scale, with large reductions in height classes < 7 m. Differences in tree height distributions and treefall rates across sites were underpinned by species-specific responses to fire frequency. Acacia nigrescens displayed the highest rates of treefall, most likely related to elephant activity, with losses exceeding 40% in the 6-9 m height classes. Synthesis. Our findings indicate that fire history imparts demographic legacies not only on vegetation structure, but also on current vegetation dynamics. Current treefall rates of certain tree species are exacerbated by a history of higher fire frequency. Species-specific and context-conscious investigations are critical for elucidating the driving mechanisms underlying broader community patterns.

Data from: The effects of Medieval dams on genetic divergence and demographic history in brown trout populations

Background: Habitat fragmentation has accelerated within the last century, but may have been ongoing over longer time scales. We analyzed the timing and genetic consequences of fragmentation in two isolated lake-dwelling brown trout populations. They are from the same river system (the Gudenå River, Denmark) and have been isolated from downstream anadromous trout by dams established ca. 600-800 years ago. For reference, we included ten other anadromous populations and two hatchery strains. Based on analysis of 44 microsatellite loci we investigated if the lake populations have been naturally genetically differentiated from anadromous trout for thousands of years, or have diverged recently due to the establishment of dams. Results: Divergence time estimates were based on 1) Approximate Bayesian Computation and 2) a coalescent-based isolation-with-gene-flow model. Both methods suggested divergence times ca. 600-800 years bp, providing strong evidence for establishment of dams in the Medieval as the factor causing divergence. Bayesian cluster analysis showed influence of stocked trout in several reference populations, but not in the focal lake and anadromous populations. Estimates of effective population size using a linkage disequilibrium method ranged from 244 to > 1,000 in all but one anadromous population, but were lower (153 and 252) in the lake populations. Conclusions: We show that genetic divergence of lake-dwelling trout in two Danish lakes reflects establishment of water mills and impassable dams ca. 600-800 years ago rather than a natural genetic population structure. Although effective population sizes of the two lake populations are not critically low they may ultimately limit response to selection and thereby future adaptation. Our results demonstrate that populations may have been affected by anthropogenic disturbance over longer time scales than normally assumed.

opencc-zeroDec 2009View details →

Data from: Nuclear and mitochondrial sequence data reveal and conceal different demographic histories and population genetic processes in Caribbean reef fishes

Mitochondrial and nuclear sequence data should recover historical demographic events at different temporal scales due to differences in their effective population sizes and substitution rates. This expectation was tested for two closely related coral reef fish, the tube blennies Acanthemblemaria aspera and A. spinosa. These two have similar life histories and dispersal potentials, and co-occur throughout the Caribbean. Sequence data for one mitochondrial and two nuclear markers were collected for 168 individuals across the species' Caribbean ranges. While both species shared a similar pattern of genetic subdivision, A. spinosa had 20-25-times greater nucleotide sequence divergence among populations than A. aspera at all three markers. Substitution rates estimated using a relaxed clock approach revealed that mitochondrial COI is evolving at 11.2% pairwise sequence divergence per million years. This rapid mitochondrial rate had obscured the signal of old population expansions for both species, which were only recovered using the more slowly evolving nuclear markers. However, the rapid COI rate allowed the recovery of a recent expansion in A. aspera corresponding to a period of increased habitat availability. Only by combining both nuclear and mitochondrial data were we able to recover the complex demographic history of these fishes.

Data from: The complex effects of demographic history on the estimation of substitution rate: concatenated gene analysis results in no more than twofold overestimation

Our recent estimation of the divergence time and isolation of Death Valley pupfishes, including the iconic Devil's Hole pupfish (DHP), rewrote widespread assumptions about this group. These species were previously assumed to be relic populations isolated over millions of years; our genomic analyses indicated recent colonization of Devil's Hole within the past 105–830 years and frequent gene flow among Death Valley populations [1]. These results understandably attracted substantial attention given the iconic battle for conservation and intense management of DHP [2]; nonetheless, a young age for this species should not diminish its conservation value. Indeed, we argue that the unique natural history of this species makes it a prime candidate for exhibiting one of the fastest mutation rates observed in any vertebrate [3].

opencc-zeroDec 2012View details →

Data from: The demographic history of populations experiencing asymmetric gene flow: combining simulated and empirical data.

Population structure can significantly affect genetic-based demographic inferences, generating spurious bottleneck-like signals. Previous studies have typically assumed island or stepping-stone models, which are characterized by symmetric gene flow. However, many organisms are characterized by asymmetric gene flow. Here, we combined simulated and empirical data to test whether asymmetric gene flow affects the inference of past demographic changes. Through the analysis of simulated genetic data with three methods (i.e. bottleneck, M-ratio and msvar), we demonstrated that asymmetric gene flow biases past demographic changes. Most biases were towards spurious signals of expansion, albeit their strength depended on values of effective population size and migration rate. It is noteworthy that the spurious signals of demographic changes also depended on the statistical approach underlying each of the three methods. For one of the three methods, biases induced by asymmetric gene flow were confirmed in an empirical multispecific data set involving four freshwater fish species (Squalius cephalus, Leuciscus burdigalensis, Gobio gobio and Phoxinus phoxinus). However, for the two other methods, strong signals of bottlenecks were detected for all species and across two rivers. This suggests that, although potentially biased by asymmetric gene flow, some of these methods were able to bypass this bias when a bottleneck actually occurred. Our results show that population structure and dispersal patterns have to be considered for proper inference of demographic changes from genetic data.

opencc-zeroDec 2015View details →

Data from: Tropical rainforests that persisted: inferences from the Quaternary demographic history of eight tree species in the Guiana shield

How Quaternary climatic and geological disturbances influenced the composition of Neotropical forests is hotly debated. Rainfall and temperature changes during and/or immediately after the last glacial maximum (LGM) are thought to have strongly affected the geographical distribution and local abundance of tree species. The paucity of the fossil records in Neotropical forests prevents a direct reconstruction of such processes. To describe community-level historical trends in forest composition, we turned therefore to inferential methods based on the reconstruction of past demographic changes. In particular, we modelled the history of rainforests in the eastern Guiana Shield over a timescale of several thousand generations, through the application of approximate Bayesian computation and maximum-likelihood methods to diversity data at nuclear and chloroplast loci in eight species or subspecies of rainforest trees. Depending on the species and on the method applied, we detected population contraction, expansion or stability, with a general trend in favour of stability or expansion, with changes presumably having occurred during or after the LGM. These findings suggest that Guiana Shield rainforests have globally persisted, while expanding, through the Quaternary, but that different species have experienced different demographic events, with a trend towards the increase in frequency of light-demanding, disturbance-associated species.

opencc-zeroDec 2014View details →

Data from: The impact of selection, gene flow and demographic history on heterogeneous genomic divergence: threespine sticklebacks in divergent environments

Heterogeneous genomic divergence between populations may reflect selection, but should also be seen in conjunction with gene flow and drift, particularly population bottlenecks. Marine and freshwater threespine stickleback (Gasterosteus aculeatus) populations often exhibit different lateral armor plate morphs. Moreover, strikingly parallel genomic footprints across different marine-freshwater population pairs are interpreted as parallel evolution and gene reuse. Nevertheless, in some geographic regions like the North Sea and Baltic Sea different patterns are observed. Freshwater populations in coastal regions are often dominated by marine morphs, suggesting that gene flow overwhelms selection, and genomic parallelism may also be less pronounced. We used RAD sequencing for analyzing 28,888 SNPs in two marine and seven freshwater populations in Denmark, Europe. Freshwater populations represented a variety of environments: river populations accessible to gene flow from marine sticklebacks and large and small isolated lakes with and without fish predators. Sticklebacks in an accessible river environment showed minimal morphological and genome-wide divergence from marine populations, supporting the hypothesis of gene flow overriding selection. Allele frequency spectra suggested bottlenecks in all freshwater populations, and particularly two small lake populations. However, genomic footprints ascribed to selection could nevertheless be identified. No genomic regions were consistent freshwater-marine outliers, and parallelism was much lower than in other comparable studies. Two genomic regions previously described to be under divergent selection in freshwater and marine populations were outliers between different freshwater populations. We ascribe these patterns to stronger environmental heterogeneity among freshwater populations in our study as compared to most other studies, although the demographic history involving bottlenecks should also be considered in the interpretation of results.

Data from: Multilocus coalescent analyses reveal the demographic history and speciation patterns of mouse lemur sister species

Background: Debate continues as to whether allopatric speciation or peripatric speciation through a founder effect is the predominant force driving evolution in vertebrates. The mouse lemurs of Madagascar are a system in which evolution has generated a large number of species over a relatively recent time frame. Here, we examine speciation patterns in a pair of sister species of mouse lemur, Microcebus murinus and M. griseorufus. These two species have ranges that are disparately proportioned in size, with M. murinus showing a much more extensive range that marginally overlaps that of M. griseorufus. Given that these two species are sister taxa, the asymmetric but overlapping geographic ranges are consistent with a model of peripatric speciation. To test this hypothesis, we analyze DNA sequence data from four molecular markers using coalescent methods. If the peripatric speciation model is supported, we predict substantially greater genetic diversity in M. murinus, relative to M. griseorufus. Further, we expect a larger effective population size in M. murinus and in the common ancestor of the two species than in M. griseorufus, with a concomitant decrease in gene tree/species tree incongruence in the latter and weak signs of demographic expansion in M. murinus. Results: Our results reject a model of peripatric divergence. Coalescent effective population size estimates were similar for both extant species and larger than that estimated for their most recent common ancestor. Gene tree results show similar levels of incomplete lineage sorting within species with respect to the species tree, and locus-specific estimates of genetic diversity are concordant for both species. Multilocus demographic analyses suggest range expansions for M. murinus, with this species also experiencing more recent population declines over the past 160 thousand years. Conclusions: Results suggest that speciation occurred in allopatry from a common ancestor narrowly distributed throughout southwest Madagascar, with subsequent range expansion for M. murinus. Population decline in M. murinus is likely related to patterns of climate change in Madagascar throughout the Pleistocene, potentially exacerbated by continual anthropogenic perturbation. Genome-level data are needed to quantify the role of niche specialization and adaptation in shaping the current ranges of these species.

opencc-zeroDec 2010View details →

Data from: Demographic history of an elusive carnivore: using museums to inform management

Elusive carnivores present a challenge to managers because traditional survey methods are not suitable. We applied a genetic approach using museum specimens to examine how historical and recent conditions influenced the demographic history of Puma concolor in western and southern Texas, USA. We used 10 microsatellite loci and indexed population trends by estimating historical and recent genetic diversity, genetic differentiation, and effective population size. Mountain lions in southern Texas exhibited a 10% decline in genetic diversity, whereas diversity remained stable in western Texas. Genetic differentiation between western and southern Texas was minimal historically (FST = 0.04, P < 0.01), but increased 2-2.5 times in our recent sample. An index of genetic drift for southern Texas was 7-8 times that of western Texas, presumably contributing to the current differentiation between western and southern Texas. Furthermore, southern Texas exhibited a > 50% temporal decline in effective population size, whereas western Texas showed no change. Our results illustrate that population declines and genetic drift have occurred in southern Texas, likely because of contemporary habitat loss and predator control. Population monitoring may be needed to ensure the persistence of mountain lions in the southern Texas region. This study highlights the utility of sampling museum collections to examine evolutionary processes and inform wildlife management.

Data from: Demographic modelling reveals a history of divergence with gene flow for a glacially tied stonefly in a changing post-Pleistocene landscape

Aim: Climate warming is causing extensive loss of glaciers in mountainous regions, yet our understanding of how glacial recession influences evolutionary processes and genetic diversity is limited. Linking genetic structure with the influences shaping it can improve understanding of how species respond to environmental change. Here, we used genome-scale data and demographic modelling to resolve the evolutionary history of Lednia tumana, a rare, aquatic insect endemic to alpine streams. We also employed a range of widely used data filtering approaches to quantify how they influenced population structure results. Location: Alpine streams in the Rocky Mountains of Glacier National Park, Montana, USA. Taxon: Lednia tumana, a stonefly (Order Plecoptera) in the family Nemouridae. Methods: We generated single nucleotide polymorphism data through restriction-site associated DNA sequencing to assess contemporary patterns of genetic structure for 11 L. tumana populations. Using identified clusters, we assessed demographic history through model selection and parameter estimation in a coalescent framework. During population structure analyses, we filtered our data to assess the influence of singletons, missing data and total number of markers on results. Results: Contemporary patterns of population structure indicate that L. tumana exhibits a pattern of isolation-by-distance among populations within three genetic clusters that align with geography. Mean pairwise genetic differentiation (FST) among populations was 0.033. Coalescent-based demographic modelling supported divergence with gene flow among genetic clusters since the end of the Pleistocene (~13-17 kya), likely reflecting the south-to-north recession of ice sheets that accumulated during the Wisconsin glaciation. Main conclusions: We identified a link between glacial retreat, evolutionary history and patterns of genetic diversity for a range-restricted stonefly imperiled by climate change. This finding included a history of divergence with gene flow, an unexpected conclusion for a mountaintop species. Beyond L. tumana, this study demonstrates the complexity of assessing genetic structure for weakly differentiated species, shows the degree to which rare alleles and missing data may influence results, and highlights the usefulness of genome-scale data to extend population genetic inquiry in non-model species.

Data from: Distinguishing the effects of selection from demographic history in the genetic variation of two sister passerines based on mitochondrial-nuclear comparison

Determining the mechanisms responsible for the distribution of genetic diversity in natural populations has occupied a central role in molecular evolution. Our study was motivated by the unprecedented observation that a widespread Eurasian flycatcher, Ficedula albicilla, exhibited no variation at the mitochondrial DNA (mtDNA) ND2 gene in 75 individuals sampled over a 5000-km distance. In contrast, its sister species, F. parva, had low but considerably higher levels of mtDNA variation. We assessed whether natural selection or demographic factors could explain the absence of mtDNA variation in F. albicilla. Eighteen nuclear genes were sequenced to estimate the two species' phylogeographic histories, and for comparison to the mtDNA data. Multilocus coalescence analyses suggested that F. albicilla experienced a population expansion perhaps following a population bottleneck. Simulations based on this demographic history, however, did not replicate the extremely low level of mtDNA variation. Historical range changes based on ecological niche models also failed to explain the observed mtDNA patterns. Neutrality tests (DHEW and ML-HKA) suggested a non-neutral pattern in the mtDNA of F. albicilla. We found a transmembrane-skewed distribution of nonsynonymous substitutions between the two species, three of which caused functional change; the results implied that positive selection could have targeted mtDNA. Several lines of evidence support selection rather than demographic history as the main force influencing the patterns of mtDNA variation. Despite the influence of natural selection, many of the phylogeographic inferences derived from mtDNA were robust, including species limits and a high level of gene flow among populations within species.