PT - JOURNAL ARTICLE AU - E. Andrew Bennett AU - Sophie Champlot AU - Joris Peters AU - Benjamin S. Arbuckle AU - Silvia Guimaraes AU - Mélanie Pruvost AU - Shirli Bar-David AU - Simon S.M. Davis AU - Mathieu Gautier AU - Petra Kaczensky AU - Ralph Kuehn AU - Marjan Mashkour AU - Arturo Morales-Muñiz AU - Erich Pucher AU - Jean-François Tournepiche AU - Hans-Peter Uerpmann AU - Adrian Bălăşescu AU - Mietje Germonpré AU - Can Y. Gündem AU - Mahmoud-Reza Hemami AU - Pierre-Elie Moullé AU - Aliye Ötzan AU - Margarete Uerpmann AU - Chris Walzer AU - Thierry Grange AU - Eva-Maria Geigl TI - Taming the Late Quaternary phylogeography of the Eurasiatic wild ass through ancient and modern DNA AID - 10.1101/090928 DP - 2016 Jan 01 TA - bioRxiv PG - 090928 4099 - http://biorxiv.org/content/early/2016/12/02/090928.short 4100 - http://biorxiv.org/content/early/2016/12/02/090928.full AB - Taxonomic over-splitting of extinct or endangered taxa, due to an incomplete knowledge of both skeletal morphological variability and the geographical ranges of past populations, continues to confuse the link between isolated extant populations and their ancestors. This is particularly problematic with the genus Equus. To more reliably determine the evolution and phylogeographic history of the endangered Asiatic wild ass, we studied the genetic diversity and inter-relationships of both extinct and extant populations over the last 100,000 years, including samples throughout its previous range from Western Europe to Southwest and East Asia. Using 229 bp of the mitochondrial hypervariable region, an approach which allowed the inclusion of information from extremely poorly preserved ancient samples, we classify all non-African wild asses into nine clades that show a clear phylogeographic structure revealing their phylogenetic history. This study places the extinct European wild ass, E. hydruntinus, the phylogeny of which has been debated since the end of the 19th century, into its phylogenetic context within the Asiatic wild asses and reveals recent gene flow events between populations currently regarded as separate species. The phylogeographic organization of clades resulting from these efforts can be used not only to improve future taxonomic determination of a poorly characterized group of equids, but also to identify historic ranges, interbreeding events between various populations, and the impact of ancient climatic changes. In addition, appropriately placing extant relict populations into a broader phylogeographic and genetic context can better inform ongoing conservation strategies for this highly endangered species.