Ancient humans interbred with other species

Our ancient human ancestors interbred with other early hominids as well as Neanderthals, new research indicates.       

Recent DNA studies have shown that interbreeding with Homo neanderthalensis took place after anatomically modern humans migrated from Africa to Eurasia, but because of the higher temperatures in Africa, DNA hasn’t survived and it’s been impossible to tell whether similar interbreeding with other extinc human forms took place there too.

But new techniques have indicated that interbreeding took place thousands of times.

“We found evidence for hybridization between modern humans and archaic forms in Africa. It looks like our lineage has always exchanged genes with their more morphologically diverged neighbors,” says Michael Hammer of the University of Arizona.

Without fossil DNA from Africa, Hammer’s team followed a computational and statistical approach, looking at DNA from modern humans belonging to African populations and searcing for unusual regions in the genome.

They used simulations to predict what ancient DNA sequences would look like had they survived within the DNA of our own cells.

“You could say we simulated interbreeding and exchange of genetic material in silico,” Hammer said. “We can simulate a model of hybridization between anatomically modern humans and some archaic form. In that sense, we simulate history so that we can see what we would expect the pattern to look like if it did occur.”

The team sequenced vast regions of human genomes from samples taken from six different populations living in Africa today and tried to match up their sequences with what they expected those sequences to look like in archaic forms. They focused on non-coding regions of the genome – stretches of DNA that don’t contain genes, and which serve as the blueprints for proteins.

“We discovered three different genetic regions fit the criteria for being archaic DNA still present in the genomes of sub-Saharan Africans,” says Hammer. “Interestingly, this signature was strongest in populations from central Africa.”

The scientists used several criteria to tag a DNA sequence as archaic. For example, a sequence differing radically from those found in a modern population was likely to be ancient. Another indication was if an unusual piece stretched over a long portion of a chromosome, implying it was brought into the population relatively recently.

Hammer said that even though the archaic DNA sequences account for only two or three percent of what is found in modern humans, that doesn’t mean the interbreeding wasn’t more extensive.

“It could be that this represents what’s left of a more extensive archaic genetic content today. Many of the sequences we looked for would be expected to be lost over time. Unless they provide a distinct evolutionary advantage, there is nothing keeping them in the population and they drift out.”

Next, Hammer’s team wants to look for ancient DNA regions that conferred some selective advantage to the anatomically modern humans once they acquired them.

“We think there were probably thousands of interbreeding events. It happened relatively extensively and regularly,” says Hammer.

“Anatomically modern humans were not so unique that they remained separate. They have always exchanged genes with their more morphologically diverged neighbors. This is quite common in nature, and it turns out we’re not so unusual after all.”