An international team of scientists has retrieved and analyzed nuclear and mitochondrial environmental DNA of humans, wolfs (Canis lupus), and bisons (Bison bonasus) from a 25,000-year-old sediment sample from the Upper Paleolithic site of Satsurblia Cave, western Georgia, Caucasus.
Satsurblia Cave is a karst cave located 1.2 km from Kumistavi village in the Imereti region of Georgia.
Discovered in 1975 by N. Kalandadze, it is divided into several layers dated to between 32,000 and 3,000 years ago.
“In most of the Caucasus, and particularly in western Georgia, karst systems hold low and stable year-round temperatures and low acidity (no guano deposits in most systems),” said Dr. Pere Gelabert from the University of Vienna and colleagues.
The researchers analyzed six sediment samples from different archaeological layers of Satsurblia Cave.
A sample dated to 25,000 years ago (Last Glacial Maximum) yielded up to several million sequence reads from three mammalian species: humans, wolfs, and European bisons.
“The human environmental genome represents an extinct lineage that contributed to the present day West-Eurasian populations,” the scientists said.
“To validate the results, we compared the recovered genome with the genetic sequences obtained from bone remains of the nearby cave of Dzudzuana, obtaining definitive evidence of genetic similarities.”
They found that a wolf environmental genome was basal (more ancient) to extant Eurasian wolves and dogs and represented a previously unknown, likely extinct, Caucasian lineage; and that a bison environmental genome was basal to present-day populations.
The human DNA data were consistent with deriving from a female individual, or multiple female individuals.
In contrast, the wolf and bison X chromosome data were intermediate between those expected for males and females, suggesting DNA came from individuals of both sexes, again indicating multiple source individuals.
“Our results demonstrate that unbiased shotgun sequencing of sediment ancient DNA can yield genome-wide data that is informative about the ancestry of several species,” the authors said.
“The DNA retrieved here is lower in quantity, and hence resolution, compared to what is often obtained from various well-preserved bones and teeth.”
“Nonetheless, it provided information largely comparable to low-coverage ancient genome sequences and allowed us to apply complementary analyses of multiple mammalian species to reconstruct some aspects of their population histories.”
“Our results thus point to new possibilities in the study of sediment ancient DNA, demonstrating that it can serve as an additional or alternative source of genome-wide information to skeletal remains.”