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Ancient humans likely mixed it up

University of Arizona researchers used a simulation model to show that DNA from Homo sapiens contains pieces from archaic human types.

Before anatomically modern humans migrated out of Africa, they interbred with more archaic hominin forms such as Homo habilis and Homo erectus, a team of University of Arizona researchers has found.

The researchers used simulations to predict what ancient DNA sequences would look like had they survived within the DNA of our own cells, and found evidence that anatomically modern humans were not so unique that they remained separate.

Michael Hammer, who led the team, said:

We found evidence for hybridization … It looks like our lineage has always exchanged genes with their more morphologically diverged neighbors.

Artist’s illustration of Homo erectus. A new study indicates that anatomically modern humans interbred with other hominins 20,000 – 60,000 years ago. Image Credit: Henry Gilbert and Kathy Shick

Results of the study appear in a 2011 issue of the Proceedings of the National Academy of Sciences.

It is widely accepted that Homo sapiens originated in Africa and eventually spread throughout the world. But did those early humans interbreed with more ancestral forms of the genus Homo – for example Homo erectus, the “upright walking man,” Homo habilis, the “tool-using man” or Homo neanderthalensis, the first artists of cave-painting fame?

Homo erectus was probably the first human to live in a hunter-gatherer society. Image Credit: Philip72

DNA studies of Neanderthal bones suggest interbreeding did occur after anatomically modern humans had migrated from their evolutionary cradle in Africa to the cooler climates of Eurasia, but what had happened in Africa remained a mystery – until now.

Hammer explained that recent advances in molecular biology have made it possible to extract DNA from fossils tens of thousands of years old and compare it to that of modern counterparts. But he said climate makes a big difference in finding DNA to study:

We don’t have fossil DNA from Africa to compare with ours. Neanderthals lived in colder climates, but the climate in more tropical areas makes it very tough for DNA to survive that long, so recovering usable samples from fossil specimens is extremely difficult if not impossible.

So Hammer’s team followed a computational and statistical approach, looking at DNA from modern humans belonging to African populations and then searching for unusual regions in the genome.

Homo habilis was dissimilar to modern humans, being shorter and having disproportionately long arms. H. habilis may have coexisted with Homo erectus in Africa for a period of 500,000 years. Fossil evidence suggests that H. habilis was a staple in the diet of large predatory animals. Image Credit: Lillyundfreya

Because nobody knows the DNA sequences of those now-extinct archaic forms, Hammer’s team first had to figure out what features of modern DNA might represent fragments that were brought in from archaic forms. He said:

We can simulate a model of hybridization between anatomically modern humans and some archaic forms. In that sense, we simulate history so that we can see what we would expect the pattern to look like if it did occur.

First, the team sequenced vast regions of human genomes from samples taken from six different populations living in Africa today. Next they tried to match up their sequences with what they expected those sequences to look like in archaic forms. Hammer explained:

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. We discovered three different genetic regions that 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.

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 likely to be ancient in origin. Another telltale sign is how far it extends along a chromosome. If an unusual piece is found to stretch over a long portion of a chromosome, it is an indication of being brought into the population relatively recently.

Michael Hammer with an ancient fossil. Image Credit: M. F. Hammer

Hammer added:

We are talking about something that happened between 20,000 and 60,000 years ago – not that long ago in the scheme of things. If interbreeding occurs, it’s going to bring in a whole chromosome, and over time, recombination 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.

According to Hammer, the first signs of anatomically modern features appeared about 200,000 years ago.

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.

We think there were probably thousands of interbreeding events. It happened relatively extensively and regularly. This is quite common in nature, and it turns out we’re not so unusual after all.

Bottom line: Michael Hammer and a team of researchers at the University of Arizona used simulations to predict what ancient DNA sequences would look like had they survived within the DNA of our own cells. The team found evidence that anatomically modern humans probably interbred with other hominins such as Homo habilis and Homo erectus. Results of their study appear in a 2011 issue of the Proceedings of the National Academy of Sciences.

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