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 some 9 million years ago, 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 published online today by the journal Nature.
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. 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. 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 at 6.3 million years in the past, 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 descendents of the earliest known human ancestor — the 6.5 to 7.5-million-year-old "Toumai," a biped that probably didn't look much different than chimpanzee ancestors — mated with ancestral chimps and created a hybrid species.
Scientists can't say how long the hybridization carried on, but the final speciation occurred around 5.3 million years ago, possibly because the two species' genetic coded were too different to mix or the animals were simply physically unappealing to each other.
"If that occurred, they might have been compatible enough on X that it would fix out to one species or another," Patterson said. "As it happened, it fixed to chimps, but it could have gone the other way."
This is just one possible explanation for the gap in speciation time, Patterson said, and is not meant to be interpreted as the full answer. Researchers at the Broad Institute are currently working on sequencing gorilla and other primate genomes and searching for similar patterns of evolution to help better tell the whole story.
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