Some West Africans may have genes from an ancient ‘ghost’ hominid

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An ancient, humanlike population still undiscovered in fossils
left a genetic legacy in present-day West Africans, a new study suggests.

These extinct relatives of Homo sapiens passed genes to
African ancestors
of modern Yoruba and Mende people starting around 24,000
years ago or later, say UCLA geneticists Arun Durvasula and Sriram Sankararaman.
Surviving DNA of those ancient hominids is different enough from that of
Neandertals and Denisovans to suggest an entirely different hominid was the
source.

Yoruba and Mende groups’ genomes contain from 2 to 19
percent of genetic material from this mysterious “ghost population,” the
scientists report February 12 in Science
Advances
. Some DNA segments passed down from the mysterious Homo species influence
survival-enhancing functions, including tumor suppression and hormone
regulation. Those genes likely spread rapidly among modern West Africans, the
investigators suspect.

DNA from Han Chinese in Beijing as well as Utah residents
with northern and western European ancestry also showed signs of ancestry from
the ancient ghost population, Durvasula and Sankararaman found. But DNA from
those two groups was not studied as closely as that from the Yoruba and Mende
people.

The report adds to recent evidence that interbreeding of
ancient people with various Homo
species played a bigger role in the evolution of modern Africans than has
generally been assumed. For instance, after leaving Africa around 60,000 to
80,000 years ago, H. sapiens groups
interbred with European Neandertals before taking
Neandertal DNA
back to Africa starting around 20,000 years ago, another
team has concluded (SN: 1/30/20). That
study found that Neandertal DNA accounts for, on average, about 0.5 percent of
individual Africans’ genomes, far more than reported in earlier studies. Most
present-day people outside Africa carry about three times as much Neandertal
DNA as Africans do.

Ghost hominid DNA and Neandertal DNA appear to have made
separate inroads among African H. sapiens
at around the same time, says geneticist Iain Mathieson of the University of
Pennsylvania Perelman School of Medicine, who did not participate in the new
study.

Although ancient humans trekking back to Africa already might
have mated with members of the ancient ghost population, “it is more likely
that interbreeding happened in Africa,” Sankararaman says. That possibility is
supported by the fact that several late Stone Age African
H. sapiens fossils
— some dating
to as late as around 16,000 years ago — display traits like those of much older
Homo species, including Neandertals,
he says.

Precisely how these genetic exchanges played out is hard to
know because researchers lack any fossils from the ancient ghost population
from which to extract examples of its DNA, says geneticist Pontus Skoglund of
the Francis Crick Institute in London. But the new study makes a good case for
DNA transmission from a poorly understood hominid population to ancestors of
West Africans today, he says.

Durvasula and Sankararaman compared genomes of 405 West
Africans — more than half either Yoruba or Mende — with ancient DNA from a
roughly 44,000-year-old Eastern European Neandertal fossil and a Denisovan
fossil from Siberia dating to at least around 51,000 years ago. Patterns of
single DNA unit changes, or SNPs, enabled the researchers to identify areas
across Yoruba and Mende genomes that were inherited from a line of ancient
hominids other than Neandertals and Denisovans. That ghost population diverged
from direct ancestors of present-day Yoruba and Mende more than 1 million years
ago, the scientists estimate.

A
2012 investigation
suggested that 15 modern African hunter-gatherers had inherited
about 2 percent of their DNA from an unknown hominid species that split from ancestors
of people today around 1.1 million years ago (SN: 7/31/12). It’s unclear whether ancient DNA identified in that
study and in the new report trace back to the same hominid species,
Sankararaman says.

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