Human environmental genome recovered in the absence of skeletal remains

Ancient sediments from caves have already been proven to preserve DNA for thousands of years. The amount of recovered sequences from environmental sediments, however, is generally low, which confounds the analyses performed with these sequences. A study led by Ron Pinhasi and Pere Gelabert of the University of Vienna and published in Current Biology successfully retrieved three mammalian environmental genomes from a single 25,000-year-old soil sample obtained from the cave of Satsurblia in the Caucasus (Georgia).


The cave of Satsurblia was inhabited by humans in different periods of the Paleolithic. Until now, only a single human individual dated from 15,000 years ago has been sequenced from the site. No other human remains have been discovered in the older layers of the cave.


The innovative approach used by the international team led by Pinhasi and Gelabert with Susanna Sawyer of the University of Vienna in collaboration with Pontus Skoglund and Anders Bergström of the Francis Crick Institute in London permits the identification of DNA in samples of environmental material, by applying extensive sequencing and huge data analysis resources. This technique has allowed the recovery of an environmental human genome from the BIII layer of the cave, which is dated before the Ice Age, about 25,000 years ago.


This new approach has evidenced the feasibility of recovering human-environmental genomes in the absence of skeletal remains. The analysis of the genetic material has revealed that the SAT29 human-environmental genome represents a human extinct lineage that contributed to the present-day West-Eurasian populations. To validate the results, the researchers compared the recovered genome with the genetic sequences obtained from bone remains of the nearby cave of Dzudzuana, obtaining definitive evidence of genetic similarities. This fact validates the results and excludes the possibility of modern contamination of the samples.


Along with the identified human genome, other genomes such as wolf and bison have also been recovered from the environmental samples. The sequences have been used to reconstruct the wolf and bison Caucasian population history and will help better understand the population dynamics of these species.


The team now plans to perform further analyses of soil samples from the cave of Satsurbia with the objective of revealing interactions between extinct fauna and humans and the effect of climatic changes on mammalian populations. The ability to recover DNA from soil samples allows us to reconstruct the evolution of whole past ecosystems.



Journal Information: Pere Gelabert et al, Genome-scale sequencing and analysis of human, wolf, and bison DNA from 25,000-year-old sediment, Current Biology (2021). DOI: 10.1016/j.cub.2021.06.023

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