Population structure in Hispanics (Bryc et al. 2010)

From the public release:

The study, published in the May 3 online issue of the Proceedings of the National Academy of Sciences, tested the genetic makeup of 100 individuals of Hispanic/Latino background in the New York tri-state area, including Dominicans, Columbians and Ecuadorians, as well as Mexicans and Puerto Ricans, the two largest Hispanic/Latino ethnic groups in the United States. Currently, Hispanic/Latino Americans comprise 15.4% of the total United States population, or 46.9 million people, and account for the largest ethnic minority in the United States.

"It is important to quantify the relative contributions of ancestry in relation to disease outcome in the Hispanic/Latino population," says study co-author Christopher Velez, a medical student at NYU School of Medicine. "This ethnically appropriate genetic research will be critical to the understanding of disease onset and severity in the United States and in Latin America. It will allow for the development of appropriate genetic tests for this population."

Through their analysis of the entire genome, the researchers found evidence of a significant sex bias consistent with the disproportionate contribution of European male and Native American female ancestry to present day populations. The scientists also found that the patterns of genes in the Hispanic/Latino populations were impacted by proximity to the African slave trade. In fact, Puerto Ricans, Dominicans and Columbians from the Caribbean coast had higher proportions of African ancestry, while Mexicans and Ecuadorians showed the lowest level of African ancestry and the highest Native American ancestry.

European migrant contributors were mostly from the Iberian Peninsula and Southern Europe. Evidence was also found for Middle Eastern and North African ancestry, reflecting the Moorish and Jewish (as well as European) origins of the Iberian populations at the time of colonization of the New World. The Native Americans that most influenced the Hispanic/Latino populations were primarily from local indigenous populations.

The paper has plentiful supplementary material online. Here is the result of the frappe analysis in a broader context:

As we can see, Hispanic individuals are a variable mix of Caucasoid (red/orange), Amerindian/Mongoloid (blue, teal) and Sub-Saharan (green) components. The orange Caucasoid component seems centered on Sardinia while the red one in NE Europe.

PNAS doi:10.1073/pnas.0914618107

Genome-wide patterns of population structure and admixture among Hispanic/Latino populations

Katarzyna Bryc et al.

Abstract

Hispanic/Latino populations possess a complex genetic structure that reflects recent admixture among and potentially ancient substructure within Native American, European, and West African source populations. Here, we quantify genome-wide patterns of SNP and haplotype variation among 100 individuals with ancestry from Ecuador, Colombia, Puerto Rico, and the Dominican Republic genotyped on the Illumina 610-Quad arrays and 112 Mexicans genotyped on Affymetrix 500K platform. Intersecting these data with previously collected high-density SNP data from 4,305 individuals, we use principal component analysis and clustering methods FRAPPE and STRUCTURE to investigate genome-wide patterns of African, European, and Native American population structure within and among Hispanic/Latino populations. Comparing autosomal, X and Y chromosome, and mtDNA variation, we find evidence of a significant sex bias in admixture proportions consistent with disproportionate contribution of European male and Native American female ancestry to present-day populations. We also find that patterns of linkage-disequilibria in admixed Hispanic/Latino populations are largely affected by the admixture dynamics of the populations, with faster decay of LD in populations of higher African ancestry. Finally, using the locus-specific ancestry inference method LAMP, we reconstruct fine-scale chromosomal patterns of admixture. We document moderate power to differentiate among potential subcontinental source populations within the Native American, European, and African segments of the admixed Hispanic/Latino genomes. Our results suggest future genome-wide association scans in Hispanic/Latino populations may require correction for local genomic ancestry at a subcontinental scale when associating differences in the genome with disease risk, progression, and drug efficacy, as well as for admixture mapping.

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