Alongside Neanderthal and Denisovan DNA, human genomes preserve traces of two other relatives no one can identify. Neither has a sequenced genome or a confirmed fossil, and part of one may be sitting in your DNA.
Researchers call one the “ghost” lineage. A new study found one of its signals in a region containing FOXP2, a gene involved in speech and language. Very little Neanderthal or Denisovan DNA has been found there, so the region often seemed distinctly modern human. Yet at one point, ghost ancestry appeared in about 13 out of every 100 copies of that region researchers analyzed.
Published in Science, the research maps both lineages and estimates when their DNA entered other human groups. The ghost lineage interbred directly with our ancestors in Africa, while the much older “super-archaic” lineage reached Homo sapiens through Denisovans.
“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,” said senior author Priya Moorjani in a press release.
How Ghost and Super-Archaic DNA Reached Modern Humans
Ghost DNA appeared in every population examined, placing the interbreeding before modern humans spread beyond Africa around 50,000 years ago. It accounts for approximately 0.5 to 1.1 percent of their genomes.
The lineage split from ours around 830,000 years ago. Its age overlaps with Middle Pleistocene Homo groups in Africa, possibly including Homo heidelbergensis, but no genetic match exists.
The super-archaic lineage separated from ours around 1.8 million years ago. Its DNA entered Denisovans more than 200,000 years ago before reaching Homo sapiens through later interbreeding.
Researchers followed the trail through 92 genomes containing high levels of Denisovan ancestry. Super-archaic fragments represented about 0.3 percent of the Denisovan ancestry detected, a figure the team considers a conservative minimum.
Homo erectus lived during the right period to be a possible source, although the connection remains unconfirmed.
“The super-archaic finding is particularly exciting because it reveals genetic contributions from a human lineage that lived over a million years ago, despite the absence of any sequenced DNA from that population,” said Arjun Biddanda, co-first author of the study.
Read More: Genomes Across Japan Reveal Traces of Neanderthal and Denisovan DNA — and a Hidden Third Ancestry
Finding Human Relatives Without Ancient Genomes
Neanderthal and Denisovan ancestry can be recognized by comparing living DNA with genomes recovered from their remains. That approach cannot work for unidentified groups with no reference genome.
The Berkeley team developed TRACE to reconstruct the family history of DNA segments using present-day genomes alone. Working with 503 genomes from the 1000 Genomes Project, it searched for branches extending far into the past.
The team first tested TRACE on known Neanderthal and Denisovan ancestry. Once it recovered those established patterns without using the ancient genomes as references, researchers turned to segments that matched neither group.
A Human Family Tree With Reconnecting Branches
Some common ghost segments overlap regions involved in immunity and metabolism. Interbreeding could have introduced useful genetic variation as humans encountered new foods and diseases, but researchers do not yet know what these specific variants do.
Ghost ancestry also appeared in regions researchers had labeled Neanderthal and Denisovan ancestry deserts. Those areas were often treated as candidates for Homo sapiens-specific evolution. But if DNA from another ancient population survived there, natural selection may have acted against Neanderthal and Denisovan ancestry specifically rather than removing every ancient contribution.
Adding genomes from more populations may reveal other unknown lineages. For now, the FOXP2 region shows what earlier methods missed: DNA from an unidentified relative in a region researchers once thought belonged only to modern humans.
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- This article references information from a study published in Science:Recovering signatures of archaic hominin introgression using ancestral recombination graphs