How the White Sands lizards lost their stripes

In molecular ecology, most of us work with study systems that are messy, uncooperative, or just plain difficult (note the fecal samples incubating on my lab bench). What I wouldn’t give for a nice, elegant study system — like the White Sands lizards featured in a recent article by Laurent et al.*
Laurent et al. work in the recently formed White Sands system, where ~275 square miles of white dunes are surrounded by the dark Chihuahuan Desert. Several species in this region (reptiles, arthopods, and mammals) have rapidly evolved blanched color morphs to blend into the white sands.
The White Sands system provides a ready-made opportunity to study the genomics of rapid adaptation, which is exactly what Laurent et al. did using two different species of White Sands lizards, each with light and dark color morphs.

The authors collected individuals from both white and dark sands for each of the two species (Sceloporus cowlesi and Aspidoscelis inornata). Using a sequence capture approach, they looked at the population structure and demographic histories of each species (notably, the two species have remarkably different demographic histories!).
But the really interesting bit was their investigation of selection in the 1-kb coding region of the melanocortin-1 receptor gene (Mc1r), which is responsible for color variation in many species (including red hair in humans).
In their lizards, the authors compared the Mc1r region to anonymous loci and they found several differences that scream “selective sweep!”:

1. Much higher F_ST values between dark and light populations at the Mc1r locus compared to neutral regions.
2. A reduction of diversity in the Mc1r locus of the White Sands populations.
3. Negative values of Tajima’s D in the Mc1r region of the White Sands populations (significantly lower than the genomic background average).
4. A significant rejection of neutrality in the White Sands Mc1r region, but not in other populations or genomic regions, using the CLR test (Kim & Stephan 2002).

To put the icing on the cake, they also identified two specific structural variants under selection (THR¹⁷⁰ILE and HIS²⁰⁸TYR).
*Laurent et al. would probably say that their research is just as messy, uncooperative, and difficult as the rest of ours – but they sure have a great system for studying recent, parallel adaptation.
References:
Laurent, Stefan, et al. (2016) “The population genomics of rapid adaptation: disentangling signatures of selection and demography in white sands lizards.” Molecular Ecology 25: 306-323. doi: http://dx.doi.org/10.1111/mec.13385
Kim, Y., & Stephan, W. (2002) Detecting a local signature of genetic hitchhiking along a recombining chromosome. Genetics, 160: 765-777. doi: http://dx.doi.org/10.3410/f.1008369.104907