Genetic isolation of wolverine (Gulo gulo) populations at the eastern periphery of their North American distribution

Genetic analysis of hog deer (Axis porcinus) in Victoria, Australia, and its applications to invasive species and game management

Hog deer were introduced to Australia in the 1860s, where they have spread across the Gippsland region of Victoria. Due to its status as an introduced species and an important game animal within Victoria, management of the species is complex. Given this complexity, genetic studies can provide important information regarding population structure and diversity which can assist in controlling problematic populations of hog deer, while also ensuring viable game stock in sites managed as game reserves. The aim of this study was to investigate the population genetic structure and diversity of the Victorian hog deer 150 years after introduction using short tandem repeats (STRs). Hog deer samples were collected across 15 sites of differing management regimes in the Gippsland region of Victoria and genotyped for 13 polymorphic STR loci. Up to four distinct genetic clusters were identified across the sites sampled, suggesting that despite low observed genetic diversity, population structure is present across their range. It was also possible to detect evidence of recent translocations among populations. This study suggests that the presence of distinct genetic clusters may enable management of separate genetic units, considering invasive species and game management objectives.

The Centre–Periphery Model, a Possible Explanation for the Distribution of Some Pinus spp. in the Sierra Madre Occidental, Mexico

Genetic diversity is key to survival of species. In evolutionary ecology, the general centre–periphery theory suggests that populations of species located at the margins of their distribution areas display less genetic diversity and greater genetic differentiation than populations from central areas. The aim of this study was to evaluate the genetic diversity and differentiation in six of the main pine species of the Sierra Madre Occidental (northern Mexico). The species considered were Pinus arizonica, P. cembroides, P. durangensis, Pinus engelmannii, P. herrerae and P. leiophylla, which occur at the margins and centre of the geographic distribution. We sampled needles from 2799 individuals belonging to 80 populations of the six species. We analysed amplified fragment length polymorphisms (AFLPs) to estimate diversity and rarity indexes, applied Principal Coordinate Analysis (PCoA), and used the Kruskal–Wallis test to detect genetic differences. Finally, we calculated Spearman’s correlation for association between variables. The general centre–periphery model only explained the traits in P. herrerae. The elevation gradient was an important factor that influenced genetic diversity. However, for elevation as partitioning criterion, most populations showed a central distribution. This information may be useful for establishing seed collections of priority individuals for maintenance in germplasm banks and their subsequent sustainable use.

Population genetics of the wolverine in Finland: the road to recovery?

After decades, even centuries of persecution, large carnivore populations are widely recovering in Europe. Considering the recent recovery of the wolverine (Gulo gulo) in Finland, our aim was to evaluate genetic variation using 14 microsatellites and mtDNA control region (579 bp) in order (1) to determine whether the species is represented by a single genetic population within Finland, (2) to quantify the genetic diversity, and (3) to estimate the effective population size. We found two major genetic clusters divided between eastern and northern Finland based on microsatellites (FST = 0.100) but also a significant pattern of isolation by distance. Wolverines in western Finland had a genetic signature similar to the northern cluster, which can be explained by former translocations of wolverines from northern to western Finland. For both main clusters, most estimates of the effective population size Ne were below 50. Nevertheless, the genetic diversity was higher in the eastern cluster (HE = 0.57, AR = 4.0, AP = 0.3) than in the northern cluster (HE = 0.49, AR = 3.7, AP = 0.1). Migration between the clusters was low. Two mtDNA haplotypes were found: one common and identical to Scandinavian wolverines; the other rare and not previously detected. The rare haplotype was more prominent in the eastern genetic cluster. Combining all available data, we infer that the genetic population structure within Finland is shaped by a recent bottleneck, isolation by distance, human-aided translocations and postglacial recolonization routes.

Determining causes of genetic isolation in a large carnivore (Ursus americanus) population to direct contemporary conservation measures

The processes leading to genetic isolation influence a population’s local extinction risk, and should thus be identified before conservation actions are implemented. Natural or human-induced circumstances can result in historical or contemporary barriers to gene flow and/or demographic bottlenecks. Distinguishing between these hypotheses can be achieved by comparing genetic diversity and differentiation in isolated vs. continuous neighboring populations. In Ontario, American black bears (Ursus americanus) are continuously distributed, genetically diverse, and exhibit an isolation-by-distance structuring pattern, except on the Bruce Peninsula (BP). To identify the processes that led to the genetic isolation of BP black bears, we modelled various levels of historical and contemporary migration and population size reductions using forward simulations. We compared simulation results with empirical genetic indices from Ontario black bear populations under different levels of geographic isolation, and conducted additional simulations to determine if translocations could help achieve genetic restoration. From a genetic standpoint, conservation concerns for BP black bears are warranted because our results show that: i) a recent demographic bottleneck associated with recently reduced migration best explains the low genetic diversity on the BP; and ii) under sustained isolation, BP black bears could lose between 70% and 80% of their rare alleles within 100 years. Although restoring migration corridors would be the most effective method to enhance long-term genetic diversity and prevent inbreeding, it is unrealistic to expect connectivity to be re-established. Current levels of genetic diversity could be maintained by successfully translocating 10 bears onto the peninsula every 5 years. Such regular translocations may be more practical than landscape restoration, because areas connecting the peninsula to nearby mainland black bear populations have been irreversibly modified by humans, and form strong barriers to movement.

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.

Lack of Spatial Immunogenetic Structure among Wolverine (Gulo gulo) Populations Suggestive of Broad Scale Balancing Selection

Elucidating the adaptive genetic potential of wildlife populations to environmental selective pressures is fundamental for species conservation. Genes of the major histocompatibility complex (MHC) are highly polymorphic, and play a key role in the adaptive immune response against pathogens. MHC polymorphism has been linked to balancing selection or heterogeneous selection promoting local adaptation. However, spatial patterns of MHC polymorphism are also influenced by gene flow and drift. Wolverines are highly vagile, inhabiting varied ecoregions that include boreal forest, taiga, tundra, and high alpine ecosystems. Here, we investigated the immunogenetic variation of wolverines in Canada as a surrogate for identifying local adaptation by contrasting the genetic structure at MHC relative to the structure at 11 neutral microsatellites to account for gene flow and drift. Evidence of historical positive selection was detected at MHC using maximum likelihood codon-based methods. Bayesian and multivariate cluster analyses revealed weaker population genetic differentiation at MHC relative to the increasing microsatellite genetic structure towards the eastern wolverine distribution. Mantel correlations of MHC against geographical distances showed no pattern of isolation by distance (IBD: r = -0.03, p = 0.9), whereas for microsatellites we found a relatively strong and significant IBD (r = 0.54, p = 0.01). Moreover, we found a significant correlation between microsatellite allelic richness and the mean number of MHC alleles, but we did not observe low MHC diversity in small populations. Overall these results suggest that MHC polymorphism has been influenced primarily by balancing selection and to a lesser extent by neutral processes such as genetic drift, with no clear evidence for local adaptation. This study contributes to our understanding of how vulnerable populations of wolverines may respond to selective pressures across their range.

Isolation of peripheral populations of Canada lynx (Lynx canadensis)

Landscape barriers to gene flow, such as rivers, can affect animal populations by limiting the potential for rescue of these isolated populations. We tested the riverine barrier hypothesis, predicting that the St. Lawrence River in eastern Canada would cause genetic divergence of Canada lynx (Lynx canadensis Kerr, 1792) populations by restricting dispersal and gene flow. We sampled 558 lynx from eastern Canada and genotyped these at 14 microsatellite loci. We found three genetic clusters, defined by the St. Lawrence River and the Strait of Belle Isle, a waterway separating Newfoundland from mainland Canada. However, these waterways were not absolute barriers, as we found 24 individuals that appeared to have crossed them. Peripheral populations of lynx are threatened in parts of Canada and the USA, and it is thought that these populations are maintained by immigration from the core. Our findings suggest that in eastern North America, rescue might be less likely because the St. Lawrence River restricts dispersal. We found that ice cover was often sufficient to allow lynx to walk across the ice in winter. If lynx used ice bridges in winter, then climate warming could cause a reduction in the extent and longevity of river and sea ice, further isolating these peripheral lynx populations.

Enzyme immunoassays as a method for quantifying hair reproductive hormones in two felid species

Non-invasive monitoring of wild felid reproductive states is important, given that many species reproduce poorly in captivity. Despite extensive work in faecal hormone analysis in felids, continued development of techniques is necessary, particularly with wild populations. In this study, our aims were as follows: (i) biochemical validation of enzyme immunoassays for estrogen, testosterone and progesterone in Canada lynx and domestic cat hair extracts; (ii) assessment of the use of hair reproductive hormones to differentiate between reproductive states (intact, estrus, pregnant and spayed/neutered), using domestic cats as a model; and (iii) assessment of the use of hair reproductive hormones to differentiate between age and sex, accounting for potential regional variability in wild lynx populations. Analysis of hair hormone levels showed prospective value in detecting pregnancy states, with pregnant domestic cats having higher levels of progesterone than spayed females. However, intact and pregnant cats did not differ in progesterone levels. Yet, two female domestic cats had higher levels of hair progesterone following a 38-day oral progestin treatment, perhaps providing a preliminary pharmacological validation of the method. Estrogen and testosterone did not differ statistically according to reproductive states of domestic cats, although intact males had higher levels of hair testosterone than neutered males. When we applied these techniques to lynx fur, we determined that hormone levels were not sufficiently precise to differentiate age classes. Hair reproductive hormone ratios differed between sexes, with the estrogen-to-progesterone ratio demonstrating the highest accuracy in differentiating males from females. Hair hormone levels differed regionally for wild lynx, indicating that spatial variability should be a consideration in wildlife hormone studies spanning large spatial scales. We conclude that use of hair hormone analysis by enzyme immunoassay may hold promise for differentiating sex in felids, but the technique will require further refinement and validation before it can be applied broadly and reliably.

Phylogeography and post-glacial recolonization in wolverines (Gulo gulo) from across their circumpolar distribution

Interglacial-glacial cycles of the Quaternary are widely recognized in shaping phylogeographic structure. Patterns from cold adapted species can be especially informative - in particular, uncovering additional glacial refugia, identifying likely recolonization patterns, and increasing our understanding of species' responses to climate change. We investigated phylogenetic structure of the wolverine, a wide-ranging cold adapted carnivore, using a 318 bp of the mitochondrial DNA control region for 983 wolverines (n=209 this study, n=774 from GenBank) from across their full Holarctic distribution. Bayesian phylogenetic tree reconstruction and the distribution of observed pairwise haplotype differences (mismatch distribution) provided evidence of a single rapid population expansion across the wolverine's Holarctic range. Even though molecular evidence corroborated a single refugium, significant subdivisions of population genetic structure (0.01< ΦST <0.99, P<0.05) were detected. Pairwise ΦST estimates separated Scandinavia from Russia and Mongolia, and identified five main divisions within North America - the Central Arctic, a western region, an eastern region consisting of Ontario and Quebec/Labrador, Manitoba, and California. These data are in contrast to the nearly panmictic structure observed in northwestern North America using nuclear microsatellites, but largely support the nuclear DNA separation of contemporary Manitoba and Ontario wolverines from northern populations. Historic samples (c. 1900) from the functionally extirpated eastern population of Quebec/Labrador displayed genetic similarities to contemporary Ontario wolverines. To understand these divergence patterns, four hypotheses were tested using Approximate Bayesian Computation (ABC). The most supported hypothesis was a single Beringia incursion during the last glacial maximum that established the northwestern population, followed by a west-to-east colonization during the Holocene. This pattern is suggestive of colonization occurring in accordance with glacial retreat, and supports expansion from a single refugium. These data are significant relative to current discussions on the conservation status of this species across its range.

Influence of adrenocorticotrophin hormone challenge and external factors (age, sex, and body region) on hair cortisol concentration in Canada lynx (Lynx canadensis)

Land use changes are a significant factor influencing the decline of felid populations. However, additional research is needed to better understand how these factors influence populations in the wild. Hormone analysis can provide valuable information on the basic physiology and overall health of an animal, and enzyme immunoassays (EIA) are generally used for hair hormone analysis but must first be validated for the substrate of choice and species of interest. To date, hormone assays from hair have not been validated for Felidae, despite that the method holds considerable promise for non-invasive sampling of free-ranging animals. We sought to: (1) evaluate whether increased adrenocorticotrophin hormone (ACTH) during the period of hair growth results in elevated hair cortisol; (2) validate the enzyme immunoassay used; and (3) identify any variations in hair cortisol between age, sex and body regions, using Canada lynx. We quantified hair cortisol concentrations in captive animals through an ACTH challenge and collected samples from legally harvested lynx to compare variability between body regions. An EIA was validated for the analysis of hair cortisol. Lynx (n=3) had a qualitative increase in hair cortisol concentration following an ACTH challenge in captive animals (20 IU/kg of body weight weekly for 5 weeks), thereby supporting the use of an EIA to quantify cortisol values in hair. Based on our analysis of sampled lynx pelts, we found that hair cortisol did not vary between age and sex, but varied within the foot/leg region to a greater extent than between individuals. We recommend that future studies identify a standardized location for hair cortisol sampling.

Impact of population expansion on genetic diversity and structure of river otters (Lontra canadensis) in Central North America

Populations of North American river otters (Lontra canadensis) declined throughout large portions of the continent during the early 1900s due to habitat degradation and unregulated trapping. River otters had been extirpated in North Dakota (ND), but the Red River Valley has since been recolonized, with potential source populations including the neighboring states of Minnesota or South Dakota, or the Canadian province of Manitoba (MB). We genotyped 9 microsatellite loci in 121 samples to determine the source population of river otters in the Red River Valley of ND, as well as to assess population structure and diversity of river otters in central North America. Overall, genetic diversity was high, with an average observed heterozygosity of 0.58. Genetic differentiation was low (F ST < 0.05) between river otters in ND and those of Minnesota, suggesting that eastern ND was recolonized by river otters from Minnesota. River otters from MB were genetically distinct from all other sampled populations. Low genetic differentiation (F ST = 0.044) between South Dakota and Louisiana (LA) suggested that reintroductions using LA stock were successful. The genetic distinctiveness of river otters from different geographic regions should be considered when deciding on source populations for future translocations.