Please use this identifier to cite or link to this item: http://hdl.handle.net/1893/22222
Appears in Collections:Aquaculture Journal Articles
Peer Review Status: Refereed
Title: The genomic substrate for adaptive radiation in African cichlid fish
Authors: Brawand, David
Wagner, Catherine E
Lee, Yang I
Malinsky, Milan
Keller, Irene
Fan, Shaohua
Simakov, Oleg
Ng, Alvin Y
Lim, Zhi Wei
Bezault, Etienne
Turner-Maier, Jason
Johnson, Jeremy
Alcazar, Rosa
Noh, Hyun Ji
Penman, David
Contact Email: d.j.penman@stir.ac.uk
Keywords: Genome evolution
Evolution
Comparative genomics
Evolutionary biology
Issue Date: Sep-2014
Publisher: Nature Publishing Group
Citation: Brawand 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.
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.
Type: Journal Article
URI: http://hdl.handle.net/1893/22222
DOI Link: http://dx.doi.org/10.1038/nature13726
Rights: This 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 http://creativecommons.org/licenses/by-nc-sa/3.0
Notes: Additional 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 Palma
Affiliation: University of Oxford
University of Bern
University of Oxford
The Wellcome Trust
University of Bern
University of Konstanz
European Molecular Biology Laboratory
Institute of Molecular and Cell Biology - A*STAR
Institute of Molecular and Cell Biology - A*STAR
Reed College
Broad Institute of MIT and Harvard
Broad Institute of MIT and Harvard
Stanford University
Broad Institute of MIT and Harvard
Aquaculture

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