Posted on January 3, 2012

Genome Study Points to Adaptation in Early African-Americans

Nicholas Wade, New York Times, January 2, 2012

Researchers scanning the genomes of African-Americans say they see evidence of natural selection as their ancestors adapted to the harsh conditions of their new environment in America.

The scientists, led by Li Jin of the Chinese Academy of Sciences in Shanghai, report in the journal Genome Research that certain disease-causing variant genes became more common in African-Americans after their ancestors reached American shores — perhaps because they conferred greater, offsetting benefits. Other gene variants have become less common, the researchers say, like the gene for sickle cell hemoglobin, which in its more common single-dose form protects against malaria. The Shanghai team suggests the gene has become less common in African-Americans because malaria is much less of a threat.

The purpose of studying African-American genomes is largely medical. Most searches for variant genes that cause disease take place in people of European ancestry, and physicians want to make sure they have not missed variants that may be more common in African-Americans and helpful for developing treatments or diagnosis.


The unusually common variants identified by the Shanghai team are associated with higher risk of hypertensionprostate cancer, sclerosis and bladder cancer.

“Most of the genes associated with African-American ethnic diseases,” they write, “may have played an important role in African-Americans’ adaptation to local environment.” But the authors have not yet been able to identify the benefits they believe such genes conferred.


The Shanghai researchers used a method for studying admixture, a geneticist’s term for when two populations or races intermarry; China has several such populations, perhaps accounting for the team’s interest. Using gene chips that analyze common variations in the human genome, researchers can deconstruct the chromosomes of an African-American, say, assigning each chunk of DNA to an African or European origin.

The scientists found that of the African-American genomes in their sample, 22 percent of the DNA came from Europeans, on average, and the rest from African ancestors, a figure in line with other estimates.


{snip} Meanwhile, the ancestry of each segment can be identified from its pattern of single-nucleotide polymorphisms, or SNPs, the sites on the human genome where there is commonly variation in the A, T, C and G units that make up DNA.

Among human populations, there are very few absolute differences, meaning those in which all members of one population will have, for example, unit T at a site and all members of another will have unit G. But populations do have characteristic percentages. Among Europeans, 70 percent may have C and 30 percent A at a particular SNP site, whereas in Africans the ratio may be 40 percent C and 60 percent A. So a section of genome with C at this SNP site is somewhat more likely to be European.

This is hardly decisive in itself. But take a row of 10 SNPs, and if European ancestry is more likely for most of them, then that section of DNA is probably European in origin.

Geneticists can thus deconstruct the genomes of admixed populations into a mosaic in which each segment can be traced back to one or the other of the two parent populations. This is the basis of the Shanghai team’s approach. {snip}