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

Mule deer (Odocoileus hemionus) are an excellent non-model 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 re-sequencing of 5,935 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, 6,886 exons in 3,559 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 re-sequencing 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 non-model organisms.

骡鹿（Mule deer，*Odocoileus hemionus*）因种群规模庞大（遗传漂变程度较低）、分布相对连续、栖息生境类型多样且表型变异丰富，是开展景观基因组学与种群基因组学实证假说检验的优质非模式生物。鉴于当前该物种的基因组学资源较为匮乏，本研究借助牛（Bos taurus）参考基因组的外显子（exon）数据，对骡鹿的5935个基因开展靶向重测序。研究团队对7只骡鹿个体进行测序，每个个体的测序覆盖度最低不低于20X，共获得约3.75兆碱基对（Mbp）的有效序列，最终在3559个基因的6886个外显子内部或邻近区域，鉴定得到23204个单核苷酸多态性（single nucleotide polymorphisms，SNPs）位点。研究发现，在骡鹿的两个主要支系（骡鹿与黑尾鹿）之间，共有91个SNP位点（来自69个基因）存在推测性的固定等位基因频率差异；本研究估算的两支系间平均遗传分化程度（全基因组FST=0.123）与此前基于微卫星位点（microsatellite loci）得到的研究结果一致。在那些携带两支系间潜在固定等位基因频率差异的SNP位点的基因中，研究团队检测到配子发生与氨基酸转运相关基因存在显著富集现象。本研究采用的外显子捕获（exon capture）靶向重测序策略，鉴定得到了一套分子标记位点，可用于后续探究黑尾鹿与骡鹿之间适应性分化与遗传分化的基因组学基础。本研究同时验证了相关技术（及外显子捕获芯片（exon capture array））的实用性，可为其他鹿科动物（cervids）及非模式生物的种群基因组学研究提供助力。