Kissing Cousins

Genome comparisons reveal that the evolutionary split between humans and chimpanzees may have been more recent and more convoluted than expected.

A new study raises questions about the evolutionary interpretations that stem from this famous "Toumaï" fossil.
Credit: Broad Institute

One of the most fascinating chapters in evolutionary history involves the details of how, and when, our own species first appeared – at its birth, just a scrawny twig in the great tree of life. Now, there are new findings, described in the May 17 online edition of Nature, that shed light on the mysterious ways whereby humans first split from chimpanzees, our closest living sister species. By comparing the DNA of several primates, including humans and chimps, scientists have revealed some surprising genetic patterns, which suggest the species’ divergence was much more recent than previously thought. Further analyses indicate that this separation was complex, with possible interbreeding between the ancient ancestors of the two modern species.

To gain insight into human speciation – the process through which the human species evolved from chimpanzees – a team of Broad Institute scientists led by David Reich, an assistant professor in the Department of Genetics at Harvard Medical School, an associate member of the Broad and the study’s senior author, examined the evidence deposited within the two species’ genomes. Differences in DNA sequence between two closely related species result from genetic mutations, which often accumulate at a steady rate and therefore can be used to measure the time passed since the species diverged. The researchers directly compared the complete genome sequences of humans and chimpanzees, as well as partial information from the genomes of other closely related primates, including gorillas, orangutans, and macaques. With these large-scale resources, the researchers could scrutinize genetic variation – and "genetic age" – at discrete locations across the entire human genome. This enabled them to determine the range of ages present throughout the genome, a key observation not possible in previous studies.

"The study gave unexpected results about how we separated from our closest relatives, the chimpanzees. We found that the population structure that existed around the time of human-chimpanzee speciation was unlike any modern ape population. Something very unusual happened at the time of speciation," said Reich.

The idea that some pieces of the human genome may be older than others is not new. However, the degree to which age fluctuates from one region to the next had not been previously explored and yielded some big surprises. The scientists discovered that the age range of the human genome relative to chimp spans a period of more than 4 million years, a much larger window than expected. In addition, they found that the youngest of regions are much younger than anticipated – no older than 6.3 million years and perhaps less than 5.4 million years old.

Notably, this estimate puts the time of human-speciation about 1 to 2 million years earlier than previous predictions, which are based in part on a well-known fossil nicknamed "Toumaï." This fossil exhibits several characteristics thought to be human-like, such as its dentition and skeletal features indicative of an upright posture. Because of these, Toumaï is classified as a hominid, part of the ancestral line of humans that appeared subsequent to the split from chimpanzees.

"It is possible that the Toumaï fossil is more recent than previously thought," said Nick Patterson, a senior research scientist and statistician at the Broad Institute and first author of the Nature paper. "But if the dating is correct, the Toumaï fossil would precede the human-chimp split. The fact that it has human-like features suggest that human-chimp speciation may have occurred over a long period with episodes of hybridization between the emerging species."

 

Georgia Tech scientists found that the rate of molecular evolution of chimpanzees is closer to that of humans than it is to other apes.

Hybridization, that is, the interbreeding of two different species, could also reconcile a second surprising finding. While the DNA that makes up the human autosomes shows the expected age range (the 4 million-year interval noted in the initial phase of the study) the researchers found that the nearly all of the DNA on the X chromosome sits at the youthful extreme of this spectrum. In fact, they predict the X chromosome to be younger on average than the others by some 1.2 million years. Such a stark age difference can signify a particularly unusual evolutionary past, and hybridization, which exposes the sex chromosomes to stronger evolutionary selection than its autosomal counterparts, could be a likely explanation.

From their findings, the scientists propose that ancestral humans initially separated from chimps, but that the two populations continued to interbreed before finally splitting from each other, less than 5.4 million years ago. Future efforts, including the completion of the gorilla genome as well as sequencing of other more distantly related primates, will help scientists at the Broad and elsewhere to further test the timing and proposed mechanisms of human speciation put forth in the Nature paper. However, the current model stands in contrast to classical views of how one animal species evolves from another, which consider hybridization to be a negligible influence, largely because the evidence for it has been lacking. Yet, the fact "that such evolutionary events have not been seen more often in animal species may simply be due to the fact that we have not been looking for them," said Reich.


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