An international team of scientists has developed new methods for the enrichment and analysis of nuclear DNA from sediments, and applied them to cave deposits in Europe and Siberia dated to between approximately 200,000 and 50,000 years ago.
Skeletal remains are important sources of Pleistocene hominin DNA, but are rarely recovered at archaeological sites.
Mitochondrial DNA (mtDNA) has been retrieved from cave sediments, but provides limited value for studying population relationships.
Although nuclear DNA contains far more information, its retrieval from sediments presents substantial challenges. It’s far less abundant than mtDNA and difficult to distinguish from other non-hominin mammalian and microbial DNA, which dominates the genetic material often present in ancient sediments.
To address these challenges, Dr. Benjamin Vernot from the Department of Evolutionary Genetics at the Max-Planck-Institute for Evolutionary Anthropology and his colleagues developed methods to recover, enrich and analyze nuclear DNA from cave sediments.
“There are lots of places in the human genome that are very similar to a bear’s DNA, for example,” Dr. Vernot said.
“We specifically targeted regions in the genome where we could be confident of isolating only human DNA, and we also designed methods to measure our success in removing non-human DNA.”
“We wanted to be confident that we weren’t accidentally looking at some unknown species of hyena.”
Specifically, the researchers applied their approach to extract nuclear DNA from more than 150 sediment samples from three caves: Galería de las Estatuas in northern Spain and Chagyrskaya and Denisova caves in the Altai Mountains of southern Siberia.
They detected a population replacement in Spain approximately 100,000 years ago, accompanied by a turnover of mtDNA.
They also identified two radiation events in Neanderthal history during the early part of the Late Pleistocene.
“The dawn of nuclear DNA analysis of sediments massively extends the range of options to tease out the evolutionary history of ancient humans,” Dr. Vernot said.
“By freeing the field of ancient DNA from the constraints of finding human remains and expanding the number of sites potentially suitable for investigation, we can now study the DNA from many more human populations, and from many more places, than has previously been thought possible,” added Dr. Matthias Meyer, also from the Department of Evolutionary Genetics at the Max-Planck-Institute for Evolutionary Anthropology.
The findings were published in the journal Science.
Benjamin Vernot et al. Unearthing Neanderthal population history using nuclear and mitochondrial DNA from cave sediments. Science, published online April 15, 2021; doi; 10.1126/science.abf1667