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Molecular phylogeography of a human autosomal skin color locus under natural selection.

Canfield VA, Berg A, Peckins S, Wentzel SM, Ang KC, Oppenheimer S, Cheng KC - G3 (Bethesda) (2013)

Bottom Line: The C11 haplotype was most likely created by a crossover between two haplotypes, followed by the A111T mutation.The two parental precursor haplotypes are found from East Asia to the Americas but are nearly absent in Africa.The distributions of C11 and its parental haplotypes make it most likely that these two last steps occurred between the Middle East and the Indian subcontinent, with the A111T mutation occurring after the split between the ancestors of Europeans and East Asians.

View Article: PubMed Central - PubMed

Affiliation: Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania 17033.

ABSTRACT
Divergent natural selection caused by differences in solar exposure has resulted in distinctive variations in skin color between human populations. The derived light skin color allele of the SLC24A5 gene, A111T, predominates in populations of Western Eurasian ancestry. To gain insight into when and where this mutation arose, we defined common haplotypes in the genomic region around SLC24A5 across diverse human populations and deduced phylogenetic relationships between them. Virtually all chromosomes carrying the A111T allele share a single 78-kb haplotype that we call C11, indicating that all instances of this mutation in human populations share a common origin. The C11 haplotype was most likely created by a crossover between two haplotypes, followed by the A111T mutation. The two parental precursor haplotypes are found from East Asia to the Americas but are nearly absent in Africa. The distributions of C11 and its parental haplotypes make it most likely that these two last steps occurred between the Middle East and the Indian subcontinent, with the A111T mutation occurring after the split between the ancestors of Europeans and East Asians.

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Related in: MedlinePlus

Relationships between local haplotypes in B and C regions. For each HapMap population, the distribution of haplotype combinations is shown as a heat map (scale on right). Recurrent recombination between core- and B-region is apparent. Predominant association of C11 with B6 contrasts with associations of C10 (B2) and C9 (B2, B7). Counts are shown in File S2.
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fig5: Relationships between local haplotypes in B and C regions. For each HapMap population, the distribution of haplotype combinations is shown as a heat map (scale on right). Recurrent recombination between core- and B-region is apparent. Predominant association of C11 with B6 contrasts with associations of C10 (B2) and C9 (B2, B7). Counts are shown in File S2.

Mentions: Initial analysis of regions A and B used only single-nucleotide polymorphisms (SNPs) from HapMap Phase 3, Release 27 (Altshuler et al. 2010) that had been genotyped and phased in each included population (11 and 6 SNPs, respectively), whereas for regions C and D, SNPs lacking data for the TSI and/or MEX samples also were included (16 and 8 SNPs, respectively); these SNPs are listed in Table S2. Phased haplotypes were retrieved from HapMap and compared with raw genotype data for consistency. For the core region C, the absence of genotypes for SNPs c1 and c13 prevented distinguishing between members of the C2/C3 haplotype pair (in TSI) and the C6/C7 pair (in TSI and MEX), respectively. For TSI and GIH, which were phased on the basis of CEU, a small number of individuals heterozygous for the ancestral allele of A111T (1/1 and 3/8, respectively) were misphased. Corrected haplotype assignments are shown in all figures and tables except Figure 5 and those in which haplotype combinations are displayed (Figure S2, Figure S3, File S2, File S3, and File S4). For subregion D, only 1 of 8 SNPs was genotyped in TSI, precluding haplotype assignment for this sample.


Molecular phylogeography of a human autosomal skin color locus under natural selection.

Canfield VA, Berg A, Peckins S, Wentzel SM, Ang KC, Oppenheimer S, Cheng KC - G3 (Bethesda) (2013)

Relationships between local haplotypes in B and C regions. For each HapMap population, the distribution of haplotype combinations is shown as a heat map (scale on right). Recurrent recombination between core- and B-region is apparent. Predominant association of C11 with B6 contrasts with associations of C10 (B2) and C9 (B2, B7). Counts are shown in File S2.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3815065&req=5

fig5: Relationships between local haplotypes in B and C regions. For each HapMap population, the distribution of haplotype combinations is shown as a heat map (scale on right). Recurrent recombination between core- and B-region is apparent. Predominant association of C11 with B6 contrasts with associations of C10 (B2) and C9 (B2, B7). Counts are shown in File S2.
Mentions: Initial analysis of regions A and B used only single-nucleotide polymorphisms (SNPs) from HapMap Phase 3, Release 27 (Altshuler et al. 2010) that had been genotyped and phased in each included population (11 and 6 SNPs, respectively), whereas for regions C and D, SNPs lacking data for the TSI and/or MEX samples also were included (16 and 8 SNPs, respectively); these SNPs are listed in Table S2. Phased haplotypes were retrieved from HapMap and compared with raw genotype data for consistency. For the core region C, the absence of genotypes for SNPs c1 and c13 prevented distinguishing between members of the C2/C3 haplotype pair (in TSI) and the C6/C7 pair (in TSI and MEX), respectively. For TSI and GIH, which were phased on the basis of CEU, a small number of individuals heterozygous for the ancestral allele of A111T (1/1 and 3/8, respectively) were misphased. Corrected haplotype assignments are shown in all figures and tables except Figure 5 and those in which haplotype combinations are displayed (Figure S2, Figure S3, File S2, File S3, and File S4). For subregion D, only 1 of 8 SNPs was genotyped in TSI, precluding haplotype assignment for this sample.

Bottom Line: The C11 haplotype was most likely created by a crossover between two haplotypes, followed by the A111T mutation.The two parental precursor haplotypes are found from East Asia to the Americas but are nearly absent in Africa.The distributions of C11 and its parental haplotypes make it most likely that these two last steps occurred between the Middle East and the Indian subcontinent, with the A111T mutation occurring after the split between the ancestors of Europeans and East Asians.

View Article: PubMed Central - PubMed

Affiliation: Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania 17033.

ABSTRACT
Divergent natural selection caused by differences in solar exposure has resulted in distinctive variations in skin color between human populations. The derived light skin color allele of the SLC24A5 gene, A111T, predominates in populations of Western Eurasian ancestry. To gain insight into when and where this mutation arose, we defined common haplotypes in the genomic region around SLC24A5 across diverse human populations and deduced phylogenetic relationships between them. Virtually all chromosomes carrying the A111T allele share a single 78-kb haplotype that we call C11, indicating that all instances of this mutation in human populations share a common origin. The C11 haplotype was most likely created by a crossover between two haplotypes, followed by the A111T mutation. The two parental precursor haplotypes are found from East Asia to the Americas but are nearly absent in Africa. The distributions of C11 and its parental haplotypes make it most likely that these two last steps occurred between the Middle East and the Indian subcontinent, with the A111T mutation occurring after the split between the ancestors of Europeans and East Asians.

Show MeSH
Related in: MedlinePlus