Study finds DNA from ‘ghost ancestors’ in all humans

A previously unknown ancient human relative interbred with our ancestors in Africa more than 50,000 years ago, leaving genetic traces that persist in every living person on Earth, according to a study published Thursday in the journal Science.science+1

Researchers at UC Berkeley and Johns Hopkins University used a new computational method to identify DNA from two extinct hominin lineages embedded in the modern human genome — neither of them Neanderthal or Denisovan. The findings reshape the picture of human evolution from a simple branching tree into what the researchers describe as "a complex web of populations connected by repeated episodes of migration and mixing".news.berkeley

A Ghost in Every Genome

The first lineage, dubbed a "ghost ancestor" because no fossil or sequenced ancient DNA exists for it, split from the modern human lineage roughly 800,000 years ago. Despite evolving separately for hundreds of thousands of years, it interbred with Homo sapiens in Africa before the major migration out of the continent. The resulting DNA — comprising about 0.5% to 1% of each person's genome, comparable to Neanderthal contributions — then spread worldwide as humans dispersed into Europe and Asia.scientificamerican+2

"We were actually able to find and map genomic locations in modern humans that are from this ghost lineage and show that this ghost ancestry is in all modern humans, not only in Africans," said Yulin Zhang, a Berkeley graduate student and co-first author of the study.news.berkeley

A Super-Archaic Surprise

The second lineage is older still. The researchers call it "super-archaic," tracing it to a hominin group that descended from a lineage dating back 1.8 million years. This population interbred with Denisovans in Eurasia more than 200,000 years ago, and fragments of its DNA later passed into Homo sapiens when Denisovans and modern humans themselves interbred.ara+1

"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, a postdoctoral researcher at Johns Hopkins and the study's other co-first author.news.berkeley

A New Frontier

The discoveries were made possible by a technique called TRACE, which reconstructs ancient genealogical relationships using only present-day genomes, bypassing the need for ancient DNA samples. Many of the archaic DNA segments the team identified are concentrated in genomic regions associated with immunity and metabolism — functions that would have given early humans adaptive advantages as they encountered new pathogens and food sources.science+1

"I think these new computational methods that allow us to reconstruct genealogical relationships are really the next frontier in this field," said Priya Moorjani, a Berkeley associate professor and senior author of the study, "because they are allowing us to uncover hidden episodes from our past without requiring ancient DNA".news.berkeley