Not just Neanderthals: Ghost lineage in Africa left its mark on our DNA - Ars Technica

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When the history of our ancestry is written, the fact that we’ve interbred with some of our closest relatives, the Neanderthals and Denisovans, will have a central role. And it will be tempting to write it as a very tidy story: Once we got genomes from these other groups, it was possible to identify the sequences in our genomes that we shared with them.

But in reality, as scientists started poking large enough collections of data, there were regular hints of some strange ancestry in our genomes. It was hard to pin down, though, at least in part because the 2 percent on average of Neanderthal DNA found in many populations does not guarantee that any two individuals will have the same 2 percent. So having the genomes of those two groups made sense of some things researchers had already been seeing.

But knowing what we do about Neanderthal and Denisovan DNA is now allowing researchers to answer a somewhat different question: Is there anything else? Using recently developed analytical techniques, they find evidence of a third lineage that we apparently interbred with before any modern humans left Africa. Again, there were hints of this earlier, but so far, there’s been no genome from a modern human relative to help us understand the details—the source of this DNA remains a “ghost lineage.”

Old, and yet young

The new work, done by a group largely based at Berkeley, relies on developments from elsewhere in the field of genomic analysis. Any site in a given person’s genome is the product of a mixture of common descent and random mutations, and its relationship to its neighbors can be mixed up by recombination, when pairs of chromosomes swap segments of DNA.

With enough genomic data, computers can be used to reconstruct what are called ancestral recombination graphs that try to reconstruct this history. For each base in the genome, ancestral recombination graphs estimate its history: How many generations back that particular base first appeared in the genome and when it has been involved with recombinations. Because of the randomness of some of these things and complexities like deletions, many of the individual inferences about history will be wrong. But those are likely to be the exceptions, and the average picture across the genome’s three billion bases should be informative.

The Berkeley team made a few inferences about what these ancestral recombination graphs should look like in cases where a separate lineage contributed DNA to modern humans (a process called “introgression”). One is that there should be a cluster of sequences that look consistently old, since they shouldn’t have as many of the same variants that the modern human genomes have picked up while the lineages were separate.

Normally, sequences that have been around for a while have more chances to be involved in a recombination. But these sequences were reintroduced to the human genome later in our history, so recombination should be far less frequent relative to a genome that’s been in the modern human lineage the whole time.

So any part of the genome that introgressed from a separate lineage should have two properties: Many of its bases should look “old” in the sense of how far back their common ancestry can be traced, yet they should look “young” in terms of how much recombination has taken place. So the researchers developed a software tool they call TRACE to look for these sequences.

Like a ghost

To test the tool, they had convenient examples: the Neanderthal and Denisovan sequences we’ve already identified in the human genome. If TRACE couldn’t pick those out, it wouldn’t find anything else useful. The development of ancestral recombination graphs is still a work in progress, so the researchers used two different tools to generate them and stuck with the one that produced the best results. The combination produced a very low false discovery rate (less than a quarter of a percent) while having an accuracy of over 90 percent.

In another demonstration, the researchers performed the analysis on African populations, which only received Neanderthal and Denisovan DNA when individuals from Eurasia migrated back. TRACE found only 0.1 percent of ancestry from these archaic lineages in these African genomes, consistent with its low false error rate.

Given about 500 modern human genomes, TRACE pulled out the expected Neanderthal and Denisovan segments. But it also revealed a lot of DNA from a ghost lineage. The...