We sequenced the genome of each living member of the non-caballine equids, and also that of the extinct quagga zebra. Genome sequencing

Horses, asses and zebras belong to a single genus, Equus, which emerged 4.0-4.5 million years ago (mya). Although the equine fossil record represents a textbook example of evolution, the succession of events that gave rise to the diversity of species existing today remains unclear. Here, we present 6 genomes from each living species of asses and zebras. This completes the set of genomes available for all extant species in the genus, which was hitherto only represented by the horse and the domestic donkey. Additionally, we used a museum specimen to characterize the genome of the Quagga zebra, which was driven to extinction in the early 1900s. We scan the genomes for lineage specific adaptations and identify 48 genes that have evolved under positive selection and are involved in olfaction, immune response, development, locomotion and behavior. Our extensive genome dataset reveals a highly dynamic demographic history with synchronous expansions and collapses on different continents during the last 400 thousand years (kyr) following major climatic events. We show that the earliest speciation occurred with gene flow in Northern America and that the ancestor of present-day asses and zebras dispersed into the Old World 2.1-3.4 mya. Strikingly, we also find evidence for gene flow involving three contemporary equine species despite chromosomal numbers varying from 16 to 31 pairs. These findings challenge the claim that the accumulation of chromosomal rearrangements drive complete reproductive isolation and promote equids as a fundamental model for understanding the interplay between chromosomal structure, gene flow and, ultimately, speciation.

马、驴与斑马同属于马属（Equus），其起源可追溯至400万至450万年前（百万年前，million years ago，缩写mya）。尽管马科动物的化石记录堪称演化生物学的经典教科书案例，但造就现今多样马属物种的演化历程仍不明晰。本研究首次发布所有现生驴类与斑马物种各6套基因组数据，至此马属所有现生物种的基因组数据集合已完整——此前该属仅覆盖家马与家驴两个物种。此外，本研究借助博物馆馆藏标本，完成了20世纪初灭绝的斑驴（Quagga）的基因组解析。我们对所有基因组开展谱系特异性适应性扫描，共鉴定出48个受正向选择的基因，这些基因分别参与嗅觉、免疫应答、生长发育、运动机能与行为调控等生理过程。本研究的大规模基因组数据集揭示了马属动物极为动态的种群演化历史：在过去40万年（千年，kiloyear，缩写kyr）间，其种群规模随重大气候事件在不同大陆同步发生扩张与收缩。研究表明，最早的物种分化事件发生于北美地区，且伴随基因流；现今驴类与斑马的共同祖先于210万至340万年前扩散至旧大陆。尤为值得关注的是，本研究还发现，尽管现存马属动物的染色体数目从16对到31对不等，但三个现生马属物种间仍存在基因流的证据。上述研究结果挑战了"染色体重排积累会导致完全生殖隔离"的主流论断，并推动马科动物成为解析染色体结构、基因流与物种分化三者间相互作用机制的核心研究模型。