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Researchers to Use Arrays to Study Impact of European Contact on Native American Genomic Diversity

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NEW YORK (GenomeWeb) – The National Science Foundation has awarded a team of researchers from the University of Texas at Austin a two-year, $212,000 grant to investigate the impact of European contact on Native American genomic diversity.

Using microarrays and next-generation sequencing, the investigators will compare DNA collected from pre-contact burial sites with samples obtained from present day Native Americans residing in the southern US, with the aims of understanding the degree of European and African admixture that has occurred since first contact as well as the way in which migration, epidemics, demographic collapse, and selection have impacted Native American genomic diversity during the past five centuries.

"We are trying to obtain a better understanding of how more recent history has shaped diversity in these populations," said Deborah Bolnick, principal investigator on the study and assistant professor of anthropology at UT Austin. "Though we have a lot of information about the social, political, and economic impact of European contact and the colonial era, we have little idea of what the biological effects of those events were for Native peoples," she told BioArray News.

According to Bolnick, much of the genetic research that has been performed with Native North American groups to date has involved Y chromosome and mitochondrial DNA testing, which can be used to determine the haplotype of an individual's direct paternal and maternal ancestry, respectively. However, Y and mtDNA results "may not represent what we see across the genome," Bolnick said. Indeed, a 2010 study involving participants from the Seaconke Wampanoag in Massachusetts, the University of Pennsylvania, and National Geographic's Genographic Project found that much of the direct paternal and maternal ancestry in the tribe was actually European and African in origin.

By using genotyping arrays as well as targeted sequencing to assess the autosomal DNA of these present day Native Americans, Bolnick and her team hope to be able to better characterize contemporary patterns in Native groups than ever before. "This will give us for the first time a more accurate picture of genome-wide diversity in Native communities from the southern US," she said.

Bolnick's team plans to use the Affymetrix Axiom Human Origins Array for its work, in part because it was designed using the genomic data of an indigenous person from the Americas.

"If you have an array that is designed for European populations, a lot of the SNPs on that array won't be variable in Native American populations and then there will be a fair amount of variation in Native American populations that you won't be able to assay," she said.

Designed together with David Reich, an associate professor of genetics at Harvard Medical School, Affymetrix launched the array nearly three years ago. It contains approximately 629,000 SNPs ascertained from individuals belonging to 11 populations, including San Bushmen, Yoruba, Mbuti Pygmies, French, Sardinian, Han, Cambodian, Mongolian, Papuan, Bougainville, and Karitania, a small tribe located in western Brazil that has had limited contact with the outside world, making it an ideal reference for Bolnick's project.

"This array was specifically designed for population genetics research," said Bolnick. "It's an array where the SNPs were ascertained from 13 genomes from around the world, including a South American individual," she said.

Bolnick's team will also used targeted Illumina sequencing to survey SNPs found on the Human Origins Array in pre-European contact samples from the southern US. Resulting array and sequencing data will be combined with other population data in the ensuing analysis, she said.

Along with aiming to measure general changes in the genetic structure of indigenous populations in the southern US, including admixture, Bolnick's team is also interested in understanding how specific historical events, such as epidemics, may have reshaped that genetic structure, allowing the researchers to potentially construct an evolutionary history of the groups in question. Although Bolnick declined to name participating tribes, citing confidentiality agreements, most indigenous groups experienced population declines following European contact. For example, a smallpox epidemic wiped out half of the Cherokee population in the 1730s. Using information collected from pre-contact samples and contemporary subjects, Bolnick could potentially identify genetic patterns in the surviving population that may have played a role in selection in response to those epidemics, as well as to identify the population bottlenecks that resulted, causing genetic drift and reduced diversity.

In the grant abstract, Bolnick and her colleagues noted that existing datasets are insufficient for such analyses because few studies have examined genome-wide variation and relatively few pre-contact samples have been analyzed. It is their goal that the resulting array and sequencing data will be "unprecedented in combining genome-wide coverage with population samples spanning a wide temporal range," making it "possible to measure the effects of drift, selection, and admixture following European contact, and providing the first comprehensive test of the hypothesis that European contact reshaped the genetic structure of Native American populations."

While the current project is focused on Native groups in the southern US, she said that her group is working with those in other regions who are conducting similar studies, enabling the researchers to construct a broader map of Native American genomic diversity.

"There have been different colonial powers, the effects of epidemics have been different, and there are a lot of reasons we'd expect to see regional variation," said Bolnick.

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