title: Mitochondrial genomes reveal the extinct Hippidion as an outgroup to all living equids.
abstract: 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 reveals that the two morphospecies 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.
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark.
authors.forename: Clio
authors.identifier: http://orcid.org/0000-0003-4312-9085
authors.initials: C
authors.lastname: Der Sarkissian
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark.
authors.forename: Julia T
authors.identifier: http://orcid.org/0000-0001-6534-8452
authors.initials: JT
authors.lastname: Vilstrup
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark.
authors.forename: Mikkel
authors.identifier: http://orcid.org/0000-0003-2401-9921
authors.initials: M
authors.lastname: Schubert
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark Danish National High-throughput DNA Sequencing Centre, Øster Farimagsgade 2D, 1353 Copenhagen K, Denmark.
authors.forename: Andaine
authors.initials: A
authors.lastname: Seguin-Orlando
authors.affiliation: Université de Lyon, UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés, Université Claude Bernard Lyon 1, ENTPE, CNRS, 6 rue Raphaël Dubois, 69622 Villeurbanne, France.
authors.forename: David
authors.initials: D
authors.lastname: Eme
authors.affiliation: Faculty of Humanities, University of Southampton, Avenue Campus, Highfield, Southampton SO17 1BF, UK.
authors.forename: Jacobo
authors.initials: J
authors.lastname: Weinstock
authors.affiliation: Departamento de Paleobiología, Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal 2, 28006 Madrid, Spain.
authors.forename: Maria Teresa
authors.initials: MT
authors.lastname: Alberdi
authors.affiliation: Centro de Estudios del Hombre Austral, Universidad de Magallanes, Instituto de la Patagonia, Av. Bulnes 01890, Punta Arenas CP 6200000, Chile.
authors.forename: Fabiana
authors.initials: F
authors.lastname: Martin
authors.affiliation: Instituto de Investigaciones Arqueológicas y Museo Gustavo Le Paige, Universidad Católica del Norte, Calle Gustavo Le Paige No. 380, San Pedro de Atacama, Chile.
authors.forename: Patricio M
authors.initials: PM
authors.lastname: Lopez
authors.affiliation: INCUAPA, CONICET-UNICEN, Del Valle 5737, Olavarría B7400JWI, Argentina.
authors.forename: Jose L
authors.initials: JL
authors.lastname: Prado
authors.affiliation: Campus Puerto Natales, Km 1.5 Norte, Universidad de Magallanes, Puerto Natales, Chile.
authors.forename: Alfredo
authors.initials: A
authors.lastname: Prieto
authors.affiliation: Université de Lyon, UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés, Université Claude Bernard Lyon 1, ENTPE, CNRS, 6 rue Raphaël Dubois, 69622 Villeurbanne, France.
authors.forename: Christophe J
authors.initials: CJ
authors.lastname: Douady
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark.
authors.forename: Tom W
authors.initials: TW
authors.lastname: Stafford
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark.
authors.forename: Eske
authors.initials: E
authors.lastname: Willerslev
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark Laboratoire AMIS, Université Paul Sabatier 3, Université de Toulouse, UMR CNRS 5288, 37 Allées Jules Guesde, 31073 Toulouse cedex 3, France lorlando@snm.ku.dk.
authors.forename: Ludovic
authors.initials: L
authors.lastname: Orlando
mesh_terms: D000818:Animals; D001483:Base Sequence; D004272:DNA, Mitochondrial / Q000235:genetics*; D018397:Equidae / Q000145:classification* / Q000235:genetics; D019143:Evolution, Molecular; D005580:Fossils; D054629:Genome, Mitochondrial; D009656:North America; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D013020:South America
chemical_list: D004272:DNA, Mitochondrial
keywords: Great American Biotic Interchange; Hippidion; ancient DNA; mitochondrial genomes