The genomic substrate for adaptive radiation in African cichlid fish

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Brawand, David (author)

The genomic substrate for adaptive radiation in African cichlid fish

Article/chapterEnglish2014

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2014-09-03
Springer Science and Business Media LLC,2014
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LIBRIS-ID:oai:DiVA.org:uu-235066
https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-235066URI
https://doi.org/10.1038/nature13726DOI

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Language:English
Summary in:English

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Subject category:art swepub-publicationtype

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De tre sista författarna delar sistaförfattarskapet.
Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand themolecular 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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Wagner, Catherine E. (author)
Li, Yang I. (author)
Malinsky, Milan (author)
Keller, Irene (author)
Fan, Shaohua (author)
Simakov, Oleg (author)
Ng, Alvin Y. (author)
Lim, Zhi Wei (author)
Bezault, Etienne (author)
Turner-Maier, Jason (author)
Johnson, Jeremy (author)
Alcazar, Rosa (author)
Noh, Hyun Ji (author)
Russell, Pamela (author)
Aken, Bronwen (author)
Alfoeldi, Jessica (author)
Amemiya, Chris (author)
Azzouzi, Naoual (author)
Baroiller, Jean-Francois (author)
Barloy-Hubler, Frederique (author)
Berlin, Aaron (author)
Bloomquist, Ryan (author)
Carleton, Karen L. (author)
Conte, Matthew A. (author)
D'Cotta, Helena (author)
Eshel, Orly (author)
Gaffney, Leslie (author)
Galibert, Francis (author)
Gante, Hugo F. (author)
Gnerre, Sante (author)
Greuter, Lucie (author)
Guyon, Richard (author)
Haddad, Natalie S. (author)
Haerty, Wilfried (author)
Harris, Rayna M. (author)
Hofmann, Hans A. (author)
Hourlier, Thibaut (author)
Hulata, Gideon (author)
Jaffe, David B. (author)
Lara, Marcia (author)
Lee, Alison P. (author)
MacCallum, Iain (author)
Mwaiko, Salome (author)
Nikaido, Masato (author)
Nishihara, Hidenori (author)
Ozouf-Costaz, Catherine (author)
Penman, David J. (author)
Przybylski, Dariusz (author)
Rakotomanga, Michaelle (author)
Renn, Suzy C. P. (author)
Ribeiro, Filipe J. (author)
Ron, Micha (author)
Salzburger, Walter (author)
Sanchez-Pulido, Luis (author)
Santos, M. Emilia (author)
Searle, Steve (author)
Sharpe, Ted (author)
Swofford, Ross (author)
Tan, Frederick J. (author)
Williams, Louise (author)
Young, Sarah (author)
Yin, Shuangye (author)
Okada, Norihiro (author)
Kocher, Thomas D. (author)
Miska, Eric A. (author)
Lander, Eric S. (author)
Venkatesh, Byrappa (author)
Fernald, Russell D. (author)
Meyer, Axel (author)
Ponting, Chris P. (author)
Streelman, J. Todd (author)
Lindblad-Toh, KerstinUppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi,Science for Life Laboratory, SciLifeLab(Swepub:uu)kerli865 (author)
Seehausen, Ole (author)
Di Palma, Federica (author)
Uppsala universitetInstitutionen för medicinsk biokemi och mikrobiologi (creator_code:org_t)

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In:Nature: Springer Science and Business Media LLC513:7518, s. 375-3810028-08361476-4687

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By the author/editor: Brawand, David; Wagner, Catherin ...; Li, Yang I.; Malinsky, Milan; Keller, Irene; Fan, Shaohua; show more...; Simakov, Oleg; Ng, Alvin Y.; Lim, Zhi Wei; Bezault, Etienne; Turner-Maier, Ja ...; Johnson, Jeremy; Alcazar, Rosa; Noh, Hyun Ji; Russell, Pamela; Aken, Bronwen; Alfoeldi, Jessic ...; Amemiya, Chris; Azzouzi, Naoual; Baroiller, Jean- ...; Barloy-Hubler, F ...; Berlin, Aaron; Bloomquist, Ryan; Carleton, Karen ...; Conte, Matthew A ...; D'Cotta, Helena; Eshel, Orly; Gaffney, Leslie; Galibert, Franci ...; Gante, Hugo F.; Gnerre, Sante; Greuter, Lucie; Guyon, Richard; Haddad, Natalie ...; Haerty, Wilfried; Harris, Rayna M.; Hofmann, Hans A.; Hourlier, Thibau ...; Hulata, Gideon; Jaffe, David B.; Lara, Marcia; Lee, Alison P.; MacCallum, Iain; Mwaiko, Salome; Nikaido, Masato; Nishihara, Hiden ...; Ozouf-Costaz, Ca ...; Penman, David J.; Przybylski, Dari ...; Rakotomanga, Mic ...; Renn, Suzy C. P.; Ribeiro, Filipe ...; Ron, Micha; Salzburger, Walt ...; Sanchez-Pulido, ...; Santos, M. Emili ...; Searle, Steve; Sharpe, Ted; Swofford, Ross; Tan, Frederick J ...; Williams, Louise; Young, Sarah; Yin, Shuangye; Okada, Norihiro; Kocher, Thomas D ...; Miska, Eric A.; Lander, Eric S.; Venkatesh, Byrap ...; Fernald, Russell ...; Meyer, Axel; Ponting, Chris P ...; Streelman, J. To ...; Lindblad-Toh, Ke ...; Seehausen, Ole; Di Palma, Federi ...; show less...

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