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

E Andrew Bennett,Petra Kaczensky,Marjan Mashkour,Ralph Kuehn,Thierry Grange,Sophie Champlot,Mietje Germonpré,Mathieu Gautier,Joris Peters,Aliye Ötzan,Erich Pucher,Mélanie Pruvost,Benjamin S Arbuckle,Margarete Uerpmann,Chris Walzer,Hans‐Peter Uerpmann ,Shirli Bar‐David ,Pierre-Élie Moullé ,Arturo Morales Muñiz ,Jean‐François Tournepiche ,Sílvia Guimarães ,Adrian Bălăşescu ,Simon Davis ,Can Yumni Gündem ,Mahmoud‐Reza Hemami ,Eva-María Geigl

doi:10.1371/journal.pone.0174216

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.

Highlights

The Asiatic wild ass (Equus hemionus), once widely distributed over a vast geographical area, is witnessing a dramatic range reduction leaving most of the remaining but isolated populations endangered
Modern and historical specimens were processed in a laboratory of the Jacques Monod Institute (IJM) dedicated to modern, non-amplified DNA analysis, which is physically separated from the ancient DNA facility and post-amplification laboratory, using aDNA procedures
The various summary statistics were computed using DNASP v5.1 [46] and Arlequin v3.5.1.3 [47] and are presented in Tables 1–3 using the 229-bp-long HVR sequences and in Table E in S1 File using the 295-bp-long HVR sequence of the historical and present-day kiangs and dziggetais

Summary

Introduction

The Asiatic wild ass (Equus hemionus), once widely distributed over a vast geographical area, is witnessing a dramatic range reduction leaving most of the remaining but isolated populations endangered. Asiatic wild asses are subdivided into two species, Equus kiang–the kiang of Tibet, and Equus hemionus with four living and one extinct subspecies, i.e., E. h. The two largest surviving populations, the dziggetais in the Mongolian Gobi Desert [3] and the kiangs of the Tibetan plateau [4], still occur over large parts of their former distribution range. The Iranian onagers, the Turkmen kulans, and the Indian khurs are reduced to small pocket populations with contracted distributions in protected areas located either in endemic centers or in refuge zones in Iran, Turkmenistan and northwest India, respectively [3,5,6]

Methods

Results

Conclusion