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Neanderthal DNA from cave mud shows two waves of migration through Eurasia

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

Analysis of three-cave genetic material in two countries suggests that an early wave of Neanderthals about 135,000 years ago could have been replaced by genetically and potentially anatomically successors 30,000 years later, according to researchers April 15 in Science. The timing of this latest wave suggests possible links to climate and environmental change.

By extracting genetic material from clay, "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, population geneticist at the Max Planck Institute for Anthropology. Evolutionary in Leipzig, Germany.

A few years ago, scientists demonstrated that it is possible to extract prehistoric human DNA from dirt, which contains genetic material left by our ancestors from skin flakes, hair, or dry stools or body fluids such as sweat or blood. Genetic analysis of ancient sediments could therefore provide valuable information on human evolution, given that ancient human fossils with sufficient DNA suitable for analysis are extremely rare (SN: 26/06/19).

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

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

After the team compared their data with previously collected DNA from Neanderthal fossils of about the same age, the findings suggested that all of these Neanderthals split into two genetically distinct waves that both dispersed through Eurasia. One emerged about 135,000 years ago, while the other emerged about 105,000 years ago, with a branch of the previous wave giving rise to all later groups examined.

In the Spanish cave, researchers found genetic evidence from both groups, with the subsequent wave replacing the previous one. “There have been signs based on the mitochondrial DNA of this turnover, but seeing it clearly with nuclear DNA is really exciting,” says paleogeneticist Qiaomei Fu of the Beijing Institute of Paleontology and Paleoanthropology of Vertebrates, who did not participate in this study.

The posterior wave may be related to the appearance of the last "classical" stage of Neanderthal anatomy, skeletal features such as a bulge in the back of the skull that may indicate strong neck muscles or enlarged brain regions linked to vision, the researchers say. This last wave may have coincided with the cooling and other environmental changes that occurred with the arrival of the last glacial era.

This research emphasizes that scientists working on possible Neanderthal sites should not throw away dirt as is traditionally done, says paleogenetic Carles Lalueza-Fox of the Barcelona Institute of Evolutionary Biology, who did not participate in this study. Instead, special protocols may be needed to avoid contaminating these areas with modern DNA.

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