The genomic substrate for adaptive radiation in African cichlid fish

Brawand, David and Wagner, Catherine E. and Li, Yang I. and Malinsky, Milan and Keller, Irene and Fan, Shaohua and Simakov, Oleg and Ng, Alvin Y. and Lim, Zhi Wei and Bezault, Etienne and Turner-Maier, Jason and Johnson, Jeremy and Alcazar, Rosa and Noh, Hyun Ji and Russell, Pamela and Aken, Bronwen and Alföldi, Jessica and Amemiya, Chris and Azzouzi, Naoual and Baroiller, Jean-François and Barloy-Hubler, Frederique and Berlin, Aaron and Bloomquist, Ryan and Carleton, Karen L. and Conte, Matthew A. and D'Cotta, Helena and Eshel, Orly and Gaffney, Leslie and Galibert, Francis and Gante, Hugo F. and Gnerre, Sante and Greuter, Lucie and Guyon, Richard and Haddad, Natalie S. and Haerty, Wilfried and Harris, Rayna M. and Hofmann, Hans A. and Hourlier, Thibaut and Hulata, Gideon and Jaffe, David B. and Lara, Marcia and Lee, Alison P. and MacCallum, Iain and Mwaiko, Salome and Nikaido, Masato and Nishihara, Hidenori and Ozouf-Costaz, Catherine and Penman, David J. and Przybylski, Dariusz and Rakotomanga, Michaelle and Renn, Suzy C. P. and Ribeiro, Filipe J. and Ron, Micha and Salzburger, Walter and Sanchez-Pulido, Luis and Santos, M. Emilia and Searle, Steve and Sharpe, Ted and Swofford, Ross and Tan, Frederick J. and Williams, Louise and Young, Sarah and Yin, Shuangye and Okada, Norihiro and Kocher, Thomas D. and Miska, Eric A. and Lander, Eric S. and Venkatesh, Byrappa and Fernald, Russell D. and Meyer, Axel and Ponting, Chris P. and Streelman, J. Todd and Lindblad-Toh, Kerstin and Seehausen, Ole and Di Palma, Federica. (2014) The genomic substrate for adaptive radiation in African cichlid fish. Nature, Vol. 513, H. 7518. pp. 375-381.

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Official URL: http://edoc.unibas.ch/dok/A6338931

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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.

Faculties and Departments:	05 Faculty of Science > Departement Umweltwissenschaften > Integrative Biologie > Evolutionary Biology (Salzburger)
UniBasel Contributors:	Salzburger, Walter
Item Type:	Article, refereed
Article Subtype:	Research Article
Publisher:	Macmillan
ISSN:	0028-0836
Note:	Publication type according to Uni Basel Research Database: Journal article
Related URLs:	Document Document
Identification Number:	pmid: 25186727 doi: 10.1038/nature13726
Last Modified:	07 Aug 2015 12:06
Deposited On:	07 Aug 2015 12:06

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