Antler characteristics are highly heritable but influenced by maternal factors

Genomic architecture of phenotypic extremes in a wild cervid

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 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 after controlling for age. Our results revealed a largely homogenous population but detected highly divergent windows between pools for both traits, with the mean allele frequency difference of 14% for and 13% for antler and body SNPs in outlier windows, respectively. Genes in outlier antler windows were enriched for pathways associated with cell death and protein metabolism and some of the most differentiated windows included genes associated with oncogenic pathways and reproduction, processes consistent with antler evolution and growth. Genes associated with body size were more nuanced, suggestive of a highly complex trait. Overall, this study revealed the complex genomic make-up of both antler morphology and body size in free-ranging white-tailed deer and identified target loci for additional analyses.

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 genome-wide single-nucleotide polymorphism (SNP) data are available. We estimated the heritability of 5 body and 3 antler traits in a free-ranging population of white-tailed deer (Odocoileus virginianus) on Anticosti Island, Quebec, Canada. We generated classic and robust GRMs from >10,000 SNPs: hind foot length, dressed body mass, and peroneus muscle mass had high h2 values of 0.62, 0.44, and 0.55, respectively. Heritability in male-only antler features ranged from 0.07 to 0.33. We explored the influence of filtering by minor allele frequency and data completion 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, specifically many unrelated individuals, can 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 as these traits could respond to selection.

Cohort antler size signals environmental stress in a moderate climate

Research in northern latitudes confirms that climate teleconnections exert important influences on ungulate fitness, but studies from regions with milder climates are lacking. We explored the influence of the Pacific Decadal Oscillation (PDO), Northern Atlantic Oscillation (NAO), and El Niño-Southern Oscillation (ENSO) on male, 2.5-year-old white-tailed deer (Odocoileus virginianus) antler and body mass in Mississippi, USA, a region with mild winters and warm, humid summers. Explanatory variables were seasonal averages of each climate index extending back to 3 years prior to account for possible maternal and lag effects. Seasonal climate indices from the period of gestation and the first year of life were correlated with deer morphometrics. Reduced antler mass was largely correlated (R² = 0.52) with PDO values indicating dry conditions during parturition and neonatal development and NAO values indicating warmer than normal winters during gestation and the first year of life. Body mass was less correlated (R² = 0.16) to climate indices, responding negatively to warmer winter weather during the first winter of life. Climate may promote variable fitness among cohorts through long-term effects on male competition for dominance and breeding access. Because broad-scale climate indices simplify complex weather systems, they may benefit management at larger scales. Although this study compared climate with morphological variables, it is likely that demographic characteristics can likewise be modeled using climate indices. As climate change in this region is projected to include greater variability in summer precipitation, we may see concomitantly greater variability in fitness among cohorts of white-tailed deer.