Metagenomic analysis of carnivores samples of upper Pleistocene and their diet


Coprolites have long been used in palynology for paleoenvironments reconstruction. They also are an important source of information on the DNA of the producing species and its diet. Using numerous archeological samples from several caves, including the Chauvet-Pont d’Arc cave, we studied coprolites for two species: the wolf, Canis lupus and the cave hyena, Crocuta crocuta spelaea. Using a canid coprolite from the Chauvet cave, dated back to 34 500 years, we obtained a complete mitochondrial genome sequence. Phylogenetic analyses highlight a maternal lineage that positions outside the diversity of extant dogs and wolfs. Then, analyzes conducted on the nuclear genes showed that the Chauvet Canis lupus specimen does not display obvious indication of domestication. Analysing the coprolite for other species to indicate the diet of this specimen, we detected cave bear (Ursus spelaeus) DNA sequences. Second, using many cave hyena coprolites, a flexible diet consisting of large as well as small animals was demonstrated for this extinct carnivore. Focusing the analysis on a coprolite samples that contained large amounts of bovine DNA, we obtained for the first time a complete mitochondrial genome sequence for the extinct European forest bison, Bison schoetensacki. In parallel, a bone sample for the extinct steppe bison provided the first complete mitochondrial genome sequence for Bison priscus. These two genome sequences shed new lights on the phylogeny of Bovinae.