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

Milan Malinsky, Richard Challis, Alexandra Tyers, Stephan Schiffels, Yohey Terai, Benjamin Ngatunga, Eric Miska, Richard Durbin, Martin J Genner, George Turner

Research output: Contribution to journalArticle (Academic Journal)peer-review

232 Citations (Scopus)
466 Downloads (Pure)


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.
Original languageEnglish
Pages (from-to)1493-1498
Number of pages6
Issue number6267
Publication statusPublished - 18 Dec 2015


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