Hello, I'm new here, I really like the Eupedia website and all the Maciamo works; I'm not fluent in english, so sorry if in my messages I do mistakes.
Welcome to the forum, Drax and thank you for the kind words.
About the subject, for Indians peoples with light eyes, that have already proven and explained of the IE invaders/migration, so I don't think it's a valid comparaison with the curious cro-magon with brown skin and blue eyes...or maybe not.
What we want to ascertain by looking into the genomes of blue-eyed South Asians is what genes have an influence on eye pigmentation without affecting skin pigmentation (or vice versa). There are two main genes for blue eyes (HERC2, OCA2), but one of them (OCA2) is also known to influence skin colour and hair colour. Many South Asians also carry the light skin allele of SLC24A5 gene, but have nevertheless darker skin than Europeans. Some South Asians have very dark skin and blue eyes. Since all Europeans have light skin, it is hard to determine just how much influence the various genes for light skin and light eyes have on each others. The only way to be sure that Mesolithic Europeans could have had dark skin and blue eyes is to try to find individuals with the same mutations for dark skin and blue eyes, and such people can probably only be found in South Asia nowadays.
I'm not a specialist, so sorry if I do a big mistake, but if they have similar maternal lineage already in 3000 BC, that made them technically more or less "cousin" genetically ? if during this time they has already the same mtdna haplogroups, I suppose we can say that they were already mixed way before this date ? We know blue eyes are from one single woman ancestor...so how we can be sure that not among the IE the blue eyes have appeared first (among peoples with light skins and light hairs like...today), and have passed of others cro-magnons with their wives ? The majority of cro-magnons were described, until this CM with blue eyes, like tanned, brown eyes and hairs, imho, it's not judicious to transform all of them with blue eyes just because of an indvidual case.
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My third hypthosis, is maybe the simple ones, because of their mtdna, both of them has blue eyes, the IE invaders improves the presences of blue eyes appearances in all the Europe but in others places in the world, that explains how a recessive traits are so present among europeans and why it's seem exclusively, at least physically, to the Europeans peoples.
Yes and no. U4 and U5 are extremely old lineages, especially U which could be over 50,000 years old, i.e. older than the presence of Homo Sapiens in Europe. So saying that people are close cousins because they both possess U5 lineages devoid of sense. Nevertheless, R1a tribes surely absorbed a lot of European maternal lineages when they arrived in Eastern Europe from Central Asia or Siberia. Skeletons from Mesolithic or Neolithic Russia and Ukraine show that a lot of individuals were of proto-Europoid type, in other words anatomically intermediary between Mesolithic Europeans and Siberians.
As for the genes for blue eyes, there is a high likelihood that they were inherited from Neanderthal, rather than having appeared independently in Europeans fairly recently. It hasn't been proven yet that Neanderthals had blue eyes. Actually Neanderthals evolved for 300,000 years in Europe and were probably more genetically diverse than modern humans, who all share a more recent ancestry. If blue eyes indeed originated in Neanderthal, different Neanderthal populations could have passed blue eyes genes many times to Homo sapiens in Europe, the Middle East or Central Asia. It's not even granted that the two main genes, OCA2 and HERC2 were passed at the same time or to the same people. They might only have converged later in Europeans. Another alternative is that only one of these genes came from Neanderthal while the other arose in Homo sapiens.
In my opinion, both Mesolithic Europeans and Proto-Indo-Europeans possessed blue eyes. It is clear that PIE people had blue eyes because blue eyes spread to North, Central and South Asia. But the La Brana sample also confirms that blue eyes were already present in Mesolithic Europe.