Biology subjects

Shafer, A. B.

Publications and source records attributed to Shafer, A. B..

6 recordsLinked to original sources

bioRxiv2026

Measuring American black bear genetic load in fixed structural variants and runs of homozygosity

Populations living in geographically isolated regions are expected to have reduced gene flow, increased genetic drift, and elevated levels of inbreeding, influencing both genetic load and possibly the distribution of structural variants. The American black bear (Ursus americanus) is widely found across Ontario, Canada, where populations inhabit diverse landscapes ranging from relatively intact contiguous forested landscapes to isolated regions such as the Saugeen Peninsula. Here, we investigated the population genomic history across five Ontario black bear populations using a combination of short-read (SR) and long-read (LR) sequencing data. We compared population genetic metrics including nucleotide diversity ({pi}), Tajimas D, runs of homozygosity (ROH), and genome-wide structural variants (SVs) to assess population health and identify signatures of isolation. Our results showed that the isolated Saugeen Peninsula population is genetically distinct and exhibited reduced nucleotide diversity, greater ROH and SV abundance compared with mainland populations. The population also showed elevated genetic load in all genomic features, suggesting increased exposure of deleterious variation that are expressed in ROH and population specific SVs. We further discuss the integration of ROH, SVs and genetic load in conservation assessments.

genomics↗

bioRxiv2023

Unravelling the complex biogeographic and anthropogenic history of Alaska's mountain goats

AimWe used genetic tools to examine the population structure of mountain goats in Alaska, USA and assessed the demographic history of this species in relation to the natural and anthropogenic forces. LocationAlaska, USA TaxonNorth American mountain goat (Oreamnos americanus) MethodsSamples were collected between 2006 - 2020 from harvested animals and live captures. We genotyped 816 mountain goats at 18 microsatellite loci and identified the number of genetically distinct subpopulations across the state and assessed their genetic diversity. We used Bayesian computation software to investigate the demographic history relative to the known biogeographic history of the state. We also simulated island translocation events and compared simulations to empirical data to address the hypothesis that Baranof Island was a cryptic refugia. ResultsWe showed that Alaska has four genetically distinct subpopulations of mountain goats with some additional genetic structure within those subpopulations. The main split of mountain goats between Southcentral and Southeast Alaska occurred [~]14,000 years ago. Simulations of translocation events largely aligned with the current populations observed today except for Baranof Island which showed greater diversity than the translocation simulation. Main ConclusionsThe distribution and genetic structure of mountain goats in Alaska reflects a combination of natural and anthropogenic forces. A rapid northerly expansion through an ice-free corridor in combination with the isolated nature of the landscape led to low diversity and isolation 14,000 years ago in Southcentral Alaska and higher diversity in Southeast Alaska. Two of the three islands where mountain goat translocations have occurred match genetically with their source population, while Baranof Island appears to have a divergent population, consistent with the hypothesis of an endemic or cryptic population prior to the translocation event. This study highlights the value of considering both the natural and anthropogenic forces when assessing the biogeographic history of a species.

evolutionary biology↗

bioRxiv2023

Island demographics and trait associations in white-tailed deer

When a population is isolated and composed of few individuals, genetic drift is the paramount evolutionary force that results in the loss of genetic diversity. Inbreeding might also occur, resulting in genomic regions that are identical by descent, manifesting as runs of homozygosity (ROHs) and the expression of recessive traits. Likewise, the genes underlying traits of interest can be revealed by comparing fixed SNPs and divergent haplotypes between affected and unaffected individuals. Populations of white-tailed deer (Odocoileus virginianus) on islands of Saint Pierre and Miquelon (SPM, France) have high incidences of leucism and malocclusions, both considered genetic defects; on the Florida Keys islands (USA) deer exhibit smaller body sizes, a polygenic trait. Here we aimed to reconstruct island demography and identify the genes associated with these traits in a pseudo case-control design. The two island populations showed reduced levels of genomic diversity and a build-up of deleterious mutations compared to mainland deer; there was also significant genome-wide divergence in Key deer. Key deer showed higher inbreeding levels, but not longer ROHs, consistent with long-term isolation. We identified multiple trait-related genes in ROHs including LAMTOR2 which has links to pigmentation changes, and NPVF which is linked to craniofacial abnormalities. Our mixed approach of linking ROHs, fixed SNPs and haplotypes matched a high number ([~]50) of a-priori body size candidate genes in Key deer. This suite of biomarkers and candidate genes should prove useful for population monitoring, noting all three phenotypes show patterns consistent with a complex trait and non-Mendelian inheritance.

genomics↗

bioRxiv2022

Quantifying the effects of recent glacial history and future climate change on a unique population of mountain goats

Human disturbance and climate change can impact populations by disrupting movement corridors and reducing important habitat. Characterizing how animals respond to such environmental changes is valuable for conservation as many species, especially habitat specialists, can experience reduced genetic diversity when deleterious habitat change occurs, leading to an increased likelihood of extirpation. Mountain goats (Oreamnos americanus) exemplify this conservation challenge; their geographically isolated habitat can inhibit gene flow, making them susceptible to population declines in the face of anthropogenic-induced landscape change. To facilitate biologically informed population management of mountain goats in Glacier Bay National Park, Alaska, we characterized the fine-scale genetic population structure and examined how future climate change could impact the population density of these mountain goats. We used DNA samples to estimate diversity and depict the genealogical history. Climate response models allowed us to simulate changes to suitable habitat and predict how this might influence future population structure. Our results indicated that three genetically distinct subpopulations exist in Glacier Bay and that the population structure is reflective of the historic landscape patterns. Climate modeling predicted that demographic productivity was likely to be reduced for all subpopulations; additionally, we found that climate change likely degrades the suitability of movement corridors that facilitate gene flow between subpopulations, ultimately increasing the cost of travel. Understanding such fine-scale patterns are key to managing subpopulations, particularly with impending changes to the landscape.

evolutionary biology↗

bioRxiv2020

Characterizing the demographic history and prion protein variation to infer susceptibility to chronic wasting disease in a naïve population of white-tailed deer (Odocoileus virginianus)

Assessments of the adaptive potential in natural populations are essential for understanding and predicting responses to environmental stressors like climate change and infectious disease. Species face a range of stressors in human-dominated landscapes, often with contrasting effects. White-tailed deer (deer) are expanding in the northern part of their range following decreasing winter severity and increasing forage availability. Chronic wasting disease (CWD), a prion disease affecting cervids, is likewise expanding and represents a major threat to deer and other cervids. We obtained tissue samples from free-ranging deer across their native range in Ontario, Canada which has yet to detect CWD in wild populations of cervids. We used high-throughput sequencing to assess neutral genomic variation, and variation in the PRNP gene that is partly responsible for the protein misfolding when deer contract CWD. Neutral variation revealed a high number of rare alleles and no population structure, and demographic models suggested a rapid historical population expansion. Allele frequencies of PRNP variants associated with CWD susceptibility and disease progression were evenly distributed across the landscape and consistent with deer populations not infected with CWD. We then estimated the selection coefficient of CWD, with simulations showing an observable and rapid shift in PRNP allele frequencies that coincides with the start of a novel CWD epidemic. Sustained surveillance of genomic and PRNP variation can be a useful tool for CWD-free regions where deer are managed for ecological and economic benefits.

molecular biology↗

bioRxiv2019

Genomic architecture of artificially and sexually selected traits in a wild cervid

Characterization of the genomic architecture of fitness-related traits such as body size and male ornamentation in mammals provides tools for conservation and management: as both indicators of quality and health, these traits are often subject to sexual and artificial selective pressures. Here we performed high-depth whole genome re-sequencing on pools of individuals representing the phenotypic extremes in our study system for antler and body size in white-tailed deer (Odocoileus virginianus). Samples were selected from a tissue repository containing phenotypic data for 4,466 male white-tailed deer from Anticosti Island, Quebec, with four pools representing the extreme phenotypes for antler and body size in the population, after controlling for age. Our results revealed a largely panmictic population, but detected highly diverged windows between pools for both traits with high shifts in allele frequency (mean allele frequency difference of 14% for and 13% for antler and body SNPs in outlier windows). These regions often contained putative genes of small-to-moderate effect consistent with a polygenic model of quantitative traits. Genes in outlier antler windows had known direct or indirect effects on growth and pathogen defence, while body genes, overall GO terms, and transposable element analyses were more varied and nuanced. Through qPCR analysis we validated both a body and antler gene. Overall, this study revealed the polygenic nature of both antler morphology and body size in free-ranging white-tailed deer and identified target loci for additional analyses.

genomics↗