22Characterization of the complex genomic architecture underlying quantitative 23 traits can provide valuable insights into the study, conservation, and management of 24 natural populations. This is particularly true for fitness-related traits such as body size 25 and male ornamentation in mammals because as indicators of quality and health, these 26 traits are often subject to sexual and artificial selective pressures. Here we performed 27 high-depth whole genome re-sequencing on pools of individuals representing the 28 phenotypic extremes in our study system for antler and body size in white-tailed deer 29 (Odocoileus virginianus). Samples were selected from a database containing 30 phenotypic data for 4,466 male white-tailed deer from Anticosti Island, Quebec, with 31 four pools representing the extreme phenotypes for antler and body size in the 32 population. Our results revealed a largely panmictic population (F ST ~ 0.01), but also 33 detected diverged regions (F ST > 0.11) between pools for both traits. These regions 34 revealed genomic islands with signatures of positive selection and demographic 35 expansion (negative Tajima's D), and contained putative genes of small-to-moderate 36 effect. Through qPCR analysis we genotyped an intron variant on gene SRP54 that is a 37 potential QTL for antler size, and propose two missense variants on the MYADM and 38 SPATA31E1 genes known to influence body size in mammals and reproductive success 39 as potential QTL. This study revealed the polygenic nature of both antler morphology 40 and body size in white-tailed deer and identified target loci for additional analyses. 41
Study area 126Anticosti Island (49°N, 62°W; 7,943 km 2 ) is located in the Gulf of St. Lawrence, Québec 127 (Canada) at the northeastern limit of the white-tailed deer range (Figure 1). The island is 128 within the balsam fir-white birch bioclimatic region with a maritime sub-boreal climate 129 characterized by cool and rainy summers (630mm/year), and long and snowy winters 130 (406 cm/year;Environment Canada, 2006;Simard et al., 2010). The deer population 131 was introduced in 1896 with ca. 220 animals and rapidly increased. Today, densities are 132 7 >20 deer/km 2 and can exceed 50 deer/km 2 locally (Potvin and Breton 2005) with an 133 estimated population >160,000 individuals. 134
Sample Collection and Modeling 135We collected tissue samples and phenotypic data on 4,466 male deer harvested by 136 hunters from September to early December, 2002-2014. We used cementum layers in 137 incisor teeth to age individuals (Hamlin et al., 2000). Two metrics of antler size were 138 selected: the number of antler tines or points (>2.5 cm) and beam diameter (measured 139