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A cup of mud that has been buried under the floor of a cave for millennia has just delivered the genome of an ancient human.
Analysis reveals traces of a woman who lived 25,000 years ago, before the last Ice Age; and, although we don’t know much about it, it represents an important scientific achievement: the ability to identify ancient human populations even when there is no bone to recover.
The sample also provided DNA from species of wolves and bison, which an international team of scientists was able to place in the context of the history of their populations.
“Our results,” they wrote in their paper, “provide new information on the Upper Pleistocene genetic histories of these three species and demonstrate that direct sequencing of DNA from sediments without target enrichment methods , can provide informative genome-wide data on ancestry and phylogenetic relationships. “
Collecting old DNA usually relies heavily on bones and luck. First, you need the bones to have survived and intact enough to preserve DNA for several thousand years.
Then you need to be able to find them and collect enough genetic material for sequencing. It is painstaking work, but rewarding – ancient DNA is capable of filling many gaps in the history of evolution, not only of humans, but of other life forms as well.
However, many archaeological sites have more evidence of hominid use than bones. One such site is Satsurblia Cave in Georgia. Artifacts like stone tools survive the rigors of time better than bones, so it’s not surprising. Even so, the cave has been used by ancient humans for thousands of years, and yet only the genome of a single individual at the site has been sequenced, from a human who lived 15,000 ago. years.
Environmental DNA, which is found preserved in sediments, is increasingly seen as a great way to learn more about the past. It settles in feces, as we saw with the collection of ancient bear DNA earlier this year, or in bone fragments that have been reduced to dust.
Thus, a team of scientists led by evolutionary biologist Pere Gelabert and archaeologist Ron Pinhasi from the University of Vienna in Austria set out to search for environmental DNA in the Satsurblia cave. They obtained six soil samples and carefully sifted them, looking for traces of genetic material.
They found them in the form of mitochondrial DNA. Fragmentary and incomplete, but, when painstakingly reconstructed, sufficient to provide new information on the populations that once inhabited the region.
First, the woman. Only a tiny fraction of her genome has been recovered, but from there, researchers were able to deduce that she was a member of a previously unknown group of modern humans. This group is now extinct, but it has contributed to current populations in Europe and Asia, as was discovered when the old genome was compared to current human genomes.
The wolf genome also represents a previously unknown, now extinct lineage, the researchers said. This suggests that wolf populations changed and reshaped dramatically at the end of the last ice age, around 11,000 years ago, with lineages like this completely extinct.
Finally, mitochondrial DNA found in the bison genome can also be found in living bison today. Researchers found that its genome was more closely related to European bison and Eurasian bison than to North American bison – an important finding, as it suggests that the two lineages diverged before the time of the Satsurblia cave bison. According to the team’s analysis, the American bison came first and diverged into other populations.
It is not known if the three species lived together in the cave – at the moment it is very difficult to refine the dating with enough certainty. In addition, the study of environmental DNA still has significant limitations, such as the fragmentary nature of any genetic material recovered and the high possibility of contamination.
Nonetheless, the discovery shows that, thanks to cheap and accessible technology, digging in the earth can be much more revealing than we might have thought possible.
“Our results demonstrate that impartial sequencing of ancient DNA from sediments can provide genome-wide data that is informative about the ancestry of several taxa,” the researchers wrote in their paper.
“Ancient sedimentary DNA at the genome scale could open up new avenues for the study of entire ecosystems, including interactions between different species and aspects of human practices related to the use of animals or plants . “
The research was published in Current biology.
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