Landscape genetics of the blotched tiger salamander (Ambystoma tigrinum melanostictum)

The field of landscape genetics has great potential to identify habitat features that influence population genetic structure. To identify landscape correlates of genetic differentiation in a quantitative fashion, we developed a novel approach using geographical information systems analysis. We present data on blotched tiger salamanders (Ambystoma tigrinum melanostictum) from 10 sites across the northern range of Yellowstone National Park in Montana and Wyoming, USA. We used eight microsatellite loci to analyse population genetic structure. We tested whether landscape variables, including topographical distance, elevation, wetland likelihood, cover type and number of river and stream crossings, were correlated with genetic subdivision (F(ST)). We then compared five hypothetical dispersal routes with a straight-line distance model using two approaches: (i) partial Mantel tests using Akaike's information criterion scores to evaluate model robustness and (ii) the BIOENV procedure, which uses a Spearman rank correlation to determine the combination of environmental variables that best fits the genetic data. Overall, gene flow appears highly restricted among sites, with a global F(ST) of 0.24. While there is a significant isolation-by-distance pattern, incorporating landscape variables substantially improved the fit of the model (from an r2 of 0.3 to 0.8) explaining genetic differentiation. It appears that gene flow follows a straight-line topographic route, with river crossings and open shrub habitat correlated with lower F(ST) and thus, decreased differentiation, while distance and elevation difference appear to increase differentiation. This study demonstrates a general approach that can be used to determine the influence of landscape variables on population genetic structure.     

Landscape genetics and least-cost path analysis reveal unexpected dispersal routes in the California tiger salamander (Ambystoma californiense)

A major goal of landscape genetics is to understand how landscapes structure genetic variation in natural populations. However, landscape genetics still lacks a framework for quantifying the effects of landscape features, such as habitat type, on realized gene flow. Here, we present a methodology for identifying the costs of dispersal through different habitats for the California tiger salamander ( Ambystoma californiense ), an endangered species restricted to grassland/vernal pool habitat mosaics. We sampled larvae from all 16 breeding ponds in a geographically restricted area of vernal pool habitat at the Fort Ord Natural Reserve, Monterey County, California. We estimated between-pond gene flow using 13 polymorphic microsatellite loci and constructed GIS data layers of habitat types in our study area. We then used least-cost path analysis to determine the relative costs of movement through each habitat that best match rates of gene flow measured by our genetic data. We identified four measurable rates of gene flow between pairs of ponds, with between 10.5% and 19.9% of larvae having immigrant ancestry. Although A. californiense is typically associated with breeding ponds in grassland habitat, we found that dispersal through grassland is nearly twice as costly as dispersal through chaparral and that oak woodland is by far the most costly habitat to traverse. With the increasing availability of molecular resources and GIS data, we anticipate that these methods could be applied to a broad range of study systems, particularly those with cryptic life histories that make direct observation of movement challenging.     

The effect of cost surface parameterization on landscape resistance estimates

A cost or resistance surface is a representation of a landscape's permeability to animal movement or gene flow and is a tool for measuring functional connectivity in landscape ecology and genetics studies. Parameterizing cost surfaces by assigning weights to different landscape elements has been challenging however, because true costs are rarely known; thus, expert opinion is often used to derive relative weights. Assigning weights would be made easier if the sensitivity of different landscape resistance estimates to relative costs was known. We carried out a sensitivity analysis of three methods to parameterize a cost surface and two models of landscape permeability: least cost path and effective resistance. We found two qualitatively different responses to varying cost weights: linear and asymptotic changes. The most sensitive models (i.e. those leading to linear change) were accumulated least cost and effective resistance estimates on a surface coded as resistance (i.e. where high-quality elements were held constant at a low-value, and low-quality elements were varied at higher values). All other cost surface scenarios led to asymptotic change. Developing a cost surface that produces a linear response of landscape resistance estimates to cost weight variation will improve the accuracy of functional connectivity estimates, especially when cost weights are selected through statistical model fitting procedures. On the other hand, for studies where cost weights are unknown and model selection is not being used, methods where resistance estimates vary asymptotically with cost weights may be more appropriate, because of their relative insensitivity to parameterization.     

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.     

Population structure of Columbia spotted frogs (Rana luteiventris) is strongly affected by the landscape

Landscape features such as mountains, rivers, and ecological gradients may strongly affect patterns of dispersal and gene flow among populations and thereby shape population dynamics and evolutionary trajectories. The landscape may have a particularly strong effect on patterns of dispersal and gene flow in amphibians because amphibians are thought to have poor dispersal abilities. We examined genetic variation at six microsatellite loci in Columbia spotted frogs (Rana luteiventris) from 28 breeding ponds in western Montana and Idaho, USA, in order to investigate the effects of landscape structure on patterns of gene flow. We were particularly interested in addressing three questions: (i) do ridges act as barriers to gene flow? (ii) is gene flow restricted between low and high elevation ponds? (iii) does a pond equal a ‘randomly mating population’ (a deme)? We found that mountain ridges and elevational differences were associated with increased genetic differentiation among sites, suggesting that gene flow is restricted by ridges and elevation in this species. We also found that populations of Columbia spotted frogs generally include more than a single pond except for very isolated ponds. There was also evidence for surprisingly high levels of gene flow among low elevation sites separated by large distances. Moreover, genetic variation within populations was strongly negatively correlated with elevation, suggesting effective population sizes are much smaller at high elevation than at low elevation. Our results show that landscape features have a profound effect on patterns of genetic variation in Columbia spotted frogs.     

Climate variables explain neutral and adaptive variation within salmonid metapopulations: the importance of replication in landscape genetics

Understanding how environmental variation influences population genetic structure is important for conservation management because it can reveal how human stressors influence population connectivity, genetic diversity and persistence. We used riverscape genetics modelling to assess whether climatic and habitat variables were related to neutral and adaptive patterns of genetic differentiation (population‐specific and pairwise F_ST) within five metapopulations (79 populations, 4583 individuals) of steelhead trout (Oncorhynchus mykiss) in the Columbia River Basin, USA. Using 151 putatively neutral and 29 candidate adaptive SNP loci, we found that climate‐related variables (winter precipitation, summer maximum temperature, winter highest 5% flow events and summer mean flow) best explained neutral and adaptive patterns of genetic differentiation within metapopulations, suggesting that climatic variation likely influences both demography (neutral variation) and local adaptation (adaptive variation). However, we did not observe consistent relationships between climate variables and F_ST across all metapopulations, underscoring the need for replication when extrapolating results from one scale to another (e.g. basin‐wide to the metapopulation scale). Sensitivity analysis (leave‐one‐population‐out) revealed consistent relationships between climate variables and F_ST within three metapopulations; however, these patterns were not consistent in two metapopulations likely due to small sample sizes (N = 10). These results provide correlative evidence that climatic variation has shaped the genetic structure of steelhead populations and highlight the need for replication and sensitivity analyses in land and riverscape genetics.     

Landscape genetics of California mule deer (Odocoileus hemionus): the roles of ecological and historical factors in generating differentiation

Landscape genetics is an emerging discipline that utilizes environmental and historical data to understand geographic patterns of genetic diversity. Niche modelling has added a new dimension to such efforts by allowing species–environmental associations to be projected into the past so that hypotheses about historical vicariance can be generated and tested independently with genetic data. However, previous approaches have primarily utilized DNA sequence data to test inferences about historical isolation and may have missed very recent episodes of environmentally mediated divergence. We type 15 microsatellite loci in California mule deer and identify five genetic groupings through a Structure analysis that are also well predicted by environmental data. We project the niches of these five deer ecotypes to the last glacial maximum (LGM) and show they overlap to a much greater extent than today, suggesting that vicariance associated with the LGM cannot explain the present-day genetic patterns. Further, we analyse mitochondrial DNA (mtDNA) sequence trees to search for evidence of historical vicariance and find only two well-supported clades. A coalescence-based analysis of mtDNA data shows that the genetic divergence of the mule deer genetic clusters in California is recent and appears to be mediated by ecological factors. The importance of environmental factors in explaining the genetic diversity of California mule deer is unexpected given that they are highly mobile species and have a broad habitat distribution. Geographic differences in the timing of reproduction and peak vegetation as well as habitat choice reflecting natal origin may explain the persistence of genetic subdivision.     

Molecular road ecology: exploring the potential of genetics for investigating transportation impacts on wildlife

Transportation infrastructures such as roads, railroads and canals can have major environmental impacts. Ecological road effects include the destruction and fragmentation of habitat, the interruption of ecological processes and increased erosion and pollution. Growing concern about these ecological road effects has led to the emergence of a new scientific discipline called road ecology. The goal of road ecology is to provide planners with scientific advice on how to avoid, minimize or mitigate negative environmental impacts of transportation. In this review, we explore the potential of molecular genetics to contribute to road ecology. First, we summarize general findings from road ecology and review studies that investigate road effects using genetic data. These studies generally focus only on barrier effects of roads on local genetic diversity and structure and only use a fraction of available molecular approaches. Thus, we propose additional molecular applications that can be used to evaluate road effects across multiple scales and dimensions of the biodiversity hierarchy. Finally, we make recommendations for future research questions and study designs that would advance molecular road ecology. Our review demonstrates that molecular approaches can substantially contribute to road ecology research and that interdisciplinary, long-term collaborations will be particularly important for realizing the full potential of molecular road ecology.     

Regional gene flow and population structure of the wind-dispersed plant species Hypochaeris radicata (Asteraceae) in an agricultural landscape

Using microsatellites, we investigated population structure and gene flow of the short-lived, wind-dispersed plant species Hypochaeris radicata in a fragmented agricultural landscape where more than 99% of the nutrient-poor grasslands have disappeared over the last century. We sampled populations in the few remaining high density populations in conservation areas, as well as individuals that occurred, with lower densities, in linear landscape elements, at two spatial scales. In a re-inventory of the landscape, after 3 years, both extinctions and colonizations of populations were observed. Contrary to expectations, no differences in genetic diversity between high and low density populations were observed. Both types of populations had relatively high levels of diversity. Overall genetic differentiation (theta) was 0.04 and significantly different from zero (P < 0.01). A significant isolation-by-distance pattern was found when all populations were simultaneously analysed (r = 0.24, P = 0.013). Isolation by distance was (marginally) significant at the small scale (r = 0.32, P = 0.06), whereas nonsignificant at the large spatial scale (r = -0.05, P = 0.66). A maximization-of-explained-variance procedure resulted in a threshold distance of 3.5 km above which populations were effectively genetically isolated. An additional partial exclusion Bayesian-based assignment test showed that overall 32.3% of the individuals were assigned to their population of origin, 48% were assigned to another population in the area and 19.7% were not assigned. Together, these results suggest high levels of gene flow. Seed dispersal contributes to the observed gene flow up to several hundred metres, which is higher than previously modelled using aerodynamic models on seed dispersal of H. radicata. We discuss the consequences of these results for an evaluation of the probability of persistence of this species in the fragmented landscape.     

Conservation genetics and demographic history of the endangered Cape Fear shiner (Notropis mekistocholas)

We examined allelic variation at 22 nuclear-encoded markers (21 microsatellites and one anonymous locus) and mitochondrial (mt)DNA in two geographical samples of the endangered cyprinid fish Notropis mekistocholas (Cape Fear shiner). Genetic diversity was relatively high in comparison to other endangered vertebrates, and there was no evidence of small population effects despite the low abundance reported for the species. Significant heterogeneity (following Bonferroni correction) in allele distribution at three microsatellites and in haplotype distribution in mtDNA was detected between the two localities. This heterogeneity may be due to reduced gene flow caused by a dam built in the early 1900 s. Bayesian coalescent analysis of microsatellite variation indicated that effective population size of Cape Fear shiners has declined in recent times (11-25 435 years ago, with highest posterior probabilities between 126 and 2007 years ago) by one-two orders of magnitude, consistent with the observed decline in abundance of the species. A decline in effective size was not indicated by analysis of mtDNA, where sequence polymorphism appeared to carry the signature of an older expansion phase that dated to the Pleistocene ( approximately 12 700 > 1 million years ago). Cape Fear shiners thus appear to have undergone an expansion phase following a glacial cycle but to have declined significantly in more recent times. These results suggest that rapidly evolving markers such as microsatellites may constitute a suitable tool when inferring recent demographic dynamics of populations.     

Fragmentation shapes nest density and social structure but not genetic diversity of Temnothorax crassispinus (Formicidae)

Human activities affect biodiversity by reducing the area of habitats, altering their shape, and increasing their isolation. Ants are particularly sensitive to habitat fragmentation, as it may locally change abiotic conditions, the availability of food and nest sites, the abundance of mutualists, competitors and predators, and also restrict gene flow between patches. As a result, the genetic population and colony structure of ants is expected to show signs of fragmentation. In the present study, we investigated the impact of fragmentation on the ant Temnothorax crassispinus in 45 forest patches across the Franconian Jura, Germany. Based on 283 colonies, of which 156 were genetically analyzed, we evidenced the presence of two putative distinct genetic clusters in the study area. Both the nest densities and the presence of queen were impacted by the number of adjacent forest patches within 400 m around the focal patch, but neither by patch shape nor patch size. We could not detect any effect of fragmentation on the genetic diversity, probably because the high dispersal abilities of T. crassispinus counterbalance any detrimental genetic consequences of fragmentation. Nevertheless, fragmentation still impacts the species density as well as the social structure of its colonies. Further investigations regarding the drivers of occurrence at a finer spatial scale might clarify the role of edge effects on the occurrence of this species.     

景观遗传学原理及其在生境片断化遗传效应研究中的应用

景观遗传学是近年来在景观生态学和种群遗传学之间形成的一个交叉领域,强调景观的组成、空间构型和环境梯度对基因流、种群遗传空间结构和局域种群适应的影响。景观遗传学尚未成为一门独立的学科,其理论基础主要来自分子遗传学、种群生物学和景观生态学。现代分子遗传标记技术、遥感和GIS支持下的景观分析和空间统计方法的综合运用是景观遗传学主要研究途径。系统介绍了景观遗传学的基础概念,关键科学问题,基本理论框架,及其与相邻研究领域的关系,综述了景观遗传学最为关注的现实课题——景观碎裂化的种群遗传效应的研究进展,主要涉及生境片断化的遗传效应、不同属性的物种响应、以及生境片断化过程的选择作用等方面。通过采取一种跨尺度的视角,景观遗传学研究显著深化了关于景观碎裂化对生物多样性影响的理解。     

The influence of contemporary and historic landscape features on the genetic structure of the sand dune endemic,Cirsium pitcheri (Asteraceae)

Narrow endemics are at risk from climate change because of their restricted habitat preferences, lower colonization ability and dispersal distances. Landscape genetics combines new tools and analyses that allow us to test how both past and present landscape features have facilitated or hindered previous range expansion and local migration patterns, and thereby identifying potential limitations to future range shifts. We have compared current and historic habitat corridors in Cirsium pitcheri, an endemic of the linear dune ecosystem of the Great Lakes, to determine the relative contributions of contemporary migration and post-glacial range expansion on genetic structure. We used seven microsatellite loci to characterize the genetic structure for 24 populations of Cirsium pitcheri, spanning the center to periphery of the range. We tested genetic distance against different measures of geographic distance and landscape permeability, based on contemporary and historic landscape features. We found moderate genetic structure (Fst=0.14), and a north–south pattern to the distribution of genetic diversity and inbreeding, with northern populations having the highest diversity and lowest levels of inbreeding. High allelic diversity, small average pairwise distances and mixed genetic clusters identified in Structure suggest that populations in the center of the range represent the point of entry to the Lake Michigan and a refugium of diversity for this species. A strong association between genetic distances and lake-level changes suggests that historic lake fluctuations best explain the broad geographic patterns, and sandy habitat best explains local patterns of movement.     

Different landscape effects on the genetic structure of two broadly distributed woody legumes,Acacia salicina and A. stenophylla (Fabaceae)

Restoring degraded landscapes has primarily focused on re‐establishing native plant communities. However, little is known with respect to the diversity and distribution of most key revegetation species or the environmental and anthropogenic factors that may affect their demography and genetic structure. In this study, we investigated the genetic structure of two widespread Australian legume species (Acacia salicina and Acacia stenophylla) in the Murray–Darling Basin (MDB), a large agriculturally utilized region in Australia, and assessed the impact of landscape structure on genetic differentiation. We used AFLP genetic data and sampled a total of 28 A. salicina and 30 A. stenophylla sampling locations across southeastern Australia. We specifically evaluated the importance of four landscape features: forest cover, land cover, water stream cover, and elevation. We found that both species had high genetic diversity (mean percentage of polymorphic loci, 55.1% for A. salicina versus. 64.3% for A. stenophylla) and differentiation among local sampling locations (A. salicina: Φ_PT = 0.301, 30%; A. stenophylla: Φ_PT = 0.235, 23%). Population structure analysis showed that both species had high levels of structure (6 clusters each) and admixture in some sampling locations, particularly A. stenophylla. Although both species have a similar geographic range, the drivers of genetic connectivity for each species were very different. Genetic variation in A. salicina seems to be mainly driven by geographic distance, while for A. stenophylla, land cover appears to be the most important factor. This suggests that for the latter species, gene flow among populations is affected by habitat fragmentation. We conclude that these largely co‐occurring species require different management actions to maintain population connectivity. We recommend active management of A. stenophylla in the MDB to improve gene flow in the adversity of increasing disturbances (e.g., droughts) driven by climate change and anthropogenic factors.     

Molecular ecology of the Neotropical otter (Lontra longicaudis): non‐invasive sampling yields insights into local population dynamics

Non‐invasive genetic analysis has been frequently employed to estimate ecological and population parameters for many secretive and/or threatened species. However, Neotropical carnivores have so far been scarcely targeted by such studies. The Neotropical otter (Lontra longicaudis) is a poorly‐known species for which local levels of genetic diversity and demographic parameters are virtually absent. We employed non‐invasive sampling and amplification of microsatellite loci to investigate population size and density, spatial organization, and relatedness of a wild Neotropical otter population in an Atlantic forest area in southern Brazil. We directly identified 28 individuals and estimate a rather high population density at the study site. Spatial organization analysis indicated that male cumulative displacement was higher than that of females, with the latter sex showing evidence of philopatric behaviour. Also, the reconstruction of genealogical relationships suggests that spatial organization in this otter appears to be influenced by relatedness. By allowing the testing of specific hypothesis targeting these issues, our results provided important glimpses into the Neotropical otter's population biology. Moreover, the findings of the present study reaffirm the power of non‐invasive genetics to investigate the biology of this elusive species, and open up new avenues for ecological and demographic studies of other Neotropical carnivores. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 932–948.     

Contemporary gene flow and the spatio-temporal genetic structure of subdivided newt populations (Triturus cristatus, T. marmoratus)

Gene flow and drift shape the distribution of neutral genetic diversity in metapopulations, but their local rates are difficult to quantify. To identify gene flow between demes as distinct from individual migration, we present a modified Bayesian method to genetically test for descendants between an immigrant and a resident in a nonmigratory life stage. Applied to a metapopulation of pond-breeding European newts (Triturus cristatus, T. marmoratus) in western France, the evidence for gene flow was usually asymmetric and, for demes of known census size (N), translated into maximally seven reproducing immigrants. Temporal sampling also enabled the joint estimation of the effective demic population size (Ne) and the immigration rate m (including nonreproductive individuals). Ne ranged between 4.1 and 19.3 individuals, Ne/N ranged between 0.05 and 0.65 and always decreased with N; m was estimated as 0.19-0.63, and was possibly biased upwards. We discuss how genotypic data can reveal fine-scale demographic processes with important microevolutionary implications.     

Population structure and gene flow reversals in Atlantic salmon (Salmo salar) over contemporary and long-term temporal scales: effects of population size and life history

Metapopulation dynamics are increasingly invoked in management and conservation of endangered species. In this context, asymmetrical gene flow patterns can be density dependent, with migration occurring mainly from larger into smaller populations, which may depend on it for their persistence. Using genetic markers, such patterns have recently been documented for various organisms including salmonids, suggesting this may be a more general pattern. However, metapopulation theory does not restrict gene flow asymmetry to 'source-sink' structures, nor need these patterns be constant over longer evolutionary timescales. In anadromous salmonids, gene flow can be expected to be shaped by various selective pressures underlying homing and dispersal ('straying') behaviours. The relative importance of these selective forces will vary spatially and for populations of different census size. Furthermore, the consequences of life-history variation among populations for dispersal and hence gene flow remain poorly quantified. We examine population structure and connectivity in Atlantic salmon (Salmo salar L.) from Newfoundland and Labrador, a region where populations of this species are relatively pristine. Using genetic variation at 13 microsatellite loci from samples (N=1346) collected from a total of 20 rivers, we examine connectivity at several regional and temporal scales and test the hypothesis that the predominant direction of gene flow is from large into small populations. We reject this hypothesis and find that the directionality of migration is affected by the temporal scale over which gene flow is assessed. Whereas large populations tend to function as sources of dispersal over contemporary timescales, such patterns are often changed and even reversed over evolutionary, coalescent-derived timescales. These patterns of population structure furthermore vary between different regions and are compatible with demographic and life-history attributes. We find no evidence for sex-biased dispersal underlying gene flow asymmetry. Our findings caution against generalizations concerning the directionality of gene flow in Atlantic salmon and emphasize the need for detailed regional study, if such information is to be meaningfully applied in conservation and management of salmonids.     

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.     

Isolation and characterization of microsatellite loci from the coppertail skink (Ctenotus taeniolatus)

We report on the isolation and characterization of eight microsatellite markers for the coppertail skink (Ctenotus taeniolatus). From a sample of 27 individuals, the number of alleles per locus ranged from seven to 13 and observed and expected heterozygosities ranged from 0.714 to 0.818 and from 0.738 to 0.899, respectively. These loci will be used to assess anthropogenic disturbance on coppertail skink populations. These are the first microsatellites reported for the genus Ctenotus, despite being the most speciose genus of lizards in Australia.     

Landscape effects on the contemporary genetic structure of Ruffed Grouse (Bonasa umbellus) populations

The amount of dispersal that occurs among populations can be limited by landscape heterogeneity, which is often due to both natural processes and anthropogenic activity leading to habitat loss or fragmentation. Understanding how populations are structured and mapping existing dispersal corridors among populations is imperative to both determining contemporary forces mediating population connectivity, and informing proper management of species with fragmented populations. Furthermore, the contemporary processes mediating gene flow across heterogeneous landscapes on a large scale are understudied, particularly with respect to widespread species. This study focuses on a widespread game bird, the Ruffed Grouse (Bonasa umbellus), for which we analyzed samples from the western extent of the range. Using three types of genetic markers, we uncovered multiple factors acting in concert that are responsible for mediating contemporary population connectivity in this species. Multiple genetically distinct groups were detected; microsatellite markers revealed six groups, and a mitochondrial marker revealed four. Many populations of Ruffed Grouse are genetically isolated, likely by macrogeographic barriers. Furthermore, the addition of landscape genetic methods not only corroborated genetic structure results, but also uncovered compelling evidence that dispersal resistance created by areas of unsuitable habitat is the most important factor mediating population connectivity among the sampled populations. This research has important implications for both our study species and other inhabitants of the early successional forest habitat preferred by Ruffed Grouse. Moreover, it adds to a growing body of evidence that isolation by resistance is more prevalent in shaping population structure of widespread species than previously thought.