Neandertal DNA recovered from cave mud reveals that these ancient humans spread across Eurasia in two different waves.

Analysis of genetic material from three caves in two countries suggests an early wave of Neandertals about 135,000 years ago may have been replaced by genetically and potentially anatomically distinct successors 30,000 years later, researchers report April 15 in Science. The timing of this later wave suggests potential links to climate and environmental shifts.

By extracting genetic material from mud, “we can get human DNA from people who lived in a cave without having to find their remains, and we can learn interesting things about those people from that DNA,” says Benjamin Vernot, a population geneticist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

A few years ago, scientists showed that it’s possible to extract prehistoric human DNA from dirt, which contains genetic material left behind by our ancestors from skin flakes, hair or dried excrement or bodily fluids such as sweat or blood. Genetic analysis of ancient sediments could therefore yield valuable insights on human evolution, given that ancient human fossils with enough DNA suitable for analysis are exceedingly rare (SN: 6/26/19).

Until now, the ancient human DNA analyzed from sediments came from mitochondria — the organelles that act as energy factories in our cells — not the chromosomes in cell nuclei, which contain the actual genetic instructions for building and regulating the body. Although chromosomes hold far more information, retrieving samples of this nuclear DNA from caves proved challenging because of its relative scarcity. A human cell often possesses thousands of copies of its mitochondrial genome for every one set of chromosomes, and the vast majority of any DNA found in ancient dirt belongs to other animals and to microbes.

To extract ancient human chromosomal DNA from caves, Vernot and colleagues identified regions in chromosomes rich in mutations specific to hominids to help the team filter out nonhuman DNA. This helped the researchers successfully analyze Neandertal chromosomal DNA from more than 150 samples of sediment roughly 50,000 to 200,000 years old from a cave in Spain and two caves in Siberia.

After the team compared its data with DNA previously collected from Neandertal fossils of about the same age, the findings suggested that all these Neandertals were split into two genetically distinct waves that both dispersed across Eurasia. One emerged about 135,000 years ago, while the other arose roughly 105,000 years ago, with one branch of the earlier wave giving rise to all the later groups examined.

In the Spanish cave, the researchers found genetic evidence of both groups, with the later wave apparently replacing the earlier one. “There were signs based on the mitochondrial DNA of this turnover, but seeing it clearly with the nuclear DNA is really exciting,” says paleogeneticist Qiaomei Fu at the Institute of Vertebrate Paleontology and Paleoanthropology in Beijing, who did not take part in this study.

The later wave may be linked with the emergence of the last “classic” stage of Neandertal anatomy, skeletal features such as a bulge at the back of the skull that may indicate strong neck muscles or enlarged brain regions linked to vision, the researchers say. This later wave may have coincided with cooling and other environmental changes that came with the advent of the last ice age, they note.

This research emphasizes how scientists working at potential Neandertal sites should not throw away dirt as is traditionally done, says paleogeneticist Carles Lalueza-Fox at the Institute of Evolutionary Biology in Barcelona, who did not take part in this study. Instead, he says, special protocols may be needed to avoid contaminating these areas with modern DNA.