Data from: Candidate adaptive genes associated with lineage divergence: identifying SNPs via next-generation targeted resequencing in mule deer (Odocoileus hemionus)

Mule deer (Odocoileus hemionus) are an excellent nonmodel species for empirically testing hypotheses in landscape and population genomics due to their large population sizes (low genetic drift), relatively continuous distribution, diversity of occupied habitats and phenotypic variation. Because few genomic resources are currently available for this species, we used exon data from a cattle (Bos taurus) reference genome to direct targeted resequencing of 5935 genes in mule deer. We sequenced approximately 3.75 Mbp at minimum 20X coverage in each of the seven mule deer, identifying 23 204 single nucleotide polymorphisms (SNPs) within, or adjacent to, 6886 exons in 3559 genes. We found 91 SNP loci (from 69 genes) with putatively fixed allele frequency differences between the two major lineages of mule deer (mule deer and black-tailed deer), and our estimate of mean genetic divergence (genome-wide FST = 0.123) between these lineages was consistent with previous findings using microsatellite loci. We detected an over-representation of gamete generation and amino acid transport genes among the genes with SNPs exhibiting potentially fixed allele frequency differences between lineages. This targeted resequencing approach using exon capture techniques has identified a suite of loci that can be used in future research to investigate the genomic basis of adaptation and differentiation between black-tailed deer and mule deer. This study also highlights techniques (and an exon capture array) that will facilitate population genomic research in other cervids and nonmodel organisms.

骡鹿（Odocoileus hemionus）是用于景观基因组学与种群基因组学假说实证检验的优质非模式生物，这得益于其种群规模庞大（遗传漂变程度低）、分布相对连续、栖息生境多样且表型变异丰富。由于当前该物种的基因组学资源相对匮乏，本研究以牛（Bos taurus）参考基因组的外显子数据为参照，开展骡鹿5935个基因的靶向重测序。本研究对7只骡鹿个体进行测序，每个个体的测序覆盖度至少为20倍，共获得约3.75 Mbp的序列数据，最终在3559个基因的6886个外显子及其侧翼区域内，鉴定得到23204个单核苷酸多态性（single nucleotide polymorphisms, SNPs）位点。我们发现91个SNP位点（涉及69个基因），其等位基因频率在骡鹿的两个主要支系（骡鹿与黑尾鹿）间呈现推定的固定差异；本研究估算的支系间平均遗传分化水平（全基因组FST=0.123）与此前基于微卫星位点获得的研究结果一致。在支系间存在潜在固定等位基因频率差异的基因中，我们检测到配子发生与氨基酸转运相关基因显著富集。本研究采用的外显子捕获靶向重测序策略，鉴定得到一套可用于后续研究的位点，用于解析黑尾鹿与骡鹿间适应性分化的基因组基础。本研究同时验证了相关技术（及外显子捕获芯片）的实用性，可为其他鹿科动物及非模式生物的种群基因组学研究提供重要助力。