title: Revising the recent evolutionary history of equids using ancient DNA.
abstract: The rich fossil record of the family Equidae (Mammalia: Perissodactyla) over the past 55 MY has made it an icon for the patterns and processes of macroevolution. Despite this, many aspects of equid phylogenetic relationships and taxonomy remain unresolved. Recent genetic analyses of extinct equids have revealed unexpected evolutionary patterns and a need for major revisions at the generic, subgeneric, and species levels. To investigate this issue we examine 35 ancient equid specimens from four geographic regions (South America, Europe, Southwest Asia, and South Africa), of which 22 delivered 87-688 bp of reproducible aDNA mitochondrial sequence. Phylogenetic analyses support a major revision of the recent evolutionary history of equids and reveal two new species, a South American hippidion and a descendant of a basal lineage potentially related to Middle Pleistocene equids. Sequences from specimens assigned to the giant extinct Cape zebra, Equus capensis, formed a separate clade within the modern plain zebra species, a phenotypicically plastic group that also included the extinct quagga. In addition, we revise the currently recognized extinction times for two hemione-related equid groups. However, it is apparent that the current dataset cannot solve all of the taxonomic and phylogenetic questions relevant to the evolution of Equus. In light of these findings, we propose a rapid DNA barcoding approach to evaluate the taxonomic status of the many Late Pleistocene fossil Equidae species that have been described from purely morphological analyses.
authors.affiliation: Institut de Génomique Fonctionnelle de Lyon, Université de Lyon 1, Ecole Normale Supérieure de Lyon, and Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, 69364 Lyon Cédex 07, France. ludovic.orlando@ens-lyon.fr
authors.forename: Ludovic
authors.initials: L
authors.lastname: Orlando
authors.forename: Jessica L
authors.initials: JL
authors.lastname: Metcalf
authors.forename: Maria T
authors.initials: MT
authors.lastname: Alberdi
authors.forename: Miguel
authors.initials: M
authors.lastname: Telles-Antunes
authors.forename: Dominique
authors.initials: D
authors.lastname: Bonjean
authors.forename: Marcel
authors.initials: M
authors.lastname: Otte
authors.forename: Fabiana
authors.initials: F
authors.lastname: Martin
authors.forename: Véra
authors.initials: V
authors.lastname: Eisenmann
authors.forename: Marjan
authors.initials: M
authors.lastname: Mashkour
authors.forename: Flavia
authors.initials: F
authors.lastname: Morello
authors.forename: Jose L
authors.initials: JL
authors.lastname: Prado
authors.forename: Rodolfo
authors.initials: R
authors.lastname: Salas-Gismondi
authors.forename: Bruce J
authors.initials: BJ
authors.lastname: Shockey
authors.forename: Patrick J
authors.initials: PJ
authors.lastname: Wrinn
authors.forename: Sergei K
authors.initials: SK
authors.lastname: Vasil'ev
authors.forename: Nikolai D
authors.initials: ND
authors.lastname: Ovodov
authors.forename: Michael I
authors.initials: MI
authors.lastname: Cherry
authors.forename: Blair
authors.initials: B
authors.lastname: Hopwood
authors.forename: Dean
authors.initials: D
authors.lastname: Male
authors.forename: Jeremy J
authors.initials: JJ
authors.lastname: Austin
authors.forename: Catherine
authors.initials: C
authors.lastname: Hänni
authors.forename: Alan
authors.initials: A
authors.lastname: Cooper
mesh_terms: D000818:Animals; D005075:Biological Evolution; D004247:DNA / Q000235:genetics*; D005580:Fossils; D006736:Horses / Q000145:classification / Q000235:genetics*; D008969:Molecular Sequence Data
chemical_list: D004247:DNA