'Mystery population' of human ancestors gave us 20% of our genes and may have boosted our brain function

The ancestors of all modern humans split off from a mystery population 1.5 million years ago and then reconnected with them 300,000 years ago, a new genetic model suggests. The unknown population contributed 20% of our DNA and may have boosted humans' brain function.

"The fact that we can reconstruct events from hundreds of thousands or millions of years ago just by looking at DNA today is astonishing, and it tells us that our history is far richer and more complex than we imagined," study co-author Aylwyn Scally, a geneticist at the University of Cambridge, said in a statement.

In a study published Tuesday (March 18) in the journal Nature Genetics, researchers presented a new method of modeling genomic data, called "cobraa," that has allowed them to trace the evolution of modern humans (Homo sapiens).

By applying their new method to modern human DNA data published in the 1000 Genomes Project and the Human Genome Diversity Project, the researchers discovered that there were two main ancestral groups that split around 1.5 million years ago, which they called Population A and Population B.

Just after that split, Population A experienced a bottleneck when the population plummeted and likely lost a significant amount of genetic diversity. But Population A grew over time, and Neanderthals and Denisovans branched off from it.

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Then, around 300,000 years ago, Population A mixed with Population B, the researchers found. Their genetic analysis suggests that 80% of the genome of all present-day humans comes from Population A, while 20% of our genome comes from Population B.

Some of the genes from Population B, "particularly those related to brain function and neural processing, may have played a crucial role in human evolution," study co-author Trevor Cousins, a postgraduate student in genetics at the University of Cambridge, said in the statement. In general, the genetic material from Population B reduced the ability of individuals to have children, Cousins told Live Science in an email, but "the genome is a complicated place, and regions outside of genes can still do important things."

The new model suggests that, around 300,000 years ago, Population A, which eventually gave rise to humans, had "deep structure," Cousins said, meaning it was formed from "two or more genetically distinct populations that mixed with each other."

Who those populations were, however, is not clear. In the study, the researchers noted that "various Homo erectus and Homo heidelbergensis populations that are potential candidates for lineages A and B existed both in Africa and elsewhere in the relevant period."

But "the genetic model cannot indicate which fossils should be assigned to Population A or B," Cousins said. "We can only speculate."

Some experts use the term "ghost populations" to talk about groups that branched off and then reconnected later through interbreeding resulting in gene flow, John Hawks, a biological anthropologist at the University of Wisconsin-Madison who was not involved in the study, told Live Science by email.

"What is interesting about this paper is that the pattern in the model is a deep African structure that is shared by everyone living today," Hawks said. "It is not 'ghost populations' contributing to one particular group, it is one big ghost that merged in with the African source population for all modern humans."

But one of the drawbacks to the new model, according to Hawks, is that it is based on the 1000 Genomes Project, which has a low representation of African populations. "So I see this as more a proof of principle than a real guide to what ancient humans were doing," Hawks said.

The origin of modern humans is a long-standing question in paleoanthropology, and improvements in DNA and genomic analysis in the past two decades have provided new insights and raised new questions.

"What's becoming clear is that the idea of species evolving in clean, distinct lineages is too simplistic," Cousins said in the statement. "Interbreeding and genetic exchange have likely played a major role in the emergence of new species repeatedly across the animal kingdom."

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