Selection signatures at melanogenic genes TYR, TYRP1, and DCT

First, they find no difference in expression profiles between dark and light skinned melanocytes and between irradiated vs. unirradiated melanocytes. They attribute this to the presence of a growth factor in the media, but also say:

In any case, the homogeneity found in the gene expression profiles of human
melanocytes grown in BSE-containing media suggests that melanocytes from both
light and dark pigmentation donors may have the same genetic ability to produce
melanin if subject to the same level of external (paracrine) signaling molecules, at least above a certain concentration.

I haven't heard of this before!:

Alternative mechanisms to explain a possible adaptive advantage of dark pigmentation involve concealment [39]...
39. Robins AH: Biological perspectives on human pigmentation.
Cambridge Studies in Biological Anthropology. Cambridge, UK: Cambridge
University Press; 1991.

and

However, in the light of the apparent vagaries that occur in the pigmentation of mammalian skin, including primates, others [41] suggest that dark skin may have outlived its usefulness.
41. Montagna W, Prota G, Kenney JA: Black skin: structure and function.
New York: Academic Press; 1993.

They also sequence TYR, TYRP1 and DCT among Africans, Europeans, Asians, and Australian Aboriginies

In addition, it seems likely that nondirectional selection is acting too. For instance, overdominance seems compatible with the diversity patterns observed for DCT in Europeans. Similarly, the high frequency of the ancestral TYR haplotype within the Senegalese suggests that purifying selection at this locus may have been of some importance within Africa, although the large number of TYR mutations associated with oculocutaneous albinism 1 (OCA1) (OMIM#230100) suggest that TYR may be a gene under purifying selection in all populations.

in conclusion:

As a result, the lighter skin pigmentation phenotype in Europeans and East Asians may have been acquired by alternative mechanisms and thus, as previously suggested [11, 12, 13, 15], light skin would be the result of convergent evolution. Similarly, the diversity profile of Australian Aborigines suggests that this may also be the case for dark skin.

I think it's kind of weird how this paper seems like two separate studies put together, one on expression profiles of melanocytes and one on sequencing the three genes in different populations.

Complex signatures of selection for the melanogenic loci TYR, TYRP1 and DCT in humans
Santos Alonso, Neskuts Izagirre, Isabel Smith-Zubiaga, Jesus Gardeazabal, Jose Luis Diaz-Ramon, Jose Luis Diaz-Perez, Diana Zelenika, Maria Dolores Boyano, Nico Smit and Concepcion de la Rua
BMC Evolutionary Biology 2008, 8:74doi:10.1186/1471-2148-8-74

Abstract (provisional) 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 a-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. Conclusions 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.