Taming the late Quaternary phylogeography of the Eurasiatic wild ass through ancient and modern DNA

Abstract

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 eleven 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 mitochondrial introgression 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.

Biostratigraphy and Palaeoecology of European Equus

“…The palaeogenetical study (Bennett et al, 2017) supports the hypothesis that hydruntine population could have gone through a bottleneck during the last two glacial periods and that Europe could have been recolonized from a refugial population, as proposed earlier on morphological grounds (Boulbes, 2009).…”

“…The rise of palaeogenetics allowed this affiliation to be confirmed by many mitochondrial sequences (Orlando et al, 2006(Orlando et al, , 2009. The last palaeogenetic studies to date do not definitively support the classification of E. hydruntinus as a distinct species and places it among the Asiatic wild asses (Bennett et al, 2017).…”

“…At the maximum extent of its geographical expansion in the Late Pleistocene, the distribution of Equus hydruntinus extended from Europe to the south-west of Asia (Middle East, Caucasus) and probably into North Africa (Uerpmann, 1987;Wilms, 1989;Orlando et al, 2006). During the Holocene, the contraction of the steppe, the significant fragmentation of its geographical distribution and distinct subpopulations, and human exploitation progressively caused its disappearance between the Neolithic and the Iron Age (Spassov and Iliev, 2002;Crees and Turvey, 2014), more precisely, according to palaeogenetic information, during the Bronze Age (Bennett et al, 2017). As this hypothesis is subject to certain limitations (cf.…”

“…altidens or E. wuesti in western and central Europe and E. mygdoniensis-E. apolloniensis around the eastern Mediterranean. The latter seems not to be linked to stenonid s. s. or E. suessenbornensis but could represent a step within the lineage of asses soon after their differentiation (Eisenmann and Boulbes, in preparation) in accordance with DNA and palaeogenetic projections (Jonsson et al, 2014;Bennett et al, 2017). These lineages finally were replaced by the more generalist caballoid horse group at the beginning of Middle Pleistocene.…”

“…Over the past 15 years, the discovery of new fossils and the revision of reference collections, added to the increased precision of the dating of certain deposits, have led to a reconsideration of the biochronology of the equids of the Pleistocene (Alberdi et al, 1998;Forsten, 1999a;Eisenmann, 2004aEisenmann, , 2006aEisenmann, , 2010Alberdi and Palombo, 2013;Van der Made et al, 2017). In addition, the progress of palaeogenetics has made it possible to calibrate evolutionary models proposed by paleontology (Orlando et al, 2013;Jonsson et al, 2014;Bennett et al, 2017).…”