Aaron B A Shafer

Aaron B A Shafer
Trent University · Forensics & Environmental and Life Sciences

Ph.D., M.Sc., B.Sc.

About

112
Publications
26,618
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
2,644
Citations
Citations since 2016
58 Research Items
1991 Citations
2016201720182019202020212022050100150200250300
2016201720182019202020212022050100150200250300
2016201720182019202020212022050100150200250300
2016201720182019202020212022050100150200250300
Additional affiliations
September 2012 - present
Uppsala University
Position
  • Pinniped speciation and demographic history
May 2012 - September 2012
University of Alberta
Position
  • Grizzly bear evolutionary ecology
September 2007 - April 2012
University of Alberta
Position
  • Comparative phylogeography and mountain goat evolutionary ecology
Education
September 2007 - April 2012
University of Alberta
Field of study
  • Biological Sciences: Systematics and Evolution
September 2005 - April 2007
Acadia University
Field of study
  • Biological Sciences
September 2001 - April 2005
McMaster University
Field of study
  • Biology

Publications

Publications (112)
Article
Geographically isolated populations, specifically island-mainland counterparts, tend to exhibit phenotypic variation in many species. The so-called island syndrome occurs when different environmental pressures lead to insular divergence from mainland populations. This phenomenon can be seen in an island population of Nova Scotia masked shrews (Sore...
Article
Full-text available
The loss of genetic diversity is a challenge many species are facing, with genomics being a potential tool to inform and prioritize decision‐making. Most caribou (Rangifer tarandus) populations have experienced significant recent declines throughout Québec, Canada, and are considered of concern, threatened or endangered. Here, we calculated the anc...
Preprint
Full-text available
Geographically isolated populations, specifically island-mainland counterparts, tend to exhibit phenotypic variation in many species. The so-called island syndrome occurs when different environmental pressures lead to insular divergence from mainland populations. This phenomenon can be seen in an island population of Nova Scotia masked shrews (Sore...
Article
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 can experience reduced genetic diversity when deleterious habitat change occurs, leading to an increased likelihood...
Article
Full-text available
Context Deciphering how the complex environmental dynamics of highland temperate forests drive local patterns of genetic variation is key to understanding species diversity and distribution. Objectives Evaluate how the environmental complexity of La Malinche volcano influences patterns of genomic variation in Peromyscus melanotis, across two mount...
Preprint
Animal migrations are some of the most ubiquitous and one of the most threatened ecological processes. A wide range of migratory behaviours occur in nature, and this behaviour is not uniform between and within species, where even individuals in the same population can exhibit differentiation. While the environment largely drives migratory behaviour...
Article
Full-text available
Identifying the genes underlying fitness-related traits such as body size and male ornamentation can provide tools for conservation and management and are often subject to various selective pressures. Here we performed high-depth whole genome re-sequencing of pools of individuals representing the phenotypic extremes for antler and body size in whit...
Article
Full-text available
Potential negative artificial selection on horn size is a concern for many harvested ungulates. The mountain goat (Oreamnos americanus) has distinct black horns, but targeting animals based on horn size in the field can be challenging. We analyzed over 23,000 horn records that included base circumference and total length, from which we also derived...
Article
Three orders represent the South American fauna of marsupials. Of these, Microbiotheria was until recently known as a monotypic genus with the only surviving species Dromiciops gliroides (monito del monte). The recent proposal of a new Dromiciops species (Dromiciops bicinovici), together with new information on the origin and diversification of liv...
Article
Full-text available
Cattails (Typha species) comprise a genus of emergent wetland plants with a global distribution. Typha latifolia and Typha angustifolia are two of the most widespread species, and in areas of sympatry can interbreed to produce the hybrid Typha × glauca. In some regions, the relatively high fitness of Typha × glauca allows it to outcompete and displ...
Article
Full-text available
The gut microbiome of animals varies by age, diet, and habitat, and directly influences an individual's health. Similarly, variation in home ranges is linked to feeding strategies and fitness. Ungulates (hooved mammals) exhibit species-specific microbiomes and habitat use patterns. We combined gut microbiome and movement data to assess relationship...
Article
Full-text available
Sexual selection is a well-known biological process, yet the genomic basis and patterns of sexual selection are not fully understood. The extravagant ornamental plumage of peacock ( Pavo cristatus ) was instrumental in shaping Charles Darwin's theory of sexual selection and is considered to be an honest signal of its immunocompetence. Here, we used...
Article
Full-text available
Many lakes across Canada and northern Europe have experienced declines in ambient phosphorus (P) and calcium (Ca) supply for over 20 years. While these declines might create or exacerbate nutrient limitation in aquatic food webs, our ability to detect and quantify different types of nutrient stress on zooplankton remains rudimentary. Here, we used...
Article
Full-text available
Acquisition of field data and analytical methods needed for conservation and management of wildlife populations represent significant challenges, particularly for species that inhabit landscapes that are difficult to access or species that persist in small, isolated populations. In such instances, integrating diverse and complementary data streams,...
Article
Full-text available
Amphibians are experiencing worldwide declines due to increasing anthropogenetic disturbances. However, the genetic variability and hence adaptability are still unknown for most frogs. We integrated the mitochondrial (ND2 gene), nuclear (TYR gene) and major histocompatibility complex (MHC) loci, to clarify the demographic patterns and immune-gene d...
Preprint
Full-text available
Here, we combined fecal microbiome and movement data to assess the relationship between space use and the gut microbiome in a specialist and a generalist ungulate. We captured and GPS radiocollared 24 mountain goats (Oreamnos americanus) and 34 white-tailed deer (Odocoileus virginianus). This is the first study to relate core range size to gut div...
Article
Full-text available
The effective size of a population (Ne), which determines its level of neutral variability, is a key evolutionary parameter. Ne can substantially depart from census sizes of present-day breeding populations (NC) as a result of past demographic changes, variation in life-history traits and selection at linked sites. Using genome-wide data we estimat...
Article
Estimating heritability (h2) is required to predict the response to selection and is useful in species that are managed or farmed using trait information. Estimating h2 in free-ranging populations is challenging due to the need for pedigrees; genomic-relatedness matrices (GRMs) circumvent this need and can be implemented in nearly any system where...
Article
Full-text available
Species that inhabit fragmented habitats are expected to exhibit spatial genetic structure with respect to geographic distance and landscape features. These patterns are also shaped by a variety of temporal processes, namely post-glacial recolonization, and those operating at more contemporary scales, such as sex-biased dispersal. We quantified the...
Article
Full-text available
The North American mountain goat (Oreamnos americanus) is an iconic alpine species that faces stressors from climate change, industrial development, and recreational activities. This species' phylogenetic position within the Caprinae lineage has not been resolved and their phylogeographic history is dynamic and controversial. Genomic data will be u...
Article
Full-text available
The community of microorganisms in the gut is affected by host species, diet, and environment and is linked to normal functioning of the host organism. Although the microbiome fluctuates in response to host demands and environmental changes, there are core groups of microorganisms that remain relatively constant throughout the hosts lifetime. Rumin...
Preprint
Full-text available
The community of microorganisms in the gut is affected by host species, diet, and environment and is linked to normal functioning of the host organism. Although the microbiome fluctuates in response to host demands and environmental changes, there are core groups of microorganisms that remain relatively constant throughout the hosts lifetime. Rumin...
Article
Full-text available
The unique ornamental features and extreme sexual traits of Peacock have always intrigued scientists and naturalists for centuries. However, the genomic basis of these phenotypes are yet unknown. Here, we report the first genome sequence and comparative analysis of peacock with the high quality genomes of chicken, turkey, duck, flycatcher and zebra...
Article
The genomics revolution has sparked interest in using our increased understanding of the loci involved in phenotypic variation and adaptation to advance the conservation of biodiversity. Despite much interest and discussion, it remains unclear whether, when, and how such analyses should be used to guide conservation action. Such 'gene-targeted' con...
Chapter
Humans have long relied on ungulates for food, clothing, manual labor, and transportation. Ungulates were among the first species to be domesticated and managed in the wild, but more than one-third of species are currently of conservation concern. Starting in the late twentieth century, ungulate research and management began employing genetic tools...
Article
Full-text available
Forest musk deer (Moschus berezovskii; FMD) are both economically valuable and highly endangered. A problem for FMD captive breeding programs has been the susceptibility of FMD to abscesses. To investigate the mechanisms of abscess development in FMD, the blood transcriptomes of three purulent and three healthy individuals were generated. A total o...
Article
Full-text available
Food resources are often not sufficient to satisfy the nutritional and energetic requirements during winter conditions at high latitudes. Dietary analysis is a prerequisite to fully understanding the feeding ecology of a species and the nature of trophic interactions. Previous dietary studies of Asian Great Bustard (Otis tarda dybowskii) relied on...
Chapter
Characterizing population histories has been a major focus in evolutionary and conservation biology for decades. Driven by a desire to understand population histories, researchers have been modeling simple demographic scenarios with genetic data since the 1970s. In the last decade, the availability of genomic data and the number of demographic infe...
Data
The rarefaction curves of OTUs and Shannon index for the 40 samples. JA1–JA10 represent the samples collected from the juvenile alpine musk deer, AA1–AA10 represent the samples collected from the adult alpine musk deer, JF1–JF10 represent the samples collected from the juvenile forest musk deer, AF1–AF10 represent the samples collected from the adu...
Data
Pairwise non-metric multidimensional scaling (NMDS) of the dissimilarity between different sample groups. Distance between the samples, based on dissimilarity in OTU composition of each sample was calculated using the Bray–Curtis dissimilarity index. Each point represents a different sample and a greater distance between two points infers a higher...
Data
The operational taxonomic unit (OTU) numbers of classified and unclassified bacterial phylotypes among four sample groups. JA, juvenile alpine musk deer; AA, adult alpine musk deer; JF, juvenile forest musk deer; AF, adult forest musk deer.
Article
Full-text available
The gut ecosystem is characterized by dynamic and reciprocal interactions between the host and bacteria. Although characterizing microbiota for herbivores has become recognized as important tool for gauging species health, no study to date has investigated the bacterial communities and evaluated the age-related bacterial dynamics of musk deer. More...
Article
Full-text available
Wintering areas affect population processes and genetic structuring of many bird species. The Asian Great Bustard (Otis tarda dybowskii) is declining across its range as its breeding and wintering grounds become more fragmented. No genetic information for this vulnerable subspecies in the wild exists. We used noninvasive fecal sampling and mitochon...
Article
Restriction site-associated DNA sequencing (RAD-seq) provides high-resolution population genomic data at low cost, and has become an important component in ecological and evolutionary studies. As with all high-throughput technologies, analytic strategies require critical validation to ensure accurate and unbiased interpretation. . To test for the i...
Article
Full-text available
Cross-species application of single-nucleotide polymorphism (SNP) chips is a valid, relatively cost-effective alternative to the high-throughput sequencing methods generally required to obtain a genome-wide sampling of polymorphisms. Kharzinova et al. (2015) examined the applicability of SNP chips developed in domestic bovids (cattle and sheep) to...
Article
Transcontinental migration is a fascinating example of how animals can respond to climatic oscillation. Yet, quantitative data on fitness components are scarce, and the resulting population genetic consequences poorly understood. Migratory divides, hybrid zones with a transition in migratory behaviour, provide a natural setting to investigate the m...
Article
Full-text available
Recent advancements in animal tracking technology and high-throughput sequencing are rapidly changing the questions and scope of research in the biological sciences. The integration of genomic data with high-tech animal instrumentation comes as a natural progression of traditional work in ecological genetics, and we provide a framework for linking...
Article
Full-text available
The letter by Garner et al. [1] continued an important discussion regarding the role genomics might play in conservation biology. In general, we do not see a dichotomy between our point of view [2] and that put forth by Garner et al. [1]. At the heart of the issue is how to define an actual impact of genomics on applied conservation and find suitab...
Article
Full-text available
The forest musk deer (Moschus berezovskii) is a high elevation species distributed across western China and northern Vietnam. Once abundant, habitat loss and poaching has led to a dramatic decrease in population numbers prompting the IUCN to list the species as endangered. Here, we characterized the genetic diversity of a Major Histocompatibility C...
Article
The global loss of biodiversity continues at an alarming rate. Genomic approaches have been suggested as a promising tool for conservation practice, and we discuss how scaling-up to genome-wide inference can benefit traditional conservation genetic approaches and provide qualitatively novel insights. Yet, the generation of genomic data and subseque...
Article
The global loss of biodiversity continues at an alarming rate. Genomic approaches have been suggested as a promising tool for conservation practice as scaling up to genome-wide data can improve traditional conservation genetic inferences and provide qualitatively novel insights. However, the generation of genomic data and subsequent analyses and in...