Researchers have delved back further than ever into the genetic history of humans, and found that the ancient population that gave rise to modern humans may have been nearly twice as genetically diverse than humans today, according a study published this week in Proceedings of the National Academy of Sciences.

Scientific reconstruction of a Homo erectus Image: Wikimedia commons, Lillyundfreya

While most studies on the genetics of ancient humans have focused on the last half million years, this study looks at particularly old areas of the genome, allowing the researchers to look at the more distant past, said molecular geneticist Prescott Deininger of the Tulane Cancer Center in New Orleans, LA, who was not involved in the research. "This [study] is a little window to look back a little bit further," he said.

When examining genetic diversity, scientists often use a measure called the effective population size, which describes how big a population has to be to carry its level of genetic diversity. Modern humans have an effective population size of about 10,000 -- a relatively low level of diversity. Chimps and gorillas, for example, both have effective population sizes of greater than 20,000. This estimate of 10,000 has been regarded as stable for about 200,000 to 400,000, maybe "as far back as a million" years, said population geneticist Chad Huff of the University of Utah. But looking deeper into human history, Huff and his colleagues determined that before about 1.2 million years ago, the effective population size of our ancestral populations was actually around 18,500.

The researchers gained their insight by looking at mobile elements -- bits of DNA that can insert themselves into the genome -- known as Alus. Occurring in an estimated 1 in 21 to 22 births, Alus, which are about 300 base pairs long and the most abundant mobile elements in the human genome, insert into the genome at a rate at least three orders of magnitude rarer than the single nucleotide mutation rate. Because of this rarity, any particular Alu is likely to be much older than an average mutation. Furthermore, because the DNA just outside of these Alu inserts is closely linked to the mobile element, that surrounding DNA is also likely to be relatively old.

The researchers can thus "use these elements they call molecular fossils to dig down through the strata of the human genome and arrive at some conclusions about human origin," explained molecular biologist John Goodier of the University of Pennsylvania School of Medicine, who did not participate in the research.

Comparing these ancient areas of the human reference genome with the genome of a particular individual -- that of genomics guru Craig Venter, as it happens -- the team found that much of the DNA surrounding the Alu inserts was older than would be expected if the effective population size had always been 10,000. Based on their results, they concluded that the effective population size had been nearly double its current level before about 1.2 million years ago. While this is clearly a substantial difference, Huff said he was actually surprised the diversity of the ancient population wasn't even greater. "It is unusual that our [effective population size] is so small for so long," Huff said, especially given the success of our species. If our ancestors "really did live on three continents," he added, "you would expect a much larger [effective] population size."

"I also wouldn't have expected our [effective population size] to be 10,000 for so long," Huff added. The small effective population size of modern humans was attributed to a bottleneck event that eliminated a great deal of ancient diversity sometime in the last 400,000 years. But if humans have maintained such low diversity for more than a million years, "I'm wondering if maybe it hasn't been [a] series of bottlenecks or if it's always been relatively small," Huff said.

While the exact mechanisms shaping the diversity of ancient humans will undoubtedly require further research, this study makes a good start by identifying a potential tool that can be used to see further back into our history, Deininger said. "I'm always a little bit impressed by how sophisticated some of these population biology studies can be in terms of unraveling ancient details," he said. "It's fun to look at the dynamics of our history."


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The 0.1% Portrait of Human History
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Genetic Variation Illuminates Murky Human History
[24th July 2000]