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Why aren't green eyes more prevalent, given that the green allele is dominant over the blue one?

My understanding is that human eye colour is determined by two genes:

1) HERC2, with alleles Bx, BB or xx,
2) gey, with alleles GG, Gb or bb,

where

  • B means brown
  • x means not brown (this is less confusing than using b for blue here, because having no B allele in HERC2 doesn't necessarily give someone blue eyes; their eyes will be either blue or green depending on the gey gene)
  • G means green
  • b means blue.

Capital letters stand for alleles that are dominant; lower case, ones that are recessive.

So the 'algorithm' goes:

  • 1) look at HERC2; if it's anything other than xx, you've got BROWN eyes
  • 2) if HERC2 is xx, look at gey; if it's anything other than bb, you've got GREEN eyes
  • 3) still here? then you've got BLUE eyes

My question is this: why is it that green eyes are so rare if the green allele is dominant over the blue one? When a blue-eyed person and a green-eyed person interbreed, their offspring will either be equally likely to have green eyes as blue (if the green-eyed parent is Gb) or always have green (if that parent is GG).

But many more people have blue eyes than green eyes, despite blue being recessive to green.

The obvious answer is that people with blue eyes (xx bb) and people with green eyes (other xx-ers) have tended to avoid breeding with each other to a large extent. Is any other explanation in the ring? Perhaps the greens are catching up?

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  • $\begingroup$ The gene which is important for the eye color is actually OCA2. In HERC2 is a regulatory region located which regulates the OCA2 expression. And there is a polymorphism which affects this. $\endgroup$ – Chris Feb 9 '15 at 14:38
  • $\begingroup$ Thanks @Chris. Will the question I'm trying to ask be more accurate if I (or you) amend HERC2 to OCA2? (That said, if HERC2 regulates the OCA2 expression, then HERC2 must be important for eye colour.) $\endgroup$ – h34 Feb 9 '15 at 14:50
  • $\begingroup$ No, it's not HERC2 that regulates OCA2, it is a regulatory region which is located inside the HERC2 gene. $\endgroup$ – Chris Feb 9 '15 at 16:19
  • $\begingroup$ @Chris - Part of HERC2, then? If the question needs correcting, please do correct it. $\endgroup$ – h34 Feb 9 '15 at 20:57
  • $\begingroup$ It's not correct that human eye colour is determined by two genes. Eye color is a polygenic trait. See for example (Sulem,..., Stefansson, 2007). $\endgroup$ – Eff Jul 25 '18 at 10:56
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A gene being dominant does not necessarily imply the gene is also common.

An easy counterexample is Huntington's disease. The gene is dominant, and only one mutant allele of huntingtin would result in development of the disease. However, the allele prevalence of the mutant is low in the general population.

In the absence of a selective advantage of green eyes over blue eyes, the two alleles of the gey gene should remain in genetic equilibrium, and therefore the number of people with green eyes will not increase. In fact, a similar misunderstanding applies to the disappearance of blondes/redheads. In both cases, the allele frequencies will remain unchanged in the absence of selection pressure.

The initial imbalance in the allele frequency could be due to many reasons. Population bottlenecks, genetic drift, and historical selection pressure could all be valid answers.

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