DNA from cave dirt tells how some Neanderthals disappeared | Science

By Ann GibbonsApril 15, 2021, 2:00 p.m.

The cave of the States of northern Spain was a hive of activity 105,000 years ago. Artifacts show that its Neanderthals raised stone tools, slaughtered red deer and could have caused fires. They also shed, bled, and removed more subtle clues on the cave floor: their own DNA. “You can imagine sitting in a cave making tools, 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 could have been colored by the cries of his own child during a call Zoom. “All the DNA that accumulates in the dirt floors.”

He and MPI-EVA geneticist Matthias Meyer report today in Science that the dirt in the United States produced a molecular treasure: the first nuclear DNA from an ancient man that was extracted from sediment. Previous studies have reported shorter, more abundant human mitochondrial DNA (mtDNA) on the cave floor, but nuclear DNA, previously available only from bones and teeth, may be much more informative. “Now, it seems possible to extract nuclear DNA from dirt and we have a lot of dirt in archeological sites,” says archaeologist Marie Soressi of Leiden University.

“This is a beautiful work,” agrees population geneticist Pontus Skoglund of the Francis Crick Institute. The sequences reveal the genetic identity and sex of the inhabitants of ancient caves and show that a group of Neanderthals replaced another in the Spanish cave about 100,000 years ago, perhaps after a cooling climate. “I can see a change in Neanderthal populations in the same place, which is quite nice,” says Skoglund.

To date, paleogeneticists have been able to extract ancient DNA from the bones or teeth of only 23 archaic humans, including 18 Neanderthals from 14 sites in Eurasia. In search of more, the Vernot and Meyer team took sediments from well-dated strata in three caves where ancient people are known to have lived: the Denisova and Chagyrskaya caves in Siberia and the Estatas cave in Atapuerca, Spain.

In what Skoglund calls “an amazing technical demonstration,” they have developed new genetic probes to fish for hominin DNA, allowing them to ignore the abundant sequences from plants, animals and bacteria. They then used statistical methods to enter the unique DNA for Neanderthals and to compare it with the reference genomes of Neanderthals in a phylogenetic tree.

All three sites produced Neanderthal nuclear and mtDNA, the biggest surprise coming from the small amount of nuclear DNA in several Neanderthals in the United States Cave. The nuclear DNA from a Neanderthal man in the deepest layer, dating back about 113,000 years, linked him to the first Neanderthals who lived about 120,000 years ago in the Denisova Cave and in the caves of Belgium and Germany.

But two Neanderthal women who lived in the cave in the United States later, about 100,000 years ago, had more appropriate nuclear DNA than later “classical” Neanderthals, including those who lived more recently. less than 70,000 years in the Vindija Cave in Croatia and 60,000 to 80,000 years now in the Chagyrskaya Cave, says co-author and paleoanthropologist Juan Luis Arsuaga of the Complutense University of Madrid.

At the same time, the more abundant mtDNA in the States Cave shows a declining diversity. Neanderthals in the cave 113,000 years ago had at least three types of mtDNA. But the Neanderthals of the cave 80,000 and 107,000 years ago had only one type. Old Neanderthal bone and tooth DNA also indicated a decrease in genetic diversity over the same period.

Arsuaga suggests that Neanderthals prospered and diversified during the hot and humid interglacial period that began 130,000 years ago. But about 110,000 years ago, temperatures in Europe dropped sharply as a new ice age set in. Soon, all but one line of Neanderthals disappeared. Members of the surviving offspring repopulated Europe in later, relatively warm times, with some taking refuge in the United States Cave.

Those survivors and their descendants include what Arsuaga calls the “famous” Neanderthal classic, such as the skulls of Vindija and La Ferrassie of France. He noticed that they had larger brains – up to 1750 cubic centimeters (cm³) – than the earlier Neanderthals, whose cranial capacities did not exceed 1400 cm³. Arsuaga says this reflects a similar pattern to modern people in Africa, who have also experienced an increase in brain size and multiple population replacements with the onset of the ice age.

“This pattern – long-distance dispersal and perhaps population replacement or mixing – is one we find almost everywhere we look” in humans or other mammals, says Beth Shapiro, a molecular biologist at the University of California, Santa Cruz.

Cave dirt DNA is likely to give more clues. Paleogeneticist Viviane Slon, co-author of Science A newspaper now at Tel Aviv University says she and the MPI-EVA team are analyzing ancient sediment DNA at dozens of sites around the world. “We hope that soon we will begin to get a high-resolution, fine-scale vision of ancient people and who they are at the moment,” she says.