Hippidions were equids with very distinctive anatomical features. They lived in South America 2.5 million years ago (Ma) until their extinction approximately 10 000 years ago. The evolutionary origin of the three known Hippidion morphospecies is still disputed. Based on palaeontological data, Hippidion could have diverged from the lineage leading to modern equids before 10 Ma. In contrast, a much later divergence date, with Hippidion nesting within modern equids,was indicated by partial ancient mitochondrial DNA sequences. Here, we characterized eight Hippidion complete mitochondrial genomes at 3.4–386.3-fold coverage using target-enrichment capture and next-generation sequencing. Our dataset revealsthat the twomorphospecies sequenced(H.saldiasi and H. principale) formed a monophyletic clade, basal to extant and extinct Equus lineages. This contrasts with previous genetic analyses and supports Hippidion as a distinct genus, in agreement with palaeontological models.We date the Hippidion split from Equus at 5.6–6.5 Ma, suggesting an early divergence in North America prior to the colonization of South America, after the formation of the Panamanian Isthmus 3.5 Ma and the Great American Biotic Interchange.

This research was supported by the Marie Curie Career-Integration Grant (293845), the Danish Council for Independent Research (Natural Sciences), the Danish National Research Foundation (DNRF94), the “Chaires d’Attractivite´ 2014” IDEX programme (University of Toulouse), and the Lundbeck Foundation (R52-A5062). F.M. was supported by the FONDECYT 1100822 and CD MAG0901 grants.

Clio Der Sarkissian et al.

Peer reviewed