the polymorphism is likely a tissue-specific regulatory mutation, and that it might have been picked up recently from the grey junglefowl.
regarding the implications of what they find:
In contrast, the minimal sequence divergence between the grey junglefowl BCDO2 sequence and the domestic yellow skin allele makes it highly unlikely that the divergence between the white and yellow skin alleles predates the speciation of the red and grey junglefowl; the Y sequence would have accumulated numerous sequence differences since the split between the red and grey junglefowl. We cannot exclude the possibility that yellow skin was introgressed to the red junglefowl by hybridization with grey junglefowl prior to domestication, but it is much more plausible that introgression was facilitated by human activities. The red and grey junglefowls are full species as demonstrated by the fact that hybridization does not occur in the wild  and when attempted in captivity, only a cross between grey cocks and red hens produced mostly sterile offspring . Hybridization between grey junglefowl and domesticated fowl, however, have been reported in the vicinity of villages within the area of contact between the two wild species , suggesting that the introgression of yellow skin into domestic birds took place after chickens were initiallyThey mention that consumers in the US, Mexico and China prefer yellow skinned chickens ...interesting... , also:
During lay, carotenoids are mobilized and deposited in the yolk of the egg. It is therefore worth speculating that the bright yellow skin color, expressed by well-fed yellow skin homozygotes but not by well-fed white skin birds, has been associated with high production and good health at some point during domestication and was therefore favored by early farmers. Of course, yellow skin may also have been selected purely for cosmetic reasons.Identification of the Yellow Skin Gene Reveals a Hybrid Origin of the Domestic Chicken
Jonas Eriksson, et al.
Abstract: Yellow skin is an abundant phenotype among domestic chickens and is caused by a recessive allele (W*Y) that allows deposition of yellow carotenoids in the skin. Here we show that yellow skin is caused by one or more cis-acting and tissue-specific regulatory mutation(s) that inhibit expression of BCDO2 (beta-carotene dioxygenase 2) in skin. Our data imply that carotenoids are taken up from the circulation in both genotypes but are degraded by BCDO2 in skin from animals carrying the white skin allele (W*W). Surprisingly, our results demonstrate that yellow skin does not originate from the red junglefowl (Gallus gallus), the presumed sole wild ancestor of the domestic chicken, but most likely from the closely related grey junglefowl (Gallus sonneratii). This is the first conclusive evidence for a hybrid origin of the domestic chicken, and it has important implications for our views of the domestication process.