Study Finds Two Ghost Human Lineages in Modern Humans’ DNA, Including Africa Interbreeding

A new study published in Science reports that modern humans carry DNA traces from two previously unidentified ancient human populations, including a “ghost” lineage and a much older “super-archaic” lineage.

“The study identified a “ghost” lineage that appears to have interbred with modern humans in Africa more than 50,000 years ago”

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The “ghost” lineage is described as interbreeding with modern humans in Africa more than 50,000 years ago, with its DNA now accounting for approximately 0.5% to 1% of each modern human genome.

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The study also finds evidence of a “super-archaic” lineage that separated from other human ancestors around 1.8 million years ago and likely interbred with Denisovans in Eurasia more than 200,000 years ago.

Researchers say the “ghost” ancestry is present in all modern humans, not only in Africans, and they estimate the ghost lineage diverged from modern human ancestors around 800,000 years ago.

The work is based on a computational technique called TRACE, developed by researchers at the University of California, Berkeley, which reconstructs ancient genealogical relationships using hundreds of present-day human genomes without requiring DNA recovered from fossils.

To detect the unknown contributions, the study introduces TRACE, short for “TRacking Archaic Contributions via ARG Estimation,” which reconstructs ancestral recombination graphs using present-day genomes alone.

The method is described as reference- and outgroup-free, using features of ancestral recombination graphs to identify archaic ancestry even when no reference genome exists for the unidentified groups.

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In the analysis of 503 genomes from the 1000 Genomes Project, TRACE recovered established Neanderthal and Denisovan patterns and then flagged DNA that matched neither group.

One reported signal is that the ghost ancestry appeared in about 13 out of every 100 copies of a region researchers analyzed, and the study estimates it accounts for approximately 0.5 to 1.1 percent of their genomes.

Researchers also report that ghost ancestry appeared in regions labeled “Neanderthal and Denisovan ancestry deserts,” including a chromosome 7 region with a ghost peak of 13.3% and a chromosome 3 region with a ghost peak near 20%.

The study’s model places the ghost lineage’s split from the lineage leading to Homo sapiens at around 830,000 years ago, and it says the ghost DNA appeared in every population examined before modern humans spread beyond Africa around 50,000 years ago.

“It accounts for approximately 0.5 to 1.1 percent of their genomes.”

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For the older super-archaic signal, the study describes a separation from the modern human lineage around 1.8 million years ago and says its DNA entered Denisovans more than 200,000 years ago before reaching Homo sapiens through later interbreeding.

Researchers also report that the super-archaic fragments represented about 0.3 percent of the Denisovan ancestry detected, which the team considers a conservative minimum.

The study frames the findings as evidence that human evolution involved repeated episodes of migration and mixing rather than a simple branching tree, with senior author Priya Moorjani saying, “We often think of human evolution as a branching tree, but new genomic data and analytical methods reveal a much more interconnected history — more like a complex web of populations connected by repeated episodes of migration and mixing.”

The paper’s authors say the identities of both populations remain unknown, but they note that the ghost lineage’s age overlaps with Middle Pleistocene Homo groups in Africa and that Homo erectus is a possible source for the super-archaic lineage, while the connection remains unconfirmed.