By NICHOLAS WADE
Published: January 2, 2012
Kean Collection/Getty Images
HARSH NEW WORLD Slaves in Georgia, circa 1850. A new environment apparently brought genetic change.
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.
Such searches often reveal events in a population’s history by pinpointing genes that have changed under the pressure of natural selection.
The unusually common variants identified by the Shanghai team are associated with higher risk of hypertension, prostate 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.
Mark D. Shriver, a geneticist at Penn State, said it was plausible that some versions of a gene would become more common as African-Americans adjusted to a new environment. “It’s very valid to expect that there will be factors subject to genetic adaptation and that are now more prevalent in contemporary African-Americans than in the ancestral group,” he said.
But Alkes L. Price, a geneticist at the Harvard School of Public Health, said the Shanghai team’s results, though plausible, fell short of proof. “This paper does not provide evidence of selection having occurred post-Africa,” he said.
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.
They then looked for sites along the genome where either European or African ancestry was present at statistically significant levels above the average, finding four regions with very common European ancestry and two with very common African ancestry. Most of these sites harbored genes of unknown function, but one, of European origin, holds a gene that combats influenza, suggesting it has become more common in African-Americans by conferring protection from the disease.
Dr. Price, however, said that two other research teams had applied the same method to African-American genomes without finding any statistically significant excess of European or African ancestry. The Chinese team, in his view, should have applied a correction factor to their statistics and, had they done so, would have obtained the same result.
In another approach, the Shanghai team focused on all the DNA segments of the African origin in the African-American genomes, discarding all the European DNA. They then compared the African component of African-American genomes with the DNA of the Yoruba of Nigeria, a well-studied population that happens to be genetically very close to the West African population from which many slaves were taken.
full-text:Such searches often reveal events in a population’s history by pinpointing genes that have changed under the pressure of natural selection.
The unusually common variants identified by the Shanghai team are associated with higher risk of hypertension, prostate 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.
Mark D. Shriver, a geneticist at Penn State, said it was plausible that some versions of a gene would become more common as African-Americans adjusted to a new environment. “It’s very valid to expect that there will be factors subject to genetic adaptation and that are now more prevalent in contemporary African-Americans than in the ancestral group,” he said.
But Alkes L. Price, a geneticist at the Harvard School of Public Health, said the Shanghai team’s results, though plausible, fell short of proof. “This paper does not provide evidence of selection having occurred post-Africa,” he said.
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.
They then looked for sites along the genome where either European or African ancestry was present at statistically significant levels above the average, finding four regions with very common European ancestry and two with very common African ancestry. Most of these sites harbored genes of unknown function, but one, of European origin, holds a gene that combats influenza, suggesting it has become more common in African-Americans by conferring protection from the disease.
Dr. Price, however, said that two other research teams had applied the same method to African-American genomes without finding any statistically significant excess of European or African ancestry. The Chinese team, in his view, should have applied a correction factor to their statistics and, had they done so, would have obtained the same result.
In another approach, the Shanghai team focused on all the DNA segments of the African origin in the African-American genomes, discarding all the European DNA. They then compared the African component of African-American genomes with the DNA of the Yoruba of Nigeria, a well-studied population that happens to be genetically very close to the West African population from which many slaves were taken.
Genome Research Points to Adaptation Among Early African-Americans - NYTimes.com
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