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, 81 (3), 626-33

Recent Genetic Selection in the Ancestral Admixture of Puerto Ricans

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Recent Genetic Selection in the Ancestral Admixture of Puerto Ricans

Hua Tang et al. Am J Hum Genet.

Abstract

Recent studies have used dense markers to examine the human genome in ancestrally homogeneous populations for hallmarks of selection. No genomewide studies have focused on recently admixed groups--populations that have experienced admixing among continentally divided ancestral populations within the past 200-500 years. New World admixed populations are unique in that they represent the sudden confluence of geographically diverged genomes with novel environmental challenges. Here, we present a novel approach for studying selection by examining the genomewide distribution of ancestry in the genetically admixed Puerto Ricans. We find strong statistical evidence of recent selection in three chromosomal regions, including the human leukocyte antigen region on chromosome 6p, chromosome 8q, and chromosome 11q. Two of these regions harbor genes for olfactory receptors. Interestingly, all three regions exhibit deficiencies in the European-ancestry proportion.

Figures

Figure  1.
Figure 1.
Genomewide variation of ancestry in Puerto Ricans. The X-axis denotes the physical location of SNPs; the Y-axis indicates the excess/deficiency in ancestry at the corresponding SNP, averaged for 192 Puerto Ricans. The red, blue, and green curves represent African, European, and Native American ancestries, respectively.
Figure  2.
Figure 2.
Comparison of observed (histogram) and simulated (line) variation in ancestry across the genome. A population model was assumed in which, for the first 5 generations, Europeans and Native Americans admix at a ratio of 0.82:0.18, with a total population size of 1,000. At generation 5, Africans enter the gene pool, bringing N to 1,250. This trihybrid population is then allowed to mate randomly for 10 generations at constant population size. The density curve for each population is based on 107 independent simulations.
Figure  3.
Figure 3.
Extreme variations of ancestry on chromosomes 6 (a), 8 (b), and 11 (c). SNPs were divided into two sets (even-numbered vs. odd-numbered markers), which were analyzed separately with use of SABER. The red and green points are the excess African and Native American ancestries, respectively, on the two marker subsets, whereas the black points are the results with use of all available markers on that chromosome.
Figure  4.
Figure 4.
Display of estimated ancestry on chromosome 6. Each pair of horizontal strips represents an (unphased) individual, with the vertical height proportional to the marker-specific ancestry estimates of African (red), European (blue), and Native American (green) ancestries. Left, Ancestry estimates around the peak on 6p21-22. Right, Randomly selected region of chromosome 6.

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