Reconstructing the evolutionary history of an endangered subspecies across the changing landscape of the Great Central Valley of California

Identifying historic patterns of population genetic diversity and connectivity is a primary challenge in efforts to re‐establish the processes that have generated and maintained genetic variation across natural landscapes. The challenge of reconstructing pattern and process is even greater in highly altered landscapes where population extinctions and dramatic demographic fluctuations in remnant populations may have substantially altered, if not eliminated, historic patterns. Here, we seek to reconstruct historic patterns of diversity and connectivity in an endangered subspecies of woodrat that now occupies only 1–2 remnant locations within the highly altered landscape of the Great Central Valley of California. We examine patterns of diversity and connectivity using 14 microsatellite loci and sequence data from a mitochondrial locus and a nuclear intron. We reconstruct temporal change in habitat availability to establish several historical scenarios that could have led to contemporary patterns of diversity, and use an approximate Bayesian computation approach to test which of these scenarios is most consistent with our observed data. We find that the Central Valley populations harbour unique genetic variation coupled with a history of admixture between two well‐differentiated species of woodrats that are currently restricted to the woodlands flanking the Valley. Our simulations also show that certain commonly used analytical approaches may fail to recover a history of admixture when populations experience severe bottlenecks subsequent to hybridization. Overall our study shows the strength of combining empirical and simulation analyses to recover the history of populations occupying highly altered landscapes.     

Population genetic differences along a latitudinal cline between original and recently colonized habitat in a butterfly

BACKGROUND: Past and current range or spatial expansions have important consequences on population genetic structure. Habitat-use expansion, i.e. changing habitat associations, may also influence genetic population parameters, but has been less studied. Here we examined the genetic population structure of a Palaeartic woodland butterfly Pararge aegeria (Nymphalidae) which has recently colonized agricultural landscapes in NW-Europe. Butterflies from woodland and agricultural landscapes differ in several phenotypic traits (including morphology, behavior and life history). We investigated whether phenotypic divergence is accompanied by genetic divergence between populations of different landscapes along a 700 km latitudinal gradient. METHODOLOGY/PRINCIPAL FINDINGS: Populations (23) along the latitudinal gradient in both landscape types were analyzed using microsatellite and allozyme markers. A general decrease in genetic diversity with latitude was detected, likely due to post-glacial colonization effects. Contrary to expectations, agricultural landscapes were not less diverse and no significant bottlenecks were detected. Nonetheless, a genetic signature of recent colonization is reflected in the absence of clinal genetic differentiation within the agricultural landscape, significantly lower gene flow between agricultural populations (3.494) than between woodland populations (4.183), and significantly higher genetic differentiation between agricultural (0.050) than woodland (0.034) pairwise comparisons, likely due to multiple founder events. Globally, the genetic data suggest multiple long distance dispersal/colonization events and subsequent high intra- and inter-landscape gene flow in this species. Phosphoglucomutase deviated from other enzymes and microsatellite markers, and hence may be under selection along the latitudinal gradient but not between landscape types. Phenotypic divergence was greater than genetic divergence, indicating directional selection on some flight morphology traits. MAIN CONCLUSIONS/SIGNIFICANCE: Clinal differentiation characterizes the population structure within the original woodland habitat. Genetic signatures of recent habitat expansion remain, notwithstanding high gene flow. After differentiation through drift was excluded, both latitude and landscape were significant factors inducing spatially variable phenotypic variation.     

Landscape genetic structure of coastal tailed frogs (Ascaphus truei) in protected vs. managed forests

Habitat loss and fragmentation are the leading causes of species’ declines and extinctions. A key component of studying population response to habitat alteration is to understand how fragmentation affects population connectivity in disturbed landscapes. We used landscape genetic analyses to determine how habitat fragmentation due to timber harvest affects genetic population connectivity of the coastal tailed frog (Ascaphus truei), a forest-dwelling, stream-breeding amphibian. We compared rates of gene flow across old-growth (Olympic National Park) and logged landscapes (Olympic National Forest) and used spatial autoregression to estimate the effect of landscape variables on genetic structure. We detected higher overall genetic connectivity across the managed forest, although this was likely a historical signature of continuous forest before timber harvest began. Gene flow also occurred terrestrially, as connectivity was high across unconnected river basins. Autoregressive models demonstrated that closed forest and low solar radiation were correlated with increased gene flow. In addition, there was evidence for a temporal lag in the correlation of decreased gene flow with harvest, suggesting that the full genetic impact may not appear for several generations. Furthermore, we detected genetic evidence of population bottlenecks across the Olympic National Forest, including at sites that were within old-growth forest but surrounded by harvested patches. Collectively, this research suggests that absence of forest (whether due to natural or anthropogenic changes) is a key restrictor of genetic connectivity and that intact forested patches in the surrounding environment are necessary for continued gene flow and population connectivity.     

Do landscape processes predict phylogeographic patterns in the wood frog?

Understanding factors that influence population connectivity and the spatial distribution of genetic variation is a major goal in molecular ecology. Improvements in the availability of high-resolution geographic data have made it increasingly possible to quantify the effects of landscape features on dispersal and genetic structure. However, most studies examining such landscape effects have been conducted at very fine (e.g. landscape genetics) or broad (e.g. phylogeography) spatial scales. Thus, the extent to which processes operating at fine spatial scales are linked to patterns at larger scales remains unclear. Here, we test whether factors impacting wood frog dispersal at fine spatial scales are correlated with genetic structure at regional scales. Using recently developed methods borrowed from electrical circuit theory, we generated landscape resistance matrices among wood frog populations in eastern North America based on slope, a wetness index, land cover and absolute barriers to wood frog dispersal. We then determined whether these matrices are correlated with genetic structure based on six microsatellite markers and whether such correlations outperform a landscape-free model of isolation by resistance. We observed significant genetic structure at regional spatial scales. However, topography and landscape variables associated with the intervening habitat between sites provide little explanation for patterns of genetic structure. Instead, absolute dispersal barriers appear to be the best predictor of regional genetic structure in this species. Our results suggest that landscape variables that influence dispersal, microhabitat selection and population structure at fine spatial scales do not necessarily explain patterns of genetic structure at broader scales.     

The scale of genetic differentiation in the Dunes Sagebrush-Lizard (Sceloporus arenicolus), an endemic habitat specialist

The Dunes Sagebrush-Lizard (Sceloporus arenicolus) is a North American species endemic to sand-shinnery oak habitats of the Mescalero and Monahans sand dunes in eastern New Mexico and western Texas. This lizard is listed as Endangered in New Mexico and exhibits habitat specificity at several geographic scales. Dunes Sagebrush-Lizards are only found in topographically complex shinnery oak (Quercus havardii) dominated landscapes within their small geographic distribution and are not found in surrounding human-altered landscapes. Within suitable sand-shinnery oak habitat, individuals predominantly occupy non-vegetated sand dune blowouts and utilize blowouts with particular physical characteristics due to thermoregulatory, reproduction, and foraging requirements. Here, we examined historical and contemporary patterns of genetic differentiation with respect to the current distribution of suitable habitat at multiple spatial scales using mitochondrial DNA sequences and microsatellite data from individuals throughout the entire range. We found three genetic clusters of individuals generally concordant with geographic regions and low sequence divergence at mitochondrial loci suggesting a recent origin of these populations. We also found high levels of genetic structure at microsatellite loci among populations within each of these groups indicating restricted gene flow at intermediate scales. Despite high habitat specificity, we did not detect genetic structure among sand blowouts at finer spatial scales. Within each population, matrices comprised of both sand blowouts and vegetated shinnery oak patches are necessary for genetic connectivity, but the fine scale spatial arrangement of blowouts may not be as critical. We discuss our results with respect to the scale of landscape heterogeneity and habitat connectivity and consider the conservation implications for this threatened taxon.     

Limited Population Structure,Genetic Drift and Bottlenecks Characterise an Endangered Bird Species in a Dynamic,Fire-Prone Ecosystem

Fire is a major disturbance process in many ecosystems world-wide, resulting in spatially and temporally dynamic landscapes. For populations occupying such environments, fire-induced landscape change is likely to influence population processes, and genetic patterns and structure among populations. The Mallee Emu-wren Stipiturus mallee is an endangered passerine whose global distribution is confined to fire-prone, semi-arid mallee shrublands in south-eastern Australia. This species, with poor capacity for dispersal, has undergone a precipitous reduction in distribution and numbers in recent decades. We used genetic analyses of 11 length-variable, nuclear loci to examine population structure and processes within this species, across its global range. Populations of the Mallee Emu-wren exhibited a low to moderate level of genetic diversity, and evidence of bottlenecks and genetic drift. Bayesian clustering methods revealed weak genetic population structure across the species'' range. The direct effects of large fires, together with associated changes in the spatial and temporal patterns of suitable habitat, have the potential to cause population bottlenecks, serial local extinctions and subsequent recolonisation, all of which may interact to erode and homogenise genetic diversity in this species. Movement among temporally and spatially shifting habitat, appears to maintain long-term genetic connectivity. A plausible explanation for the observed genetic patterns is that, following extensive fires, recolonisation exceeds in-situ survival as the primary driver of population recovery in this species. These findings suggest that dynamic, fire-dominated landscapes can drive genetic homogenisation of populations of species with low-mobility and specialised habitat that otherwise would be expected to show strongly structured populations. Such effects must be considered when formulating management actions to conserve species in fire-prone systems.     

Effects of slope and riparian habitat connectivity on gene flow in an endangered Panamanian frog, Atelopus varius

Aim Understanding how heterogeneous landscapes shape genetic structure not only sheds light on processes involved in population divergence and speciation, but can also guide management strategies to promote and maintain genetic connectivity of populations of endangered species. This study aimed to (1) identify barriers and corridors for gene flow among populations of the endangered frog, Atelopus varius and (2) assess the relative contributions of alternative landscape factors to patterns of genetic variation among these populations in a hypothesis testing framework. Location This study took place in western Panama and included all nine of the remaining known populations of A. varius at the time of study. Methods The influence of landscape variables on gene flow among populations was examined by testing for correlations between alternative landscape‐resistance scenarios and genetic distance. Fifteen alternative hypotheses about the influence of (1) riparian habitat corridors, (2) steep slopes, and (3) climatic suitability on patterns of genetic structure were tested in a causal modelling framework, using Mantel and partial‐Mantel tests, along with an analysis of molecular variation. Results Only the hypothesis attributing resistance to dispersal across steep slopes (genetic isolation by slope distance) was fully supported by the causal modelling approach. However, the analysis of molecular variance and the paths of least‐slope among populations suggest that riparian habitat connectivity may influence genetic structure as well. Main conclusions These results suggest that patterns of genetic variation among A. varius populations are affected by the slope of the landscape such that areas with steep slopes act as barriers to gene flow. In contrast, areas of low slope, such as streams and mountain ridges, appear to be important corridors for gene flow, especially among high elevation populations. These results engender important considerations for the management of this critically endangered species.     

Watershed characteristics shape the landscape genetics of brook stickleback (Culaea inconstans) in shallow prairie lakes

Investigating the consequences of landscape features on population genetic patterns is increasingly important to elucidate the ecological factors governing connectivity between populations and predicting the evolutionary consequences of landscapes. Small prairie lakes in Alberta, Canada, and the brook stickleback (Culaea inconstans) that inhabit them, provide a unique aquatic system whereby populations are highly isolated from one another. These heterogeneous and extreme environments are prone to winterkills, an event whereby most of the fish die and frequent bottlenecks occur. In this study, we characterized the genetic population structure of brook stickleback among several lakes, finding that the species is hierarchically influenced by within‐lake characteristics in small‐scale watersheds. Landscape genetic analyses of the role of spatial features found support for basin characteristics associated with genetic diversity and bottlenecks in 20% of the sampled lakes. These results suggest that brook stickleback population genetic patterns may be driven, at least in part, by ecological processes that accelerate genetic drift and landscape patterns associated with reduced dispersal. Collectively, these results reinforce the potential importance of connectivity in the maintenance of genetic diversity, especially in fragmented landscapes.     

A multiscale analysis of gene flow for the New England cottontail,an imperiled habitat specialist in a fragmented landscape

Landscape features of anthropogenic or natural origin can influence organisms' dispersal patterns and the connectivity of populations. Understanding these relationships is of broad interest in ecology and evolutionary biology and provides key insights for habitat conservation planning at the landscape scale. This knowledge is germane to restoration efforts for the New England cottontail (Sylvilagus transitionalis), an early successional habitat specialist of conservation concern. We evaluated local population structure and measures of genetic diversity of a geographically isolated population of cottontails in the northeastern United States. We also conducted a multiscale landscape genetic analysis, in which we assessed genetic discontinuities relative to the landscape and developed several resistance models to test hypotheses about landscape features that promote or inhibit cottontail dispersal within and across the local populations. Bayesian clustering identified four genetically distinct populations, with very little migration among them, and additional substructure within one of those populations. These populations had private alleles, low genetic diversity, critically low effective population sizes (3.2–36.7), and evidence of recent genetic bottlenecks. Major highways and a river were found to limit cottontail dispersal and to separate populations. The habitat along roadsides, railroad beds, and utility corridors, on the other hand, was found to facilitate cottontail movement among patches. The relative importance of dispersal barriers and facilitators on gene flow varied among populations in relation to landscape composition, demonstrating the complexity and context dependency of factors influencing gene flow and highlighting the importance of replication and scale in landscape genetic studies. Our findings provide information for the design of restoration landscapes for the New England cottontail and also highlight the dual influence of roads, as both barriers and facilitators of dispersal for an early successional habitat specialist in a fragmented landscape.     

Connectivity and gene flow among Eastern Tiger Salamander (Ambystoma tigrinum) populations in highly modified anthropogenic landscapes

Fragmented landscapes resulting from anthropogenic habitat modification can have significant impacts on dispersal, gene flow, and persistence of wildlife populations. Therefore, quantifying population connectivity across a mosaic of habitats in highly modified landscapes is critical for the development of conservation management plans for threatened populations. Endangered populations of the eastern tiger salamander (Ambystoma tigrinum) in New York and New Jersey are at the northern edge of the species’ range and remaining populations persist in highly developed landscapes in both states. We used landscape genetic approaches to examine regional genetic population structure and potential barriers to migration among remaining populations. Despite the post-glacial demographic processes that have shaped genetic diversity in tiger salamander populations at the northern extent of their range, we found that populations in each state belong to distinct genetic clusters, consistent with the large geographic distance that separates them. We detected overall low genetic diversity and high relatedness within populations, likely due to recent range expansion, isolation, and relatively small population sizes. Nonetheless, landscape connectivity analyses reveal habitat corridors among remaining breeding ponds. Furthermore, molecular estimates of population connectivity among ponds indicate that gene flow still occurs at regional scales. Further fragmentation of remaining habitat will potentially restrict dispersal among breeding ponds, cause the erosion of genetic diversity, and exacerbate already high levels of inbreeding. We recommend the continued management and maintenance of habitat corridors to ensure long-term viability of these endangered populations.     

Nonequilibrium conditions following landscape rearrangement: the relative contribution of past and current hydrological landscapes on the genetic structure of a stream-dwelling fish

Interpreting patterns of population structure in nature is often challenging, especially in dynamic landscapes where population genetic connectivity evolves over time. In this study, we document the absence of migration-drift equilibrium in a stream-dwelling euryhaline fish resulting from past fine-scale drainage rearrangements and evaluate the relative contribution of past and current hydrological landscapes on observed population structure. Based on allelic variation at nine microsatellite loci, genetic relationships among 12 populations of brook charr, Salvelinus fontinalis, from Gros Morne National Park of Canada (GMNP, Newfoundland, Canada) did not reflect current stream hierarchical structure. In addition, we observed no correlation between population differentiation and contemporary landscape features (waterway distance and sums of altitudinal differences). Instead, population relationships were consistent with historical hydrological structure predicted a priori based on geomorphological and biogeographical evidences. Also, population differentiation was strongly correlated with inferred historical landscape features. Contemporary barriers have apparently preserved the signature of past genetic connectivity by constraining gene flow. Based on the relationships between population differentiation and current and past landscape features at various spatial scales, we suggest that brook charr genetic diversity in GMNP is mostly the result of small distance migrations at the time of colonization and subsequent differentiation through drift. This study highlights the potential of approaching landscapes from a combination of contemporary and historical perspectives when interpreting nonequilibrium population structures resulting from landscape rearrangement.     

Genetic connectivity and diversity in inselberg populations of Acacia woodmaniorum,a rare endemic of the Yilgarn Craton banded iron formations

Historically rare plant species with disjunct population distributions and small population sizes might be expected to show significant genetic structure and low levels of genetic diversity because of the effects of inbreeding and genetic drift. Across the globe, terrestrial inselbergs are habitat for rich, often rare and endemic flora and are valuable systems for investigating evolutionary processes that shape patterns of genetic structure and levels of genetic diversity at the landscape scale. We assessed genetic structure and levels of genetic diversity across the range of the historically rare inselberg endemic Acacia woodmaniorum. Phylogeographic and genetic structure indicates that connectivity is not sufficient to produce a panmictic population across the limited geographic range of the species. However, historical levels of gene flow are sufficient to maintain a high degree of adaptive connectivity across the landscape. Genetic diversity indicates gene flow is sufficient to largely counteract any negative genetic effects of inbreeding and random genetic drift in even the most disjunct or smallest populations. Phylogeographic and genetic structure, a signal of isolation by distance and a lack of evidence of recent genetic bottlenecks suggest long-term stability of contemporary population distributions and population sizes. There is some evidence that genetic connectivity among disjunct outcrops may be facilitated by the occasional long distance dispersal of Acacia polyads carried by insect pollinators moved by prevailing winds.     

Understanding the genetic effects of recent habitat fragmentation in the context of evolutionary history: phylogeography and landscape genetics of a southern California endemic Jerusalem cricket (Orthoptera: Stenopelmatidae: Stenopelmatus)

Habitat loss and fragmentation due to urbanization are the most pervasive threats to biodiversity in southern California. Loss of habitat and fragmentation can lower migration rates and genetic connectivity among remaining populations of native species, reducing genetic variability and increasing extinction risk. However, it may be difficult to separate the effects of recent anthropogenic fragmentation from the genetic signature of prehistoric fragmentation due to previous natural geological and climatic changes. To address these challenges, we examined the phylogenetic and population genetic structure of a flightless insect endemic to cismontane southern California, Stenopelmatus'mahogani' (Orthoptera: Stenopelmatidae). Analyses of mitochondrial DNA sequence data suggest that diversification across southern California began during the Pleistocene, with most haplotypes currently restricted to a single population. Patterns of genetic divergence correlate with contemporary urbanization, even after correcting for (geographical information system) GIS-based reconstructions of fragmentation during the Pleistocene. Theoretical simulations confirm that contemporary patterns of genetic structure could be produced by recent urban fragmentation using biologically reasonable assumptions about model parameters. Diversity within populations was positively correlated with current fragment size, but not prehistoric fragment size, suggesting that the effects of increased drift following anthropogenic fragmentation are already being seen. Loss of genetic connectivity and diversity can hinder a population's ability to adapt to ecological perturbations commonly associated with urbanization, such as habitat degradation, climatic changes and introduced species. Consequently, our results underscore the importance of preserving and restoring landscape connectivity for long-term persistence of low vagility native species.     

Genetic variation and structure in the Mediterranean shrubs Myrtus communis and Pistacia lentiscus in different landscape contexts

Studies concerning different habitat configurations can provide insights into the complex interactions between species’ life‐history traits and the environment and can help to predict patterns in population genetics. In this study, we compared patterns of genetic variation in two Mediterranean shrub species (Myrtus communis and Pistacia lentiscus) that co‐occur in populations within three contrasting landscape contexts: continuous, fragmented‐connected and fragmented‐isolated populations. Analysing variation at microsatellites loci, our results revealed weak responses to the landscape contexts. We rather found a population‐specific response in both study species. However, despite both study species sharing similar levels of genetic diversity, Myrtus displayed higher levels of homozygosity and genetic differentiation among populations, stronger patterns of within‐population spatial genetic structure, lower values of mutation‐scaled effective population size and stronger evidence for recent genetic bottlenecks than Pistacia. This result highlights the influence of past events (e.g. historical connectivity, fluctuations in population size) and local factors (e.g. microhabitat availability for recruitment, habitat quality, plant density, native fauna) and that the landscape configuration per se (i.e. fragment size and/or isolation) might not completely determine the species’ genetic patterns.     

Divergent landscape effects on population connectivity in two co-occurring amphibian species

The physical and environmental attributes of landscapes often shape patterns of population connectivity by influencing dispersal and gene flow. Landscape effects on movement are typically evaluated for single species. However, inferences from multiple species are required for multi‐species management strategies increasingly being applied in conservation. In this study, I compared the spatial genetic patterns of two amphibian species across the northeastern United States and estimated the influence of specific landscape features on the observed genetic structure. The spotted salamander (Ambystoma maculatum) and wood frog (Rana sylvatica) share many ecological attributes related to habitat use, phenology and site fidelity. However, I hypothesized that important differences in their movement patterns and life history would create distinct genetic patterns for each species. Using 14 microsatellite loci, I tested for differences in the level of genetic differentiation between the two species across 22 breeding ponds. The effects of eight landscape features were also estimated by evaluating 32 landscape resistance models. Spotted salamanders exhibited significantly higher genetic differentiation than wood frogs. Different landscape features were also identified as potential drivers of the genetic patterns in each species, with little overlap in model support between species. Collectively, these results provide strong evidence that these two amphibian species interact with the landscape in measurably different ways. The distinct genetic patterns observed are consistent with key differences in movement ability and life history between A. maculatum and R. sylvatica. These results highlight the importance of considering more than one species when assessing the impacts of the landscape matrix on population connectivity, even for ecologically similar species within the same habitats.     

Fine-scale population structure in a desert amphibian: landscape genetics of the black toad (Bufo exsul)

Environmental variables can strongly influence a variety of intra- and inter-population processes, including demography, population structure and gene flow. When environmental conditions are particularly harsh for a certain species, investigating these effects is important to understanding how populations persist under difficult conditions. Furthermore, species inhabiting challenging environments present excellent opportunities to examine the effects of complex landscapes on population processes because these effects will often be more pronounced. In this study, I use 16 microsatellite loci to examine population structure, gene flow and demographic history in the black toad, Bufo exsul , which has one of the most restricted natural ranges of any amphibian. Bufo exsul inhabits four springs in the Deep Springs Valley high desert basin and has never been observed more than several meters from any source of water. My results reveal limited gene flow and moderately high levels of population structure ( F _ST = 0.051–0.063) between all but the two closest springs. I found that the geographic distance across the arid scrub habitat between springs is significantly correlated with genetic structure when distance accounts for topography and barriers to dispersal. I also found very low effective population sizes ( N _e = 7–30) and substantial evidence for historical population bottlenecks in all four populations. Together, these results suggest that the desert landscape and B.   exsul 's high habitat specificity contribute significantly to population structure and demography in this species and emphasize the importance of considering behavioural and landscape data in conservation genetic studies of natural systems.     

Habitat fragmentation in coastal southern California disrupts genetic connectivity in the cactus wren (Campylorhynchus brunneicapillus)

Achieving long‐term persistence of species in urbanized landscapes requires characterizing population genetic structure to understand and manage the effects of anthropogenic disturbance on connectivity. Urbanization over the past century in coastal southern California has caused both precipitous loss of coastal sage scrub habitat and declines in populations of the cactus wren (Campylorhynchus brunneicapillus). Using 22 microsatellite loci, we found that remnant cactus wren aggregations in coastal southern California comprised 20 populations based on strict exact tests for population differentiation, and 12 genetic clusters with hierarchical Bayesian clustering analyses. Genetic structure patterns largely mirrored underlying habitat availability, with cluster and population boundaries coinciding with fragmentation caused primarily by urbanization. Using a habitat model we developed, we detected stronger associations between habitat‐based distances and genetic distances than Euclidean geographic distance. Within populations, we detected a positive association between available local habitat and allelic richness and a negative association with relatedness. Isolation‐by‐distance patterns varied over the study area, which we attribute to temporal differences in anthropogenic landscape development. We also found that genetic bottleneck signals were associated with wildfire frequency. These results indicate that habitat fragmentation and alterations have reduced genetic connectivity and diversity of cactus wren populations in coastal southern California. Management efforts focused on improving connectivity among remaining populations may help to ensure population persistence.     

Geographical variation in genetic structure of an Atlantic Coastal Forest frog reveals regional differences in habitat stability

Climatic oscillations throughout the Pleistocene combined with geological and topographic complexity resulted in extreme habitat heterogeneity along the Atlantic coast of Brazil. Inferring how these historic landscape patterns have structured the current diversity of the region's biota is important both for our understanding of the factors promoting diversification, as well as the conservation of this biodiversity hotspot. Here we evaluate potential historical scenarios of diversification in the Atlantic Coastal Forest of Brazil by investigating the population genetic structure of a frog endemic to the region. Using mitochondrial and nuclear sequences, we generated a Bayesian population-level phylogeny of the Thoropa miliaris species complex. We found deep genetic divergences among five geographically distinct clades. Southern clades were monophyletic and nested within paraphyletic northern clades. Analyses of historical demographic patterns suggest an overall north to south population expansion, likely associated with regional differences in habitat stability during the Pliocene and early Pleistocene. However, genetic structure among southern populations is less pronounced and likely represents more recent vicariant events resulting from Holocenic sea-level oscillations. Our analyses corroborate that the Atlantic Coastal Forest has been a biogeographically dynamic landscape and suggest that the high diversity of its fauna and flora resulted from a combination of climatic and geologic events from the Pliocene to the present.     

Effects of landscape and history on diversification of a montane, stream-breeding amphibian

Aim The aim of this study was to understand the roles of landscape features in shaping patterns of contemporary and historical genetic diversification among populations of the Andean tree frog (Hypsiboas andinus) across spatial scales. Location Andes mountains, north‐western Argentina, South America. Methods Mitochondrial DNA control region sequences were utilized to assess genetic differentiation among populations and calculate population pair‐wise genetic distances. Three models of movement, namely traditional straight‐line distance and two effective distances based on habitat classification, were examined to determine which of these explained the most variation in pair‐wise population genetic differentiation. The two habitat classifications were based on digital vegetation and hydrology layers that were generated from a 90‐m resolution digital elevation model (DEM) and known relationships between elevation and habitat. Mantel tests were conducted to test for correlations between geographic and genetic distance matrices and to estimate the percentage variation explained by each type of geographic distance. To investigate the location of possible barriers to gene flow, we used Monmonier’s maximum difference algorithm as implemented in barrier 2.2. Results At both geographic scales, effective distances explained more variation in genetic differentiation than did straight‐line distance. The least‐cost distances based on the simple classification performed better than the more detailed habitat classification. We controlled for the effects of historical range fragmentation determined from previous nested clade analyses, and therefore evaluated the effect of different distances on the genetic variation attributable to more recent factors. Effective distances identified populations that were highly divergent as a result of isolation in unsuitable habitats. The proposed locations of barriers to gene flow identified using Monmonier’s maximum difference algorithm corresponded well with earlier analyses and supported findings from our partial Mantel tests. Main conclusions Our results indicate that landscape features have been important in both historical and contemporary genetic structuring of populations of H. andinus at both large and small spatial scales. A landscape genetic perspective offers novel insights not provided by traditional phylogeographic studies: (1) effective distances can better explain patterns of differentiation in populations, especially in heterogeneous landscapes where barriers to dispersal may be common; and (2) least‐cost path analysis can help to identify corridors of movement between populations that are biologically more realistic.     

Genetic structure of the marsh frog (Pelophylax ridibundus) populations in urban landscape

Urbanization is a pervasive process causing habitat fragmentation, spatial isolation of populations, and reduction of biological diversity. In this study, we applied 11 microsatellite loci and Bayesian analyses to investigate genetic diversity and population structure in marsh frogs (Pelophylax ridibundus) living in two types of environment—highly fragmented urban landscapes, and landscapes characterized by the presence of a river and artificial canals. Our results show reduced genetic diversity, lower effective population sizes, and higher genetic differentiation for spatially isolated urban populations in comparison with populations outside intensely urbanized areas. Reduction of allelic diversity in urban localities isolated for 13–37 generations is more conspicuous than reduction of expected heterozygosity. Populations living close to the River Danube, its branches, and artificial canals are genetically more homogenous. Our results also suggest that the Danube in Bratislava is not a natural barrier to gene flow. In contrast, it acts as a natural corridor for water frog dispersal. Population structure of P. ridibundus also shows higher genetic connectivity within water paths than between them, suggesting limited overland dispersal, and reflects the historical landscape structure associated with the distribution of the lost river branches.