Jónsson Hákon, Schubert Mikkel, Seguin-Orlando Andaine, Ginolhac Aurélien, Petersen Lillian, Fumagalli Matteo, Albrechtsen Anders, Petersen Bent, Korneliussen Thorfinn S, Vilstrup Julia T, Lear Teri, Myka Jennifer Leigh, Lundquist Judith, Miller Donald C, Alfarhan Ahmed H, Alquraishi Saleh A, Al-Rasheid Khaled A S, Stagegaard Julia, Strauss Günter, Bertelsen Mads Frost, Sicheritz-Ponten Thomas, Antczak Douglas F, Bailey Ernest, Nielsen Rasmus, Willerslev Eske, Orlando Ludovic
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen K, Denmark;
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen K, Denmark; National High-Throughput DNA Sequencing Center, DK-1353 Copenhagen K, Denmark;
Proc Natl Acad Sci U S A. 2014 Dec 30;111(52):18655-60. doi: 10.1073/pnas.1412627111. Epub 2014 Dec 1.
Horses, asses, and zebras belong to a single genus, Equus, which emerged 4.0-4.5 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 six 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 represented only by the horse and the domestic donkey. In addition, 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 ky after 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 pairs 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、驴和斑马属于单属物种马属（Equus），该属出现于400万至450万年前。尽管马科动物化石记录是进化的典型教科书示例，但导致当今现存物种多样性的一系列事件仍不清楚。在此，我们展示了来自每个现存驴和斑马物种的六个基因组。这完善了该属所有现存物种的基因组集合，此前该集合仅由马和家驴代表。此外，我们利用一个博物馆标本对斑驴的基因组进行了特征分析，斑驴于20世纪初灭绝。我们在基因组中搜索特定谱系的适应性变化，并确定了48个在正选择下进化且涉及嗅觉、免疫反应、发育、运动和行为的基因。我们广泛的基因组数据集揭示了一个高度动态的种群历史，在过去40万年的主要气候事件之后，不同大陆上出现了同步的扩张和衰退。我们表明，最早的物种形成发生在北美洲且伴随着基因流动，并且当今驴和斑马的祖先在210万至340万年前扩散到了旧世界。引人注目的是，我们还发现了涉及三种当代马科动物基因流动的证据，尽管它们的染色体对数从16对到31对不等。这些发现挑战了关于染色体重排积累导致完全生殖隔离的说法，并推动马科动物成为理解染色体结构、基因流动以及最终物种形成之间相互作用的基础模型。
