Research article

Complex signatures of selection for the melanogenic loci TYR, TYRP1 and DCT in humans

Santos Alonso¹ , Neskuts Izagirre¹ , Isabel Smith-Zubiaga² , Jesús Gardeazabal³ , José Luís Díaz-Ramón³ , José Luís Díaz-Pérez³ , Diana Zelenika⁴ , María Dolores Boyano⁵ , Nico Smit⁶ and Concepción de la Rúa¹

¹Dept. Genetics, Physical Anthropology and Animal Physiology. University of the Basque Country. Barrio Sarriena s/n. 48940 Leioa, Bizkaia, Spain

²Dept. Zoology and Animal Cell Biology. University of the Basque Country. Barrio Sarriena s/n. 48940 Leioa, Bizkaia, Spain

³Dermatology Service. Cruces Hospital. Plaza de Cruces s/n, 48903, Cruces-Barakaldo, Bizkaia, Spain

⁴Centre National de Génotypage (CNG). 2 Rue Gaston Cremieux. CP 5721. 91057 Evry Cedex, France

⁵Dept. Cell Biology and Histology. University of the Basque Country. Barrio Sarriena s/n. 48940 Leioa, Bizkaia, Spain

⁶Department of Clinical Chemistry, L01-036 Leiden University Medical Center, Albinusdreef 2, 2333 AZ Leiden, The Netherlands

author email corresponding author email

BMC Evolutionary Biology 2008, 8:74doi:10.1186/1471-2148-8-74

Published:	29 February 2008

Abstract

Background

The observed correlation between ultraviolet light incidence and skin color, together with the geographical apportionment of skin reflectance among human populations, suggests an adaptive value for the pigmentation of the human skin. We have used Affymetrix U133a v2.0 gene expression microarrays to investigate the expression profiles of a total of 9 melanocyte cell lines (5 from lightly pigmented donors and 4 from darkly pigmented donors) plus their respective unirradiated controls. In order to reveal signatures of selection in loci with a bearing on skin pigmentation in humans, we have resequenced between 4 to 5 kb of the proximal regulatory regions of three of the most differently expressed genes, in the expectation that variation at regulatory regions might account for intraespecific morphological diversity, as suggested elsewhere.

Results

Contrary to our expectations, expression profiles did not cluster the cells into unirradiated versus irradiated melanocytes, or into lightly pigmented versus darkly pigmented melanocytes. Instead, expression profiles correlated with the presence of Bovine Pituitary Extract (known to contain α-MSH) in the media. This allowed us to differentiate between melanocytes that are synthesizing melanin and those that are not. TYR, TYRP1 and DCT were among the five most differently expressed genes between these two groups. Population genetic analyses of sequence haplotypes of the proximal regulatory flanking-regions included Tajima's D, HEW and DHEW neutrality tests analysis. These were complemented with EHH tests (among others) in which the significance was obtained by a novel approach using extensive simulations under the coalescent model with recombination. We observe strong evidence for positive selection for TYRP1 alleles in Africans and for DCT and TYRP1 in Asians. However, the overall picture reflects a complex pattern of selection, which might include overdominance for DCT in Europeans.

Conclusion

Diversity patterns clearly evidence adaptive selection in pigmentation genes in Africans and Asians. In Europeans, the evidence is more complex, and both directional and balancing selection may be involved in light skin. As a result, different non-African populations may have acquired light skin by alternative ways, and so light skin, and perhaps dark skin too, may be the result of convergent evolution.