title: The genomic substrate for adaptive radiation in African cichlid fish.
abstract: Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.|MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK.
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authors.affiliation: Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution & Biogeochemistry, CH-6047 Kastanienbaum, Switzerland.|Division of Aquatic Ecology, Institute of Ecology & Evolution, University of Bern, CH-3012 Bern, Switzerland.
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authors.lastname: Wagner
authors.affiliation: MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK.
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authors.affiliation: Gurdon Institute, Cambridge CB2 1QN, UK.|Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.
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authors.affiliation: Division of Aquatic Ecology, Institute of Ecology & Evolution, University of Bern, CH-3012 Bern, Switzerland.
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authors.lastname: Keller
authors.affiliation: Department of Biology, University of Konstanz, D-78457 Konstanz, Germany.
authors.forename: Shaohua
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authors.lastname: Fan
authors.affiliation: Department of Biology, University of Konstanz, D-78457 Konstanz, Germany.|European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
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authors.lastname: Simakov
authors.affiliation: Institute of Molecular and Cell Biology, ASTAR, 138673 Singapore.
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authors.affiliation: Institute of Molecular and Cell Biology, ASTAR, 138673 Singapore.
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authors.affiliation: Department of Biology, Reed College, Portland, Oregon 97202, USA.
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authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
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authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
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authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
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authors.affiliation: Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.
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authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
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authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
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authors.affiliation: Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution & Biogeochemistry, CH-6047 Kastanienbaum, Switzerland.|Division of Aquatic Ecology, Institute of Ecology & Evolution, University of Bern, CH-3012 Bern, Switzerland.
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authors.affiliation: MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK.
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authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
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authors.affiliation: MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK.
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authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.|Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden.
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authors.affiliation: Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution & Biogeochemistry, CH-6047 Kastanienbaum, Switzerland.|Division of Aquatic Ecology, Institute of Ecology & Evolution, University of Bern, CH-3012 Bern, Switzerland.
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authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.|Vertebrate and Health Genomics, The Genome Analysis Centre, Norwich NR18 7UH, UK.
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mesh_terms: D000351:Africa, Eastern; D000818:Animals; D023681:Cichlids / Q000145:classification* / Q000235:genetics*; D004251:DNA Transposable Elements / Q000235:genetics; D019143:Evolution, Molecular; D020440:Gene Duplication / Q000235:genetics; D005786:Gene Expression Regulation / Q000235:genetics; D049810:Genetic Speciation; D016678:Genome / Q000235:genetics*; D023281:Genomics; D060106:Lakes; D035683:MicroRNAs / Q000235:genetics; D010802:Phylogeny; D011110:Polymorphism, Genetic / Q000235:genetics
chemical_list: D004251:DNA Transposable Elements; D035683:MicroRNAs