The genome and diet of a 35,000-year-old Canis lupus specimen from the Palaeolithic painted cave of Chauvet-Pont d'Arc

Libraries of ancient DNA were produced from a 36,000-year-old coprolite collected in the Paleolithic painted cave of Chauvet-Pont-d'Arc (Ardeche, France). Shotgun DNA sequencing demonstrated that the predominant mammalian DNA correspond to that of a canid specimen. Aligning the DNA reads to the dog mitochondrial and nuclear reference genomes sequences yielded 83x and 2.7x coverages for the mitochondrial and the nuclear genome, respectively. Phylogenetic analysis of the mitochondrial genome sequence indicated that it lies outside the diversity of that recorded among extant dogs and Holarctic wolves and belongs to a clade that only includes European wolves of the same time period. As regards the nuclear genome, the similar coverage of the autosomes and of the X chromosome demonstrates that the feces was produced by a female individual. Principal component analysis and admixture analysis indicated that the nuclear genome of the Chauvet specimen is much more related to the genomes of old-world wolves, especially central Europe and Middle-East wolves, than to the genomes of dogs and new-world wolves. We conclude that the coprolite corresponds to feces produced 36,000 years ago by a female Holarctic wolf in the Chauvet cave. The presence of small amounts of Ursus spelaeus mitochondrial DNA (0.4% of Canis lupus mitochondrial DNA) in the coprolite also indicates that the extinct cave bear was part of the diet of the Chauvet wolf specimen.