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Neanderthal Population Replacement Detected Using Spanish Cave Sediments

NEW YORK – Using a method to interrogate nuclear and mitochondrial DNA left behind in cave sediment samples, an international research team has defined two Late Pleistocene Neanderthal groups at a site in northern Spain, placing a shift between the populations at roughly 100,000 years ago.

The researchers reasoned that improved sediment sequencing methods would make it possible to get a more accurate look at the hominins that once inhabited archaeological sites where DNA-containing bones or teeth are no longer found.

"Usually, we find no human remains at caves, even when it's obvious that someone lived there," first and corresponding author Benjamin Vernot, an evolutionary genetics researcher at the Max Planck Institute for Evolutionary Anthropology, said in an email.

As they reported in Science on Thursday, the investigators used hybridization capture targeting to search for and sequence informative Neanderthal or Denisovan DNA sequences in more than 150 cave sediment samples from three Paleolithic sites dated at between 50,000 and 200,000 years ago in western Europe and southern Siberia: the Denisova and Chagyrskaya Caves in southern Siberia's Altai Mountains, where Denisova or Neanderthal bones were profiled previously, and the Galeria de las Estatuas site in northern Spain, where Neanderthal-related artefacts have been found.

"[W]e set out to retrieve hominin nuclear genomic sequences from sediments by targeting, via hybridization capture, regions in the nuclear genome with high mammalian sequence diversity," the authors wrote, "and used these sequences to explore the history of Neanderthal populations in western Europe and southern Siberia."

After identifying hominin DNA in the sediment, or stratigraphic, layers that collected over time at these sites, the team put together hundreds of sequencing libraries, generating data at 1.6 million SNPs in the Neanderthal nuclear genome and across the mitochondrial genome. To weed out DNA contaminants from other animals, that set included nearly 98,900 sites in the genome that are fixed in hominins, chimps, and bonobos.

Sequence data from Denisova and Chagyrskaya samples made it possible to compare sediment-based samples to sites where bones have been tested in the past, senior author Matthias Meyer, an evolutionary genetics researcher at the Max Planck Institute for Evolutionary Anthropology, explained in a statement.

"The techniques we developed are very new, and we wanted to be able to test them in places where we knew what to expect," Meyer said.

At the Denisova Cave, for example, the researchers found sequences falling in the Altai Neanderhtal lineage. But phylogenetic analyses on sediment sequences from the bone-poor Estatuas pit in Spain also pointed to a previously unappreciated Neanderthal population turnover that took place an estimated 100,000 years ago, they reported, while spelling out genetic differences between Neanderthals from two apparent radiations in the Estatuas area in Spain.

The team noted that additional research will be needed to dig into relationships between the Neanderthal forms found in Spain and morphological types proposed in the past, along with the reasons behind the Neanderthal population replacement.

"These radiation events … occurred during the early part of the Late Pleistocene and may be associated with changes in climate and environmental conditions during the last interglacial," the authors wrote, adding that "methods presented here open the possibility to obtain such data independently of the fossil record, limited only by biochemical constraints on long-term DNA preservation."

More generally, the authors noted, the study "lays the ground for studying the population history of ancient hominins from trace amounts of nuclear DNA in sediments."