Ancient clues. Yakut DNA shows signs of a genetic bottleneck.

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How We Lost Our Diversity

Modern humans are a lot alike--at least at the genetic level--compared with other primates. If you compare any two people from far-flung corners of the globe, their genomes will be much more similar than those of any pair of chimpanzees, gorillas, or other apes from different populations. Now, evolutionary geneticists have shown that our ancestors lost much of their genetic diversity in two dramatic bottlenecks that sharply squeezed down the population of modern humans as they moved out of Africa between 60,000 and 50,000 years ago.

Researchers have known since the 1990s that Africans are the most genetically diverse people in the world. Humans outside of Africa are missing many genetic variants found only in Africans and, indeed, the farther a traditional group lives from Africa, the less diversity it has in its genes and morphological traits, including skull shape (Science, 6 January 1995, p. 35). Genetic diversity is usually considered a good thing: the more a population has, the more likely individuals will have gene variants that will help them adapt better to new climates, diets, and life-threatening diseases, such as malaria or smallpox. Many scientists have suggested that those who left Africa went through a bottleneck, where only a small number of individuals had offspring, thus reducing genetic diversity. But until recently, little research has been done to pinpoint how that diversity was lost.

Large, new genetic databases from diverse populations have given researchers new tools to study this problem, but, so far, they have produced mixed results. One model proposes that genetic diversity was lost in two distinct bottlenecks, where groups of hundreds or thousands of migrating people were quickly decimated by disease, starvation, warfare, or some other cause, dramatically reducing the number of adults who bore children that survived. Another suggests that genetic diversity was reduced in a stepwise fashion as an initial group of about 100,000 or so people moved out around the globe, gradually leaving behind more and more people in settlements along the way.

With the recent publication of a large data set of 763 microsatellite markers--short stretches of DNA that are repeated in the genome--from 53 populations in the Human Genome Diversity Project, evolutionary geneticists William Amos and Joe Hoffman of the University of Cambridge in the United Kingdom had enough genomic data to test both models. Using a software program called BOTTLENECK, the two searched for the signature of bottlenecks or founder effects in each population to see if the loss of diversity occurred suddenly or gradually as adjacent populations moved farther from Africa. Different genetic markers of diversity decline at different rates, creating an imbalance. The larger the imbalance, the stronger the evidence of a bottleneck.

The team uncovered strong signs of this imbalance between rare alleles and heterozygosity in two populations--one, in people living today in the Middle East, and the other in the Yakut, who live near the Bering Strait. That indicated to the researchers that the first bottleneck occurred as people migrated out of Africa to the Middle East about 50,000 to 60,000 years ago, and the second, 19,000 kilometers away, when they crossed the ancient land bridge in the Bering Strait to the Americas. The scientists report their conclusions online today in the Proceedings of the Royal Society B: Biological Sciences.

What caused the bottlenecks? Amos suggests that obstacles--such as the sea, glaciers, or mountains--on the route from Africa to the Middle East, across the Himalayas and over the Bering Strait, held many migrants back, so that a much smaller group moved on, producing offspring to inhabit new parts of the globe. Changes in climate may also have opened and closed new routes out of Africa, creating new barriers. The results are convincing, says anthropologist Henry Harpending of the University of Utah in Salt Lake City. "This paper is a "nerd's delight, for the clever statistical technology."