Hunting the Extinct Steppe Bison (Bison priscus) Mitochondrial Genome in the Trois-Frères Paleolithic Painted Cave

Abstract

Despite the abundance of fossil remains for the extinct steppe bison (Bison priscus), an animal that was painted and engraved in numerous European Paleolithic caves, a complete mitochondrial genome sequence has never been obtained for this species. In the present study we collected bone samples from a sector of the Trois-Frères Paleolithic cave (Ariège, France) that formerly functioned as a pitfall and was sealed before the end of the Pleistocene. Screening the DNA content of the samples collected from the ground surface revealed their contamination by Bos DNA. However, a 19,000-year-old rib collected on a rock apart the pathway delineated for modern visitors was devoid of such contaminants and reproducibly yielded Bison priscus DNA. High-throughput shotgun sequencing combined with conventional PCR analysis of the rib DNA extract enabled to reconstruct a complete mitochondrial genome sequence of 16,318 bp for the extinct steppe bison with a 10.4-fold coverage. Phylogenetic analyses robustly established the position of the Bison priscus mitochondrial genome as basal to the clade delineated by the genomes of the modern American Bison bison. The extinct steppe bison sequence, which exhibits 93 specific polymorphisms as compared to the published Bison bison mitochondrial genomes, provides an additional resource for the study of Bovinae specimens. Moreover this study of ancient DNA delineates a new research pathway for the analysis of the Magdalenian Trois-Frères cave.

Early cave art and ancient DNA record the origin of European bison

“…Contrary to previous palaeontological interpretations, the ancestors of modern wisent were present in Europe throughout the Late Pleistocene, and the two different bison morphs depicted in Paleolithic art suggest that early artists recorded the replacement of the steppe bison by the hybrid form (including CladeX) in Western Europe around the LGM. Two bison individuals have been genotyped from European caves during this period: a 19-kyr-old steppe bison from Southern France 24 and a 16-kyr-old wisent (CladeX) from Northern Italy (present study), corresponding to the timing of the morphological transition from steppe bison-like to wisent-like morphotypes apparent in cave art.…”

A mobile laboratory for ancient DNA analysis

“…To set up a rapid DNA extraction procedure, we used the methods described above to analyze two samples previously published: a steppe bison rib [48], and a cave hyena coprolite [11]. Briefly, 300 mg of bone or coprolite powder was recovered using a single-use surgical blade, divided in two 150 mg samples that were transferred into 2-ml Eppendorf tube, and 1.5 ml of DNA extraction buffer was added.…”

“…genome sequence for the steppe bison has been deciphered using shotgun DNA sequencing [48]; and a cave hyena coprolite (CC8) from which shotgun DNA sequencing yielded a complete cave hyena and a partial red deer (Cervus elaphus) mitochondrial genome sequence [11]. For each sample, we performed two experiments: one experiment aiming to compare the DNA extracts recovered after a 1-h, 3-h, or 16-h incubation period; and one experiment aiming to compare extracts recovered after a 1-h, 2-h, or 16-h incubation period.…”

Past climate changes, population dynamics and the origin of Bison in Europe

“…Indeed, mitochondrial sequences of the American bison and the yak Poephagus mutus f. grunniens (Linnaeus, 1758) form a distinct cluster, while the wisent occupies a phylogenetic position closer to Bos primigenius f. taurus (Linnaeus, 1758), a phenomenon that has been explained by incomplete lineage sorting or ancient hybridization [ 21 , 22 ]. European, Siberian, and American B. priscus mitogenomes were shown to be phylogenetically closer to B. bison than to B. bonasus [ 7 , 14 , 23 ].…”