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dc.contributor.authorBrawand, David-
dc.contributor.authorWagner, Catherine E-
dc.contributor.authorLee, Yang I-
dc.contributor.authorMalinsky, Milan-
dc.contributor.authorKeller, Irene-
dc.contributor.authorFan, Shaohua-
dc.contributor.authorSimakov, Oleg-
dc.contributor.authorNg, Alvin Y-
dc.contributor.authorLim, Zhi Wei-
dc.contributor.authorBezault, Etienne-
dc.contributor.authorTurner-Maier, Jason-
dc.contributor.authorJohnson, Jeremy-
dc.contributor.authorAlcazar, Rosa-
dc.contributor.authorNoh, Hyun Ji-
dc.contributor.authorPenman, David-
dc.description.abstractCichlid 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.en_UK
dc.publisherNature Publishing Group-
dc.relationBrawand D, Wagner CE, Lee YI, Malinsky M, Keller I, Fan S, Simakov O, Ng AY, Lim ZW, Bezault E, Turner-Maier J, Johnson J, Alcazar R, Noh HJ & Penman D (2014) The genomic substrate for adaptive radiation in African cichlid fish, Nature, 513 (7518), pp. 375-381.-
dc.rightsThis work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported licence. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons licence, users will need to obtain permission from the licence holder to reproduce the material. To view a copy of this licence, visit
dc.subjectGenome evolutionen_UK
dc.subjectComparative genomicsen_UK
dc.subjectEvolutionary biologyen_UK
dc.titleThe genomic substrate for adaptive radiation in African cichlid fishen_UK
dc.typeJournal Articleen_UK
dc.type.statusPublisher version (final published refereed version)-
dc.description.notesAdditional co-authors: Pamela Russell, Bronwen Aken, Jessica Alföldi, Chris Amemiya, Naoual Azzouzi, Jean-François Baroiller, Frederique Barloy-Hubler, Aaron Berlin, Ryan Bloomquist, Karen L. Carleton, Matthew A. Conte, Helena D'Cotta, Orly Eshel, Leslie Gaffney, Francis Galibert, Hugo F. Gante, Sante Gnerre, Lucie Greuter, Richard Guyon, Natalie S. Haddad, Wilfried Haerty, Rayna M. Harris, Hans A. Hofmann, Thibaut Hourlier, Gideon Hulata, David B. Jaffe, Marcia Lara, Alison P. Lee, Iain MacCallum, Salome Mwaiko, Masato Nikaido, Hidenori Nishihara, Catherine Ozouf-Costaz, Dariusz Przybylski, Michaelle Rakotomanga, Suzy C. P. Renn, Filipe J. Ribeiro, Micha Ron, Walter Salzburger, Luis Sanchez-Pulido, M. Emilia Santos, Steve Searle, Ted Sharpe, Ross Swofford, Frederick J. Tan, Louise Williams, Sarah Young, Shuangye Yin, Norihiro Okada, Thomas D. Kocher, Eric A. Miska, Eric S. Lander, Byrappa Venkatesh, Russell D. Fernald, Axel Meyer, Chris P. Ponting, J. Todd Streelman, Kerstin Lindblad-Toh, Ole Seehausen & Federica Di Palmaen_UK
dc.contributor.affiliationUniversity of Oxford-
dc.contributor.affiliationUniversity of Bern-
dc.contributor.affiliationUniversity of Oxford-
dc.contributor.affiliationThe Wellcome Trust-
dc.contributor.affiliationUniversity of Bern-
dc.contributor.affiliationUniversity of Konstanz-
dc.contributor.affiliationEuropean Molecular Biology Laboratory-
dc.contributor.affiliationInstitute of Molecular and Cell Biology - A*STAR-
dc.contributor.affiliationInstitute of Molecular and Cell Biology - A*STAR-
dc.contributor.affiliationReed College-
dc.contributor.affiliationBroad Institute of MIT and Harvard-
dc.contributor.affiliationBroad Institute of MIT and Harvard-
dc.contributor.affiliationStanford University-
dc.contributor.affiliationBroad Institute of MIT and Harvard-
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