June 2011, Cover Stories, Daily News

Before They Left Africa, Modern Humans Interbred With Archaic Humans, Reports DNA Study

By Dan McLerran   Mon, Sep 05, 2011

It has become increasingly clear through DNA studies that modern humans may have interbred with Neanderthals in Eurasia following their migration from their ancestral African homeland. Now, based on new DNA research conducted by a team of scientists from the University of Arizona and the University of California, San Francisco, it seems that modern humans had already established a pattern of mixing it up with their more archaic cousins before they even left their southerly African climes. 

Says team leader Michael Hammer, associate professor and research scientist with the University of Arizona's Arizona Research Labs, "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". This conclusion and the study details and results were published in the Proceedings of the National Academy of Sciences. 

Using a computational and statistical approach through simulations of gene sequences, the researchers were able to identify unusual regions in the genome that would be indicative of "fragments" of archaic human genomes inherited by anatomically modern humans. DNA samples from modern sub-Saharan populations were taken for the testing.

The methodology differs from that used recently by other scientists in genetic studies of modern and Neanderthal humans. While DNA samples can be successfully extracted for testing from Neanderthal fossils, DNA samples from the remains of archaic humans in Africa cannot be successfully obtained, as the more tropical environmental conditions in Africa did not permit sufficient preservation of their DNA through time. The team thus used simulation techniques based on predictions of what archaic human genome sequences would look like had they survived within the DNA of modern human cells, as a substitute for the lack of available DNA. The team sequenced genomes of samples from six different populations living in Africa today and matched their sequences with the simulated model sequences that contained archaic forms.  

"What we do know is that the sequences of those forms, even the Neanderthals, are not that different from modern humans," Hammer said. "They have certain characteristics that make them different from modern DNA. 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."  One tell-tale sign of an archaic genome sequence is that if a sequence found in a modern population sample differed radically from the others found in the modern population, it was likely to be ancient in origin. 

"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. Interestingly, this signature was strongest in populations from central Africa."

When interbreeding occurs, whole new chromosomes are introduced into the mix.  Over time, these chromosomes are "chopped" into smaller fragments through recombination during subsequent breeding events, resulting in the short, unusual fragments that provide the traces of ancient interbreeding in modern populations. The longer the "fragment", generally, the more ancient the interbreeding event. In this study, the team is identifying events that take place between 20,000 and 60,000 years ago. "We think there were probably thousands of interbreeding events," Hammer said. "It happened relatively extensively and regularly.

Next, and perhaps even more critical to our understanding of how human evolution worked, Hammer and his team plan to search for and identify ancient DNA that afforded selective advantages to anatomically modern humans after they acquired them.

The paper, Genetic Evidence for Archaic Admixture in Africa, published in the Proceedings of the National Academy of Sciences, was co-authored by August Woerner from the UA's ARL Division of Biotechnology, Fernando Mendez from the UA's department of ecology and evolutionary biology, Joseph Watkins from the UA's Mathematics Department and Jeffrey Wall from the Institute for Human Genetics at the University of California San Francisco.

Cover Photo, Top Left: University of Arizona's Michael F. Hammer with an ancient hominid fossil. Credit: M. F. Hammer

By Dan McLerran

As Founder and Editor of Popular Archaeology Magazine, Dan is a freelance writer and journalist specializing in archaeology.  He studied anthropology and archaeology in undergraduate and graduate school and has been an active participant on archaeological excavations in the U.S. and abroad.  He is the creator and administrator of Archaeological Digs, a popular weblog about archaeological excavation and field school opportunities.