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）是开展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，其种群规模庞大（遗传漂变程度低）、分布相对连续、栖息生境类型多样且表型变异丰富。由于目前该物种可用的基因组学资源较为匮乏，我们借助牛（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。我们对7只骡鹿个体分别进行测序，每个个体的测序覆盖度最低不低于20倍，最终在3559个基因的6886个外显子内部或邻近区域，共鉴定出23204个单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）。我们在骡鹿的两个主要支系——骡鹿与黑尾鹿——之间，发现了91个源自69个基因的SNP位点，这些位点的等位基因频率差异推测为固定差异；我们对这两个支系间的平均遗传分化（全基因组FST = 0.123）的估算结果，与此前利用微卫星位点得到的研究结论一致。我们还发现，在携带等位基因频率可能存在固定差异的SNP的基因中，配子发生与氨基酸转运相关基因的占比显著偏高。本研究采用的外显子捕获靶向重测序策略，筛选出了一系列可用于后续探究黑尾鹿与骡鹿适应性分化基因组基础的位点。本研究同时验证了相关技术（及一套外显子捕获芯片）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助力。