Using several genetic analytical methods, an international research team has identified an interbreeding event between Neanderthals and modern humans that occurred about 100,000 years ago – tens of thousands of years earlier than previous scientific estimates. Dr. FU Qiaomei, a researcher at the Institute of Vertebrate Paleontology and Paleoanthropology (IVPP) of the Chinese Academy of Sciences, is part of the team that made this ground-breaking discovery, which was published February 17 in the journal Nature.
The authors have pieced together the first genetic evidence supporting the scenario that some modern humans may have left Africa in an early migration and admixed with archaic hominids in Eurasia before the ancestors of present-day non-Africans migrated out of Africa less than 65,000 years ago. The breakthrough involves a specific “Altai Neanderthal” (Figure 1), whose remains were found in a cave in the Altai Mountains in southern Siberia.
The individual shows signs of gene flow from modern humans. In comparison, the two Neanderthals from European caves who were also sequenced for this study, as well as a Denisovan, all appeared to lack specific DNA derived from modern humans.
Some of their findings reveal that alleles in the windows of the Altai Neanderthal genome with low divergence from Africans have higher divergence from the Denisovan than Denisovan windows with low divergence from Africans. The latter windows in the Altai Neanderthal genome have higher heterozygosity than in the Denisovan genome.
Research also found that a demographic model that estimates gene flow from these early modern humans into the ancestors of the Altai Neanderthal to be about 1.0–7.1%. Although the exact source is unclear, the authors suspect that it may have come from a deep population that either split off from the ancestors of present-day Africans or from one of the early African lineages. The study finds that complex computer simulations also support the data.
The team was able to further calculate that early modern human introgression into the Altai Neanderthal lineage occurred 100,000–230,000 years ago, based on the amount of shared haplotypes (50 kilobases or longer in length) between modern humans and the Altai Neanderthal. This introgression is much earlier than previously reported gene flow from Neanderthals into modern humans outside Africa (47,000–65,000 years ago).
Possibly, there was an extended lag between when this group branched off from the modern human family tree, roughly 200,000 years ago, and when its members left their genetic mark in the Altai Neanderthal, about 100,000 years ago, before the group became extinct.
This research was partly supported by the Special Foundation of the President of the Chinese Academy of Sciences.
Dorsal view of the Denisova Neandertal toe bone. (Image by Bence Viola)
(Text & Images’ Source: article by Chen Na, Chinese Academy of Sciences)
First genetic evidence of modern human DNA in a Neanderthal individual
Cold Spring Harbor, NY – Using several different methods of DNA analysis, an international research team has found what they consider to be strong evidence of an interbreeding event between Neanderthals and modern humans that occurred tens of thousands of years earlier than any other such event previously documented.
Today in Nature the team publishes evidence of interbreeding that occurred an estimated 100,000 years ago. More specifically the scientists provide the first genetic evidence of a scenario in which early modern humans left the African continent and mixed with archaic (now-extinct) members of the human family prior to the migration “out of Africa” of the ancestors of present-day non-Africans, less than 65,000 years ago.
Scenario of interbreeding between modern humans and Neanderthals: Neanderthal DNA in present-day humans outside Africa originates from interbreeding that occurred 47,000 – 65,000 years ago (green arrow). Modern human DNA in Neanderthals is likely a consequence of earlier contact between the two groups roughly 100,000 years ago (red arrow). © Ilan Gronau
“It’s been known for several years, following the first sequencing of the Neanderthal genome in 2010, that Neanderthals and humans must have interbred,” says Professor Adam Siepel, a co-team leader and Cold Spring Harbor Laboratory (CSHL) quantitative biologist. “But the data so far refers to an event dating to around 47,000-65,000 years ago, around the time that human populations emigrated from Africa. The event we found appears considerably older than that event.”
In addition to Siepel, who is Chair of CSHL’s Simons Center for Quantitative Biology, the team included several members of the Max Plank Institute for Evolutionary Anthropology, including Martin Kuhlwilm, Svante Pääbo, Matthias Meyer and co-team leader Sergi Castellano. Kuhlwilm was co-first author of the new paper with Ilan Gronau, a former member of Siepel’s Lab who is now at the Herzliya Interdisciplinary Center, Israel. Melissa Hubisz, a Ph.D. student with Siepel at Cornell University, also made major contributions to the work. The full international research team included 15 additional co-authors.
“One very interesting thing about our finding is that it shows a signal of breeding in the ‘opposite’ direction from that already known,” Siepel notes. “That is, we show human DNA in a Neanderthal genome, rather than Neanderthal DNA in human genomes.”
This finding, the result of several kinds of advanced computer modeling algorithms comparing complete genomes of hundreds of contemporary humans with complete and partial genomes of four archaic humans, has implications for our knowledge of human migration patterns.