Data from: Genome-wide set of SNPs reveals evidence for two glacial refugia and admixture from postglacial recolonization in an alpine ungulate

Past glaciation events have played a major role in shaping the genetic diversity and distribution of wild sheep in North America. The advancement of glaciers can isolate populations in ice-free refugia, where they can survive until the recession of ice sheets. The major Beringian refugium is thought to have held thinhorn sheep (Ovis dalli) populations during times of glacial advance. While isolation in the major refugium can account for much of the genetic and morphological diversity seen in extant thinhorn sheep populations, mounting evidence suggests the persistence of populations in smaller minor refugia. We investigated the refugial origins of thinhorn sheep using ~10 000 SNPs obtained via a cross-species application of the domestic sheep ovine HD BeadChip to genotype 52 thinhorn sheep and five bighorn sheep (O. canadensis) samples. Phylogenetic inference revealed a distinct lineage of thinhorn sheep inhabiting British Columbia, which is consistent with the survival of a group of thinhorn sheep in a minor refugium separate from the Beringian refugium. Isolation in separate glacial refugia probably mediated the evolution of the two thinhorn sheep subspecies, the white Dall's sheep (O. d. dalli), which persisted in Beringia, and the dark Stone's sheep (O. d. stonei), which utilized the minor refugium. We also found the first genetic evidence for admixture between sheep from different glacial refugia in south-central Yukon as a consequence of post glacial expansion and recolonization. These results show that glaciation events can have a major role in the evolution of species inhabiting previously glaciated habitats and the need to look beyond established refugia when examining the evolutionary history of such species.

过去的冰期事件对北美野生绵羊的遗传多样性与分布格局塑造起到了关键作用。冰川扩张会将种群隔离在无冰避难所中，使其得以存活直至冰盖消退。学界普遍认为，冰川扩张时期，主要的白令海峡冰期避难所（Beringian refugium）曾栖息着石羊（*Ovis dalli*）种群。尽管主要避难所内的隔离作用足以解释现存石羊种群中绝大多数的遗传与形态多样性，但越来越多的证据表明，小型次级避难所中也曾存在石羊种群的存续。本研究借助跨物种应用家绵羊HD基因分型芯片（ovine HD BeadChip）获得的约10000个单核苷酸多态性位点（Single Nucleotide Polymorphism，SNPs），对52份石羊样本与5份大角羊（*O. canadensis*）样本进行基因分型，以此探究石羊的避难所起源。系统发育推断结果显示，栖息于不列颠哥伦比亚省的石羊构成了一个独立演化支，这与石羊种群在独立于白令海峡避难所的次级避难所中存续的推论相符。独立冰期避难所内的隔离作用促成了两种石羊亚种的演化：一类是存续于白令海峡地区的白色达氏羊（*O. d. dalli*），另一类是依托次级避难所的深色斯通羊（*O. d. stonei*）。本研究还在育空地区中南部发现了首个遗传学证据，证明冰期后扩张与再定居过程中，来自不同冰期避难所的绵羊种群发生了基因交流。本研究结果表明，冰期事件对曾经历冰川作用的栖息地物种的演化具有关键塑造作用，同时提示在探究此类物种的演化历史时，需突破既有避难所框架的局限。