Both Neandertals that they sequenced had a version of MC1R that is not found among modern humans (at least 3,700 of them). This variant is likely to have led to lighter skin/hair. It looks like this will be coming out in Science soon.
A Melanocortin 1 Receptor Allele Suggests Varying Pigmentation Among Neanderthals
Carles Lalueza-Fox, Holger Römpler, David Caramelli, Claudia Stäubert, Giulio Catalano, David Hughes, Nadin Rohland, Elena Pilli, Laura Longo, Silvana Condemi, Marco de la Rasilla, Javier Fortea, Antonio Rosas, Mark Stoneking, Torsten Schöneberg, Jaume Bertranpetit, Michael Hofreiter
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 ~3,700 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.