title: Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake.
abstract: 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.
authors.affiliation: Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, UK.|Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, CB2 1QN, UK.
authors.forename: Milan
authors.initials: M
authors.lastname: Malinsky
authors.affiliation: School of Biological Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK.
authors.forename: Richard J
authors.initials: RJ
authors.lastname: Challis
authors.affiliation: School of Biological Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK.
authors.forename: Alexandra M
authors.initials: AM
authors.lastname: Tyers
authors.affiliation: Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, UK.
authors.forename: Stephan
authors.initials: S
authors.lastname: Schiffels
authors.affiliation: Department of Evolutionary Studies of Biosystems, SOKENDAI, Kanagawa 240-0193, Japan.
authors.forename: Yohey
authors.initials: Y
authors.lastname: Terai
authors.affiliation: Tanzania Fisheries Research Institute, Box 9750, Dar es Salaam, Tanzania.
authors.forename: Benjamin P
authors.initials: BP
authors.lastname: Ngatunga
authors.affiliation: Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, UK.|Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, CB2 1QN, UK.
authors.forename: Eric A
authors.initials: EA
authors.lastname: Miska
authors.affiliation: Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, UK.
authors.forename: Richard
authors.initials: R
authors.lastname: Durbin
authors.affiliation: School of Biological Sciences, Life Sciences Building, 24 Tyndall Avenue, University of Bristol, Bristol, BS8 1TQ, UK.
authors.forename: Martin J
authors.initials: MJ
authors.lastname: Genner
authors.affiliation: School of Biological Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK.
authors.forename: George F
authors.initials: GF
authors.lastname: Turner
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D000818:Animals; D023681:Cichlids / Q000145:classification / Q000235:genetics* / Q000502:physiology*; D044404:Genomic Islands; D060106:Lakes; D052586:Mating Preference, Animal; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D013045:Species Specificity; D013636:Tanzania