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Among Many Peoples, Little Genomic Variety

By David Brown
Washington Post Staff Writer
Monday, June 22, 2009

There is a simplicity and all-inclusiveness to the number three -- the triangle, the Holy Trinity, three peas in a pod. So it's perhaps not surprising that the Family of Man is divided that way, too.

All of Earth's people, according to a new analysis of the genomes of 53 populations, fall into just three genetic groups. They are the products of the first and most important journey our species made -- the walk out of Africa about 70,000 years ago by a small fraction of ancestral Homo sapiens.

One group is the African. It contains the descendants of the original humans who emerged in East Africa about 200,000 years ago. The second is the Eurasian, encompassing the natives of Europe, the Middle East and Southwest Asia (east to about Pakistan). The third is the East Asian, the inhabitants of Asia, Japan and Southeast Asia, and -- thanks to the Bering Land Bridge and island-hopping in the South Pacific -- of the Americas and Oceania as well.

The existence of this ancient divergence has long been known.

What is new is a subtle but important insight into what happened on a genomic level as the human species spilled across the landscape, eventually occupying every habitable part of the planet.

People adapted to what they encountered the way all living organisms do: through natural selection. A small fraction of the mutations constantly creeping into our genes happened by chance to prove beneficial in the new circumstances outside the African homeland. Those included differences in climate, altitude, latitude, food availability, parasites, infectious diseases and lots of other things.

A person who carried, by chance, a helpful mutation was more likely to survive and procreate than someone without it. The person's offspring would then probably be endowed with the same beneficial mutation. Over thousands of generations, the new variant (what geneticists call the "derived allele") could go from being rare to being common as its carriers fared better than their brethren and contributed more descendants to the population.

Scientists have long known that regardless of ancestral home or ethnic group, everyone's genes are pretty much alike. We're all Homo sapiens. Everything else is pretty much details.

Recent research has produced a surprise, however. Population geneticists expected to find dramatic differences as they got a look at the full genomes -- about 25,000 genes -- of people of widely varying ethnic and geographic backgrounds. Specifically, they expected to find that many ethnic groups would have derived alleles that their members shared but that were uncommon or nonexistent in other groups. Each regional, ethnic group or latitude was thought to have a genomic "signature" -- the record of its recent evolution through natural selection.

But as analyses of genomes from dozens of distinct populations have rolled in -- French, Bantu, Palestinian, Yakut, Japanese -- that's not what scientists have found. Dramatic genome variation among populations turns out to be extremely rare.

Instead, it is "random genetic drift" that appears to be more important in sculpting our genes. Drift describes the chance loss of genetic variation that occurred not only in the out-of-Africa migration, but through all of human history as famine, climate change or war caused populations to crash and then recover.

Despite those calamities, it appears that all contemporary populations ended up largely the same, or only crudely distinguishable from one another, on the genome level.

Of course, small variations can result in dramatic differences. Skin color is perhaps the most obvious.

Vitamin D is made in the skin through a chemical reaction requiring ultraviolet light. Mutations in genes that lighten skin pigment -- at least a half-dozen have been found -- swept through populations as they moved away from the Equator and had less-constant sunlight.

Among West Africans, a chance mutation in the blood protein hemoglobin turned out to partially protect against malaria. It rapidly became common in places where malaria was a huge threat to survival. Similarly, a mutation allowing adults to digest milk became valuable when Middle Easterners and Europeans domesticated cattle. About 90 percent of Scandinavians now carry it.

Such clear ethnic distinctions are the exception, however, defying the expectations of many researchers. That may have been a product of the way scientists have studied genes over the last century.

Bacteria, fruit flies and other rapidly reproducing organisms were (and still are) the workhorses of genetic research.

When experimenters subject populations of them to extreme conditions, mutant genes can become pervasive in just a few generations.

Not so for people, it appears.

"When it comes to the question, 'What is the main process by which adaptation is happening?', the answers may be very different for humans and flies," said Jonathan K. Pritchard, a computational biologist at the University of Chicago. He is the senior author of a paper on the subject this month in the online journal PLoS Genetics.

In human beings, natural selection appears to work most of the time on dozens of genes in small and hard-to-detect ways. In contrast to fruit flies in the lab, useful traits involving body size, immunity, metabolism and behavior do not come about because one or two genes become ascendant.

The short stature of rain-forest dwellers such as the pygmies of central Africa, for example, appears not to be the product of a single derived allele for shortness carried by virtually everyone in the population. Instead, dozens of gene variants that slightly decrease height have each become slightly more common, and it is their total effect that results in the group's dramatically shorter stature.

"Adaptations to the environment absolutely do occur," said Joseph K. Pickrell, a graduate student at the University of Chicago who, with Graham Coop of the University of California at Davis, co-authored the recent study. "But they don't occur according to this simple model that we and others have been looking for."

Which brings us back to the tripartite Family of Man.

When a small number of people left Africa 70,000 years ago, they carried with them only a sample of the genetic diversity that had evolved on that continent in the preceding 130,000 years.

When the descendants of those migrants in turn divided into two groups 40,000 years ago, the westward-turning Eurasians and the eastward-turning East Asians each took by chance only some of the genetic diversity of their forebears.

As a result, African populations today have greater genetic diversity -- more variants in more genes -- than Eurasians or East Asians, and Eurasians somewhat more than East Asians.

But each had more than enough diversity for the trip.

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