Research Article

Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake

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Science  18 Dec 2015:
Vol. 350, Issue 6267, pp. 1493-1498
DOI: 10.1126/science.aac9927

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Cichlids diverge within a crater lake

It is not clear how populations diversify and new species form at the genomic level, especially when they coexist in the same location. Malinsky et al. investigated how two ecomorphs of cichlid fish in a small lake in Tanzania are diversifying relative to each other. Although there is gene flow between the two forms, major regions of genetic divergence, known as genomic islands, separate the populations. Within these islands, the authors found genes likely to be associated with mate choice, supporting the idea that genetic changes related to breeding preferences are the first to diverge during speciation.

Science, this issue p. 1493


The genomic causes and effects of divergent ecological selection during speciation are still poorly understood. Here we report the discovery and detailed characterization of early-stage adaptive divergence of two cichlid fish ecomorphs in a small (700 meters in diameter) isolated crater lake in Tanzania. The ecomorphs differ in depth preference, male breeding color, body shape, diet, and trophic morphology. With whole-genome sequences of 146 fish, we identified 98 clearly demarcated genomic “islands” of high differentiation and demonstrated the association of genotypes across these islands with divergent mate preferences. The islands contain candidate adaptive genes enriched for functions in sensory perception (including rhodopsin and other twilight-vision–associated genes), hormone signaling, and morphogenesis. Our study suggests mechanisms and genomic regions that may play a role in the closely related mega-radiation of Lake Malawi.

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