A new report in Science this week reveals that Neanderthals have a variant in a receptor involved in skin and hair color that made some of them look like modern northern Europeans: Lalueza-Fox, Carles, et al. "A Melanocortin 1 Receptor Allele Suggest Varying Pigmentation Among Neanderthals" Science Express (Advance of Print) 25 October 2007.
Abstract: The melanocortin 1 receptor (MC1R) regulates pigmentation in humans and other vertebrates. Variants of MC1R with reduced function are associated with pale skin color and red hair in humans primarily of European origin. We amplified and sequenced a fragment of the MC1R gene (mc1r) from two Neanderthal remains. Both specimens have a mutation not found in ~3700 modern humans. Functional analyses show that this variant reduces MC1R activity to a level that alters hair and/or skin pigmentation in humans. The impaired activity of this variant suggests that Neanderthals varied in pigmentation levels, potentially to the scale observed in modern humans. Our data suggest that inactive MC1R variants evolved independently in both modern humans and Neanderthals.
Certain mutations in the melanocortin 1 receptor effects pigmentation in humans, changing the levels of color in both skin and hair (particularly red hair, freckling, and sun-sensitivity (1). The variant that was found in one of the Neanderthal specimens is different than any seen in modern humans. The Neanderthal variant also causes changes in hair and skin pigmentation, resulting in red hair and fair skin, but this mutation arose independently of the ones in modern humans. The mutations evolved independently but the physical outcome (phenotype) is similar. Red hair in modern humans is not a trait we've inherited from Neanderthals, because this study, as others before it have shown, Neanderthals and modern humans did not interbreed.
The variant is a point mutation: one base in the DNA sequence is G instead of the expected A. This results in a single amino acid change at this position, from arginine (R) to Glycine (G) at position 307. This is abbreviated in the paper (and this is typical shorthand) Arg307Gly. This mutation affects the function of the resultant receptor and the pigmentation difference occurs.
The authors were also able to calculate that the frequency of red hair in Neanderthals would be about 1 in 100 if the individual was homozygous for the allele (two identical copies of the mutated gene).
(1) J.L. Rees. "Genetics of Hair and Skin Color". Annual Review of Genetics V37 (2003) p. 67-90.