Sept. 6, 2011
Courtesy of the University of Arizona
and World Science staff
Interbreeding between ancestors of modern humans and our extinct evolutionary relatives happened much earlier—and more extensively—than scientists have thought, a study suggests.
Scientists believe our species, Homo sapiens, originated in Africa and eventually spread worldwide. Several past studies have also indicated that after reaching Europe, Homo sapiens interbred with Neanderthal people. But the new work suggests interbreeding with other lineages had already taken place in Africa, perhaps with noted extinct human lineages such as Homo erectus, the “upright walking man,” or Homo habilis, “tool-using man.”
New research suggests ancestors of modern humans interbred with other lineages in Africa, perhaps with noted extinct lineages such as Homo erectus, the “upright walking man,” or Homo habilis, “tool-using man,” pictured above in an artist's conception. (Courtesy NASA)
“We think there were probably thousands of interbreeding events... It looks like our lineage has always exchanged genes” with others, said Michael Hammer of the University of Arizona, who led a team reporting the new findings. The research appears in this week’s early online edition of the journal Proceedings of the National Academy of Sciences.
Scientists can now extract DNA from fossils tens of thousands of years old, which has enabled research into proposed interbreeding with Neanderthals. But the Africa specimens that Hammer’s team studied were much older, Hammer noted, so “we don’t have fossil DNA from Africa to compare with ours.” Also, “Neanderthals lived in colder climates, but the climate in more tropical areas make it very tough for DNA to survive that long.”
Thus “our work is different from the research that led to the breakthroughs in Neanderthal genetics,” he explained. “We couldn’t look directly for ancient DNA that is 40,000 years old and make a direct comparison.” To get around this, Hammer’s team used computers and statistics. “We looked at DNA from modern humans belonging to African populations and searched for unusual regions in the genome,” he explained.
Because nobody knows the DNA sequences of those extinct humans, Hammer’s team first had to figure out what features of modern DNA might represent fragments brought in from archaic forms. “What we do know is that the sequences of those forms, even the Neanderthals, are not that different from modern humans,” he said. “They have certain characteristics that make them different from modern DNA.”
The researchers used simulations to predict what ancient DNA sequences would look like had they survived. “You could say we simulated interbreeding and exchange of genetic material,” Hammer said.
According to Hammer, the first signs of anatomically modern features appeared about 200,000 years ago.
First, 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. The researchers focused on “non-coding” regions of the genome, stretches of DNA that don’t contain actual genes.
“Then we asked ourselves what does the general pattern of variation look like in the DNA that we sequenced in those African populations, and we started to look at regions that looked unusual,” Hammer said. “We discovered three different genetic regions fit the criteria for being archaic DNA still present in the genomes of sub-Saharan Africans. Interesting, this signature was strongest in populations from central Africa.”
The scientists applied several criteria to tag a DNA sequence as archaic. For example, if a DNA sequence differed radically from the ones found in a modern population, it was considered likely ancient in origin. Another telltale sign is how far it extends along a chromosome, Hammer and colleagues contend: if an unusual piece is found to stretch a long portion of a chromosome, it’s a sign of having entered the population relatively recently.
“We are talking about something that happened between 20,000 and 60,000 years ago – not that long ago in the scheme of things,” Hammer said. “If interbreeding occurs, it’s going to bring in a whole chromosome, and over time, recombination [genetic mixing] events will chop the chromosome down to smaller pieces. And those pieces will now be found as short, unusual fragments. By looking at how long they are we can get an estimate of how far back the interbreeding event happened.”
Hammer said that although 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.”
In a next step, Hammer’s team wants to look for ancient DNA regions that conferred some advantage to the anatomically modern humans once they acquired them. Interbreeding, he added, “is quite common in nature, and it turns out we’re not so unusual after all.”