Clues to two mysterious ‘ghost’ ancestors emerge from genetic traces found in modern human DNA - CNN

Clues emerging from DNA could unlock the mystery of human ancestors that are missing from the fossil record yet present in the genes of people living today.

Scientists found evidence years ago that our species, Homo sapiens, had interbred with now-extinct human relatives, including Neanderthals and Denisovans. But some lineages have been difficult to identify, because — unlike Neanderthals and Denisovans, whose DNA has been recovered from prehistoric remains — they are essentially genetic “ghosts,” with no DNA proof of their existence to compare with the hints spotted in our genomes.

While previous studies have discovered remnants of the ghost lineages, they could not determine when the interbreeding happened or how far back these lineages diverged from the ancestors of modern humans.

Now, researchers have developed a new method to analyze modern human genomes and uncovered evidence of two previously unknown ancestral lineages by working backward from DNA in living people to reconstruct missing parts of the human family tree. One of the lineages appears to have interbred directly with Homo sapiens in Africa more than 50,000 years ago, while the other was an even older group that passed some of its DNA to humans indirectly through Denisovans. The researchers reported their findings July 30 in the journal Science.

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The scientists’ method reconstructs genealogies, or maps showing where different pieces of DNA came from and how they were passed down, revealing branches of our evolutionary past.

“The most fundamental question that most of us have is, ‘Why are we here? Where do we come from?’ And these genealogies really allow us to look into the past in a way that we have not been able to do before,” said Priya Moorjani, study coauthor and an associate professor in the department of molecular and cell biology at the University of California, Berkeley.

Moorjani added that the discovery allows for further investigation into why some hominin groups survived while others disappeared. Understanding the genetic contributions of our various ancestors can help answer that question while also revealing how humans adapted to their environments and why certain diseases affect us today, she said.

Hunting for ghost lineages

Modern humans first moved out of Africa around 50,000 years ago. This migration of Homo sapiens is what led to interbreeding with the Neanderthals and Denisovans in Eurasia. However, the newly detected lineages add more to the story.

One of the unknown ghost ancestors described in the new study likely interbred with humans in Africa before the migration event. The researchers estimate that DNA inherited from this lineage makes up about 0.5% to 1% of the genomes of people living today — almost the same percentage as Neanderthal DNA currently found in many modern humans.

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The second lineage is much older. The researchers refer to it as a “super-archaic” ancestor because it traces back to a branch of the human family tree that split roughly 1.8 million years ago. This hominin appears to have interbred with Denisovans in Eurasia more than 200,000 years ago, with some of its DNA eventually reaching modern humans through our interbreeding with Denisovans.

To uncover these ghost ancestors, researchers developed a new computer-based method, called TRACE, that can search contemporary human genomes for clues left by long-lost populations.

“Our genomes are mosaics of little bits of DNA from all our ancestors, and so in different parts of our genome we have a different family tree,” Moorjani explained. Some branches of those family trees are relatively recent, while others extend much further into the past. DNA inherited from ancient relatives such as Neanderthals, for example, sits on these deeper branches. TRACE searches across the genome for far back lineages that could point to ancestry from previously unknown populations.

The researchers tested TRACE on more than 500 modern human genomes from current populations across Africa, Europe and Asia. They found traces of the more recent ghost ancestry in every population they studied, pointing to a lineage that must have contributed DNA to the ancestors of modern humans before our species’ major migration out of Africa.