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Does the African genome hold the secrets of a previously unknown species of hominid?

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Researchers have just finished performing the most comprehensive genetic analysis of modern day Africans ever. And they've turned up some absolutely incredible results.

Their findings suggest humans are more genetically diverse than we'd previously believed. But they also show that ancient humans may have interbred with an unknown species of hominin — what researchers surmise "could have been a sibling species to Neanderthals."

When it comes to genetic variation, there's no place on Earth like Africa. Numerous studies in recent years have revealed that human genomic diversity is greater in Africa than anywhere else on Earth. In fact, if you were to move outward from the continent along the migratory paths of early Homo sapiens, taking genetic samples along the way, you'd find that human populations tend to become more and more genetically similar the farther from Africa you get (the result of something called the founder effect).


To quote paleontologist Mike Novacek, provost of science at the American Museum of Natural History, the genes of modern day Africans "tell a very fascinating historical and evolutionary story about populations, where they once were, where they went to in migrations, and so forth." Adds Novacek, "To find out where you are, you need a map," and genetic studies of modern day African populations give us "orientation for a lot of great scientific and applied questions."


And yet, such investigations are lacking. In a groundbreaking new genomics study, published in the latest issue of Cell, a team of researchers led by geneticists Joseph Lachance and Sarah Tishkoff notes that "despite the important role that African populations have played in human evolutionary history, they remain one of the most understudied groups in human genomics." To address this disparity, the researchers decided to sequence the genomes of five males from three different African hunter-gatherer populations: Pygmies from Cameroon (pictured up top), and Khoesan-speaking Hadza and Sandawe from Tanzania.

Not All Genome Sequences are Created Equal

But wait — hang on a second. Fifteen genomes? Groundbreaking? Even if you haven't heard of initiatives like The X PRIZE in Genomics, or The 1000 Genomes Project, 15 probably doesn't sound like a whole lot. After all, rapid advances in sequencing technologies have begun to make whole-genome sequencing (wherein a person's entire genetic code is analyzed, as opposed to a small subset of genes) increasingly affordable — to the point that at least one company claims it can now accurately determine a person's full DNA blueprint for less than $1,000.


But 15 genomes is a big deal, because not all whole-genome analyses are created equal. Lachance, Tishkoff and their colleagues have acquired what are known as "high-coverage" whole-genome maps. Their method involves sequencing each strand of DNA more than 60 times in order to achieve unparalleled accuracy (a DNA blueprint examined this closely is said to have been sequenced "at >60x coverage.")

By comparison, note the researchers, "whole-genome sequencing in the 1000 Genomes Project has generally been at low coverage, and genetic diversity in many ethnically diverse populations is yet to be characterized, particularly with respect to Africa, the ancestral homeland of all modern humans." That makes the work of Lachance, Tishkoff and their colleagues the first population genomics analysis ever conducted using high-coverage whole genome sequencing.


Did Humans Interbreed with an Unknown Species of Hominid?

The researchers' investigation has led to a number of insightful observations. Results from whole-genome sequencing suggest, for example, that these hunter-gatherer populations have likely responded to distinct, region-specific environmental factors by evolving in ways that are markedly different from agricultural and pastoral populations. Analysis of Pygmy DNA sequences also revealed a collection of genes that likely underlies the population's short stature. (Male Pygmies are typically less than five feet tall; Dr. Tishkoff is pictured here with women from the Western Pygmies of Cameroon.)


Even more intriguing, however, was the discovery of over 13-million genetic variants, that is: points in the genome where a single nucleotide differed from the human genome reference sequence. At the time of their discovery, a staggering 5-million of these variants were new to science.

"It was awe-inspiring to find millions of new variants that we never knew existed in our species," said Lachance in a statement. "It's humbling but invigorating to think about how to make sense of all this diversity."


That's not to say Lachance and his colleagues aren't trying to come up with an explanation. On the contrary, in their search for answers, the researchers claim to have made a remarkable discovery: fragments of DNA, different from those found in most modern-day humans, that point to ancient interbreeding between H. sapiens and an as-yet unidentified species of hominid — not Neanderthals, mind you, but an entirely new species we've yet to discover. That's a pretty bold claim, especially in the absence of any fossilized evidence to back it up. To date, hominid remains discovered in Africa have all resembled modern humans; and while paleoanthropologists sometimes criticize geneticists for ignoring this derth of paleontological evidence (Stanford researcher Richard Klein has described Lachance and Tishkoff's publication as "irresponsible"), the researchers believe their findings to be sound:

"Fossils degrade fast in Africa so we don't have a reference genome for this ancestral lineage," explained co-author Joshua Akey in a statement; but the researchers report that they've gone to great lengths to show that the genetic traces they've discovered resemble neither human nor Neanderthal DNA, and that no genome sequences taken from outside of Africa show any evidence of the foreign genetic material. Consequently, explains Akey, "one of the things we're thinking is it could have been a sibling species to Neanderthals."


Further investigations will help substantiate these claims, and Tishkoff reports that she intends to continue sequencing the genomes of more and more Africans.

"Our study emphasizes the critically important role of next-generation genome sequencing for elucidating the genetic basis of both normal variable traits in humans as well as identifying the genetic basis of human disease risk," she said.


The researchers' findings are published in the latest issue of Cell.