Variation in pigmentation type and levels is a hallmark of myriad evolutionary radiations, and biologists have long been fascinated by the factors that promote and maintain variation in coloration across populations. Here we provide insights into the genetic basis of complex and continuous patterns of color variation in cichlid fishes, which offer a vast diversity of pigmentation patterns that have evolved in response to both natural and sexual selection. Specifically, we crossed two divergent cichlid species to generate an F2 mapping population that exhibited extensive variation in pigmentation levels and patterns. Our experimental design is robust in that it combines traditional quantitative trait locus (QTL) analysis with population genomics, which has allowed us to move efficiently from QTL interval to candidate gene. In total, we detected 41 QTL and 13 epistatic interactions that underlie melanocyte- and xanthophore-based coloration across the fins and flanks of these fishes. We also identified 2 QTL and 1 interaction for variation in the magnitude of integration among these color traits. This finding in particular is notable as there are marked differences both within and between species with respect to the complexity of pigmentation patterns. While certain individuals are characterized by more uniform “integrated” color patterns, others exhibit many more degrees of freedom with respect to the distribution of color “modules” across the fins and flank. Our data reveal, for the first time, a genetic basis for this difference. Finally, we implicate pax3a as a mediator of continuous variation in the levels of xanothophore-based color along the cichlid flank.

Albertson_et_al_QTL_datafileGenotypic and phenotypic data from the F2 population. Used for QTL analyses. Formatted for R-qtl.qPCR dataPhenotypic (average xanthophore counts on regions 'E-F' of fish) and qPCR data used for Figure S2.qPCR.xlsxallele specific expression dataData based on Sanger sequencing for estimating the relative expression of different alleles.allele specific exp data.xlsx