Data from: Whole-genome resequencing uncovers molecular signatures of natural and sexual selection in wild bighorn sheep

The identification of genes influencing fitness is central to our understanding of the genetic basis of adaptation and how it shapes phenotypic variation in wild populations. Here, we used whole-genome resequencing of wild Rocky Mountain bighorn sheep (Ovis canadensis) to >50-fold coverage to identify 2.8 million single nucleotide polymorphisms (SNPs) and genomic regions bearing signatures of directional selection (i.e. selective sweeps). A comparison of SNP diversity between the X chromosome and the autosomes indicated that bighorn males had a dramatically reduced long-term effective population size compared to females. This probably reflects a long history of intense sexual selection mediated by male–male competition for mates. Selective sweep scans based on heterozygosity and nucleotide diversity revealed evidence for a selective sweep shared across multiple populations at RXFP2, a gene that strongly affects horn size in domestic ungulates. The massive horns carried by bighorn rams appear to have evolved in part via strong positive selection at RXFP2. We identified evidence for selection within individual populations at genes affecting early body growth and cellular response to hypoxia; however, these must be interpreted more cautiously as genetic drift is strong within local populations and may have caused false positives. These results represent a rare example of strong genomic signatures of selection identified at genes with known function in wild populations of a nonmodel species. Our results also showcase the value of reference genome assemblies from agricultural or model species for studies of the genomic basis of adaptation in closely related wild taxa.

鉴定影响适合度的基因，是我们理解适应的遗传基础，以及其如何塑造野生种群表型变异的核心所在。本研究对野生落基山大角羊（Ovis canadensis）开展全基因组重测序（whole-genome resequencing），测序覆盖度达50倍以上，共鉴定出280万个单核苷酸多态性（single nucleotide polymorphisms, SNPs）以及携带定向选择（directional selection，即选择性清除selective sweeps）信号的基因组区域。通过对比X染色体与常染色体的SNP多样性，研究发现相较于雌性大角羊，雄性大角羊的长期有效种群规模显著降低。这大概率反映了长期以来由雄性间配偶竞争介导的强烈性选择历史。基于杂合度（heterozygosity）与核苷酸多样性（nucleotide diversity）的选择性清除扫描分析显示，在多个种群中共享了RXFP2基因的选择性清除信号——该基因在驯养有蹄类动物中可显著影响角的大小。大角公羊所拥有的巨型羊角，其演化似乎部分源于RXFP2基因受到的强烈正向选择。本研究还在影响早期机体生长以及细胞低氧应答（cellular response to hypoxia）的基因中，找到了单个种群内存在选择的证据；但由于当地种群内遗传漂变（genetic drift）作用较强，可能产生假阳性（false positives）结果，因此对这些结果的解读需更为谨慎。本研究结果为在非模式物种（nonmodel species）的野生种群中，鉴定到具有已知功能基因的强选择基因组信号提供了罕见范例。本研究同时证明，利用农业物种或模式物种的参考基因组组装（reference genome assemblies），可有效开展近缘野生类群的适应遗传基础研究。