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（Odocoileus hemionus）是开展景观基因组学与种群基因组学实证假说检验的优秀非模式物种（non-model species），其具备种群规模庞大（遗传漂变水平较低）、分布相对连续、栖息生境类型多样以及表型变异丰富等诸多优势。鉴于当前该物种可利用的基因组学资源相对匮乏，本研究借助牛（Bos taurus）参考基因组的外显子数据，对骡鹿的5935个基因开展靶向重测序。本研究对7只骡鹿个体分别进行了至少20倍覆盖度的约3.75 Mbp区域测序，在3559个基因的6886个外显子内部或其邻近区域，共鉴定得到23204个单核苷酸多态性位点（single nucleotide polymorphisms, SNPs）。研究发现，在骡鹿两大主要演化支系（骡鹿与黑尾鹿）之间，存在91个SNP位点（源自69个基因）呈现出疑似固定的等位频率差异；我们估算得到的支系间全基因组平均遗传分化程度（全基因组FST = 0.123），与此前利用微卫星位点（microsatellite loci）得到的研究结果一致。在那些在两大支系间呈现潜在固定等位频率差异的携带SNP的基因中，我们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。这种采用外显子捕获（exon capture）技术的靶向重测序策略，筛选得到了一系列可用于后续研究的位点，以探究黑尾鹿与骡鹿之间适应性分化与物种分化的基因组基础。本研究还明确了一套可推广的技术方案（以及一套外显子捕获芯片），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助力。