About Blue Eyes

This isn't new (the paper is twelve years old), but it caught my eye today.

The time frame for the initial mutation spans the late Mesolithic era, an era during which hunter-gatherers from Southern Europe repopulated the rest of the continent as glaciers from the last major ice age retreated to the north, and the early Neolithic era. It predates the Copper, Bronze and Iron ages. The authors of the paper on the genetics of eye color believe that the blue eye color gene is genetic fitness neutral. As a press release on the study explains in a conclusion stronger than the study itself really supports given its limited sample size and diversity:

New research shows that people with blue eyes have a single, common ancestor. Scientists have tracked down a genetic mutation which took place 6,000-10,000 years ago and is the cause of the eye color of all blue-eyed humans alive on the planet today.

The mutation is similar to an albinism mutation but more targeted and less complete.

"Originally, we all had brown eyes," said Professor Hans Eiberg from the Department of Cellular and Molecular Medicine. "But a genetic mutation affecting the OCA2 gene in our chromosomes resulted in the creation of a "switch," which literally "turned off" the ability to produce brown eyes." The OCA2 gene codes for the so-called P protein, which is involved in the production of melanin, the pigment that gives colour to our hair, eyes and skin. The "switch," which is located in the gene adjacent to OCA2 does not, however, turn off the gene entirely, but rather limits its action to reducing the production of melanin in the iris -- effectively "diluting" brown eyes to blue. The switch's effect on OCA2 is very specific therefore. If the OCA2 gene had been completely destroyed or turned off, human beings would be without melanin in their hair, eyes or skin colour -- a condition known as albinism. 

Variation in the colour of the eyes from brown to green can all be explained by the amount of melanin in the iris, but blue-eyed individuals only have a small degree of variation in the amount of melanin in their eyes. "From this we can conclude that all blue-eyed individuals are linked to the same ancestor," says Professor Eiberg. "They have all inherited the same switch at exactly the same spot in their DNA." Brown-eyed individuals, by contrast, have considerable individual variation in the area of their DNA that controls melanin production. 

Professor Eiberg and his team examined mitochondrial DNA and compared the eye colour of blue-eyed individuals in countries as diverse as Jordan, Denmark and Turkey. 

The abstract and citation to the paper are as follows:

The human eye color is a quantitative trait displaying multifactorial inheritance. Several studies have shown that the OCA2 locus is the major contributor to the human eye color variation. By linkage analysis of a large Danish family, we fine mapped the blue eye color locus to a 166 Kbp region within the HERC2 gene. By association analyses, we identified two SNPs within this region that were perfectly associated with the blue and brown eye colors: rs12913832 and rs1129038. Of these, rs12913832 is located 21.152 bp upstream from the OCA2 promoter in a highly conserved sequence in intron 86 of HERC2. The brown eye color allele of rs12913832 is highly conserved throughout a number of species. As shown by a Luciferase assays in cell cultures, the element significantly reduces the activity of the OCA2 promoter and electrophoretic mobility shift assays demonstrate that the two alleles bind different subsets of nuclear extracts. One single haplotype, represented by six polymorphic SNPs covering half of the 3′ end of the HERC2 gene, was found in 155 blue-eyed individuals from Denmark, and in 5 and 2 blue-eyed individuals from Turkey and Jordan, respectively. Hence, our data suggest a common founder mutation in an OCA2 inhibiting regulatory element as the cause of blue eye color in humans. In addition, an LOD score of Z = 4.21 between hair color and D14S72 was obtained in the large family, indicating that RABGGTA is a candidate gene for hair color.

Hans Eiberg, et al., "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." 123(2) Human Genetics 177 (March 2008). DOI: 10.1007/s00439-007-0460-x

Two subsequent papers have favored a somewhat earlier Mesolithic European hunter-gatherer origin for the genes, rather than a Neolithic one, and have refined the genetic model to include a few more genes. As Wikipedia explains:

People of European descent show the greatest variety in eye color of any population worldwide. Recent advances in ancient DNA technology have revealed some of the history of eye color in Europe. All European Mesolithic hunter-gatherer remains so far investigated have shown genetic markers for light-colored eyes, in the case of western and central European hunter-gatherers combined with dark skin color. The later additions to the European gene pool, the Early Neolithic farmers from Anatolia and the Yamnaya Copper Age/Bronze Age pastoralists (possibly the Proto-Indo-European population) from the area north of the Black Sea appear to have had much higher incidences of dark eye color alleles, and alleles giving rise to lighter skin, than the original European population.

The two  more recent papers cited are:

Haak, W.; Lazaridis, I., et al., "Massive migration from the steppe was a source for Indo-European languages in Europe". 522(7555) Nature. 207–211 (2015). arXiv:1502.02783. bioRxiv 013433. doi:10.1038/nature14317. 

Mathieson, Iain (2015). "Eight thousand years of natural selection in Europe". bioRxiv 016477.

Neanderthals probably had blue eyes, light colored hair and light colored skin, while the modern humans who co-existed and encountered with them at the end of the Upper Paleolithic era would have had brown eyes, dark hair and dark colored skin. But, genes for light pigmentation in modern humans alive today arose from mutations that took place roughly 20,000 years after Neanderthals were extinct and were not derived from Neanderthal admixture.