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

TLDR

Hispanic/Latino populations exhibit complex genetic structure reflecting recent admixture among Native American, European, and West African sources and possible ancient substructure. The study aims to quantify genome‑wide SNP and haplotype variation in 212 individuals from Ecuador, Colombia, Puerto Rico, the Dominican Republic, and Mexico. By integrating new Illumina and Affymetrix genotypes with high‑density SNP data from 4,305 individuals, the authors applied PCA, FRAPPE, STRUCTURE, and LAMP to map African, European, and Native American ancestry patterns and fine‑scale chromosomal admixture. They observed a sex‑biased admixture pattern (European male, Native American female), faster LD decay in populations with higher African ancestry, moderate ability to resolve subcontinental source populations, and highlighted the need for local ancestry correction in future Hispanic/Latino GWAS.

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.