Check this out, Angela: http://www.dailymail.co.uk/sciencet...ns-brought-Europe-Near-East-study-claims.html
It seems that western hunter-gatherers were a bit different from Scandinavian hunter-gatherers.
And this article refers to a third gene on Scandinavians: http://news.sciencemag.org/archaeology/2015/04/how-europeans-evolved-white-skin
"They also had a third gene, HERC2/OCA2, which causes blue eyes and may also contribute to light skin and blond hair. Thus ancient hunter-gatherers of the far north were already pale and blue-eyed, but those of central and southern Europe had darker skin."
That's actually not too bad as a simplistic summary of the tentative conclusions reached thus far by researchers working in the field. Usually reporters, even science reporters, get it much more wrong than this.
They're still missing some facts, however. If I'm remembering correctly (and if I'm not please correct the record) there were a few stray de-pigmentation genes in some of the WHG, and the "light genes" were not uniform among hunter gatherers in the far north. The SHG were a specific subset. (We're also not even sure how much genetic input there is from them.) Arvistro has posted about a proposed link with the EHG. However, if I remember correctly, the EHG were not all fair. Furthermore, the Central European farmers had some people with light hair, eye and skin snps, yet I don't think they're modeled with EHG, are they? (You can see the results in Gamba et al.)
That component came later, supposedly with the Indo-Europeans, yet look at their pigmentation.
I coincidentally just saw this posted on anthrogenica by "Sein". It's really apropos, so I hope he doesn't mind my posting it here.
"According to Allencroft et al., the derived mutation at rs16891982 (SLC45A2) was found at only around 25% in the Bronze Age steppe (!), and the derived mutation at rs12913832 (OCA2-HERC2) was found at 0%. To put that in perspective, that means these people were darker than living Pakistanis, who have higher percentages of the derived mutation at rs16891982, and who do display the derived mutation at rs12913832 (but at very low levels for this mutation). Same with Yamnaya in Haak et al., these people were much darker than any living population in Europe, and approached lighter South Asian populations in terms of pigmentation genetics."
If that's correct, and all of the steppe people looked like this they certainly didn't bring pale pigmentation to Europe.
There is something going on other than migration of peoples carrying these traits. As others have been pointing out, these are indeed recessive traits. It has to be down to selection, and recent selection, and that's indeed what the researchers are saying. I don't see how it can be denied.
What we don't totally understand is the mechanism. It's a little clearer for lactase persistence, because we can see the benefit in terms of nutrition in regions of Europe where you can't grow things all year long. With skin color it also makes some sense in terms of adaptation to UV light, but why the sudden acceleration? Did blue eyes serve a function we don't yet understand? Or, perhaps, it was a chance mutation that persisted in isolated hunter gatherer bands, but was selected for later on?
If I were a researcher in this field I would look at the areas around the locations for these depigmentation snps. They're all close together. What other snps are near them? What function do they serve? What other purposes could the depigmentation snps serve? Are they tied into other mechanisms, and something in the changed environment affected these other mechanisms? I think that in addition to latitude a change in diet away from seafood and more heavily cereal based may be part of the answer and should certainly be investigated, but I also think it may have something to do with lactase and that the two are somehow connected.
There's still a lot of research to be done, but what I think can't be denied is that changes were happening in these two areas, and happening quickly, and furthermore that our views of the past were wrong on so many levels. Ancient dna surprises, and surprises, and surprises.