The genomic substrate for adaptive radiation in African cichlid fish

David Brawand; Catherine E Wagner; Yang I Li; Milan Malinsky; Irene Keller; Shaohua Fan; Oleg Simakov; Alvin Y Ng; Zhi Wei Lim; Etienne Bezault; Jason Turner-Maier; Jeremy Johnson; Rosa Alcazar; Hyun Ji Noh; 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; David J Penman; 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

doi:10.1038/nature13726

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The genomic substrate for adaptive radiation in African cichlid fish

Journal article

Open access

Peer reviewed

The genomic substrate for adaptive radiation in African cichlid fish

David Brawand, Catherine E Wagner, Yang I Li, Milan Malinsky, Irene Keller, Shaohua Fan, Oleg Simakov, Alvin Y Ng, Zhi Wei Lim, Etienne Bezault, …

Nature, Vol.513(7518), pp.375–381-381

09/03/2014

DOI: https://doi.org/10.1038/nature13726

PMCID: PMC4353498

PMID: 25186727

Abstract

Comparative genomics

Genome evolution

Life Sciences

Genetics

Evolution

Evolutionary Biology

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.

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Title: The genomic substrate for adaptive radiation in African cichlid fish
Creators: David Brawand - University of Oxford [Oxford]
Catherine E Wagner - Centre of Ecology, Evolution and Biogeochemistry, Department of Fish Ecology and Evolution
Yang I Li - University of Oxford [Oxford]
Milan Malinsky - Sanger Institute
Irene Keller - Institute of Zoology, University of Bern
Shaohua Fan - Zoology and Evolutionary Biology, Department of Biology
Oleg Simakov - EMBL Heidelberg
Alvin Y Ng - Institute of Molecular and Cell Biology
Zhi Wei Lim - Institute of Molecular and Cell Biology
Etienne Bezault - Department of Biology, Reed college, Portland, OR, USA
Jason Turner-Maier - Broad Institute of MIT and Harvard
Jeremy Johnson - Broad Institute of MIT and Harvard
Rosa Alcazar - Stanford University
Hyun Ji Noh - Broad Institute of MIT and Harvard
Pamela Russell - California Institute of Technology
Bronwen Aken - Sanger Institute
Jessica Alföldi - Broad Institute of MIT and Harvard
Chris Amemiya - Benaroya Research Institute
Naoual Azzouzi - Institut de Génétique et Développement de Rennes
Jean-François Baroiller - Intensification raisonnée et écologique pour une pisciculture durable
Frederique Barloy-Hubler - Institut de Génétique et Développement de Rennes
Aaron Berlin - Broad Institute of MIT and Harvard
Ryan Bloomquist - Georgia Institute of Technology [Atlanta]
Karen L Carleton - University of Maryland [College Park]
Matthew A Conte - University of Maryland [College Park]
Helena D'Cotta - Intensification raisonnée et écologique pour une pisciculture durable
Orly Eshel - The Volcani Center
Leslie Gaffney - Broad Institute of MIT and Harvard
Francis Galibert - Institut de Génétique et Développement de Rennes
Hugo F Gante - University of Basel
Sante Gnerre - Broad Institute of MIT and Harvard
Lucie Greuter - Centre of Ecology, Evolution and Biogeochemistry, Department of Fish Ecology and Evolution
Richard Guyon - Institut de Génétique et Développement de Rennes
Natalie S Haddad - Georgia Institute of Technology [Atlanta]
Wilfried Haerty - University of Oxford [Oxford]
Rayna M Harris - University of Texas at Austin [Austin]
Hans A Hofmann - University of Texas at Austin [Austin]
Thibaut Hourlier - Sanger Institute
Gideon Hulata - The Volcani Center
David B Jaffe - Broad Institute of MIT and Harvard
Marcia Lara - Broad Institute of MIT and Harvard
Alison P Lee - Institute of Molecular and Cell Biology
Iain Maccallum - Broad Institute of MIT and Harvard
Salome Mwaiko - Centre of Ecology, Evolution and Biogeochemistry, Department of Fish Ecology and Evolution
Masato Nikaido - Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku
Hidenori Nishihara - Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku
Catherine Ozouf-Costaz - Muséum national d'Histoire naturelle
David J Penman - University of Stirling
Dariusz Przybylski - Broad Institute of MIT and Harvard
Michaelle Rakotomanga - Institut de Génétique et Développement de Rennes
Suzy C. P Renn - Department of Biology, Reed college, Portland, OR, USA
Filipe J Ribeiro - Broad Institute of MIT and Harvard
Micha Ron - The Volcani Center
Walter Salzburger - University of Basel
Luis Sanchez-Pulido - University of Oxford [Oxford]
M. Emilia Santos - University of Basel
Steve Searle - Sanger Institute
Ted Sharpe - Broad Institute of MIT and Harvard
Ross Swofford - Broad Institute of MIT and Harvard
Frederick J Tan - Carnegie Institution for Science [Washington]
Louise Williams - Broad Institute of MIT and Harvard
Sarah Young - Broad Institute of MIT and Harvard
Shuangye Yin - Science for Life Laboratory
Norihiro Okada - National Cheng Kung University
Thomas D Kocher - University of Maryland [College Park]
Eric A Miska - Wellcome Trust/Cancer Research UK Gurdon Institute
Eric S Lander - Broad Institute of MIT and Harvard
Byrappa Venkatesh - Institute of Molecular and Cell Biology
Russell D Fernald - Stanford University
Axel Meyer - Zoology and Evolutionary Biology, Department of Biology
Chris P Ponting - University of Oxford [Oxford]
J. Todd Streelman - Georgia Institute of Technology [Atlanta]
Kerstin Lindblad-Toh - Broad Institute of MIT and Harvard
Ole Seehausen - Centre of Ecology, Evolution and Biogeochemistry, Department of Fish Ecology and Evolution
Federica Di Palma - The Genome Analysis Centre
Publication Details: Nature, Vol.513(7518), pp.375–381-381
Publisher: Nature Publishing Group
Identifiers: 9924012912601921
Academic Unit: Department of Biology
Language: English
Resource Type: Journal article

The genomic substrate for adaptive radiation in African cichlid fish

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