The earliest known ancestors of modern humans might have reproduced with early chimpanzees to create a hybrid species, a new genetic analysis suggests.

Based on the study of human and chimp genomes, the scientists believe the split between the human and chimpanzee lines occurred much more recently than previously thought — no more than 6.3 million years ago and perhaps as recently as 5.4 million years ago.

Human and chimpanzee ancestors began branching apart on the primate evolutionary tree about 9 million years ago, scientists say, but there are significant gaps in the fossil record. The new analysis suggests that a full split, which scientists call speciation, wasn't achieved for nearly 4 million years and might have occurred twice.

The study was released by the journal Nature on Wednesday and will appear in a future print issue.

Researchers from Harvard Medical School and the Broad Institute of MIT and Harvard matched sequences of the human genome to the same regions of the genetic code of chimpanzees and several other primate species. DNA is made up of sequences of chemical bases, labeled A, T, G, and C. They compared the codes, letter by letter, and noted where there was a divergence.

Based on an estimated relative mutation rate, they calculated how long it would take to accrue the mutations and determined that millions of years of genetic divergence led to an initial speciation around 6.3 million years ago. From start to finish, complete speciation spanned a much longer time range than in any other modern apes.

"The variation is huge," said study lead author Nick Patterson of the Broad Institute. "There are regions of the genome that don't appear to be much more than 5 million years old, and there are regions that appear to be 4 million years older than that. The ancestral time over which humans and chimpanzees speciated, where there's no more gene flow, covers 4 million years."

X marks the spot
The team also observed that humans and chimps are very similar on the X chromosome — sometimes referred to as the female sex chromosome, even though both sexes have at least one X chromosome. The average age of the X chromosome in humans is about 1.2 million years "younger" than the rest of the chromosomes, and the final change occurred around 5.4 million years ago.

This suggests that after the first speciation 6.3 million years ago, early human ancestors may have lived and reproduced with ancestral chimps to produce hybrid primates.

"This would help explain why divergence on X between humans and chimps is so low," Patterson told LiveScience.

Mixing and matching genetic information from two species doesn't always work out well, and hybrid species often have trouble reproducing. The problem generally arises from differences on the X chromosomes.

"In a situation where it's unfavorable to have one X from one species and one from the other, which happens as hybrids reproduce among themselves, you get powerful selection for the good combination," Patterson said. "The X chromosome will fix out and everyone will have the same X."

What happened
Patterson explains one possibility for how this could have happened: The initial split occurred around 6.3 million years ago. Sometime after, the descendants of the earliest known human ancestor mated with ancestral chimps and created a hybrid species.

In this scenario, the earliest known human ancestor, a biped known as "Toumai" that probably didn't look much different than chimpanzee ancestors, would have predated the hybridization. The Toumai fossil, which was unearthed in Chad, has been dated back to somewhere between 6.5 million and 7.5 million years ago.