Population connectivity and genetic diversity of American marten (Martes americana) in the United States northern Rocky Mountains in a climate change context

Climate change is likely to alter population connectivity, particularly for species associated with higher elevation environments. The goal of this study is to predict the potential effects of future climate change on population connectivity and genetic diversity of American marten populations across a 30.2 million hectare region of the in the US northern Rocky Mountains. We use a landscape resistance model validated from empirical landscape genetics modeling to predict the current and expected future extent and fragmentation of American marten dispersal habitat under five climate change scenarios, corresponding to climatic warming of between 0.7 and 3.3 °C, consistent with expected climate change by year 2080. We predict the regions of the current and future landscapes where gene flow is expected to be governed by isolation by distance and the regions where population fragmentation is expected to limit gene flow. Finally, we predict changes in the strength and location of predicted movement corridors, fracture zones and the location of dispersal barriers across the study area in each scenario. We found that under the current climate, gene flow is predicted to be limited primarily by distance (isolation), and landscape structure does not significantly limit gene flow, resulting in very high genetic diversity over most of the study area. Projected climatic warming substantially reduces the extent and increases the fragmentation of marten populations in the western and northwestern parts of the study area. In contrast, climate change is not predicted to fragment the extensive higher elevation mountain massifs in central Idaho, the northern U.S. continental divide, and Greater Yellowstone Ecosystem. In addition, we show locations in the study area that are important corridors in the current landscape that remain intact across the climate change scenarios.     

Landscape genetics of a pollinator longhorn beetle [Typocerus v. velutinus (Olivier)] on a continuous habitat surface

Landscape connectivity, the degree to which the landscape structure facilitates or impedes organismal movement and gene flow, is increasingly important to conservationists and land managers. Metrics for describing the undulating shape of continuous habitat surfaces can expand the usefulness of continuous gradient surfaces that describe habitat and predict the flow of organisms and genes. We adopted a landscape gradient model of habitat and used surface metrics of connectivity to model the genetic continuity between populations of the banded longhorn beetle [Typocerus v. velutinus (Olivier)] collected at 17 sites across a fragmentation gradient in Indiana, USA. We tested the hypothesis that greater habitat connectivity facilitates gene flow between beetle populations against a null model of isolation by distance (IBD). We used next‐generation sequencing to develop 10 polymorphic microsatellite loci and genotype the individual beetles to assess the population genetic structure. Isolation by distance did not explain the population genetic structure. The surface metrics model of habitat connectivity explained the variance in genetic dissimilarities 30 times better than the IBD model. We conclude that surface metrology of habitat maps is a powerful extension of landscape genetics in heterogeneous landscapes.     

Temporally dynamic habitat suitability predicts genetic relatedness among caribou

Landscape heterogeneity plays a central role in shaping ecological and evolutionary processes. While species utilization of the landscape is usually viewed as constant within a year, the spatial distribution of individuals is likely to vary in time in relation to particular seasonal needs. Understanding temporal variation in landscape use and genetic connectivity has direct conservation implications. Here, we modelled the daily use of the landscape by caribou in Quebec and Labrador, Canada and tested its ability to explain the genetic relatedness among individuals. We assessed habitat selection using locations of collared individuals in migratory herds and static occurrences from sedentary groups. Connectivity models based on habitat use outperformed a baseline isolation-by-distance model in explaining genetic relatedness, suggesting that variations in landscape features such as snow, vegetation productivity and land use modulate connectivity among populations. Connectivity surfaces derived from habitat use were the best predictors of genetic relatedness. The relationship between connectivity surface and genetic relatedness varied in time and peaked during the rutting period. Landscape permeability in the period of mate searching is especially important to allow gene flow among populations. Our study highlights the importance of considering temporal variations in habitat selection for optimizing connectivity across heterogeneous landscape and counter habitat fragmentation.     

Connectivity of prairie dog colonies in an altered landscape: inferences from analysis of microsatellite DNA variation

Connectivity of populations influences the degree to which species maintain genetic diversity and persist despite local extinctions. Natural landscape features are known to influence connectivity, but global anthropogenic landscape change underscores the importance of quantifying how human-modified landscapes disrupt connectivity of natural populations. Grasslands of western North America have experienced extensive habitat alteration, fragmenting populations of species such as black-tailed prairie dogs (Cynomys ludovicianus). Population sizes and the geographic range of prairie dogs have been declining for over a century due to habitat loss, disease, and eradication efforts. In many places, prairie dogs have persisted in the face of emerging urban landscapes that carve habitat into smaller and smaller fragments separated by uninhabitable areas. In extreme cases, prairie dog colonies are completely bounded by urbanization. Connectivity is particularly important for prairie dogs because colonies suffer high probabilities of extirpation by plague, and dispersal permits recolonization. Here we explore connectivity of prairie dog populations using analyses of 11 microsatellite loci for 9 prairie dog colonies spanning the fragmented landscape of Boulder County, Colorado. Isolation-by-resistance modeling suggests that wetlands and high intensity urbanization limit movement of prairie dogs. However, prairie dogs appear to move moderately well through low intensity development (including roads) and freely through cropland and grassland. Additionally, there is a marked decline in gene flow between colonies with increasing geographic distance, indicating isolation by distance even in an altered landscape. Our results suggest that prairie dog colonies retain some connectivity despite fragmentation by urbanization and agricultural development.     

Landscape Genetics for the Empirical Assessment of Resistance Surfaces: The European Pine Marten (Martes martes) as a Target-Species of a Regional Ecological Network

Coherent ecological networks (EN) composed of core areas linked by ecological corridors are being developed worldwide with the goal of promoting landscape connectivity and biodiversity conservation. However, empirical assessment of the performance of EN designs is critical to evaluate the utility of these networks to mitigate effects of habitat loss and fragmentation. Landscape genetics provides a particularly valuable framework to address the question of functional connectivity by providing a direct means to investigate the effects of landscape structure on gene flow. The goals of this study are (1) to evaluate the landscape features that drive gene flow of an EN target species (European pine marten), and (2) evaluate the optimality of a regional EN design in providing connectivity for this species within the Basque Country (North Spain). Using partial Mantel tests in a reciprocal causal modeling framework we competed 59 alternative models, including isolation by distance and the regional EN. Our analysis indicated that the regional EN was among the most supported resistance models for the pine marten, but was not the best supported model. Gene flow of pine marten in northern Spain is facilitated by natural vegetation, and is resisted by anthropogenic landcover types and roads. Our results suggest that the regional EN design being implemented in the Basque Country will effectively facilitate gene flow of forest dwelling species at regional scale.     

Landscape genetic analyses reveal fine‐scale effects of forest fragmentation in an insular tropical bird

Within the framework of landscape genetics, resistance surface modelling is particularly relevant to explicitly test competing hypotheses about landscape effects on gene flow. To investigate how fragmentation of tropical forest affects population connectivity in a forest specialist bird species, we optimized resistance surfaces without a priori specification, using least‐cost (LCP) or resistance (IBR) distances. We implemented a two‐step procedure in order (i) to objectively define the landscape thematic resolution (level of detail in classification scheme to describe landscape variables) and spatial extent (area within the landscape boundaries) and then (ii) to test the relative role of several landscape features (elevation, roads, land cover) in genetic differentiation in the Plumbeous Warbler (Setophaga plumbea). We detected a small‐scale reduction of gene flow mainly driven by land cover, with a negative impact of the nonforest matrix on landscape functional connectivity. However, matrix components did not equally constrain gene flow, as their conductivity increased with increasing structural similarity with forest habitat: urban areas and meadows had the highest resistance values whereas agricultural areas had intermediate resistance values. Our results revealed a higher performance of IBR compared to LCP in explaining gene flow, reflecting suboptimal movements across this human‐modified landscape, challenging the common use of LCP to design habitat corridors and advocating for a broader use of circuit theory modelling. Finally, our results emphasize the need for an objective definition of landscape scales (landscape extent and thematic resolution) and highlight potential pitfalls associated with parameterization of resistance surfaces.     

Landscape-level comparison of genetic diversity and differentiation in a small mammal inhabiting different fragmented landscapes of the Brazilian Atlantic Forest

Habitat loss and fragmentation can have detrimental effects on all levels of biodiversity, including genetic variation. Most studies that investigate genetic effects of habitat loss and fragmentation focus on analysing genetic data from a single landscape. However, our understanding of habitat loss effects on landscape-wide patterns of biodiversity would benefit from studies that are based on quantitative comparisons among multiple study landscapes. Here, we use such a landscape-level study design to compare genetic variation in the forest-specialist marsupial Marmosops incanus from four 10,000-hectare Atlantic forest landscapes which differ in the amount of their remaining native forest cover (86, 49, 31, 11 %). Additionally, we used a model selection framework to evaluate the influence of patch characteristics on genetic variation within each landscape. We genotyped 529 individuals with 12 microsatellites to statistically compare estimates of genetic diversity and genetic differentiation in populations inhabiting different forest patches within the landscapes. Our study indicates that before the extinction of the specialist species (here in the 11 % landscape) genetic diversity is significantly reduced in the 31 % landscape, while genetic differentiation is significantly higher in the 49 and 31 % landscapes compared to the 86 % landscape. Results further provide evidence for non-proportional responses of genetic diversity and differentiation to increasing habitat loss, and suggest that local patch isolation impacts gene flow and genetic connectivity only in the 31 % landscape. These results have high relevance for analysing landscape genetic relationships and emphasize the importance of landscape-level study designs for understanding habitat loss effects on all levels of biodiversity.     

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.     

Genetic differentiation and gene flow among populations of the alpine butterfly, Parnassius smintheus, vary with landscape connectivity

Levels of gene flow among populations vary both inter- and intraspecifically, and understanding the ecological bases of variation in levels of gene flow represents an important link between the ecological and evolutionary dynamics of populations. The effects of habitat spatial structure on gene flow have received considerable attention; however, most studies have been conducted at a single spatial scale and without background data on how individual movement is affected by landscape features. We examined the influence of habitat connectivity on inferred levels of gene flow in a high-altitude, meadow-dwelling butterfly, Parnassius smintheus. For this species, we had background data on the effects of landscape structure on both individual movement and on small-scale population genetic differentiation. We compared genetic differentiation and patterns of isolation by distance, based on variation at seven microsatellite loci, among three regions representing two levels of connectivity of high-altitude, nonforested habitats. We found that reduced connectivity of habitats, resulting from more forest cover at high altitudes, was associated with greater genetic differentiation among populations (higher estimated FST), a breakdown of isolation by distance, and overall lower levels of inferred gene flow. These observed differences were consistent with expectations based on our knowledge of the movement behaviour of this species and on previous population genetic analyses conducted at the smaller spatial scale. Our results indicate that the role of gene flow may vary among groups of populations depending on the interplay between individual movement and the structure of the surrounding landscape.     

Using multiple landscape genetic approaches to test the validity of genetic clusters in a species characterized by an isolation‐by‐distance pattern

Bayesian clustering methods are typically used to identify barriers to gene flow, but they are prone to deduce artificial subdivisions in a study population characterized by an isolation‐by‐distance pattern (IbD). Here we analysed the landscape genetic structure of a population of wild boars (Sus scrofa) from south‐western Germany. Two clustering methods inferred the presence of the same genetic discontinuity. However, the population in question was characterized by a strong IbD pattern. While landscape‐resistance modelling failed to identify landscape features that influenced wild boar movement, partial Mantel tests and multiple regression of distance matrices (MRDMs) suggested that the empirically inferred clusters were separated by a genuine barrier. When simulating random lines bisecting the study area, 60% of the unique barriers represented, according to partial Mantel tests and MRDMs, significant obstacles to gene flow. By contrast, the random‐lines simulation showed that the boundaries of the inferred empirical clusters corresponded to the most important genetic discontinuity in the study area. Given the degree of habitat fragmentation separating the two empirical partitions, it is likely that the clustering programs correctly identified a barrier to gene flow. The differing results between the work published here and other studies suggest that it will be very difficult to draw general conclusions about habitat permeability in wild boar from individual studies.     

景观生态学:两栖动物生态学研究的新途径

全球两栖动物正以远超过自然灭绝的高速率灭绝,这与生境丧失和景观破碎化有着直接关系。生境丧失导致两栖动物的生存空间减少,使局部种群消失,而景观破碎化则导致两栖动物种群之间的隔离度增加,不利于动物的繁殖和扩散。但两者往往是同时出现,相互作用。复合种群、景观连接度、景观遗传学及景观模型模拟等理论和方法的发展,为在生境丧失与破碎化景观下两栖动物的种群结构、组成和动态变化研究提供了理论基础和技术方法。同时景观生态学中特别重视研究的尺度,生境破碎化是发生在景观尺度下的生境变化过程,因此对生境破碎化的影响应该从现有的主要集中在斑块尺度和斑块-景观尺度转变到景观尺度上来。     

Dispersal ability and habitat requirements determine landscape‐level genetic patterns in desert aquatic insects

Species occupying the same geographic range can exhibit remarkably different population structures across the landscape, ranging from highly diversified to panmictic. Given limitations on collecting population‐level data for large numbers of species, ecologists seek to identify proximate organismal traits—such as dispersal ability, habitat preference and life history—that are strong predictors of realized population structure. We examined how dispersal ability and habitat structure affect the regional balance of gene flow and genetic drift within three aquatic insects that represent the range of dispersal abilities and habitat requirements observed in desert stream insect communities. For each species, we tested for linear relationships between genetic distances and geographic distances using Euclidean and landscape‐based metrics of resistance. We found that the moderate‐disperser Mesocapnia arizonensis (Plecoptera: Capniidae) has a strong isolation‐by‐distance pattern, suggesting migration–drift equilibrium. By contrast, population structure in the flightless Abedus herberti (Hemiptera: Belostomatidae) is influenced by genetic drift, while gene flow is the dominant force in the strong‐flying Boreonectes aequinoctialis (Coleoptera: Dytiscidae). The best‐fitting landscape model for M. arizonensis was based on Euclidean distance. Analyses also identified a strong spatial scale‐dependence, where landscape genetic methods only performed well for species that were intermediate in dispersal ability. Our results highlight the fact that when either gene flow or genetic drift dominates in shaping population structure, no detectable relationship between genetic and geographic distances is expected at certain spatial scales. This study provides insight into how gene flow and drift interact at the regional scale for these insects as well as the organisms that share similar habitats and dispersal abilities.     

Mechanistic insights into landscape genetic structure of two tropical amphibians using field‐derived resistance surfaces

Conversion of forests to agriculture often fragments distributions of forest species and can disrupt gene flow. We examined effects of prevalent land uses on genetic connectivity of two amphibian species in northeastern Costa Rica. We incorporated data from field surveys and experiments to develop resistance surfaces that represent local mechanisms hypothesized to modify dispersal success of amphibians, such as habitat‐specific predation and desiccation risk. Because time lags can exist between forest conversion and genetic responses, we evaluated landscape effects using land‐cover data from different time periods. Populations of both species were structured at similar spatial scales but exhibited differing responses to landscape features. Litter frog population differentiation was significantly related to landscape resistances estimated from abundance and experiment data. Model support was highest for experiment‐derived surfaces that represented responses to microclimate variation. Litter frog genetic variation was best explained by contemporary landscape configuration, indicating rapid population response to land‐use change. Poison frog genetic structure was strongly associated with geographic isolation, which explained up to 45% of genetic variation, and long‐standing barriers, such as rivers and mountains. However, there was also partial support for abundance‐ and microclimate response‐derived resistances. Differences in species responses to landscape features may be explained by overriding effects of population size on patterns of differentiation for poison frogs, but not litter frogs. In addition, pastures are likely semi‐permeable to poison frog gene flow because the species is known to use pastures when remnant vegetation is present, but litter frogs do not. Ongoing reforestation efforts will probably increase connectivity in the region by increasing tree cover and reducing area of pastures.     

Anthropogenic Habitats Facilitate Dispersal of an Early Successional Obligate: Implications for Restoration of an Endangered Ecosystem

Landscape modification and habitat fragmentation disrupt the connectivity of natural landscapes, with major consequences for biodiversity. Species that require patchily distributed habitats, such as those that specialize on early successional ecosystems, must disperse through a landscape matrix with unsuitable habitat types. We evaluated landscape effects on dispersal of an early successional obligate, the New England cottontail (Sylvilagus transitionalis). Using a landscape genetics approach, we identified barriers and facilitators of gene flow and connectivity corridors for a population of cottontails in the northeastern United States. We modeled dispersal in relation to landscape structure and composition and tested hypotheses about the influence of habitat fragmentation on gene flow. Anthropogenic and natural shrubland habitats facilitated gene flow, while the remainder of the matrix, particularly development and forest, impeded gene flow. The relative influence of matrix habitats differed between study areas in relation to a fragmentation gradient. Barrier features had higher explanatory power in the more fragmented site, while facilitating features were important in the less fragmented site. Landscape models that included a simultaneous barrier and facilitating effect of roads had higher explanatory power than models that considered either effect separately, supporting the hypothesis that roads act as both barriers and facilitators at all spatial scales. The inclusion of LiDAR-identified shrubland habitat improved the fit of our facilitator models. Corridor analyses using circuit and least cost path approaches revealed the importance of anthropogenic, linear features for restoring connectivity between the study areas. In fragmented landscapes, human-modified habitats may enhance functional connectivity by providing suitable dispersal conduits for early successional specialists.     

Population structure and landscape genetics in the endangered subterranean rodent Ctenomys porteousi

In order to devise adequate conservation and management strategies for endangered species, it is important to incorporate a reliable understanding of its spatial population structure, detecting the existence of demographic partitions throughout its geographical range and characterizing the distribution of its genetic diversity. Moreover, in species that occupy fragmented habitats it is essential to know how landscape characteristics may affect the genetic connectivity among populations. In this study we use eight microsatellite markers to analyze population structure and gene flow patterns in the complete geographic range of the endangered rodent Ctenomys porteousi. Also, we use landscape genetics approaches to evaluate the effects of landscape configuration on the genetic connectivity among populations. In spite of geographical proximity of the sampling sites (8–27 km between the nearest sites) and the absence of marked barriers to individual movement, strong population structure and low values of gene flow were observed. Genetic differentiation among sampling sites was consistent with a simple model of isolation by distance, where peripheral areas showed higher population differentiation than those sites located in the central area of the species’ distribution. Landscape genetics analysis suggested that habitat fragmentation at regional level has affected the distribution of genetic variation among populations. The distance of sampling sites to areas of the landscape having higher habitat connectivity was the environmental factor most strongly related to population genetic structure. In general, our results indicate strong genetic structure in C. porteousi, even at a small spatial scale, and suggest that habitat fragmentation could increase the population differentiation.     

Urbanization reduces genetic connectivity in bobcats (Lynx rufus) at both intra– and interpopulation spatial scales

Urbanization is a major factor driving habitat fragmentation and connectivity loss in wildlife. However, the impacts of urbanization on connectivity can vary among species and even populations due to differences in local landscape characteristics, and our ability to detect these relationships may depend on the spatial scale at which they are measured. Bobcats (Lynx rufus) are relatively sensitive to urbanization and the status of bobcat populations is an important indicator of connectivity in urban coastal southern California. We genotyped 271 bobcats at 13,520 SNP loci to conduct a replicated landscape resistance analysis in five genetically distinct populations. We tested urban and natural factors potentially influencing individual connectivity in each population separately, as well as study–wide. Overall, landscape genomic effects were most frequently detected at the study–wide spatial scale, with urban land cover (measured as impervious surface) having negative effects and topographic roughness having positive effects on gene flow. The negative effect of urban land cover on connectivity was also evident when populations were analyzed separately despite varying substantially in spatial area and the proportion of urban development, confirming a pervasive impact of urbanization largely independent of spatial scale. The effect of urban development was strongest in one population where stream habitat had been lost to development, suggesting that riparian corridors may help mitigate reduced connectivity in urbanizing areas. Our results demonstrate the importance of replicating landscape genetic analyses across populations and considering how landscape genetic effects may vary with spatial scale and local landscape structure.     

The influence of landscape on gene flow in the eastern massasauga rattlesnake (Sistrurus c. catenatus): insight from computer simulations

Understanding how gene flow shapes contemporary population structure requires the explicit consideration of landscape composition and configuration. New landscape genetic approaches allow us to link such heterogeneity to gene flow within and among populations. However, the attribution of cause is difficult when landscape features are spatially correlated, or when genetic patterns reflect past events. We use spatial Bayesian clustering and landscape resistance analysis to identify the landscape features that influence gene flow across two regional populations of the eastern massasauga rattlesnake, Sistrurus c. catenatus. Based on spatially explicit simulations, we inferred how habitat distribution modulates gene flow and attempted to disentangle the effects of spatially confounded landscape features. We found genetic clustering across one regional landscape but not the other, and also local differences in the effect of landscape on gene flow. Beyond the effects of isolation‐by‐distance, water bodies appear to underlie genetic differentiation among individuals in one regional population. Significant effects of roads were additionally detected locally, but these effects are possibly confounded with the signal of water bodies. In contrast, we found no signal of isolation‐by‐distance or landscape effects on genetic structure in the other regional population. Our simulations imply that these local differences have arisen as a result of differences in population density or tendencies for juvenile rather than adult dispersal. Importantly, our simulations also demonstrate that the ability to detect the consequences of contemporary anthropogenic landscape features (e.g. roads) on gene flow may be compromised when long‐standing natural features (e.g. water bodies) co‐exist on the landscape.     

Landscape genetics in the subterranean rodent <Emphasis Type="Italic">Ctenomys</Emphasis> “<Emphasis Type="Italic">chasiquensis</Emphasis>” associated with highly disturbed habitats from the southeastern Pampas region,Argentina

Studies of genetic differentiation in fragmented environments help us to identify those landscape features that most affect gene flow and dispersal patterns. Particularly, the assessment of the relative significance of intrinsic biological and environmental factors affecting the genetic structure of populations becomes crucial. In this work, we assess the current dispersal patterns and population structure of Ctenomys “chasiquensis”, a vulnerable and endemic subterranean rodent distributed on a small area in Central Argentina, using 9 polymorphic microsatellite loci. We use landscape genetics approaches to assess the relationship between genetic connectivity among populations and environmental attributes. Our analyses show that populations of C. “chasiquensis” are moderately to highly structured at a regional level. This pattern is most likely the outcome of substantial gene flow on the more homogeneous sand dune habitat of the Northwest of its distributional range, in conjunction with an important degree of isolation of eastern and southwestern populations, where the optimal habitat is surrounded by a highly fragmented landscape. Landscape genetics analysis suggests that habitat quality and longitude were the environmental factors most strongly associated with genetic differentiation/uniqueness of populations. In conclusion, our results indicate an important genetic structure in this species, even at a small spatial scale, suggesting that contemporary habitat fragmentation increases population differentiation.     

Population genetic structure and connectivity in the endangered Ethiopian mountain Nyala (Tragelaphus buxtoni): recommending dispersal corridors for future conservation

Habitat fragmentation is an increasing threat to wildlife species across the globe and it has been predicted that future biodiversity will decrease rapidly without the intervention of scientifically-based management. In this study we have applied a landscape genetics approach to suggest a network design that will maintain connectivity among populations of the endangered mountain Nyala (Tragelaphus buxtoni) in the fragmented highlands of Ethiopia. DNA was obtained non-invasively from 328 individuals and genetic population structure and gene flow were estimated using 12 microsatellite markers. In addition, a 475-bp segment of the mitochondrial control region was sequenced for 132 individuals. Potential dispersal corridors were determined from least-cost path analysis based on a habitat suitability map. The genetic data indicated limited gene flow between the sampled mountain Nyala populations of the Bale Massif and the Arsi Massif. The genetic differentiation observed among five sampling areas of the Bale Massif followed a pattern of isolation by distance. We detected no impact of habitat resistance on the gene flow. In the future, however, the current expanding human population in the highlands of Ethiopia may reduce the current mountain Nyala habitat and further limit migration. Hence, maintaining habitat connectivity and facilitating survival of stepping-stone populations will be important for the future conservation of the species. The approach used here may also be useful for the study and conservation of other wildlife species inhabiting areas of increasing human encroachment.     

Isolation by distance,resistance and/or clusters? Lessons learned from a forest‐dwelling carnivore inhabiting a heterogeneous landscape

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.