Researchers who excavated the Estatuas Cave in Spain have found a long record of Neanderthal DNA in the sediments.
© JAVIER TRUEBA / MADRID SCIENTIFIC FILMS
By Ann Gibbons
Estatuas Cave in northern Spain was a hive of activity 105,000 years ago. Artifacts show that its inhabitants of Neanderthal had stone tools, felled deer, and possibly made fire. They also threw out subtle clues on the cave floor, bled and excreted: their own DNA. ‘You can imagine them sitting in the cave making tools and slaughtering animals. Maybe they cut themselves or their babies pooped, ‘says population geneticist Benjamin Vernot, a postdoctoral fellow at the Max Planck Institute for Evolutionary Anthropology (MPI-EVA), whose perspective may have been colored by the crying of his own baby during a Zoom call. “All the DNA is piled up in the dirt.”
He and the MPI-EVA geneticist, Matthias Meyer, report today in Science that dirt from Estatuas yielded molecular treasure: the first nuclear DNA of an ancient human obtained from sediments. Previous studies have reported shorter human mitochondrial DNA (mtDNA) from cave floors, but nuclear DNA, previously available only in bones and teeth, can be much more informative. “It seems possible to extract nuclear DNA from dirt, and we have a lot of dirt in archaeological sites,” says archaeologist Marie Soressi of Leiden University.
“This is a beautiful paper,” agrees population geneticist Pontus Skoglund of the Francis Crick Institute. The series reveals the genetic identity and gender of ancient cave dwellers and shows that one group of Neanderthals replaced another in the Spanish cave about 100,000 years ago, perhaps after a climate cooling. “They can see a shift in the Neanderthal population on the same site, which is quite nice,” says Skoglund.
To date, paleogeneticists have succeeded in extracting ancient DNA from the bones or teeth of only 23 archaic people, including 18 Neanderthals from 14 places across Eurasia. In search of more, the team of Vernot and Meyer sampled sediment from well-dated layers in three caves, where ancient people are known to have lived: the Denisova and Chagyrskaya caves in Siberia and Estatuas Cave in Atapuerca, Spain.
In what Skoglund calls “a wonderful technical demonstration,” they have developed new genetic probes to capture hominin DNA, enabling them to ignore the abundant sequences of plants, animals and bacteria. Thereafter, they used statistical methods to harness DNA specific to Neanderthals and compare it with reference genomes of Neanderthals in a phylogenetic tree.
All three sites yielded Neanderthal nucleus and mtDNA, with the biggest surprise due to the small amount of nuclear DNA from several Neanderthal humans in the Estatuas Cave. Nuclear DNA from a Neanderthal male in the deepest layer, dating from about 113,000 years ago, linked him to early Neanderthal humans who lived in the Denisova Cave about 120,000 years ago and in caves in Belgium and Germany.
But two female Neanderthals who later lived in Estatuas Cave, about 100,000 years ago, have nuclear DNA more similar to that of later, ‘classical’ Neanderthals, including those who lived in Vindija Cave less than 70,000 years ago Croatia lived and lived in the Chagyrskaya Cave 60,000 to 80,000 years ago, says co-author and paleoanthropologist Juan Luis Arsuaga of the Complutense University of Madrid.
At the same time, the more abundant mtDNA from the Estatuas cave shows declining diversity. Neanderthals in the cave had at least three types of mtDNA 113,000 years ago. But the Neanderthals of the cave 80,000 and 107,000 years ago had only one species. Existing ancient DNA of Neanderthal bones and teeth also indicated a decrease in genetic diversity during the same period.
Arsuaga suggests that Neanderthals thrived and diversified during the hot, humid interglacial period that began 130,000 years ago. But about 110,000 years ago, temperatures in Europe suddenly dropped as a new ice age set in. Shortly afterwards, all descendants of Neanderthals disappeared. Surviving members repopulated Europe during later, relatively warm periods, with some hiding in the Estatuas Cave.
The survivors and their descendants include what Arsuaga calls the ‘famous’ classical Neanderthals, such as skulls of Vindija and La Ferrassie in France. He notes that they had larger brains – up to 1750 cubic centimeters (cm3) – than earlier Neanderthals, whose cranial abilities did not exceed 1400 cm3. Arsuaga says this reflects a similar pattern in modern humans in Africa, which also underwent an increase in brain size and multiple population replacements with the onset of the ice age.
“This pattern – spread over perhaps long distances and population replacement or mixture – is one we find almost everywhere we look,” says humans or other mammals, says Beth Shapiro, a molecular biologist at the University of California, Santa Cruz.
Cave-dirt DNA is likely to yield more clues. Paleogeneticist Viviane Slon, co-author of the Science now at Tel Aviv University, she says, and the MPI-EVA team is analyzing old DNA from sediments at dozens of sites worldwide. “Hopefully we will soon get a very high resolution, fine – scale view of old people and who was true at what time,” she says.