Epigenome and Paleogenome>> Phylogeography of the domestication and extinction of animals

We analyze different genetic markers, in particular mitochondrial DNA, to trace the evolution under human influence of various species from the Pleistocene to the present. The analysis of these markers in a large number of individuals from different time periods and geographic locations allow us to reconstruct the evolutionary history of animal populations during processes such as domestication. We studied in particular the evolution during the last 10,000 years of bovine populations since the beginning of the Neolithic in Southwest Asia as well as along the Neolithic migration routes in Europe. First, we analysed a large body of ancient bones from around the Mediterranean, which we obtained through collaboration with archaeozoologists from 10 different countries. Our methodological efforts allowed us to obtain very interesting results even from bones originating from geographic regions that have never before yielded palaeogenetic results. We could determine that a large number of cattle was domesticated in Southwest Asia and that the Neolithic migrations. Moreover, we could demonstrate that the reduction of their diversity was not the result of the Neolithic migrations leading to their dispersal in Europe. This reduction was rather the result of a sensible climatic degradation at the end of the Bronze Age (toward the end of the 2nd millennium B.C.) that resulted in the collapse of a number of contemporary societies. Our results contribute substantially to the understanding of the domestication process (De Lima Guimaraes et al., in preparation).

We also study the genetic history of cat and ass populations during their domestication.
Moreover, we studied the phylogeography of endangered species, on one hand the cheetah (Charruau et al., 2010), on the other hand the Asiatic wild ass E. hemionus (Bennett et al., in preparation). In both cases, our palaeogenetic study of archaeological and of historical specimens conserved in Natural history collections has revised the taxonomy of these species and revealed previously unknown gene flow between the populations suggesting a revision of current species conservation strategies.
Our study of specimens the Eurasian wild ass dated to 100,000 and 12,800 years has shown that these animals used to live in France during the Pleistocene and that their depictions in several cave paintings and engravings (e.g., Lascaux cave) reflects a reality during the Pleistocene. 

In the course of the study of ancient equids we also analysed equid skeletons buried in Sumerian tombs from the 3rd millennium BCE. Our methodological progress allowed us to obtain genetic results from these remains despite their poor DNA preservation. We could show that these animals, which are depicted on the « standard of Ur », were hybrids between female domesticated donkeys and male Syrian wild asses (Bennett et al., in preparation). This result finally ends speculation on the nature of these animals, which could not be identified based on bone morphology or iconographic and textual documents. 

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