Christopher J. Kyle

Genetic nature of eastern wolves: Past, present and future

Eastern North American wolves have long been recognized as morphologically distinct from both coyotes and gray wolves. This has led to questions regarding their origins and taxonomic status. Eastern wolves are mainly viewed as: (1) a smaller subspecies of gray wolf (Canis lupus lycaon), potentially the result of historical hybridization between gray wolves (C. lupus) and red wolves (C. rufus), (2) a hybrid, the result of gray wolf (C. lupus) and coyote (C. latrans) interbreeding, or (3) a distinct species, C. lycaon, closely related to the red wolf (C. rufus). Although debate persists, recent molecular studies suggest that the eastern wolf is not a gray wolf subspecies, nor the result of gray wolf/coyote hybridization. Eastern wolves were more likely a distinct species, C. lycaon, prior to the eastward spread of coyotes in the late 1800s. However, contemporary interbreeding exits between C. lycaon to both C. lupus and C. latrans over much of its present range complicating its present taxonomic characterization. While hybridization may be reducing the taxonomic distinctiveness of C. lycaon, it should not necessarily be viewed as negative influence. Hybridization may be enhancing the adaptive potential of eastern wolves, allowing them to more effectively exploit available resources in rapidly changing environments.

Differential permeability of rivers to raccoon gene flow corresponds to rabies incidence in Ontario, Canada

The correlation of landscape features with genetic discontinuities reveals barriers to dispersal that can contribute to understanding present and future spread of wildlife diseases. This knowledge can then be used for targeting control efforts. The impact of natural barriers on raccoon dispersal was assessed through genetic analysis of samples from two regions, Niagara (N = 666) and St. Lawrence (N = 802). These areas are transected by major rivers and are at the northern front of a raccoon rabies epizootic. Genetic clusters were identified in each region using Bayesian clustering algorithms. In the Niagara region, two clusters were identified corresponding to either side of the Niagara River. For the St. Lawrence region, spatially congruent clusters were not identified, despite the presence of the intervening St. Lawrence River. These genetic data are consistent with raccoon rabies incidence data where rabies has been detected across the St. Lawrence River in Ontario while no cases have been detected in Ontario across the Niagara River. This is despite expectations of rabies incidence in Niagara before the St. Lawrence based on the progression of rabies from New York. The results from the two regions suggest different permeabilities to raccoons between New York and Ontario that may be attributed to the rivers. However, other factors have also been explored that could contribute to this difference between these study sites including the shape of the landscape and resource distribution.

Combining direct and indirect genetic methods to estimate dispersal for informing wildlife disease management decisions

Epidemiological models are useful tools for management to predict and control wildlife disease outbreaks. Dispersal behaviours of the vector are critical in determining patterns of disease spread, and key variables in epidemiological models, yet they are difficult to measure. Raccoon rabies is enzootic over the eastern seaboard of North America and management actions to control its spread are costly. Understanding dispersal behaviours of raccoons can contribute to refining management protocols to reduce economic impacts. Here, estimates of dispersal were obtained through parentage and spatial genetic analyses of raccoons in two areas at the front of the raccoon rabies epizootic in Ontario; Niagara (N = 296) and St Lawrence (N = 593). Parentage analysis indicated the dispersal distance distribution is highly positively skewed with 85% of raccoons, both male and female, moving < 3 km. The tail of this distribution indicated a small proportion (< 4%) moves more than 20 km. Analysis of spatial genetic structure provided a similar assessment as the spatial genetic correlation coefficient dropped sharply after 1 km. Directionality of dispersal would have important implications for control actions; however, evidence of directional bias was not found. Separating the data into age and sex classes the spatial genetic analyses detected female philopatry. Dispersal distances differed significantly between juveniles and adults, while juveniles in the Niagara region were significantly more related to each other than adults were to each other. Factors that may contribute to these differences include kin association, and spring dispersal. Changes to the timing and area covered by rabies control operations in Ontario are indicated based on these dispersal data.

Genetic diversity and population structure of wolverine (Gulo gulo) populations at the southern edge of their current distribution in North Americawith implications for genetic viability

The current range of wolverines (Gulo gulo) within the lower 48 states includes small, remnant populations in Idaho, Washington, Wyoming and Montana. The size and trend of each of these populations and connectivity to adjacent populations in the contiguous United States and Canada are poorly understood. In this study, levels of genetic diversity and population genetic structure were examined in three states (Idaho, Wyoming, and Montana) and two Canadian provinces (Alberta and British Columbia) using both mitochondrial (mtDNA) and nuclear microsatellite DNA. Restricted levels of gene flow were detected among these populations with mitochondrial and nuclear DNA and our observations suggest a pattern of male-mediated gene flow. Populations in the United States appear to be receiving migrants from Canada, however, substantial genetic differentiation suggests that gene flow may not be high enough to prevent genetic drift. Our analyses suggest that at least 400 breeding pairs or 1–2 effective migrants per generation would be needed to ensure genetic viability in the long-term for each of the populations in the United States. Significant matrilineal structuring and restricted female gene flow indicates that demographic viability will depend upon the movement of female wolverines into new territories. Results from this study provide guidelines for conservation and management and indicate the need for more ecological data.

MHC class II DRB diversity in raccoons (Procyon lotor) reveals associations with raccoon rabies virus (Lyssavirus).

In North America, the raccoon rabies virus (RRV) is an endemic wildlife disease which causes acute encephalopathies and is a strong selective force on raccoons (Procyon lotor), with estimates of ∼85% of the population succumbing to the disease when epizootic. RRV is regarded as a lethal disease if untreated; therefore, no evolutionary response would be expected of raccoon populations. However, variable immune responses to RRV have been observed in raccoons indicating a potential for evolutionary adaptation. Studies of variation within the immunologically important major histocompatibility complex (MHC) have revealed relationships between MHC alleles and diseases in humans and other wildlife species. This enhances our understanding of how hosts and pathogens adapt and co-evolve. In this study, we used RRV as a model system to study host–pathogen interaction in raccoons from a challenge study and from four wild populations that differ in exposure times and viral lineages. We investigated the potential role of Prlo-DRB polymorphism in relation to susceptibility/resistance to RRV in 113 RRV positive and 143 RRV negative raccoons. Six alleles were found to be associated with RRV negative status and five alleles with RRV positive animals. We found variable patterns of MHC associations given the relative number of selective RRV sweeps in the studied regions and correlations between MHC diversity and RRV lineages. The allelic associations established provide insight into how the genetic variation of raccoons may affect the disease outcome and this can be used to examine similar associations between other rabies variants and their hosts.

Comparison of 454 pyrosequencing methods for characterizing the major histocompatibility complex of nonmodel species and the advantages of ultra deep coverage.

Characterization and population genetic analysis of multilocus genes, such as those found in the major histocompatibility complex (MHC) is challenging in nonmodel vertebrates. The traditional method of extensive cloning and Sanger sequencing is costly and time‐intensive and indirect methods of assessment often underestimate total variation. Here, we explored the suitability of 454 pyrosequencing for characterizing multilocus genes for use in population genetic studies. We compared two sample tagging protocols and two bioinformatic procedures for 454 sequencing through characterization of a 185‐bp fragment of MHC DRB exon 2 in wolverines (Gulo gulo) and further compared the results with those from cloning and Sanger sequencing. We found 10 putative DRB alleles in the 88 individuals screened with between two and four alleles per individual, suggesting amplification of a duplicated DRB gene. In addition to the putative alleles, all individuals possessed an easily identifiable pseudogene. In our system, sequence variants with a frequency below 6% in an individual sample were usually artefacts. However, we found that sample preparation and data processing procedures can greatly affect variant frequencies in addition to the complexity of the multilocus system. Therefore, we recommend determining a per‐amplicon‐variant frequency threshold for each unique system. The extremely deep coverage obtained in our study (approximately 5000×) coupled with the semi‐quantitative nature of pyrosequencing enabled us to assign all putative alleles to the two DRB loci, which is generally not possible using traditional methods. Our method of obtaining locus‐specific MHC genotypes will enhance population genetic analyses and studies on disease susceptibility in nonmodel wildlife species.

Variability in the growth patterns of the cornified claw sheath among vertebrates: implications for using biogeochemistry to study animal movement

We review the role of biogeochemical signatures, such as stable isotopes and trace elements, in the cornified claw tissue as a means of studying movement and foraging behaviour of vertebrates because this approach is noninvasive and can capture contemporary and historic signatures. Because biogeochemical techniques are still relatively new in studies of animal movement, we are only beginning to understand how the growth patterns of the cornified claw sheath may affect our ability to interpret the biogeochemical signals in these tissues. To move towards resolving this, we review the morphology of the epidermal cornified claw sheath in several taxa that illustrate substantial variation in growth patterns both between taxa and between individual distinct claw regions. For instance, in mammalian claws, deposition of keratinizing cells from the epidermis is nonlinear because the claw tip is composed of old and new cornified epidermal cells, whereas the cornified blade horn covering the claw’s lateral walls is ...

Landscape modelling spatial bottlenecks: implications for raccoon rabies disease spread

A landscape genetic simulation modelling approach is used to understand factors affecting raccoon rabies disease spread in southern Ontario, Canada. Using the Ontario Rabies Model, we test the hypothesis that landscape configuration (shape of available habitat) affects dispersal, as indicated by genetic structuring. We simulated range expansions of raccoons from New York into vacant landscapes in Ontario, in two areas that differed by the presence or absence of a landscape constriction. Our results provide theoretical evidence that landscape constriction acts as a vicariant bottleneck. We discuss implications for raccoon rabies spread.

Rapid Homogenization of Multiple Sources: Genetic Structure of a Recolonizing Population of Fishers

Abstract Fishers (Martes pennanti) were extirpated from much of southern Ontario, Canada, prior to the 1950s. We hypothesised that the recent recolonization of this area originated from an expansion of the population in Algonquin Provincial Park, which historically served as a refuge for fishers. To test this hypothesis, we created a sampling lattice to encompass Algonquin and the surrounding area, and we collected contemporaneous DNA samples. We sampled fishers from each of 35 sites and genotyped them at 16 microsatellite loci. Using a Bayesian assignment approach, with no a priori geographic information, we inferred 5 discrete genetic populations and used genetic population assignment as a means to cluster sites together. We concluded that the Algonquin Park fisher population has not been a substantial source for recolonization and expansion, which has instead occurred from a number of remnant populations within Ontario, Quebec, and most recently from the Adirondacks in New York, USA. The genetic structure among sampling sites across the entire area revealed a pattern of isolation-by-distance (IBD). However, an examination of the distribution of genetic structure (FST/1−FST) at different distances showed higher rates of gene flow than predicted under a strict IBD model at small distances (40 km) within clusters and at larger distances up to 100 km among clusters. This pattern of genetic structure suggests increased migration and gene flow among expanding reproductive fronts.

Spatial patterns of neutral and functional genetic variations reveal patterns of local adaptation in raccoon (Procyon lotor) populations exposed to raccoon rabies

Local adaptation is necessary for population survival and depends on the interplay between responses to selective forces and demographic processes that introduce or retain adaptive and maladaptive attributes. Host–parasite systems are dynamic, varying in space and time, where both host and parasites must adapt to their ever‐changing environment in order to survive. We investigated patterns of local adaptation in raccoon populations with varying temporal exposure to the raccoon rabies virus (RRV). RRV infects approximately 85% of the population when epizootic and has been presumed to be completely lethal once contracted; however, disease challenge experiments and varying spatial patterns of RRV spread suggest some level of immunity may exist. We first assessed patterns of local adaptation in raccoon populations along the eastern seaboard of North America by contrasting spatial patterns of neutral (microsatellite loci) and functional, major histocompatibility complex (MHC) genetic diversity and structure. We explored variation of MHC allele frequencies in the light of temporal population exposure to RRV (0–60 years) and specific RRV strains in infected raccoons. Our results revealed high levels of MHC variation (66 DRB exon 2 alleles) and pronounced genetic structure relative to neutral microsatellite loci, indicative of local adaptation. We found a positive association linking MHC genetic diversity and temporal RRV exposure, but no association with susceptibility and resistance to RRV strains. These results have implications for landscape epidemiology studies seeking to predict the spread of RRV and present an example of how population demographics influence the degree to which populations adapt to local selective pressures.