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Given what we know of the genetics of eye color and their historical distribution, is it possible or at least plausible for a person born in the Horn of Africa during the early Neolithic (ca. 9000 BCE), assuming no recent ancestors from outside this area, to have had amber eyes (or in general anything other than brown?) If so, would one or both parents need to have that color as well, and what of siblings?

I know that today there is much less isolation and much more crossing of genetic lines, so that pretty much any combination of skin and eye color is likely possible, but no doubt it was different back then.

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There are two possibilities: First, that an individual develops a mutation de novo and is the first to carry it. When we talk about recessive expressed allels, than both parents need to have a copy of the allel, otherwise it will not show up in the kids. In this case a mixed population of siblings is to be expected (some carrying both recessive allels, some only one). However, its most likely, that the eye color at this time was brown. As far as I know, there has been no evidence so far from ancient DNA that this has been different.

The oldest DNAfrom Europe, which has been analyzed and which showed a difference for the eye color comes from Spain (La Brana-Arintero site in Valdelugueros) and is about 7.000 years old. See this report about it. This individual is thought to have an "african" type of pigmentation but blue eyes. The original publication is called "Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European."

Another paper claims that the blue eye color comes from a mutation which occured in a gene called "OCA2" in the black sea region some 6-10.000 years ago. See here: "Blue eye color in humans may be caused by a perfectly associated founder mutation in a regulatory element located within the HERC2 gene inhibiting OCA2 expression" .

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Thanks. My searches turned up nothing on genetics of amber eyes, except we apparently don't know which genes control it. It may be caused by a pigment (lipochrome) which is also present in green eyes, but I can't tell if the genes involved in brown and blue eyes have any effect on the gene(s) for amber eyes. If amber/green is caused by an entirely different pigment, shouldn't the other genes (which regulate melanin) only affect how light or dark the amber is? Or whether the result is green or amber? I assume green may be "blue+lipochrome" and amber is "brown+lipochrome", but do we know? –  adcoon Feb 7 at 21:26
    
@adcoon The eye color is build by both: Melanin and Lipochrome. Amber comes up, when you have very little melanin and a lot of Lipochrome. The deposition of Lipochrome into the eye is controlled by EYCL1 and EYCL2. Have a look on this Webpage which has a ton of references at the bottom. –  Chris Feb 8 at 20:24
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