Aaron B. A. Shafer

This study estimates mutation and recombination rates in polar bears using whole-genome sequencing, finding species-specific values that improve demographic inference for conservation.

The paper assesses genetic load and structural variation in American black bear populations, finding elevated levels in an isolated population.

This study develops epigenetic clocks for mule deer and a multi-species clock for the Odocoileus genus to analyze age-associated DNA methylation patterns and aging dynamics.

This study uses ancient DNA from North American cervids to trace genetic diversity changes over time, revealing historical population dynamics and impacts of external pressures.

This study uses genome-wide data to show that Typha species diverged allopatrically without gene flow, followed by secondary contact, with little evidence of ecological speciation driving differentiation.

This study shows spatial variability in soil necrobiome communities has little effect on PMI estimation, with temporal patterns being more significant.

The paper investigates structural variants in two deer species to understand their role in speciation and divergence, finding species-specific deletions and insertions linked to reproductive and sensory functions.

This study examines how environmental and temporal factors affect antler size and record white-tailed deer distribution in Ontario using hunter data and CAR models.

The paper uses ancient DNA from a subway deer to clarify the taxonomic status of Torontoceros hypogaeus, suggesting it may be a distinct Odocoileus species.

The paper uses genomic data to compare reproductive isolation between Typha species in Europe and North America, finding stronger isolation in Europe due to prolonged sympatry.

The paper estimates heritability of migration traits in mule deer using GPS and genomic data, finding low heritability for migration timing, distance, and duration but high heritability for movement rate.

This study identifies shrew-specific genomic variants linked to echolocation, metabolism, and body size plasticity through comparative genomics.

The paper analyzes genetic diversity and trait associations in island white-tailed deer populations to identify genes linked to leucism, malocclusions, and body size.

This study develops epigenetic clocks for three large mammals using DNA methylation data to estimate age with high accuracy and robustness.

The paper uses genomic analyses to study demographic changes in deer populations due to climate and human pressures, finding evidence of population decline and recovery.

The paper develops genomic resources for Typha, a wetland plant genus, by sequencing 140 samples and identifying SNPs and plastome sequences to study genetic diversity and hybridization.

The paper examines how demographic history affects genomic health in three ungulates by analyzing inbreeding, constrained elements, and mutational load.

This study identifies genomic regions associated with migratory direction in a cervid population, highlighting genes involved in lipid formation and epigenetic modifications.

The paper compares morphological and DNA methylation differences between island and mainland masked shrews, finding epigenetic and phenotypic divergence.

This paper develops a method to estimate time since deposition of bloodstains using RNA quality metrics from degrading blood samples without amplification.

This study quantifies secondary DNA transfer on denim using a human blood analogue and shows that friction leads to the highest DNA transfer and STR profile quality.

The paper presents a high-quality genome assembly of Typha latifolia, along with annotation and comparative analysis, providing a resource for studying hybrid dynamics in Typha species.

The paper assesses genomic variation and PRNP gene diversity in white-tailed deer to infer susceptibility to chronic wasting disease and demographic history.

This study identifies polygenic loci associated with antler and body size in white-tailed deer using whole genome re-sequencing of phenotypically extreme pools.

The paper examines the relationship between gut microbiome composition and core range size in mountain goats and white-tailed deer, finding a positive correlation between Firmicutes to Bacteroides ratios and core range area.

The paper estimates heritability of body and antler traits in free-ranging white-tailed deer using genomic-relatedness matrices and finds moderate heritability for body traits but low and variable heritability for antler traits.

The paper reports a multi-year collaboration to assess genetic and phenotypic differences in an isolated mountain goat population on the Cleveland Peninsula compared to southeast Alaska.

This study reports the first genome sequence of the Indian peacock and identifies genes under adaptive evolution that may explain its unique phenotypic traits.

The paper uses genome-wide sequencing to show that Canada lynx populations exhibit neutral genetic differentiation and cryptic epigenetic plasticity, particularly in Newfoundland, which may explain island dwarfism.