NEW YORK – New findings from independent research teams are providing previously unappreciated insights into human population history — from genetic details on a human lineage that appears to have gone extinct in Europe to a clearer view on the timing and duration of early modern human mixing with Neanderthals outside of Africa.
For the first of the studies, published in Nature on Thursday, Max Planck Institute for Evolutionary Anthropology researchers Kay Prüfer and Johannes Krause led an international team that presented findings from a whole-genome sequencing study of 42,000- to 49,000-year-old early modern human representatives at the Zlatý kůň and Ranis in Czechia and Germany, respectively.
"We analyzed the genomes of a handful of individuals from, on the one hand, a site called Ranis, which is in central Germany, and then a genome from a female skull from Zlatý kůň in the Czech Republic," Krause, co-senior and co-corresponding author and an archaeogenetic researcher and director at the Max Planck Institute of Evolutionary Anthropology, explained during a press briefing on Wednesday.
The results build on a mitochondrial DNA analysis that members of the same team described in a Nature study earlier this year, which suggested that Ranis individuals belonged to a technocomplex culture known as the Lincombian-Ranisian-Jerzmanowician (LRJ) that ranged from the UK to Poland some 45,000 years ago.
"It was discussed before whether this northern European culture was made by Neanderthals or by modern humans, or Homo sapiens," Krause said, explaining that the mitochondrial data confirmed that the LRJ was linked to modern humans, despite the cold climactic conditions in the area and relatively short time frame since apparent migrations out of Africa.
By generating high-quality genome sequences for each individual from Zlatý kůň and Ranis — together with five low-coverage genomes for 45,000-year-old individuals in Ranis — the team has now been able to show that the individuals belonged to a relatively small population with an estimated size of roughly 200 members and belonged to a genetic lineage that does not have any known descendants across present-day human populations.
Rather, that human lineage appears to have disappeared roughly 40,000 years ago, Krause said, at roughly the same time that other hominin lineages, including Neanderthals, went extinct in Europe.
"There's multiple lineages that we have identified now that did not contribute to later people, which also tells us that the human story, human history, is not just a story of success," Krause told reporters. "We actually went extinct several times, including Neanderthals going extinct around that time."
Even so, investigators explained, the extinct human group shared similar Neanderthal ancestry patterns with other human lineages, despite their otherwise distinct migration, interaction, and population survival patterns.
In the Ranis genomes, for example, the team tracked down stretches of Neanderthal sequence stemming from an admixture event that was estimated to have taken place over some 7,000 years roughly 45,000 to 49,000 years ago, based on Neanderthal DNA segment length-based analyses of the generations that have occurred since the gene flow event.
In another study, published in Science on Thursday, investigators at the University of California, Berkeley, the Max Planck Institute for Evolutionary Anthropology, the University of Rochester, and the Francis Crick Institute took a closer look at the timing and length of that early modern human-Neanderthal mixing event, which they called a "single, shared extended period of gene flow."
There, the team analyzed Neanderthal ancestry patterns in 59 published ancient genome sequences from Europe, Western Asia, and Central Asia, along with published sequences from 275 present-day humans from around the world, to assess Neanderthal ancestry patterns stretching back roughly 50,000 years.
"We created a catalog of Neanderthal ancestry segments in each individual," co-senior and co-corresponding author Priya Moorjani, a molecular and cell biology and computational biology researcher with the University of California, Berkeley, said during Wednesday's press briefing. "By comparing the segments over time and across geographic regions, we inferred that the vast majority of the Neanderthal gene flow had occurred in a single, shared, extended period."
Together, that team's results pointed to a period of gene flow from Neanderthals to modern human migrants from Africa that took place around 43,500 to 50,500 years ago.
"This was really striking because it's very consistent with the estimate from the Nature paper, as well as from archaeological evidence," Moorjani said, "which has dated the overlap of Neanderthals and modern humans in Europe."
She, too, said the results have helped to narrow the time frame for the out-of-Africa migration involving the ancestors of present-day populations, as well as human lineages that fizzled out, suggesting waves of migration that occurred earlier than 51,000 years ago likely involved individuals who did not seem to have contributed genetically to living, non-African individuals.
Investigators speculated that the human-Neanderthal mixing may have taken place in the Near East, based on the subsequent distribution of human lineages carrying Neanderthal DNA, though the precise location has not been determined.
Consistent with prior studies on selection for and against Neanderthal sequences in the human genome, they noted that Neanderthal sequences that have persisted in the human genome include Neanderthal-specific variants involved in everything from metabolism and immune function to skin pigmentation, though the precise impacts of certain variants in these regions remain unknown.
Nevertheless, the team saw signs that this selection occurred relatively quickly after early modern humans met and mingled with Neanderthals.
"By studying modern humans over time, we were able to show that the landscape of Neanderthal ancestry, as we see it in present-day individuals, probably formed relatively rapidly after the gene flow," co-first and co-corresponding author Leonardo Iasi, an evolutionary genetics researcher with the Max Planck Institute for Evolutionary Anthropology, told reporters on Wednesday. "The majority of selection — positive and negative — on Neanderthal ancestry happened very quickly after the gene flow, within roughly 100 generations."