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Six degrees of separation. Just 18,500 breeding human ancestors were alive 1.2 million years ago, even though they had colonized much of the Old World.

Greg Wakabayashi

Human Ancestors Were an Endangered Species

With 6.8 billion people alive today, it's hard to fathom that humans were ever imperiled. But 1.2 million years ago, only 18,500 early humans were breeding on the planet--evidence that there was a real risk of extinction for our early ancestors, according to a new study. That number is smaller than current figures for the effective population size (or number of breeding individuals) for endangered species such as chimpanzees (21,000) and gorillas (25,000). In fact, our toehold on the planet wasn't secure for a long time--at least 1 million years, because our ancestral stock was winnowed with the emergence of our species, Homo sapiens, 160,000 years ago or so and, again, with the migration of modern humans out of Africa. "There's this history of a precarious existence not just for our species but for our ancestors," says co-author Lynn Jorde, a human geneticist at the University of Utah in Salt Lake City.

Researchers have long known that modern humans lack the genetic variation found in other living primates, such as chimpanzees or gorillas, even though our current population size is so much larger. One explanation for this lack of variation is that our species underwent recent bottlenecks--events where a significant percentage were killed or otherwise prevented from reproducing. Some researchers proposed that the lack of variation in our maternally inherited mitochondrial DNA suggested these bottlenecks took place as our ancestors spread out of Africa relatively recently. One possibility occurred 70,000 years ago, when the Toba super-volcano erupted in Indonesia and triggered a nuclear winter that fewer than 15,000 individuals survived. Studies of diversity in other regions of the human genome, however, attributed low genetic variation to chronically low numbers, with as few as 10,000 breeding humans at different times during the past 2 million years. But the problem with all these studies is that they tracked specific genetic lineages, and not the entire genome and, hence, populations.

Now, a new method of studying markers across the entire genome is allowing geneticists to look back farther in time, before the emergence of our species 200,000 years ago, to see the population history of our really ancient ancestors, such as Homo erectus. Jorde and his colleagues used short lengths of DNA that randomly insert themselves into the genome, known as Alus, as probes to find ancient parts of the genome. Alu insertions are rare events but once inserted, they are hard to remove--a 300-basepair-length of an Alu is seldom lost in entirety, so Alu insertions work like fossils to mark ancient regions of the genome. By examining the mutations in DNA near Alu insertions in two completely sequenced modern human genomes, they could calculate how much genetic diversity existed in our ancestors. They used the number of those genetic differences between the two genomes to calculate how large the population was at that time.

As they report online this week in the Proceedings of the National Academy of Sciences, the researchers found that the ancient human effective population size 1.2 million years ago, the number who could breed--was about 18,500, and couldn't have been larger than 26,000. This means that even before the emergence of Homo sapiens in Africa, our ancestral population of Homo erectus was small even at a time that the species was spreading around the world. This implies an "unusually small population size for a species spread across the entire Old World," the authors write.

Population geneticists, including Montgomery Slatkin of the University of California, Berkeley, say that the theoretical analysis in the new method "seems correct." The findings also "wonderfully illustrate how chance events, (such as the random insertion of Alus), have contributed to patterns of human genetic variation," says population geneticist John Wakeley of Harvard University.