The genomic substrate for adaptive radiation in African cichlid fish

David Brawand 1, 2 Catherine E. Wagner 3 Yang I. Li 1 Milan Malinsky 4, 5 Irene Keller 6 Shaohua Fan 7 Oleg Simakov 8, 7 Alvin Y. Ng 9 Zhi Wei Lim 9 Etienne Bezault 10 Jason Turner-Maier 2 Jeremy Johnson 2 Rosa Alcazar 11 Hyun Ji Noh 2 Pamela Russell 12 Bronwen Aken 4 Jessica Alföldi 2 Chris Amemiya 13 Naoual Azzouzi 14 Jean-François Baroiller 15 Frederique Barloy-Hubler 14 Aaron Berlin 2 Ryan Bloomquist 16 Karen L. Carleton 17 Matthew A. Conte 17 Helena D'Cotta 15 Orly Eshel 18 Leslie Gaffney 2 Francis Galibert 14 Hugo F. Gante 19 Sante Gnerre 2 Lucie Greuter 3 Richard Guyon 14 Natalie S. Haddad 16 Wilfried Haerty 1 Rayna M. Harris 20 Hans A. Hofmann 20 Thibaut Hourlier 4 Gideon Hulata 18 David B. Jaffe 2 Marcia Lara 2 Alison P. Lee 9 Iain Maccallum 2 Salome Mwaiko 3 Masato Nikaido 21 Hidenori Nishihara 21 Catherine Ozouf-Costaz 22 David J. Penman 23 Dariusz Przybylski 2 Michaelle Rakotomanga 14 Suzy C. P. Renn 10 Filipe J. Ribeiro 2 Micha Ron 18 Walter Salzburger 19 Luis Sanchez-Pulido 1 M. Emilia Santos 19 Steve Searle 4 Ted Sharpe 2 Ross Swofford 2 Frederick J. Tan 24 Louise Williams 2 Sarah Young 2 Shuangye Yin 25 Norihiro Okada 26, 21 Thomas D. Kocher 17 Eric A. Miska 5 Eric S. Lander 2 Byrappa Venkatesh 9 Russell D. Fernald 11 Axel Meyer 7 Chris P. Ponting 1 J. Todd Streelman 16 Kerstin Lindblad-Toh 2, 25 Ole Seehausen 3, 6 Federica Di Palma 27, 2
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.
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Nature, Nature Publishing Group, 2014, 513, pp.375-381. 〈10.1038/nature13726〉
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David Brawand, Catherine E. Wagner, Yang I. Li, Milan Malinsky, Irene Keller, et al.. The genomic substrate for adaptive radiation in African cichlid fish. Nature, Nature Publishing Group, 2014, 513, pp.375-381. 〈10.1038/nature13726〉. 〈hal-01064590〉

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