Neanderthals and modern humans shared a long, fascinating history. The presence of Neanderthal DNA in the genomes of living people shows those populations were closely connected. Some scientists even argue Neanderthals shouldn’t be classified as a separate species.
Most past research focused on gene flow from Neanderthals into modern humans, which makes sense because we have far more human genetic material than Neanderthal DNA available for analysis.
Recently, an American team of geneticists led by Liming Li of Princeton University developed a method to trace gene flow from modern humans into Neanderthals by analyzing Neanderthal DNA segments preserved in modern human genomes.
What scientists have learned
Their results show a long-lasting, recurring connection between the two hominin groups starting about 250,000 years ago. The team found that this early human-to-Neanderthal gene flow means previous estimates of Neanderthal population size should be reduced by roughly 20%.
“The lower estimated population size and projected dynamics of admixtures correspond to population data on Neanderthals, whose numbers decreased over time and were ultimately absorbed into the modern human gene pool,” the paper said.
There isn’t much Neanderthal DNA left from pure Neanderthals, since they disappeared about 40,000 years ago. Tests of preserved Neanderthal genetic material haven’t found evidence of modern human DNA. However, every living person’s genome contains at least a small amount of Neanderthal DNA: between one and four percent.
Li and his colleagues used the international 1000 Genomes database to identify Neanderthal DNA in 2,000 modern human genomes, ScienceAlert reports. To extract information from these sequences, the team used IBDmix, a method developed at Princeton.
They looked for heterozygosity, a measure of genetic diversity: high heterozygosity means more diversity, low means less. So if a Neanderthal DNA segment shows unusually high heterozygosity, it likely came from an individual whose ancestors included modern humans.
They found Neanderthal DNA segments in African genomes that carried the high-heterozygosity signature — while Neanderthal segments in non-Africans did not. That pattern pointed to two pulses of gene flow from modern humans into Neanderthals: one about 250,000–200,000 years ago and another around 120,000–100,000 years ago.
The team also estimated how much modern human DNA is present in some Neanderthal lineages. For example, the genomes of Neanderthals from Croatia’s Vindija Cave and from the Altai Mountains appear to contain about 2.5% and 3.7% modern human DNA, respectively. That suggests previous studies overestimated Neanderthal population sizes, which affects explanations for their extinction.
Li and his colleagues’ work supports the idea that Neanderthals were absorbed into expanding Homo sapiens populations, and it aligns with previous findings such as the loss of the Neanderthal Y chromosome.
“The assimilation of Neanderthals into the population of modern humans as they spread across Eurasia would have effectively increased the numbers of modern human populations while simultaneously reducing the population of Neanderthals, which was already under threat,” the paper said.
The study’s conclusions were published in the journal Science.
