title: Mitochondrial phylogenomics of modern and ancient equids.
abstract: The genus Equus is richly represented in the fossil record, yet our understanding of taxonomic relationships within this genus remains limited. To estimate the phylogenetic relationships among modern horses, zebras, asses and donkeys, we generated the first data set including complete mitochondrial sequences from all seven extant lineages within the genus Equus. Bayesian and Maximum Likelihood phylogenetic inference confirms that zebras are monophyletic within the genus, and the Plains and Grevy's zebras form a well-supported monophyletic group. Using ancient DNA techniques, we further characterize the complete mitochondrial genomes of three extinct equid lineages (the New World stilt-legged horses, NWSLH; the subgenus Sussemionus; and the Quagga, Equus quagga quagga). Comparisons with extant taxa confirm the NWSLH as being part of the caballines, and the Quagga and Plains zebras as being conspecific. However, the evolutionary relationships among the non-caballine lineages, including the now-extinct subgenus Sussemionus, remain unresolved, most likely due to extremely rapid radiation within this group. The closest living outgroups (rhinos and tapirs) were found to be too phylogenetically distant to calibrate reliable molecular clocks. Additional mitochondrial genome sequence data, including radiocarbon dated ancient equids, will be required before revisiting the exact timing of the lineage radiation leading up to modern equids, which for now were found to have possibly shared a common ancestor as far as up to 4 Million years ago (Mya).
authors: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
authors: Julia T
authors: JT
authors: Vilstrup
authors: Andaine
authors: A
authors: Seguin-Orlando
authors: Mathias
authors: M
authors: Stiller
authors: Aurelien
authors: A
authors: Ginolhac
authors: Maanasa
authors: M
authors: Raghavan
authors: Sandra C A
authors: SC
authors: Nielsen
authors: Jacobo
authors: J
authors: Weinstock
authors: Duane
authors: D
authors: Froese
authors: Sergei K
authors: SK
authors: Vasiliev
authors: Nikolai D
authors: ND
authors: Ovodov
authors: Joel
authors: J
authors: Clary
authors: Kristofer M
authors: KM
authors: Helgen
authors: Robert C
authors: RC
authors: Fleischer
authors: Alan
authors: A
authors: Cooper
authors: Beth
authors: B
authors: Shapiro
authors: Ludovic
authors: L
authors: Orlando
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D005580:Fossils; D054629:Genome, Mitochondrial / Q000235:genetics*; D023281:Genomics; D006736:Horses / Q000235:genetics*; D010802:Phylogeny; D012641:Selection, Genetic / Q000235:genetics; D013997:Time Factors