Neanderthal Population Dynamics Clarified With New Sequence Data
Jun 26, 2019 | staff reporter
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NEW YORK – A team from Germany and Belgium has sequenced two new Neanderthal genomes to untangle the ancient history of the ancient hominins.

As they reported online today in Science Advances, investigators at the Max Planck Institute for Evolutionary Anthropology and elsewhere sequenced nuclear DNA from two Neanderthals whose remains were dated to about 120,000 years ago. The Neanderthals — found in caves in Germany and Belgium, respectively — had distinct mitochondrial lineages, they reported.




Even so, the Neanderthals shared closer genetic ties to Neanderthals found in Western Europe tens of thousands of years later than they did to another Neanderthal from around 120,000 years ago that was previously sequenced in Siberia.

"Our analysis shows that late Neanderthals that lived in Europe at around [40,000 years] ago trace at least part of their ancestry back to Neanderthals that lived there approximately 80,000 years earlier," senior and co-corresponding author Kay Prüfer, an evolutionary genetics researcher with the Max Planck' Institute for Evolutionary Anthropology, and his colleagues wrote. "The latter became widespread, appearing in the east at least [90,000 years] ago."

Prüfer, who is also affiliated with the Max Planck Institute for the Science of Human History, noted in a statement that the result "is truly extraordinary and a stark contrast to the turbulent history of replacements, large-scale admixtures and extinctions that is seen in modern human history."

Although past studies suggest Neanderthals in Europe and Central Asia fell into one genetically related group in the time leading up to their extinction roughly 40,000 years ago, not as much is known about the deeper population history of Neanderthals, which go back an estimated 430,000 years.

Even so, there have been clues that Neanderthals were once more genetically diverse, including genetic differences between the 120,000-year-old Altai Neanderthal and the Neanderthal ancestor of a Neanderthal-Denisovan offspring found in Russia's Denisova Cave.

To get a better look at more ancient Neanderthal population history, the researchers began by using multiple DNA extraction, library preparation, and contaminant DNA removal methods to prepare sequencing libraries for two Neanderthals, a male found in Germany's Hohlenstein-Stadel Cave and a female from the Scladina Cave in Belgium.

After focusing in on the most promising libraries from each Neanderthal, the team generated mitochondrial genomes for them, along with 168 million base pairs of nuclear sequence from one Neanderthal and 78 million base pairs of nuclear DNA from the other.

Despite the age of the remains, the researchers reported, both the Hohlenstein-Stadel Neanderthal and the Scladina Cave Neanderthal shared more alleles with a 50,000-year-old Neanderthal from Croatia than with a much older Altai Neanderthal, both sequenced to high coverage for past studies. 

Even though the Neanderthal from the Hohlenstein-Stadel Cave in Germany fell in a mtDNA lineage that appeared to have split from other lineages roughly 270,000 years ago, the team's broader nuclear DNA-based analyses suggested both the Hohlenstein-Stadel and Scladina Cave Neanderthals were ancestral to the Croatian Neanderthal and other Neanderthals from Western Europe, splitting from the Altai Neanderthal lineage roughly 122,000 to 141,000 years ago.

"The genetic continuity seen in Europe contrasts … with the deeply divergent mtDNA in [the Hohlenstein-Stadel Neanderthal], which hints at a more complex history that affected at least some of the European Neanderthals before [about 120,000 years] ago," the authors concluded. "DNA sequences from even older Neanderthals are needed to clarify whether Neanderthal substructure, gene flow from relatives to modern humans, or both are the explanation for the Hohlenstein-Stadel Neanderthal]'s peculiar mtDNA."

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