Skin color gene in humans and fish

New Science paper on allele which explains much of the difference in pigmentation between Europeans and Sub-Saharan Africans. Interestingly, Sub-Saharan Africans and East Asians both share the same ancestral allele, which means that the light pigmentation of East Asians is not caused by this gene. From an accompanying news story in the magazine:

People come in many different hues, from black to brown to white and shades in between. The chief determinant of skin color is the pigment melanin, which protects against ultraviolet rays and is found in cellular organelles called melanosomes. But the genetics behind this spectrum of skin colors have remained enigmatic. Now, on page 1782 of this week's issue of Science, an international team reports the identification of a zebrafish pigmentation gene and its human counterpart, which apparently accounts for a significant part of the difference between African and European skin tones. One variant of the gene seems to have undergone strong natural selection for lighter skin in Europeans.

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The new work is raising goose bumps among skin-color researchers. "Entirely original and groundbreaking," says molecular biologist Richard Sturm of the University of Queensland in Brisbane, Australia. Anthropologist Nina Jablonski of the California Academy of Sciences in San Francisco, California, notes that the paper "provides very strong support for positive selection" of light skin in Europeans. Researchers have not been sure whether European pale skin is the result of some selective advantage or due to a relaxation of selection for dark skin, after the ancestors of modern Europeans migrated out of Africa into less sunny climes.

Yet the authors agree that the new gene, SLC24A5, is far from the whole story: Although at least 93% of Africans and East Asians share the same allele, East Asians are usually light skinned too. This means that variation in other genes, a handful of which have been previously identified, also affects skin color.

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The team concludes that between 25% and 38% of the skin-color difference between Europeans and Africans can be attributed to SLC24A5 variants.

And from the actual paper paper:

The allele frequency for the Thr111 variant ranged from 98.7 to 100% among several European-American population samples, whereas the ancestral alanine allele (Ala111) had a frequency of 93 to 100% in African, Indigenous American, and East Asian population samples (fig. S6) (29, 30). The difference in allele frequencies between the European and African populations at rs1426654 ranks within the top 0.01% of SNP markers in the HapMap database (29), consistent with the possibility that this SNP has been a target of natural or sexual selection.

Science 16 December 2005:
Vol. 310. no. 5755, pp. 1782 - 1786

SLC24A5, a Putative Cation Exchanger, Affects Pigmentation in Zebrafish and Humans

Rebecca L. Lamason et al.

Lighter variations of pigmentation in humans are associated with diminished number, size, and density of melanosomes, the pigmented organelles of melanocytes. Here we show that zebrafish golden mutants share these melanosomal changes and that golden encodes a putative cation exchanger slc24a5 (nckx5) that localizes to an intracellular membrane, likely the melanosome or its precursor. The human ortholog is highly similar in sequence and functional in zebrafish. The evolutionarily conserved ancestral allele of a human coding polymorphism predominates in African and East Asian populations. In contrast, the variant allele is nearly fixed in European populations, is associated with a substantial reduction in regional heterozygosity, and correlates with lighter skin pigmentation in admixed populations, suggesting a key role for the SLC24A5 gene in human pigmentation.