Inferring Population Genetic Structure in Widely and Continuously Distributed Carnivores: The Stone Marten (Martes foina) as a Case Study

Large-scale assessment of genetic structure to assess risk of populations of a large herbivore to disease

Chronic wasting disease (CWD) can spread among cervids by direct and indirect transmission, the former being more likely in emerging areas. Identifying subpopulations allows the delineation of focal areas to target for intervention. We aimed to assess the population structure of white-tailed deer (Odocoileus virginianus) in the northeastern United States at a regional scale to inform managers regarding gene flow throughout the region. We genotyped 10 microsatellites in 5701 wild deer samples from Maryland, New York, Ohio, Pennsylvania, and Virginia. We evaluated the distribution of genetic variability through spatial principal component analysis and inferred genetic structure using non-spatial and spatial Bayesian clustering algorithms (BCAs). We simulated populations representing each inferred wild cluster, wild deer in each state and each physiographic province, total wild population, and a captive population. We conducted genetic assignment tests using these potential sources, calculating the probability of samples being correctly assigned to their origin. Non-spatial BCA identified two clusters across the region, while spatial BCA suggested a maximum of nine clusters. Assignment tests correctly placed deer into captive or wild origin in most cases (94%), as previously reported, but performance varied when assigning wild deer to more specific origins. Assignments to clusters inferred via non-spatial BCA performed well, but efficiency was greatly reduced when assigning samples to clusters inferred via spatial BCA. Differences between spatial BCA clusters are not strong enough to make assignment tests a reliable method for inferring the geographic origin of deer using 10 microsatellites. However, the genetic distinction between clusters may indicate natural and anthropogenic barriers of interest for management.

Genetic diversity and population structure of the Western European hedgehog, Erinaceus europaeus: conservation status of populations in the Iberian Peninsula

Anthropogenic habitat fragmentation and roadkill mortality are considered important threats to European hedgehogs. Habitat fragmentation isolates hedgehog populations and, as a consequence, reduces their genetic diversity and leads the populations to vulnerable situations. The hedgehog populations in the Iberian Peninsula represent the southern limit of the species. We used microsatellite markers to estimate the genetic diversity and population structure of Erinaceus europaeus on the Iberian Peninsula. The obtained results indicated the presence of two differentiated groups, north-western and north-eastern, which coincided with the distribution of the two phylogeographic mitochondrial lineages described in the Peninsula. Moreover, in the north-eastern group, three genetically different clusters (Girona, Central Catalonia and Zoo) were identified. The highest genetic diversity (Hs = 0.696) was detected in the north-western region. Significant genetic differentiation (FST range = 0.072–0.224) was found among the clusters, indicating that these groups are well differentiated and present low gene flow. We concluded that the north-western group is genetically stable, whereas in the north-eastern region, despite some contact among groups, some populations are isolated and vulnerable.

Intact landscape promotes gene flow and low genetic structuring in the threatened Eastern Massasauga Rattlesnake

Genetic structuring of wild populations is dependent on environmental, ecological, and life-history factors. The specific role environmental context plays in genetic structuring is important to conservation practitioners working with rare species across areas with varying degrees of fragmentation. We investigated fine-scale genetic patterns of the federally threatened Eastern Massasauga Rattlesnake (Sistrurus catenatus) on a relatively undisturbed island in northern Michigan, USA. This species often persists in habitat islands throughout much of its distribution due to extensive habitat loss and distance-limited dispersal. We found that the entire island population exhibited weak genetic structuring with spatially segregated variation in effective migration and genetic diversity. The low level of genetic structuring contrasts with previous studies in the southern part of the species' range at comparable fine scales (~7 km), in which much higher levels of structuring were documented. The island population's genetic structuring more closely resembles that of populations from Ontario, Canada, that occupy similarly intact habitats. Intrapopulation variation in effective migration and genetic diversity likely corresponds to the presence of large inland lakes acting as barriers and more human activity in the southern portion of the island. The observed genetic structuring in this intact landscape suggests that the Eastern Massasauga is capable of sufficient interpatch movements to reduce overall genetic structuring and colonize new habitats. Landscape mosaics with multiple habitat patches and localized barriers (e.g., large water bodies or roads) will promote gene flow and natural colonization for this declining species.

Spatial ecology of the stone marten in an Alpine area: combining camera-trapping and genetic surveys

A species’ potential distribution can be modelled adequately only if no factor other than habitat availability affects its occurrences. Space use by stone marten Martes foina is likely to be affected by interspecific competition with the strictly related pine marten Martes martes, the latter being able to outcompete the first species in forested habitats. Hence, to point out the environmental factors which determine the distribution and density of the stone marten, a relatively understudied mesocarnivore, we applied two non-invasive survey methods, camera-trapping and faecal-DNA based genetic analysis, in an Alpine area where the pine marten was deemed to be absent (Val Grande National Park N Italy). Camera trapping was conducted from October 2014 to November 2015, using up to 27 cameras. Marten scats were searched for between July and November 2015 and, to assess density, in spring 2017. Species identification was accomplished by a PCR-RFLP method, while 17 autosomal microsatellites were used for individual identification. The stone marten occurred in all available habitats (83% of trapping sites and 73.2% of scats); nonetheless, habitat suitability, as assessed using MaxEnt, depended on four major land cover variables—rocky grasslands, rocks and debris, beech forests and chestnut forests—, martens selecting forests and avoiding open rocky areas. Sixteen individuals were identified, of which 14 related to each other, possibly forming six different groups. Using capwire estimators, density was assessed as 0.95 (0.7–1.3) ind/km2. In the study area, the widespread stone marten selected forested areas, attaining density values like those reported for the pine marten in northern Europe and suggesting that patterns of habitat selection may depend on the relative abundance of the two competing martens.

Fine-scale landscape genetics unveiling contemporary asymmetric movement of red panda (Ailurus fulgens) in Kangchenjunga landscape, India

Wildlife management in rapid changing landscapes requires critical planning through cross cutting networks, and understanding of landscape features, often affected by the anthropogenic activities. The present study demonstrates fine-scale spatial patterns of genetic variation and contemporary gene flow of red panda (Ailurus fulgens) populations with respect to landscape connectivity in Kangchenjunga Landscape (KL), India. The study found about 1,309.54 km2 area suitable for red panda in KL-India, of which 62.21% area fell under the Protected Area network. We identified 24 unique individuals from 234 feces collected at nine microsatellite loci. The spatially explicit and non-explicit Bayesian clustering algorithms evident to exhibit population structuring and supported red panda populations to exist in meta-population frame work. In concurrence to the habitat suitability and landscape connectivity models, gene flow results supported a contemporary asymmetric movement of red panda by connecting KL-India in a crescent arc. We demonstrate the structural-operational connectivity of corridors in KL-India that facilitated red panda movement in the past. We also seek for cooperation in Nepal, Bhutan and China to aid in preparing for a comprehensive monitoring plan for the long-term conservation and management of red panda in trans-boundary landscapes.

Assessment of spatial genetic structure to identify populations at risk for infection of an emerging epizootic disease

Understanding the geographic extent and connectivity of wildlife populations can provide important insights into the management of disease outbreaks but defining patterns of population structure is difficult for widely distributed species. Landscape genetic analyses are powerful methods for identifying cryptic structure and movement patterns that may be associated with spatial epizootic patterns in such cases.We characterized patterns of population substructure and connectivity using microsatellite genotypes from 2,222 white-tailed deer (Odocoileus virginianus) in the Mid-Atlantic region of the United States, a region where chronic wasting disease was first detected in 2009. The goal of this study was to evaluate the juxtaposition between population structure, landscape features that influence gene flow, and current disease management units.Clustering analyses identified four to five subpopulations in this region, the edges of which corresponded to ecophysiographic provinces. Subpopulations were further partitioned into 11 clusters with subtle (F ST ≤ 0.041), but significant genetic differentiation. Genetic differentiation was lower and migration rates were higher among neighboring genetic clusters, indicating an underlying genetic cline. Genetic discontinuities were associated with topographic barriers, however.Resistance surface modeling indicated that gene flow was diffuse in homogenous landscapes, but the direction and extent of gene flow were influenced by forest cover, traffic volume, and elevational relief in subregions heterogeneous for these landscape features. Chronic wasting disease primarily occurred among genetic clusters within a single subpopulation and along corridors of high landscape connectivity.These results may suggest a possible correlation between population substructure, landscape connectivity, and the occurrence of diseases for widespread species. Considering these factors may be useful in delineating effective management units, although only the largest features produced appreciable differences in subpopulation structure. Disease mitigation strategies implemented at the scale of ecophysiographic provinces are likely to be more effective than those implemented at finer scales.

The Anatolian glacial refugium and human-mediated colonization: a phylogeographical study of the stone marten (Martes foina) in Turkey

The Anatolian Peninsula, comprising most of modern Turkey, is situated at the junction of Europe, the Middle East and Asia. Together with its complex geomorphological and climatic history, this has given rise to a rich fauna and flora, which exhibits a wide range of historical biogeographical patterns. The stone marten (Martes foina) is a small carnivore that is found across the temperate Palaearctic region including Anatolia, where it is often associated with habitats modified by humans, but few genetic data exist for this species. We sequenced a 1840-bp region of the mitochondrial genome from 97 martens sampled across the peninsula and intron 7 of the nuclear β-fibrinogen gene from 53 of these. Two mitochondrial lineages were recovered, with overlapping eastern and western distributions, but there was no geographical structure for the autosomal marker. Coalescent analyses indicated that both of the lineages originated during the Last Glacial Maximum, one of them within an eastern Anatolian refugium and the other in a western Anatolian or Balkan refugium. The western lineage colonized most of Europe in the Holocene, while the eastern lineage may be endemic to Anatolia, from where it colonized the Iberian Peninsula via human translocation. The presence of at least one refugial stone marten population highlights the importance of Anatolia to the preservation of genetic variation and biodiversity.

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.

Noninvasive sampling reveals population genetic structure in the Royle's pika, Ochotona roylei, in the western Himalaya

Understanding population genetic structure of climate-sensitive herbivore species is important as it provides useful insights on how shifts in environmental conditions can alter their distribution and abundance. Herbivore responses to the environment can have a strong indirect cascading effect on community structure. This is particularly important for Royle's pika (Lagomorpha: Ochotona roylei), a herbivorous talus-dwelling species in alpine ecosystem, which forms a major prey base for many carnivores in the Himalayan arc. In this study, we used seven polymorphic microsatellite loci to detect evidence for recent changes in genetic diversity and population structure in Royle's pika across five locations sampled between 8 and 160 km apart in the western Himalaya. Using four clustering approaches, we found the presence of significant contemporary genetic structure in Royle's pika populations. The detected genetic structure could be primarily attributed to the landscape features in alpine habitat (e.g., wide lowland valleys, rivers) that may act as semipermeable barriers to gene flow and distribution of food plants, which are key determinants in spatial distribution of herbivores. Pika showed low inbreeding coefficients (F IS) and a high level of pairwise relatedness for individuals within 1 km suggesting low dispersal abilities of talus-dwelling pikas. We have found evidence of a recent population bottleneck, possibly due to effects of environmental disturbances (e.g., snow melting patterns or thermal stress). Our results reveal significant evidence of isolation by distance in genetic differentiation (F ST range = 0.04-0.19). This is the first population genetics study on Royle's pika, which helps to address evolutionary consequences of climate change which are expected to significantly affect the distribution and population dynamics in this talus-dwelling species.

Genetic diversity and structure related to expansion history and habitat isolation: stone marten populating rural-urban habitats

Background

Population genetic diversity and structure are determined by past and current evolutionary processes, among which spatially limited dispersal, genetic drift, and shifts in species distribution boundaries have major effects. In most wildlife species, environmental modifications by humans often lead to contraction of species’ ranges and/or limit their dispersal by acting as environmental barriers. However, in species well adapted to anthropogenic habitat or open landscapes, human induced environmental changes may facilitate dispersal and range expansions. In this study, we analysed whether isolation by distance and deforestation, among other environmental features, promotes or restricts dispersal and expansion in stone marten (Martes foina) populations.

Results

We genotyped 298 martens from eight sites at twenty-two microsatellite loci to characterize the genetic variability, population structure and demographic history of stone martens in Poland. At the landscape scale, limited genetic differentiation between sites in a mosaic of urban, rural and forest habitats was mostly influenced by isolation by distance. Statistical clustering and multivariate analyses showed weak genetic structuring with two to four clusters and a high rate of gene flow between them. Stronger genetic differentiation was detected for one stone marten population (NE1) located inside a large forest complex. Genetic differentiation between this site and all others was 20% higher than between other sites separated by similar distances. The genetic uniqueness index of NE1 was also twofold higher than in other sites. Past demographic history analyses showed recent expansion of this species in north-eastern Poland. A decrease in genetic diversity from south to north, and MIGRAINE analyses indicated the direction of expansion of stone marten.

Conclusions

Our results showed that two processes, changes in species distribution boundaries and limited dispersal associated with landscape barriers, affect genetic diversity and structure in stone marten. Analysis of local barriers that reduced dispersal and large scale analyses of genetic structure and demographic history highlight the importance of isolation by distance and forest cover for the past colonization of central Europe by stone marten. This confirmed the hypothesis that human-landscape changes (deforestation) accelerated stone marten expansion, to which climate warming probably has also been contributing over the last few decades.

Electronic supplementary material

The online version of this article (10.1186/s12898-017-0156-6) contains supplementary material, which is available to authorized users.

Assessing Genetic Structure in Common but Ecologically Distinct Carnivores: The Stone Marten and Red Fox

The identification of populations and spatial genetic patterns is important for ecological and conservation research, and spatially explicit individual-based methods have been recognised as powerful tools in this context. Mammalian carnivores are intrinsically vulnerable to habitat fragmentation but not much is known about the genetic consequences of fragmentation in common species. Stone martens (Martes foina) and red foxes (Vulpes vulpes) share a widespread Palearctic distribution and are considered habitat generalists, but in the Iberian Peninsula stone martens tend to occur in higher quality habitats. We compared their genetic structure in Portugal to see if they are consistent with their differences in ecological plasticity, and also to illustrate an approach to explicitly delineate the spatial boundaries of consistently identified genetic units. We analysed microsatellite data using spatial Bayesian clustering methods (implemented in the software BAPS, GENELAND and TESS), a progressive partitioning approach and a multivariate technique (Spatial Principal Components Analysis-sPCA). Three consensus Bayesian clusters were identified for the stone marten. No consensus was achieved for the red fox, but one cluster was the most probable clustering solution. Progressive partitioning and sPCA suggested additional clusters in the stone marten but they were not consistent among methods and were geographically incoherent. The contrasting results between the two species are consistent with the literature reporting stricter ecological requirements of the stone marten in the Iberian Peninsula. The observed genetic structure in the stone marten may have been influenced by landscape features, particularly rivers, and fragmentation. We suggest that an approach based on a consensus clustering solution of multiple different algorithms may provide an objective and effective means to delineate potential boundaries of inferred subpopulations. sPCA and progressive partitioning offer further verification of possible population structure and may be useful for revealing cryptic spatial genetic patterns worth further investigation.