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

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 Tanz...

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Bibliographic Details
Published in:Science (American Association for the Advancement of Science) 2015-12, Vol.350 (6267), p.1493-1498
Main Authors: Malinsky, Milan, Challis, Richard J., Tyers, Alexandra M., Schiffels, Stephan, Terai, Yohey, Ngatunga, Benjamin P., Miska, Eric A., Durbin, Richard, Genner, Martin J., Turner, George F.
Format: Article
Language:English
Subjects:
Adaptation, Physiological - genetics
Animals
Aquatic ecology
Cichlidae
Cichlids
Cichlids - classification
Cichlids - genetics
Cichlids - physiology
Craters
Fish
Genes
Genetics
Genomic Islands
Genomics
Individualized Instruction
Islands
Lakes
Mating Preference, Animal
Morphology
Phylogeny
Polymorphism, Single Nucleotide
Populations
RESEARCH ARTICLE
Speciation
Species Specificity
Tanzania
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Summary: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.
ISSN:0036-8075
1095-9203
DOI:10.1126/science.aac9927