Patch occupancy by stone martens Martes foina in fragmented landscapes of central Spain: the role of fragment size,isolation and habitat structure

We studied the response to forest fragmentation of a generalist carnivore, the stone marten Martes foina, in highly fragmented landscapes of central Spain. Five different areas (n = 178 fragments) in central Spain were surveyed. This paper analyses the relationship between fragment use by martens (measured through scat presence) and a series of variables related to the size, isolation and vegetation structure of each fragment by means of stepwise logistic regression. Size and isolation have an important effect on stone marten presence in fragments. Our results were similar to those found for other marten species in landscapes with coarse-grain fragmentation, but they contrast with other studies conducted in landscapes with fine-grain fragmentation. These data suggested that in highly fragmented landscapes, size and isolation factors resulting from forest fragmentation were responsible for determining marten responses, irrespective of their habitat generalism. Management policies for the stone marten in highly fragmented scenarios require the maintenance of large forests near continuous forest tracts in mountains or riparian woodlands.     

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.     

Population genetic structure in Myrtus communis L. in a chronically fragmented landscape in the Mediterranean: can gene flow counteract habitat perturbation?

Ancient managed landscapes provide ideal opportunities to assess the consequences of habitat fragmentation on the patterns of genetic diversity and gene flow in long-lived plant species. Using amplified fragment length polymorphism (AFLP) and allozyme markers, we quantified seed-mediated gene flow and population genetic diversity and structure in 14 populations of Myrtus communis (myrtle), a common endozoochorous shrub species of forest patches in lowland agricultural Mediterranean areas. Overall, allozyme diversity for myrtle was low (P₉₅   =   25%; A   =   1.411; H_e = 0.085) compared to other known populations, and a significant portion of populations (57%) had lower levels of allelic diversity and/or heterozygosity than expected at random, as shown by simulated resampling of the whole diversity of the landscape. We found significant correlations between allozyme variability and population size and patch isolation, but no significant inbreeding in any population. Genetic differentiation among populations for both allozyme and AFLP markers was significant (Φ_ST = 0.144 and Φ_ST = 0.142, respectively) but an isolation-by-distance pattern was not detected. Assignment tests on AFLP data indicated a high immigration rate in the populations ( ca. 20–22%), likely through effective seed dispersal across the landscape by birds and mammals. Our results suggest that genetic isolation is not the automatic outcome of habitat destruction since substantial levels of seed-mediated gene flow are currently detectable. However, even moderate rates of gene flow seem insufficient in this long-lived species to counteract the genetic erosion and differentiation imposed by chronic habitat destruction.     

A comparison of the population genetic structure of parasitic Viscum album from two landscapes differing in degree of fragmentation

Parasite populations do not necessarily conform to expected patterns of genetic diversity and structure. Parasitic plants may be more vulnerable to the negative consequences of landscape fragmentation because of their specialized life history strategies and dependence on host plants, which are themselves susceptible to genetic erosion and reduced fitness following habitat change. We used AFLP genetic markers to investigate the effects of habitat fragmentation on genetic diversity and structure within and among populations of hemiparasitic Viscum album. Comparing populations from two landscapes differing in the amount of forest fragmentation allowed us to directly quantify habitat fragmentation effects. Populations from both landscapes exhibited significant isolation-by-distance and sex ratios biased towards females. The less severely fragmented landscape had larger and less isolated populations, resulting in lower levels of population genetic structure (F _ST = 0.05 vs. 0.09) and inbreeding (F _IS = 0.13 vs. 0.27). Genetic differentiation between host-tree subpopulations was also higher in the more fragmented landscape. We found no significant differences in within-population gene diversity, percentage of polymorphic loci, or molecular variance between the two regions, nor did we find relationships between genetic diversity measures and germination success. Our results indicate that increasing habitat fragmentation negatively affects population genetic structure and levels of inbreeding in V. album, with the degree of isolation among populations exerting a stronger influence than forest patch size.     

The influence of forest fragmentation and landscape pattern on American martens

1. We investigated the effects of forest fragmentation on American martens ( Martes americana Rhoads) by evaluating differences in marten capture rates (excluding recaptures) in 18 study sites with different levels of fragmentation resulting from timber harvest clearcuts and natural openings. We focused on low levels of fragmentation, where forest connectivity was maintained and non-forest cover ranged from 2% to 42%.
2. Martens appeared to respond negatively to low levels of habitat fragmentation, based on the significant decrease in capture rates within the series of increasingly fragmented landscapes. Martens were nearly absent from landscapes having > 25% non-forest cover, even though forest connectivity was still present.
3. Marten capture rates were negatively correlated with increasing proximity of open areas and increasing extent of high-contrast edges. Forested landscapes appeared unsuitable for martens when the average nearest-neighbour distance between open (non-forested) patches was <100 m. In these landscapes, the proximity of open areas created strips of forest edge and eliminated nearly all forest interior.
4. Small mammal densities were significantly higher in clearcuts than in forests, but marten captures were not correlated with prey abundance or biomass associated with clearcuts.
5. Conservation efforts for the marten must consider not only the structural aspects of mature forests, but the landscape pattern in which the forest occurs. We recommend that the combination of timber harvests and natural openings comprise <25% of landscapes ≥9 km² in size.
6. The spatial pattern of open areas is important as well, because small, dispersed openings result in less forest interior habitat than one large opening at the same percentage of fragmentation. Progressive cutting from a single patch would retain the largest amount of interior forest habitat.     

Fragmentation and Genetic Diversity in Romnalda (Dasypogonaceae), a Rare Rain forest Herbaceous Genus from New Guinea and Australia

Rain forests are expected to be amongst the ecosystem types most affected by fragmentation due to their high species diversity, high endemism, complexity of interactions, and contrast with surrounding altered matrix. Due to their shorter life cycles and dependence on canopy cover, rain forest understory herbs are expected to indicate the effects of recent fragmentation more rapidly than canopy trees. This study investigated all four known species of the genus Romnalda , all of which are rare rain forest herbaceous species, to investigate the possible effects of habitat fragmentation and isolation on genetic diversity and gene flow. Allozymes were used as genetic markers and regional remnant vegetation maps were used to compare landscape fragmentation. We found that R. strobilacea populations in a highly fragmented landscape were genetically depauperate compared with those of its congeneric species that are found within continuous rain forest habitats and that allelic diversity decreased with decreasing population size but not geographic distance in R. strobilacea . Given the similarity among the species, our results indicate that all Romnalda species are potentially susceptible to loss of genetic diversity due to habitat fragmentation within relatively short timeframes. The results indicate that populations are not highly genetically differentiated and there is little evidence of genetic provenance where the species have restricted geographic ranges. Thus, species recovery programs would be better to focus on maintaining population size and genetic diversity rather than population differentiation.     

Where to sleep in a rural landscape? A comparative study of resting sites pattern in two syntopic Martes species

The niche‐complementarity hypothesis predicts that two sympatric species must differ in their requirements for one of the three main ecological dimensions (i.e. habitat use, diet, and activity time) to coexist. European pine marten Martes martes and stone marten M. foina are syntopic medium‐sized mustelids with very similar morphology and ecology for which resting sites are a key resource. To better understand how these species coexist, we investigated whether key features of their resting site pattern (number of resting sites, area over which they are distributed, main habitat type used for resting) differed. We used diurnal telemetry to identify resident individuals (e.g. spatially stable individuals over time) and to locate them during resting periods in a fragmented forested area in France. Stone marten used fewer resting sites distributed over a smaller surface area than pine marten. Most stone marten resting sites were located in open habitat (83%) in the proximity of human habitations, whereas pine martens rested almost exclusively in forest (98%). Sex, age, and season explained some variability in both the number of resting sites and the probability of resting within forested habitat for stone marten but not pine marten. The area covered by resting sites was larger in males than in females, but age modulated this difference in an opposite way for the two species. Such a pattern was expected given the intra‐sexual territoriality and the reproductive phenology of these species. Overall, stone marten showed higher inter‐individual variability in resting site pattern than pine marten. The particular pattern observed in subadult male stone martens during summer (increase in resting site surface area and in the probability to rest in forest) may reflect an attempt to settle in forests, and we discuss these implications in the context of interspecific competition.     

Investigating genetic diversity and habitat dynamics in Plantago brutia (Plantaginaceae), implications for the management of narrow endemics in Mediterranean mountain pastures

Many factors have contributed to the richness of narrow endemics in the Mediterranean, including long-lasting human impact on pristine landscapes. The abandonment of traditional land-use practices is causing forest recovery throughout the Mediterranean mountains, by increasing reduction and fragmentation of open habitats. We investigated the population genetic structure and habitat dynamics of Plantago brutia Ten., a narrow endemic in mountain pastures of S Italy. Some plants were cultivated in the botanical garden to explore the species' breeding system. Genetic diversity was evaluated based on inter-simple sequence repeat (ISSR) polymorphisms in 150 individuals from most of known stands. Recent dynamics in the species habitat were checked over a 14-year period. Flower phenology, stigma receptivity and experimental pollinations revealed protogyny and self-incompatibility. With the exception of very small and isolated populations, high genetic diversity was found at the species and population level. amova revealed weak differentiation among populations, and the Mantel test suggested absence of isolation-by-distance. Multivariate analysis of population and genetic data distinguished the populations based on genetic richness, size and isolation. Landscape analyses confirmed recent reduction and isolation of potentially suitable habitats. Low selfing, recent isolation and probable seed exchange may have preserved P. brutia populations from higher loss of genetic diversity. Nonetheless, data related to very small populations suggest that this species may suffer further fragmentation and isolation. To preserve most of the species' genetic richness, future management efforts should consider the large and isolated populations recognised in our analyses.     

Landscape configuration determines gene flow and phenotype in a flightless forest-edge ground-dwelling bush-cricket, Pholidoptera griseoaptera

Spatial configuration of habitats influences genetic structure and population fitness whereas it affects mainly species with limited dispersal ability. To reveal how habitat fragmentation determines dispersal and dispersal-related morphology in a ground-dispersing insect species we used a bush-cricket (Pholidoptera griseoaptera) which is associated with forest-edge habitat. We analysed spatial genetic patterns together with variability of the phenotype in two forested landscapes with different levels of fragmentation. While spatial configuration of forest habitats did not negatively affect genetic characteristics related to the fitness of sampled populations, genetic differentiation was found higher among populations from an extensive forest. Compared to an agricultural matrix between forest patches, the matrix of extensive forest had lower permeability and posed barriers for the dispersal of this species. Landscape configuration significantly affected also morphological traits that are supposed to account for species dispersal potential; individuals from fragmented forest patches had longer hind femurs and a higher femur to pronotum ratio. This result suggests that selection pressure act differently on populations from both landscape types since dispersal-related morphology was related to the level of habitat fragmentation. Thus observed patterns may be explained as plastic according to the level of landscape configuration; while anthropogenic fragmentation of habitats for this species can lead to homogenization of spatial genetic structure.     

Limited effect of anthropogenic habitat fragmentation on molecular diversity in a rain forest skink, Gnypetoscincus queenslandiae

To examine the effects of recent habitat fragmentation, we assayed genetic diversity in a rain forest endemic lizard, the prickly forest skink (Gnypetoscincus queenslandiae), from seven forest fragments and five sites in continuous forest on the Atherton tableland of northeastern Queensland, Australia. The rain forest in this region was fragmented by logging and clearing for dairy farms in the early 1900s and most forest fragments studied have been isolated for 50-80 years or nine to 12 skink generations. We genotyped 411 individuals at nine microsatellite DNA loci and found fewer alleles per locus in prickly forest skinks from small rain forest fragments and a lower ratio of allele number to allele size range in forest fragments than in continuous forest, indicative of a decrease in effective population size. In contrast, and as expected for populations with small neighbourhood sizes, neither heterozygosity nor variance in allele size differed between fragments and sites in continuous forests. Considering measures of among population differentiation, there was no increase in FST among fragments and a significant isolation by distance pattern was identified across all 12 sites. However, the relationship between genetic (FST) and geographical distance was significantly stronger for continuous forest sites than for fragments, consistent with disruption of gene flow among the latter. The observed changes in genetic diversity within and among populations are small, but in the direction predicted by the theory of genetic erosion in recently fragmented populations. The results also illustrate the inherent difficulty in detecting genetic consequences of recent habitat fragmentation, even in genetically variable species, and especially when effective population size and dispersal rates are low.     

Exploring the legacy of goat grazing: signatures of habitat fragmentation on genetic patterns of endemic weevil populations in Northern Isabela Island,Galápagos (Ecuador)

Together with reduction in habitat area and quality, reduction in habitat connectivity is one of the major factors influencing species’ persistence in fragmented landscapes. We explore the consequences of recent habitat fragmentation on volcanoes across Isabela Island, Galápagos by analyzing genetic patterns of populations of endemic weevils whose host plants have been depleted by indiscriminate goat grazing. We predicted that if grazing on the weevils’ host plants has caused habitat fragmentation on the weevils populations themselves, then the effects on the genetic architecture of populations should be more severe on Galapaganus conwayensis populations from volcanoes on Northern Isabela than on those from Santa Cruz or Pinta islands where vegetation destruction was not as extensive. We used mitochondrial sequences to reveal historical colonization patterns and microsatellite variation to understand more contemporary genetic changes. We found significantly lower microsatellite genetic diversity and population size within localities and increased genetic differentiation at a small geographic scale with a stronger isolation by distance pattern and larger numbers of genetic clusters on Isabela. In the absence of long-standing mitochondrial structure within each volcano, we interpret the microsatellite results as suggesting that recent host plant habitat fragmentation may indeed influence the genetic patterns of plant feeding insects and highlight the importance of controlling the spread of introduced herbivores in the Galápagos Islands.     

Molecular and paleo-climatic data uncover the impact of an ancient bottleneck on the demographic history and contemporary genetic structure of endangered Pinus uliginosa

With the current rate of biodiversity loss, conservation management practices require a comprehensive understanding of eco-evolutionary relationships, history, and genetic structure of species. Assessments of genetic diversity are crucial, especially in rare, endemic, or threatened forest tree species with small and isolated populations, such as peat bog pine (Pinus uliginosa N.). Here, we used a novel approach, combining genetic diversity assessment, ecological niche modeling, and population demography inference to explore the complex history of a few remnant populations of this endangered pine. To asses the relative influence of isolation and fragmentation on genetic diversity in the taxonomic context, the patterns of genetic variation found in P. uliginosa were contrasted with those observed in its close relatives with much bigger distribution ranges and larger populations (Pinus sylvestris, Pinus mugo, and Pinus uncinata). We found a similar level of genetic diversity across the species at nuclear loci but contrasting patterns of variability distribution at chloroplast markers. We detected the signatures of an ancient genetic bottleneck dated at around 26 400 years ago, indicating a drastic reduction in the population size of P. uligionosa during the Last Glacial Maximum. In addition, we found substantial differentiation between current populations as a result of enhanced genetic drift during long-lasting isolation. The research suggests potential conservation management strategies for peat bog pine and emphasizes the importance of using complementary approaches for their successful development.     

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.     

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.     

Contemporary habitat loss reduces genetic diversity in an ecologically specialized butterfly

Aim This study investigated the influence of contemporary habitat loss on the genetic diversity and structure of animal species using a common, but ecologically specialized, butterfly, Theclinesthes albocincta (Lepidoptera: Lycaenidae), as a model. Location South Australia. Methods We used amplified fragment length polymorphism (AFLP) and allozyme datasets to investigate the genetic structure and genetic diversity among populations of T. albocincta in a fragmented landscape and compared this diversity and structure with that of populations in two nearby landscapes that have more continuous distributions of butterflies and their habitat. Butterflies were sampled from 15 sites and genotyped, first using 363 informative AFLP bands and then using 17 polymorphic allozyme loci (n = 248 and 254, respectively). We complemented these analyses with phylogeographic information based on mitochondrial DNA (mtDNA) haplotype information derived from a previous study in the same landscapes. Results Both datasets indicated a relatively high level of genetic structuring across the sampling range (AFLP, F_ST = 0.34; allozyme, F_ST = 0.13): structure was greatest among populations in the fragmented landscape (AFLP, F_ST = 0.15; allozyme, F_ST = 0.13). Populations in the fragmented landscape also had significantly lower genetic diversity than populations in the other two landscapes: there were no detectable differences in genetic diversity between the two continuous landscapes. There was also evidence (r² = 0.33) of an isolation by distance effect across the sampled range of the species. Main conclusions The multiple lines of evidence, presented within a phylogeographic context, support the hypothesis that contemporary habitat fragmentation has been a major driver of genetic erosion and differentiation in this species. Theclinesthes albocincta populations in the fragmented landscape are thus likely to be at greater risk of extinction because of reduced genetic diversity, their isolation from conspecific subpopulations in other landscapes, and other extrinsic forces acting on their small population sizes. Our study provides compelling evidence that habitat loss and fragmentation have significant rapid impacts on the genetic diversity and structure of butterfly populations, especially specialist species with particular habitat preferences and poor dispersal abilities.     

Small-Scale Fragmentation Effects on Local Genetic Diversity in Two Phyllostomid Bats with Different Dispersal Abilities in Panama

Habitat fragmentation is one of the greatest threats to biodiversity. Despite their importance for conservation, the genetic consequences of small-scale habitat fragmentation for bat populations are largely unknown. In this study, we linked genetic with ecological and demographic data to assess the effects of habitat fragmentation on two species of phyllostomid bats ( Uroderma bilobatum and Carollia perspicillata ) that differ in their dispersal abilities and demographic response to fragmentation. We hypothesized that population differentiation and the effect of habitat fragmentation on levels of genetic diversity will be a function of the species' mobility. We sequenced mtDNA from 232 bats caught on 11 islands in Gatún Lake, Panamá, isolated from the mainland for ca 90 yr, and in adjacent, continuous forest on the mainland. Populations of both species showed significant genetic differentiation ( F _ST). Consistent with our prediction, population subdivision was lower in the highly mobile U. bilobatum ( F _ST= 0.01) compared to the less vagile C. perspicillata ( F _ST= 0.06), and only the latter species showed a pattern indicative of isolation by distance and, in addition, an effect of fragmentation. Genetic erosion as a result of fragmentation was also only detectable in the less mobile species, C. perspicillata , where haplotype diversity was lower in island compared to mainland populations. Our results suggest that some Neotropical bat species are prone to loss of genetic variation in response to anthropogenic small-scale habitat fragmentation. In this context, our findings point toward mobility as a good predictor of a species' vulnerability to fragmentation and altered population genetic structure.     

Impacts of Restored Patch Density and Distance from Natural Forests on Colonization Success

Abstract The reduction and fragmentation of forest habitats is expected to have profound effects on plant species diversity as a consequence of the decreased area and increased isolation of the remnant patches. To stop the ongoing process of forest fragmentation, much attention has been given recently to the restoration of forest habitat. The present study investigates restoration possibilities of recently established patches with respect to their geographical isolation. Because seed dispersal events over 100 m are considered to be of long distance, a threshold value of 100 m between recent and old woodland was chosen to define isolation. Total species richness, individual patch species richness, frequency distributions in species occurrences, and patch occupancy patterns of individual species were significantly different among isolated and nonisolated stands. In the short term no high species richness is to be expected in isolated stands. Establishing new forests adjacent to existing woodland ensures higher survival probabilities of existing populations. In the long term, however, the importance of long‐distance seed dispersal should not be underestimated because most species showed occasional long‐distance seed dispersal. A clear distinction should be made between populations colonizing adjacent patches and patches isolated from old woodland. The colonization of isolated stands may have important effects on the dynamics and diversity of forest networks, and more attention should be directed toward the genetic traits and viability of founding populations in isolated stands.     

Habitat fragmentation affects genetic diversity and differentiation of the Yarkand hare

The Yarkand hare, Lepus yarkandensis, is an endemic, endangered species restricted to the Tarim Basin of the Xinjiang Uygur Autonomous Region, China. The Yarkand hare is distributed in scattered oases which are physically isolated by the desert. Its natural fragmentation habitat makes it an ideal object for studying effect of habitat fragmentation on its genetic structure. To evaluate the effects of habitat fragmentation on genetic diversity of the species, we assessed genetic diversity for 20 sampling populations based on control region and Cytb markers. Relatively low levels of gene diversity are found in most of isolated populations in the southern margin of the Taklamakan Desert. Furthermore, a positive correlation is found between gene diversity and the size of historical effective population. Significant genetic differentiation is detected among most populations by pairwise F_ST analyses, which is characterized by an isolation by distance pattern. Additionally, the AMOVA results show highly significant population structure among seven geographical groups. High migration rates are found among continuous populations, while very low levels of migration rates are found among the relatively isolated populations, suggesting that the desert may make an effective barrier against gene flow. Finally, the control region shows four clades by the phylogenetic analyses, three of which are present in nearly all sampling populations. The observed pattern of the lineage mixing, also shown by the Cytb data, may be caused by extensive gene flow among populations, and could be explained by possible demographical expansion of the Yarkand hare during the late Pleistocene interglacial period.     

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.     

American marten (Martes americana) in the Pacific Northwest: population differentiation across a landscape fragmented in time and space

American marten (Martes americana) have a close association with mature temperate forests, a habitat that expanded throughout the Pacific Northwest as glaciers receded at the end of the Pleistocene. Similar to several other forest-associated mammals in North America (e.g. black bear), genetic analysis of the marten shows a deep phylogeographical subdivision that reflects populations with distinctive evolutionary histories. Using a suite of 14 microsatellite markers, we explored the genetic structure of marten populations in two reciprocally monophyletic clades in the Pacific Northwest identified previously as M. caurina and M. americana by mitochondrial haplotypes and morphology. Microsatellite phylogeographical patterns were congruent with mitochondrial analyses. These independent data sets shed light upon hybridization patterns, population structure and evolutionary histories. Hybridization between M. caurina and M. americana individuals was documented in two regions of sympatry (Kuiu Island in southeastern Alaska and southern Montana). Northern insular populations of M. caurina exhibited higher differentiation and lower variability relative to northern populations of M. americana. Greater divergence among M. caurina populations may reflect longer isolation and persistence in coastal forest habitat that was fragmented by rising sea level in the early Holocene. Lower differentiation among northern M. americana populations and close relationship to other continental M. americana populations may reflect more recent expansion into the Pacific Northwest and/or continued gene flow among populations. Differentiation among M. caurina populations was attributed to habitat fragmentation (i.e. rising sea level), as opposed to isolation-by-distance; oceanic straits pose significant barriers to gene flow among M. caurina populations and between populations of M. caurina and M. americana.