Pigmentation patterns are one of the most recognizable forms of phenotypic diversity and an important component of organismal fitness. While much progress has been made in understanding the genes controlling pigmentation in model systems, many questions remain about the genetic basis of pigment traits observed in nature. Lake Malawi cichlid fishes are known for their diversity of male pigmentation patterns, which have been shaped by sexual selection. To begin the process of identifying the genes underlying this diversity, we quantified the number of pigment cells on the body and fins of two species of the genus Metriaclima and their hybrids. We then used the Castle-Wright equation to estimate that differences in individual pigmentation traits between these species are controlled by one to four genes each. Different pigmentation traits are highly correlated in the F(2) , suggesting shared developmental pathways and genetic pleiotropy. Melanophore and xanthophore traits fall on opposite ends of the first principal component axis of the F(2) phenotypes, suggesting a tradeoff during the development of these two pigment cell types.
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