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 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.

Subspecies hybridization as a potential conservation tool in species reintroductions

“…These results indicated that there were no genetic or behavioural barriers to subspecies hybridization and that no cryptic subpopulations have formed due to a lack of admixture. This may be due to weak genetic differentiation between the subspecies; we found that only 0.03% of the analysed SNPs were fixed for opposite alleles in the onager and kulan samples, which is consistent with previous findings demonstrating only low genetic divergence between onagers and kulans (Bennett et al, 2017). Species such as the Asiatic wild ass, which show low levels of divergence between subpopulations or subspecies may therefore present good candidates for hybridization as part of genetic management.…”

“…Both subspecies are currently classified as endangered by the IUCN and a major conservation concern is the extreme fragmentation and small sizes of remaining wild populations (Bennett et al, 2017; Kaczensky et al, 2018). Furthermore, on the basis of numerous phylogenetic analyses (Geigl & Grange, 2012; Orlando et al, 2009; Vilstrup et al, 2013), some authors advocate a revision of the separate subspecies status of E. h. onager and E. h. kulan and joint management of the remaining populations (Bennett et al, 2017; Oakenfull et al, 2000). The results presented here demonstrate that genetic or behavioural barriers are unlikely to compromise a mixed stock management approach in in situ and ex situ conservation.…”

La paléogénétique en tant qu’approche archéométrique au cours des 30 dernières années

“…Malgré ces incertitudes et limites, l'apport de la paléogénétique basé sur les méthodes de PCR à l'archéologie, la paléoanthropologie, l'archéozoologie et l'archéobotanique a été (et est toujours) multiple et riche. Il a permis de déterminer à quelles lignées maternelles ont appartenu des individus mis au jour dans des sites archéologiques et ainsi de reconstruire des migrations et remplacements de populations humaines (par exemple en Europe centrale au cours des dernières 6 500 années ; Brandt et al, 2013), mais aussi d'animaux domestiqués (par ex : les chats, Ottoni et al, 2017), des relations familiales et sociales au sein des cimetières (par ex : Keyser-Tracqui et al, 2003), identifier des pathogènes et parasites intestinaux (Côté et al, 2016), éclairer les positions phylogénétiques de certains animaux éteints emblématiques (comme le mammouth ; Debruyne et al, 2003) ou énigmatiques (comme l'hydrontin ; Bennett et al, 2017), déterminer les événements initiaux lors de la domestication des animaux (comme les chevaux ; Ludwig et al, 2009), reconstruire le paléoenvironnement grâce à l'analyse de pollens et des sédiments (comme pour le Groenland il y a environ 800 000-450 000 ans ; Willerslev et al, 2007) ou encore étudier la réponse de la mégafaune aux changements climatiques et environnementaux et l'action anthropique (Lorenzen et al, 2011).…”

The case of an arctic wild ass highlights the utility of ancient DNA for validating problematic identifications in museum collections

“…While fossils of kiang‐like wild asses are known from Pleistocene deposits in Alaska (Harington, ), the Pleistocene range of kiangs remains unknown. Wild asses during the Pleistocene spanned from present‐day France, where they were known as the European wild ass ( E. hydrintius ), to China (Figure a) in regions south of 50˚ N (Bennett et al, ).…”