Ecological genomics in full colour

Colour patterns in animals have long offered an opportunity to observe adaptive traits in natural populations. Colour plays myriad roles in interactions within and among species, from reproductive signalling to predator avoidance, leading to multiple targets of natural and sexual selection and opportunities for diversification. Understanding the genetic and developmental underpinnings of variation in colour promises a fuller understanding of these evolutionary processes, but the path to unravelling these connections can be arduous. The advent of genomic techniques suitable for nonmodel organisms is now beginning to light the way. Two new studies in this issue of Molecular Ecology use genomic sequencing of laboratory crosses to map colour traits in cichlid fishes, a remarkably diverse group in which coloration has played a major role in diversification. They illustrate how genomic approaches, specifically RAD sequencing, can rapidly identify both simple and more complex genetic variation underlying ecologically important traits. In the first, Henning et al. ( 2014 ) detect a single locus that appears to control in a Mendelian fashion the presence of horizontal stripes, a trait that has evolved in numerous cichlid lineages. In the second, Albertson et al. ( 2014 ) identify several genes and epistatic interactions affecting multiple colour traits, as well as a novel metric describing integration across colour traits. Albertson et al. ( 2014 ) go further, by quantifying differential expression of parental alleles at a candidate locus and by relating differentiation among natural populations at mapped loci to trait divergence. Herein lies the promise of ecological genomics – efficiently integrating genetic mapping of phenotypes with population genomic data to both identify functional genes and unravel their evolutionary history. These studies offer guidance on how genomic techniques can be tailored to a research question or study system, and they also add to the growing body of empirical examples addressing basic questions about how ecologically important traits evolve in natural populations.