Biology subjects

Shafer, A.

Publications and source records attributed to Shafer, A..

22 records · Page 2Linked to original sources

bioRxiv2020

Heritability estimates of antler and body traits in white-tailed deer (Odocoileus virginianus) from genomic-relatedness matrices

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 phenotypic and SNP data are available. We estimated the heritability of five body and three antler traits in a free-ranging population of white-tailed deer (Odocoileus virginianus) on Anticosti Island, Quebec, Canada. We generated GRMs from >10,000 SNPs: dressed body mass and peroneus muscle mass had moderate h2 values of 0.49 and 0.56, respectively. Heritability in male-only antler features ranged from 0.00 to 0.51 and had high standard errors. We explored the influence of minor allele frequency and data completion filters on h2: GRMs derived from fewer SNPs had reduced h2 estimates and the relatedness coefficients significantly deviated from those generated with more SNPs. As a corollary, we discussed limitations to the application of GRMs in the wild, notably how skewed GRMs increase variance around h2 estimates. This is the first study to estimate h2 on a free-ranging population of white-tailed deer and should be informative for breeding designs and management.

genomics↗

bioRxiv2019

Tau pathology in cognitively normal older adults: Associations with brain atrophy and cognitive decline

INTRODUCTIONTau pathology, a hallmark of Alzheimers disease, is observed in the brains of virtually all individuals over 70.\n\nMETHODSUsing 18F-AV-1451 (18F-flortaucipir) PET, we evaluated tau pathology in 54 cognitively normal participants (mean age 77.5, SD 8.9) from the Baltimore Longitudinal Study of Aging. We assessed associations between PET signal and age, sex, race, and amyloid positivity. We investigated relationships between regional signal and retrospective rates of change in regional volumes and cognitive function adjusting for age, sex, and amyloid status.\n\nRESULTSGreater age, male sex, black race, and amyloid positivity were associated with higher 18F-AV-1451 retention in distinct brain regions. Retention in the entorhinal cortex was associated with lower entorhinal volume ({beta} = -1.124, SE = 0.485, p = 0.025) and a steeper decline in memory performance ({beta} = -0.086, SE = 0.039, p = 0.029).\n\nDISCUSSIONAssessment of medial temporal tau pathology will provide insights into early structural brain changes associated with later cognitive impairment and Alzheimers disease.

neuroscience↗

bioRxiv2018

Extensive field-sampling reveals the uniqueness of a trophy mountain goat population

Collaborations between academic researchers and agencies is crucial for genetic data to have a tangible impact on conservation and wildlife management. Such partnerships are particularly important elusive species where the difficult terrain requires that a significant amount of resources and a combination of methods be used to estimate population parameters needed for conservation. We report and multi-year academic-agency collaboration on the North American mountain goat that used an extensive field sampling of genetic and phenotypic data to determine whether, and to what degree, genetic and phenotypic differences separate an isolated population of mountain goats on the Cleveland Peninsula form those in southeast Alaska. We observed significantly larger horns on the peninsula and the population appears demographically isolated. Isolation-by-distance accompanied by limited migration and low effective population size on the Cleveland Peninsula suggest this population will continue to lose genetic diversity. While the large horns of mountain goats have generated interest in re-opening mountain goat harvest on Cleveland Peninsula, our genetic data suggest this population is vulnerable to demographic and environmental perturbations and is unlikely to support a sustained harvest.

genetics↗

bioRxiv2018

Recent demographic histories and genetic diversity across pinnipeds are shaped by anthropogenic interactions and mediated by ecology and life-history

A central paradigm in conservation biology is that population bottlenecks reduce genetic diversity and negatively impact population viability and adaptive potential. In an era of unprecedented biodiversity loss and climate change, understanding both the determinants and consequences of bottlenecks in wild populations is therefore an increasingly important challenge. However, as most studies have focused on single species, the multitude of potential drivers and the consequences of bottlenecks remain elusive. Here, we used a comparative approach by integrating genetic data from over 11,000 individuals of 30 pinniped species with demographic, ecological and life history data to elucidate the consequences of large-scale commercial exploitation by 18th and 19th century sealers. We show that around one third of these species exhibit strong genetic signatures of recent population declines, with estimated bottleneck effective population sizes reflecting just a few tens of surviving individuals in the most extreme cases. Bottleneck strength was strongly associated with both breeding habitat and mating system variation, and together with global abundance explained a large proportion of the variation in genetic diversity across species. Overall, there was no relationship between bottleneck intensity and IUCN status, although three of the four most heavily bottlenecked species are currently endangered. Our study reveals an unforeseen interplay between anthropogenic exploitation, ecology, life history and demographic declines, sheds new light on the determinants of genetic diversity, and is consistent with the notion that both genetic and demographic factors influence population viability.

evolutionary biology↗