Stacie J. Robinson

Putting the "landscape" in landscape genetics.

Landscape genetics has emerged as a new research area that integrates population genetics, landscape ecology and spatial statistics. Researchers in this field can combine the high resolution of genetic markers with spatial data and a variety of statistical methods to evaluate the role that landscape variables play in shaping genetic diversity and population structure. While interest in this research area is growing rapidly, our ability to fully utilize landscape data, test explicit hypotheses and truly integrate these diverse disciplines has lagged behind. Part of the current challenge in the development of the field of landscape genetics is bridging the communication and knowledge gap between these highly specific and technical disciplines. The goal of this review is to help bridge this gap by exposing geneticists to terminology, sampling methods and analysis techniques widely used in landscape ecology and spatial statistics but rarely addressed in the genetics literature. We offer a definition for the term ‘landscape genetics’, provide an overview of the landscape genetics literature, give guidelines for appropriate sampling design and useful analysis techniques, and discuss future directions in the field. We hope, this review will stimulate increased dialog and enhance interdisciplinary collaborations advancing this exciting new field.

Reliability of genetic bottleneck tests for detecting recent population declines

The identification of population bottlenecks is critical in conservation because populations that have experienced significant reductions in abundance are subject to a variety of genetic and demographic processes that can hasten extinction. Genetic bottleneck tests constitute an appealing and popular approach for determining if a population decline has occurred because they only require sampling at a single point in time, yet reflect demographic history over multiple generations. However, a review of the published literature indicates that, as typically applied, microsatellite‐based bottleneck tests often do not detect bottlenecks in vertebrate populations known to have experienced declines. This observation was supported by simulations that revealed that bottleneck tests can have limited statistical power to detect bottlenecks largely as a result of limited sample sizes typically used in published studies. Moreover, commonly assumed values for mutation model parameters do not appear to encompass variation in microsatellite evolution observed in vertebrates and, on average, the proportion of multi‐step mutations is underestimated by a factor of approximately two. As a result, bottleneck tests can have a higher probability of ‘detecting’ bottlenecks in stable populations than expected based on the nominal significance level. We provide recommendations that could add rigor to inferences drawn from future bottleneck tests and highlight new directions for the characterization of demographic history.

The walk is never random: subtle landscape effects shape gene flow in a continuous white-tailed deer population in the Midwestern United States

One of the pervasive challenges in landscape genetics is detecting gene flow patterns within continuous populations of highly mobile wildlife. Understanding population genetic structure within a continuous population can give insights into social structure, movement across the landscape and contact between populations, which influence ecological interactions, reproductive dynamics or pathogen transmission. We investigated the genetic structure of a large population of deer spanning the area of Wisconsin and Illinois, USA, affected by chronic wasting disease. We combined multiscale investigation, landscape genetic techniques and spatial statistical modelling to address the complex questions of landscape factors influencing population structure. We sampled over 2000 deer and used spatial autocorrelation and a spatial principal components analysis to describe the population genetic structure. We evaluated landscape effects on this pattern using a spatial autoregressive model within a model selection framework to test alternative hypotheses about gene flow. We found high levels of genetic connectivity, with gradients of variation across the large continuous population of white‐tailed deer. At the fine scale, spatial clustering of related animals was correlated with the amount and arrangement of forested habitat. At the broader scale, impediments to dispersal were important to shaping genetic connectivity within the population. We found significant barrier effects of individual state and interstate highways and rivers. Our results offer an important understanding of deer biology and movement that will help inform the management of this species in an area where overabundance and disease spread are primary concerns.

The role of genetics in chronic wasting disease of North American cervids

Chronic wasting disease (CWD) is a major concern for the management of North American cervid populations. This fatal prion disease has led to declines in populations which have high CWD prevalence and areas with both high and low infection rates have experienced economic losses in wildlife recreation and fears of potential spill-over into livestock or humans. Research from human and veterinary medicine has established that the prion protein gene (Prnp) encodes the protein responsible for transmissible spongiform encephalopathies (TSEs). Polymorphisms in the Prnp gene can lead to different prion forms that moderate individual susceptibility to and progression of TSE infection. Prnp genes have been sequenced in a number of cervid species including those currently infected by CWD (elk, mule deer, white-tailed deer, moose) and those for which susceptibility is not yet determined (caribou, fallow deer, sika deer). Over thousands of sequences examined, the Prnp gene is remarkably conserved within the family Cervidae; only 16 amino acid polymorphisms have been reported within the 256 amino acid open reading frame in the third exon of the Prnp gene. Some of these polymorphisms have been associated with lower rates of CWD infection and slower progression of clinical CWD. Here we review the body of research on Prnp genetics of North American cervids. Specifically, we focus on known polymorphisms in the Prnp gene, observed genotypic differences in CWD infection rates and clinical progression, mechanisms for genetic TSE resistance related to both the cervid host and the prion agent and potential for natural selection for CWD-resistance. We also identify gaps in our knowledge that require future research.

Emerging prion disease drives host selection in a wildlife population

Infectious diseases are increasingly recognized as an important force driving population dynamics, conservation biology, and natural selection in wildlife populations. Infectious agents have been implicated in the decline of small or endangered populations and may act to constrain population size, distribution, growth rates, or migration patterns. Further, diseases may provide selective pressures that shape the genetic diversity of populations or species. Thus, understanding disease dynamics and selective pressures from pathogens is crucial to understanding population processes, managing wildlife diseases, and conserving biological diversity. There is ample evidence that variation in the prion protein gene (PRNP) impacts host susceptibility to prion diseases. Still, little is known about how genetic differences might influence natural selection within wildlife populations. Here we link genetic variation with differential susceptibility of white-tailed deer to chronic wasting disease (CWD), with implications for fitness and disease-driven genetic selection. We developed a single nucleotide polymorphism (SNP) assay to efficiently genotype deer at the locus of interest (in the 96th codon of the PRNP gene). Then, using a Bayesian modeling approach, we found that the more susceptible genotype had over four times greater risk of CWD infection; and, once infected, deer with the resistant genotype survived 49% longer (8.25 more months). We used these epidemiological parameters in a multi-stage population matrix model to evaluate relative fitness based on genotype-specific population growth rates. The differences in disease infection and mortality rates allowed genetically resistant deer to achieve higher population growth and obtain a long-term fitness advantage, which translated into a selection coefficient of over 1% favoring the CWD-resistant genotype. This selective pressure suggests that the resistant allele could become dominant in the population within an evolutionarily short time frame. Our work provides a rare example of a quantifiable disease-driven selection process in a wildlife population, demonstrating the potential for infectious diseases to alter host populations. This will have direct bearing on the epidemiology, dynamics, and future trends in CWD transmission and spread. Understanding genotype-specific epidemiology will improve predictive models and inform management strategies for CWD-affected cervid populations.

Estimating abundance of American black bears using DNA-based capture–mark–recapture models

Abstract Wildlife managers at Kenai Fjords (KEFJ) National Park, Alaska, are developing a comprehensive bear management plan. An important first step in this plan is to establish a baseline of bear abundance and inventory approaches for future monitoring efforts. In this study we use non-invasive genetic sampling and DNA-based capture–mark–recapture (CMR) analysis to estimate abundance of American black bears (Ursus americanus) using coastal habitats in the park. We used 2 multi-session CMR models in program MARK and 2 continuous-occasion models specifically designed for DNA-based capture data in the programs CAPWIRE and BAYESN. The latter 2 models maximize data from non-invasive sampling by allowing the entire sampling period to be considered a single continuous capture–mark–recapture occasion. Although all models yielded similar point estimates of population size, confidence intervals varied widely among methods. CAPWIRE yielded the most precise estimates of bear abundance. The number of bears estimated in each KEFJ bay ranged from 73 in the least populated to 324 in the most populated bay. Overall, the continuous-occasion CMR models provided the best estimates with our dataset, and we found that this approach offers a practical option when trapping seasons are constrained by biological or logistical factors.

Evaluating Population Structure of Black Bears on the Kenai Peninsula using Mitochondrial and Nuclear DNA Analyses

Abstract Increasing human impacts on the Kenai Peninsula, Alaska, have raised questions about potential implications for genetic diversity and population structure of local taxa. Black bears (Ursus americanus) occupy most of the Kenai Peninsula and are currently a species of public interest and management focus. In this study, we use 13 nuclear DNA (nDNA) microsatellite loci and sequence data from the mitochondrial DNA (mtDNA) control region to investigate population structure and phylogeographic patterns in black bears on the Kenai and surrounding mainland. We used both aspatial and spatial Bayesian assignment models to evaluate nDNA genetic structure and cluster individuals into genetically distinct groups. Substantial population substructure was detected, indicating restricted gene flow in recent generations as well as signatures of past barriers between the Kenai and mainland. We identified 3 genetically distinct groups that cluster geographically in the Kenai Peninsula, Alaskan mainland, and Prince William Sound areas. Connectivity among genetic groups was moderate, with Fst values ranging from 0.07 to 0.12. Five mtDNA haplotypes were detected, 2 of which were primarily restricted to the Kenai. Our results provide important information about current levels of genetic diversity and connectivity among black bears on the Kenai Peninsula and will provide a baseline for future monitoring.

ORAL RABIES VACCINE (ORV) BAIT UPTAKE BY CAPTIVE STRIPED SKUNKS

Aerial delivery of oral rabies vaccine (ORV) baits has proven effective in large-scale efforts to immunize wildlife against rabies, and in North America this strategy currently is being used to immunize foxes (Urocyon cinereoargenteus and Vulpes vulpes), raccoons (Procyon lotor), and coyotes (Canis latrans). Skunks are also a major reservoir and vector of rabies, but at present oral vaccines for use in skunks are not licensed. Furthermore, given differences in morphology (smaller jaws) and behavior (food handling and consumption), it is unknown if baits currently used in ORV campaigns would be effective for skunks. Because oral vaccine delivery is contingent upon puncture of the vaccine container (VC), baits need to be sufficiently attractive to elicit selection and consumption. Manipulation of the bait to facilitate vaccine ingestion by the target species is a critical element for an effective ORV bait. The objectives of this study were to assess manipulation and consumption of current ORV baits by striped skunks (Mephitis mephitis). We conducted four independent trials with penned animals and various baits to assess bait selection frequency, VC puncture frequency, and consumption. Video recorded trials were used to assess attractiveness of baits and consumption behavior of skunks. Bait characteristics, such as texture, size, and flavor influenced selection and consumption. Fish and chicken flavors were preferred and vaccine containers within selected baits were likely to be punctured. Vaccine ingestion seemed more likely if VCs were directly coated with the bait matrix. To make baits attractive to skunks and to ensure puncture of the VC, modifications to current baits should consider a smaller size, a meat-flavored matrix, a slightly pressurized VC, and a direct coating of matrix on the VC.

Evaluating spatial overlap and relatedness of white-tailed deer in a chronic wasting disease management zone.

Wildlife disease transmission, at a local scale, can occur from interactions between infected and susceptible conspecifics or from a contaminated environment. Thus, the degree of spatial overlap and rate of contact among deer is likely to impact both direct and indirect transmission of infectious diseases such chronic wasting disease (CWD) or bovine tuberculosis. We identified a strong relationship between degree of spatial overlap (volume of intersection) and genetic relatedness for female white-tailed deer in Wisconsin’s area of highest CWD prevalence. We used volume of intersection as a surrogate for contact rates between deer and concluded that related deer are more likely to have contact, which may drive disease transmission dynamics. In addition, we found that age of deer influences overlap, with fawns exhibiting the highest degree of overlap with other deer. Our results further support the finding that female social groups have higher contact among related deer which can result in transmission of infectious diseases. We suggest that control of large social groups comprised of closely related deer may be an effective strategy in slowing the transmission of infectious pathogens, and CWD in particular.

Diversity and Distribution of White-Tailed Deer mtDNA Lineages in Chronic Wasting Disease (CWD) Outbreak Areas in Southern Wisconsin, USA

Chronic wasting disease (CWD) is a transmissible spongiform encephalopathy affecting North American cervids. Because it is uniformly fatal, the disease is a major concern in the management of white-tailed deer populations. Management programs to control CWD require improved knowledge of deer interaction, movement, and population connectivity that could influence disease transmission and spread. Genetic methods were employed to evaluate connectivity among populations in the CWD management zone of southern Wisconsin. A 576-base-pair region of the mitochondrial DNA of 359 white-tailed deer from 12 sample populations was analyzed. Fifty-eight variable sites were detected within the sequence, defining 43 haplotypes. While most sample populations displayed similar levels of haplotype diversity, individual haplotypes were clustered on the landscape. Spatial clusters of different haplotypes were apparent in distinct ecoregions surrounding CWD outbreak areas. The spatial distribution of mtDNA haplotypes suggests that clustering of the deer matrilineal groups and population connectivity are associated with broad-scale geographic landscape features. These landscape characteristics may also influence the contact rates between groups and therefore the potential spread of CWD; this may be especially true of local disease spread between female social groups. Our results suggest that optimal CWD management needs to be tailored to fit gender-specific dispersal behaviors and regional differences in deer population connectivity. This information will help wildlife managers design surveillance and monitoring efforts based on population interactions and potential deer movement among CWD-affected and unaffected areas.