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.2007 Sep;81(3):626-33.
doi: 10.1086/520769. Epub 2007 Aug 1.

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.2007 Sep.

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.

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Figures

Figure 1.
Figure 1.
Genomewide variation of ancestry in Puerto Ricans. TheX-axis denotes the physical location of SNPs; theY-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, bringingN 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.
See this image and copyright information in PMC

Comment in

  • Long-range LD can confound genome scans in admixed populations.
    Price AL, Weale ME, Patterson N, Myers SR, Need AC, Shianna KV, Ge D, Rotter JI, Torres E, Taylor KD, Goldstein DB, Reich D.Price AL, et al.Am J Hum Genet. 2008 Jul;83(1):132-5; author reply 135-9. doi: 10.1016/j.ajhg.2008.06.005.Am J Hum Genet. 2008.PMID:18606306Free PMC article.No abstract available.

References

Web Resources

    1. ASHI,http://www.ashi-hla.org/ (for the HLA Frequency database)
    1. Tang Lab Web site,http://www.fhcrc.org/labs/tang (for FRAPPE and SABER software)

References

    1. Kimura M (2003) The neutral theory of molecular evolution. Cambridge University Press, Cambridge, United Kingdom
    1. Sabeti PC, Reich DE, Higgins JM, Levine HZ, Richter DJ, Schaffner SF, Gabriel SB, Platko JV, Patterson NJ, McDonald GJ, et al (2002) Detecting recent positive selection in the human genome from haplotype structure. Nature 419:832–837 10.1038/nature01140 - DOI - PubMed
    1. Carlson CS, Thomas DJ, Eberle MA, Swanson JE, Livingston RJ, Rieder MJ, Nickerson DA (2005) Genomic regions exhibiting positive selection identified from dense genotype data. Genome Res 15:1553–1565 10.1101/gr.4326505 - DOI - PMC - PubMed
    1. Voight BF, Kudaravalli S, Wen X, Pritchard JK (2006) A map of recent positive selection in the human genome. PLoS Biol 4:e72 10.1371/journal.pbio.0040072 - DOI - PMC - PubMed
    1. Tishkoff SA, Reed FA, Ranciaro A, Voight BF, Babbitt CC, Silverman JS, Powell K, Mortensen HM, Hirbo JB, Osman M, et al (2007) Convergent adaptation of human lactase persistence in Africa and Europe. Nat Genet 39:31–40 10.1038/ng1946 - DOI - PMC - PubMed

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