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WHEN DID NEANDERTALS AND HUMANS INTERBREED? GENOMICS CLOSES IN ON A
DATE  
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Stephanie Pappas
December 12, 2024
Scientific American
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_ Genomic sleuthing can determine how many generations have passed
since a hybridization event. The oldest human genomes ever sequenced
reveal that our Neandertal ancestry came from one “pulse” of
interbreeding and pins down the timing. _

Illustration of Zlatý kůň, who belonged to the same population as
the Ranis individuals and was closely related to two of them, Tom
Björklund ([link removed])

 

Scientists have long known that humans outside of Africa owe 2 to 3
percent of their genome to Neandertal ancestors
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But now, using the oldest modern human DNA ever analyzed, two separate
studies have traced this ancestry to a single surge of interbreeding
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between 45,000 and 49,000 years ago.

Neandertals (_Homo neanderthalensis_) and modern humans (_Homo
sapiens_)
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each other many times over tens of thousands of years: modern human
DNA is found in Neandertals who lived more than 200,000 years ago
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populations mingled further with Neandertals
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species went extinct 39,000 years ago. But not all of these
interactions left a shared imprint on all non-African populations
today. The moment that left this near-global genetic fingerprint
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period of a few thousand years, occurring between Neandertals who were
established in Europe and humans who were newly arriving in their
territory.

“The height of this interaction was, we think, 47,000 years
ago—which also gives us a rough estimate of when this out-of-Africa
migration
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have happened,” says Leonardo Iasi, a postdoctoral researcher in
evolutionary genetics at the Max Planck Institute for Evolutionary
Anthropology in Leipzig, Germany, and lead author of one of the
studies, which was published on Thursday in _Science_. He is also a
co-author of the other paper, which was published concurrently
in _Nature_.

Multiple waves of humans left Africa, where the _Homo _genus
originally evolved, over thousands of years and established
populations in the Near East and Europe. There they encountered and
sometimes bred with Neandertals, descendants of an earlier human
ancestor who had left Africa hundreds of thousands of years earlier.
The last common ancestor of Neandertals and modern humans remains
unknown, but that species likely lived between 650,000 and 500,000
years ago. Researchers still can’t quite say exactly _where_ the
Neandertal-human intermingling occurred, but the two new studies
narrow down the question of “when” considerably.

In the _Nature_ study, biochemist Johannes Krause, archaeogeneticist
Kay Prüfer and doctoral student Arev Sümer, all at the Max Planck
Institute for Evolutionary Anthropology, and their colleagues
sequenced genomes from six individuals discovered in Ranis, Germany,
and one from the Zlatý kůň site in the Czech Republic. These
people, who lived between 49,000 and 42,000 years ago, included some
of the oldest modern human genomes ever sequenced. They also turned
out to include the oldest known family of modern humans, Sümer says.
The people in Ranis included a mother and her young daughter, plus
another female individual from the same extended family. Even more
surprisingly, the person from Zlatý kůň—a female individual known
from her skull bones—was a more distant relative to this Ranis
family.

These linked populations, which probably consisted of only about 300
members spread across Central Europe, also shared 2.9 percent
Neandertal ancestry. By looking at the length of the Neandertal gene
segments in these human genomes, the researchers were able to gauge
when Neandertal ancestry was introduced. (Longer segments are more
recent additions because genetic recombination hasn’t had a chance
to scramble them. Shorter segments come from a more distant
interbreeding event.) The scientists found that these Central
Europeans were removed by about 80 generations, or between 1,500 and
1,000 years, from ancestors who mixed with Neandertals.

In the _Science_ study, researchers looked at a larger dataset of 59
ancient human genomes from between 45,000 and 2,200 years ago, plus
the genomes of a diverse group of 275 present-day humans. “We were
interested in estimating the timing of the Neandertal ancestry and
also checking if this happened over a short duration or over an
extended period of time,” says Priya Moorjani, a population
geneticist at the University of California, Berkeley, who, with
Benjamin Peter of the Max Planck Institute for Evolutionary
Anthropology, was co-senior author of the paper. (Peter is also a
co-author of the _Nature_ paper.)

Like Krause’s team, Moorjani and her colleagues found evidence of a
single pulse of Neandertal genetics entering the human genome between
approximately 50,500 and 43,500 years ago. The scientists also saw
evidence of natural selection in these genes: within about 100
generations, the human genome looked a lot like it does today, in
terms of which segments had lots of Neandertal genes and which had
very few. For example, the modern X chromosome has few Neandertal
genes.

This genetic change is fascinating, says Joshua Akey, a Princeton
University genomicist, who was not involved in the new studies,
because it points to places on the human genome where Neandertal genes
may have either boosted survival and reproduction and become
permanently incorporated or caused harm and disappeared. “Everyone
is innately fascinated by what makes us potentially different from
other types of humans that existed,” Akey says. “And if there are
genetic substrates that define differences, then these are the places
on the genome where they reside.”

The researchers also found that the people in Ranis and Zlatý kůň,
despite their connection to the out-of-Africa population that spread
across the world, left no descendants behind. “There are multiple
lineages that we have identified now that did not contribute to modern
people,” Krause says, “which also tells us that the human story is
not just a story of success. We also went extinct.”

Additionally, these findings raise new questions about the dispersion
of modern humans and the way humans gradually replaced Neandertals as
the dominant species in Europe, says Isabelle Crevecoeur, a
paleoanthropologist at the French National Center for Scientific
Research (CNRS) and the University of Bordeaux in France, who was not
involved in the new studies. “Now the big challenge for us, as
paleoanthropologists or prehistorians, is really to try to connect the
genetic results with the cultural or archaeological data—and try to
make sense of it,” she says.

_STEPHANIE PAPPAS
[[link removed]] is a
freelance science journalist based in Denver, Colo. More
by Stephanie Pappas
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