title: Ancient DNA clarifies the evolutionary history of American Late Pleistocene equids.
abstract: Hippidions are past members of the equid lineage which appeared in the South American fossil record around 2.5 Ma but then became extinct during the great late Pleistocene megafaunal extinction. According to fossil records and numerous dental, cranial, and postcranial characters, Hippidion and Equus lineages were expected to cluster in two distinct phylogenetic groups that diverged at least 10 MY, long before the emergence of the first Equus. However, the first DNA sequence information retrieved from Hippidion fossils supported a striking different phylogeny, with hippidions nesting inside a paraphyletic group of Equus. This result indicated either that the currently accepted phylogenetic tree of equids was incorrect regarding the timing of the evolutionary split between Hippidion and Equus or that the taxonomic identification of the hippidion fossils used for DNA analysis needed to be reexamined (and attributed to another extinct South American member of the equid lineage). The most likely candidate for the latter explanation is Equus (Amerhippus) neogeus. Here, we show by retrieving new ancient mtDNA sequences that hippidions and Equus (Amerhippus) neogeus were members of two distinct lineages. Furthermore, using a rigorous phylogenetic approach, we demonstrate that while formerly the largest equid from Southern America, Equus (Amerhippus) was just a member of the species Equus caballus. This new data increases the known phenotypic plasticity of horses and consequently casts doubt on the taxonomic validity of the subgenus Equus (Amerhippus).
authors.affiliation: Université de Lyon, Paleogenetics and Molecular Evolution, Institut de Génomique Fonctionnelle de Lyon, CNRS UMR 5242 - INRA - Université Claude Bernard Lyon I, Lyon Cedex 07, France. ludovic.orlando@ens-lyon.fr
authors.forename: Ludovic
authors.initials: L
authors.lastname: Orlando
authors.forename: Dean
authors.initials: D
authors.lastname: Male
authors.forename: Maria Teresa
authors.initials: MT
authors.lastname: Alberdi
authors.forename: Jose Luis
authors.initials: JL
authors.lastname: Prado
authors.forename: Alfredo
authors.initials: A
authors.lastname: Prieto
authors.forename: Alan
authors.initials: A
authors.lastname: Cooper
authors.forename: Catherine
authors.initials: C
authors.lastname: Hänni
mesh_terms: D000818:Animals; D004272:DNA, Mitochondrial / Q000737:chemistry / Q000235:genetics*; D018397:Equidae / Q000145:classification / Q000235:genetics*; D019143:Evolution, Molecular; D005580:Fossils; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA
chemical_list: D004272:DNA, Mitochondrial