Sex and landscape influence spatial genetic variation in a large fossorial mammal, the Bare-nosed Wombat (Vombatus ursinus)

Dispersal is an important process that is widely studied across species, and it can be influenced by intrinsic and extrinsic factors. Intrinsic factors commonly assessed include the sex and age of individuals, while landscape features are frequently-tested extrinsic factors. Here, we investigated the effects of both sex and landscape composition and configuration on genetic distances among bare-nosed wombats (Vombatus ursinus)-one of the largest fossorial mammals in the world and subject to habitat fragmentation, threats from disease, and human persecution including culling as an agricultural pest. We analyzed a data set comprising 74 Tasmanian individuals (30 males and 44 females), genotyped for 9,064 single-nucleotide polymorphisms. We tested for sex-biased dispersal and the influence of landscape features on genetic distances including land use, water, vegetation, elevation, and topographic ruggedness. We detected significant female-biased dispersal, which may be related to females donating burrows to their offspring due to the energetic cost of excavation, given their large body sizes. Land use, waterbodies, and elevation appeared to be significant landscape predictors of genetic distance. Land use potentially reflects land clearing and persecution over the last 200 years. If our findings based on a limited sample size are valid, retention and restoration of nonanthropogenic landscapes in which wombats can move and burrow may be important for gene flow and maintenance of genetic diversity.

Landscape genetics of an endangered salt marsh endemic: Identifying population continuity and barriers to dispersal

Preserving the genetic diversity of endangered species is fundamental to their conservation and requires an understanding of genetic structure. In turn, identification of landscape features that impede gene flow can facilitate management to mitigate such obstacles and help with identifying isolated populations. We conducted a landscape genetic study of the endangered salt marsh harvest mouse (Reithrodontomys raviventris), a species endemic to the coastal marshes of the San Francisco Estuary of California. We collected and genotyped > 500 samples from across the marshes of Suisun Bay which contain the largest remaining tracts of habitat for the species. Cluster analyses and a population tree identified three geographically discrete populations. Next, we conducted landscape genetic analyses at two scales (the entire study area and across the Northern Marshes) where we tested 65 univariate models of landscape features and used the best supported to test multivariable analyses. Our analysis of the entire study area indicated that open water and elevation (> 2 m) constrained gene flow. Analysis of the Northern Marshes, where low elevation marsh habitat is more continuous, indicated that geographic distance was the only significant predictor of genetic distance at this scale. The identification of a large, connected population across Northern Marshes achieves a number of recovery targets for this stronghold of the species. The identification of landscape features that act as barriers to dispersal enables the identification of isolated and vulnerable populations more broadly across the species range, thus aiding conservation prioritization.

Landscape of stress: Tree mortality influences physiological stress and survival in a native mesocarnivore

Climate change and anthropogenic modifications to the landscape can have both positive and negative effects on an animal. Linking landscape change to physiological stress and fitness of an animal is a fundamental tenet to be examined in applied ecology. Cortisol is a glucocorticoid hormone that can be used to indicate an animal's physiological stress response. In the Sierra Nevada Mountains of California, fishers (Pekania pennanti) are a threatened mesocarnivore that have been subjected to rapid landscape changes due to anthropogenic modifications and tree mortality related to a 4-year drought. We measured cortisol concentrations in the hair of 64 fishers (41 females, 23 males) captured and radio-collared in the Sierra National Forest, California. We addressed two main questions: (1) Is the physiological stress response of fishers influenced by anthropogenic factors, habitat type, canopy cover, and tree mortality due to drought in their home range? (2) Does the physiological stress response influence survival, reproduction, or body condition? We examined these factors within a fisher home range at 3 scales (30, 60, 95% isopleths). Using model selection, we found that tree mortality was the principle driver influencing stress levels among individual fishers with female and male fishers having increasing cortisol levels in home ranges with increasing tree mortality. Most importantly, we also found a link between physiological stress and demography where female fishers with low cortisol levels had the highest annual survival rate (0.94), whereas females with medium and high cortisol had lower annual survival rates, 0.78 and 0.81, respectively. We found no significant relationships between cortisol levels and body condition, male survival, or litter size. We concluded that tree mortality related to a 4-year drought has created a "landscape of stress" for this small, isolated fisher population.

Multiscale patterns of isolation by ecology and fine-scale population structure in Texas bobcats

Patterns of spatial genetic variation can be generated by a variety of ecological processes, including individual preferences based on habitat. These ecological processes act at multiple spatial and temporal scales, generating scale-dependent effects on gene flow. In this study, we focused on bobcats (Lynx rufus), a highly mobile, generalist felid that exhibits ecological and behavioral plasticity, high abundance, and broad connectivity across much of their range. However, bobcats also show genetic differentiation along habitat breaks, a pattern typically observed in cases of isolation-by-ecology (IBE). The IBE observed in bobcats is hypothesized to occur due to habitat-biased dispersal, but it is unknown if this occurs at other habitat breaks across their range or at what spatial scale IBE becomes most apparent. Thus, we used a multiscale approach to examine isolation by ecology (IBE) patterns in bobcats (Lynx rufus) at both fine and broad spatial scales in western Texas. We genotyped 102 individuals at nine microsatellite loci and used partial redundancy analysis (pRDA) to test if a suite of landscape variables influenced genetic variation in bobcats. Bobcats exhibited a latitudinal cline in population structure with a spatial signature of male-biased dispersal, and no clear barriers to gene flow. Our pRDA tests revealed high genetic similarity in similar habitats, and results differed by spatial scale. At the fine spatial scale, herbaceous rangeland was an important influence on gene flow whereas mixed rangeland and agriculture were significant at the broad spatial scale. Taken together, our results suggests that complex interactions between spatial-use behavior and landscape heterogeneity can create non-random gene flow in highly mobile species like bobcats. Furthermore, our results add to the growing body of data highlighting the importance of multiscale study designs when assessing spatial genetic structure.

Landscape use by fishers (Pekania pennanti): core areas differ in habitat than the entire home range

Home ranges have long been studied in animal ecology. Core areas may be used at a greater proportion than the rest of the home range, implying the core contains dependable resources. The Pacific fisher (Pekania pennanti (Erxleben, 1777)) is a rare mesocarnivore occupying a small area in the Sierra Nevada Mountains, California, USA. Once statewide, fishers declined in the 1900s due to trapping, habitat fragmentation, and development. Recently, drought induced by climate change may be affecting this population. We examined space use of fishers in their core versus their home range for levels of anthropogenic modifications (housing density, road density, silvicultural treatments), habitat types, and tree mortality. We found core areas contained more late-successional forest and minimal human activity compared with their territory. Their core had higher levels of dense canopy and higher amounts of conifer cover, while minimizing the amount of buildings, developed habitat, and low canopy cover. Fishers may in effect be seeking refugia by minimizing their exposure to these elements in their core. Conserving landscape components used by fishers in their core areas will be important for the persistence of this isolated population.

Latitudinal clines in sexual selection, sexual size dimorphism and sex-specific genetic dispersal during a poleward range expansion

Range expansions can be shaped by sex differences in behaviours and other phenotypic traits affecting dispersal and reproduction. Here, we investigate sex differences in morphology, behaviour and genomic population differentiation along a climate-mediated range expansion in the common bluetail damselfly (Ischnura elegans) in northern Europe. We sampled 65 sites along a 583-km gradient spanning the I. elegans range in Sweden and quantified latitudinal gradients in site relative abundance, sex ratio and sex-specific shifts in body size and mating status (a measure of sexual selection). Using single nucleotide polymorphism (SNP) data for 426 individuals from 25 sites, we further investigated sex-specific landscape and climatic effects on neutral genetic connectivity and migration patterns. We found evidence for sex differences associated with the I. elegans range expansion, namely (a) increased male body size with latitude, but no latitudinal effect on female body size, resulting in reduced sexual dimorphism towards the range limit, (b) a steeper decline in male genetic similarity with increasing geographic distance than in females, (c) male-biased genetic migration propensity and (d) a latitudinal cline in migration distance (increasing migratory distances towards the range margin), which was stronger in males. Cooler mean annual temperatures towards the range limit were associated with increased resistance to gene flow in both sexes. Sex ratios became increasingly male biased towards the range limit, and there was evidence for a changed sexual selection regime shifting from favouring larger males in the south to favouring smaller males in the north. Our findings suggest sex-specific spatial phenotype sorting at the range limit, where larger males disperse more under higher landscape resistance associated with cooler climates. The combination of latitudinal gradients in sex-biased dispersal, increasing male body size and (reduced) sexual size dimorphism should have emergent consequences for sexual selection dynamics and the mating system at the expanding range front. Our study illustrates the importance of considering sex differences in the study of range expansions driven by ongoing climate change.

Multiple glacial refugia and contemporary dispersal shape the genetic structure of an endemic amphibian from the Pyrenees

Historical factors (colonization scenarios, demographic oscillations) and contemporary processes (population connectivity, current population size) largely contribute to shaping species' present-day genetic diversity and structure. In this study, we use a combination of mitochondrial and nuclear DNA markers to understand the role of Quaternary climatic oscillations and present-day gene flow dynamics in determining the genetic diversity and structure of the newt Calotriton asper (Al. Dugès, 1852), endemic to the Pyrenees. Mitochondrial DNA did not show a clear phylogeographic pattern and presented low levels of variation. In contrast, microsatellites revealed five major genetic lineages with admixture patterns at their boundaries. Approximate Bayesian computation analyses and linear models indicated that the five lineages likely underwent separate evolutionary histories and can be tracked back to distinct glacial refugia. Lineage differentiation started around the Last Glacial Maximum at three focal areas (western, central and eastern Pyrenees) and extended through the end of the Last Glacial Period in the central Pyrenees, where it led to the formation of two more lineages. Our data revealed no evidence of recent dispersal between lineages, whereas borders likely represent zones of secondary contact following expansion from multiple refugia. Finally, we did not find genetic evidence of sex-biased dispersal. This work highlights the importance of integrating past evolutionary processes and present-day gene flow and dispersal dynamics, together with multilocus approaches, to gain insights into what shaped the current genetic attributes of amphibians living in montane habitats.

Multiscale landscape genetics of American marten at their southern range periphery

American marten (Martes americana) are a conservation priority in many forested regions of North America. Populations are fragmented at the southern edge of their distribution due to suboptimal habitat conditions. Facilitating gene flow may improve population resilience through genetic and demographic rescue. We used a multiscale approach to estimate the relationship between genetic connectivity and landscape characteristics among individuals at three scales in the northeastern United States: regional, subregional, and local. We integrated multiple modeling techniques and identified top models based on consensus. Top models were used to parameterize resistance surfaces at each scale, and circuit theory was used to identify potential movement corridors. Regional gene flow was affected by forest cover, elevation, developed land cover, and slope. At subregional and local scales, the effects were site specific and included subsets of temperature, elevation, developed land cover, and slope. Developed land cover significantly affected gene flow at each scale. At finer scales, lack of variance in forest cover may have limited the ability to detect a relationship with gene flow. The effect of slope on gene flow was positive or negative, depending on the site examined. Occupancy probability was a relatively poor predictor, and we caution its use as a proxy for landscape resistance. Our results underscore the importance of replication and multiscale approaches in landscape genetics. Climate warming and landscape conversion may reduce the genetic connectivity of marten populations in the northeastern United States, and represent the primary challenges to marten conservation at the southern periphery of their range.

Landscape heterogeneity in landform and land use provides functional resistance to gene flow in continuous Asian black bear populations

CONTEXT

Genetic diversity is one of the most important facets of biological diversity, and changes in the spatial pattern of habitats, often modified by human activity, are believed to have affected the genetic diversity of resident natural populations.

OBJECTIVES

We undertook a landscape genetic analysis in order to determine which landscape features influence gene flow within Asian black bear populations and to identify the underlying processes.

METHODS

In our evaluation of gene flow, we estimated four parameters of resistance with regard to landscape elevation: the mean, the difference between the highest and lowest, the standard deviation, and the coefficient of variation of elevation among individuals. We then examined the resistance effect of different land use types.

RESULTS

With the exception of mean elevation, we found that all parameters showed a significant relationship with genetic distance, indicating that unevenness in elevation provides functional resistance to gene flow. Although we found no evidence of landscape barriers (isolation-by-barrier), there was an indication of landscape resistance (isolation-by-resistance). Urban area and farmland are suggested to be the strong factors contributing to the resistance to gene flow, even though isolation-by-distance was also detected. When we examined gene flow for pairs of males and pairs of females, both isolation-by-distance and isolation-by-resistance were stronger in order of female pairs, male pairs, all individual pairs.

CONCLUSIONS

We conclude that landscape resistance was detectable with a high contrast in landscape heterogeneity and they are more influential on females than males.

OPEN PRACTICES

This article has been awarded Open Data badge. All materials and data are publicly accessible via the Open Science Framework at https://doi.org/10.5061/dryad.gn0qf16. Learn more about the Open Practices badges from the Center for Open Science: https://osf.io/tvyxz/wiki.