In a genomic study encompassing more than 300 genomes, researchers determined the time period during which Neanderthals interbred with modern humans, starting about 50,500 years ago and lasting about 7,000 years — until Neanderthals began to disappear. That interbreeding left Eurasians with many genes inherited from our Neanderthal ancestors, which in total make up between 1% and 2% of our genomes today.
Neanderthal man. Image credit: Mauro Cutrona.
To date, sequencing of Neanderthal and Denisovan genomes has revealed substantial gene flow between these archaic hominins and modern human ancestors, even as scientists have also reported that Neanderthal ancestry is unevenly distributed across the genome.
Moreover, certain regions of the genome — known as archaic deserts — completely lack Neanderthal ancestry, while others exhibit high frequencies of Neanderthal variants, potentially due to beneficial adaptive mutations.
However, much about the nature of this ancient admixture, including the role evolutionary forces like genetic drift or natural selection played in shaping these patterns, remains unclear.
“”The timing is really important because it has direct implications on our understanding of the timing of the out-of-Africa migration as most non-Africans today inherit 1-2% ancestry from Neanderthals,” said University of California, Berkeley’s Dr. Priya Moorjani.
“It also has implications for understanding the settlement of the regions outside Africa, which is typically done by looking at archeological materials or fossils in different regions of the world.”
“The longer duration of gene flow may help explain, for example, why East Asians have about 20% more Neanderthal genes than Europeans and West Asians.”
“If modern humans moved eastward about 47,000 years ago, as archeological sites suggest, they would already have had intermixed Neanderthal genes.”
In the study, Dr. Moorjani and colleagues analyzed genomic data from 59 ancient individuals sampled between 45,000 and 2,200 years before present and 275 diverse present-day individuals.
They examined the frequency, length, and distribution of Neanderthal ancestry segments over time.
They discovered that the vast majority of Neanderthal gene flow is attributable to a single, shared extended period of gene flow that likely occurred 50,500 to 43,500 years ago, which is consistent with archeological evidence for the overlap of modern humans and Neanderthals in Europe.
Additionally, their findings demonstrate that Neanderthal ancestry underwent rapid natural selection — both positive and negative — within 100 generations after gene flow, especially on the X chromosome.
“We show that the period of mixing was quite complex and may have taken a long time,” said Dr. Benjamin Peter, a researcher at the University of Rochester and the Max Planck Institute for Evolutionary Anthropology.
“Different groups could have separated during the 6,000- to 7,000-year period and some groups may have continued mixing for a longer period of time.”
“But a single shared period of gene flow fits the data best.”
“One of the main findings is the precise estimate of the timing of Neanderthal admixture, which was previously estimated using single ancient samples or in present-day individuals,” said Dr. Manjusha Chintalapati, a researcher at the University of California, Berkeley.
“Nobody had tried to model all of the ancient samples together.”
“This allowed us to build a more complete picture of the past”
“We identified some Neanderthal regions that are present at high frequency, possibly because they were beneficial as early modern humans began to explore new environments outside of Africa.”
“These include genes related to immune function, skin pigmentation and metabolism.”
“On the other hand, there are also large regions of the genome that are completely devoid of Neanderthal ancestry.”
“These regions formed rapidly after the gene flow and were also absent from the earliest modern human genomes, 30,000 to 45,000-year-old individuals.”
“Many Neanderthal sequences may have been deleterious to humans and were therefore actively and rapidly selected against by evolution.”
“Diversification of humans outside of Africa may have begun during or soon after the Neanderthal gene flow, which could partially explain the different levels of Neanderthal ancestry among non-African populations and also reconcile our dates with archaeological evidence for the presence of modern humans in Southeast Asia and Oceania by about 47,000 years,” Dr. Peter said.
“Studying more ancient genomes from Eurasia and Oceania could further our understanding of when humans spread to these regions.”
The results appear in the journal Science.
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Leonardo N.M. Iasi et al. 2024. Neanderthal ancestry through time: Insights from genomes of ancient and present-day humans. Science 386 (6727); doi: 10.1126/science.adq3010
