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The genomic substrate for adaptive radiation in African cichlid fish

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 (Oreoc...

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Autores principales: Brawand, David, Wagner, Catherine E., Li, 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, Russell, Pamela, Aken, Bronwen, Alföldi, Jessica, Amemiya, Chris, Azzouzi, Naoual, Baroiller, Jean-François, Barloy-Hubler, Frederique, Berlin, Aaron, Bloomquist, Ryan, Carleton, Karen L., Conte, Matthew A., D'Cotta, Helena, Eshel, Orly, Gaffney, Leslie, Galibert, Francis, Gante, Hugo F., Gnerre, Sante, Greuter, Lucie, Guyon, Richard, Haddad, Natalie S., Haerty, Wilfried, Harris, Rayna M., Hofmann, Hans A., Hourlier, Thibaut, Hulata, Gideon, Jaffe, David B., Lara, Marcia, Lee, Alison P., MacCallum, Iain, Mwaiko, Salome, Nikaido, Masato, Nishihara, Hidenori, Ozouf-Costaz, Catherine, Penman, David J., Przybylski, Dariusz, Rakotomanga, Michaelle, Renn, Suzy C. P., Ribeiro, Filipe J., Ron, Micha, Salzburger, Walter, Sanchez-Pulido, Luis, Santos, M. Emilia, 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, Byrappa, Fernald, Russell D., Meyer, Axel, Ponting, Chris P., Streelman, J. Todd, Lindblad-Toh, Kerstin, Seehausen, Ole, Di Palma, Federica
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4353498/
https://www.ncbi.nlm.nih.gov/pubmed/25186727
http://dx.doi.org/10.1038/nature13726
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author Brawand, David
Wagner, Catherine E.
Li, 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
Russell, Pamela
Aken, Bronwen
Alföldi, Jessica
Amemiya, Chris
Azzouzi, Naoual
Baroiller, Jean-François
Barloy-Hubler, Frederique
Berlin, Aaron
Bloomquist, Ryan
Carleton, Karen L.
Conte, Matthew A.
D'Cotta, Helena
Eshel, Orly
Gaffney, Leslie
Galibert, Francis
Gante, Hugo F.
Gnerre, Sante
Greuter, Lucie
Guyon, Richard
Haddad, Natalie S.
Haerty, Wilfried
Harris, Rayna M.
Hofmann, Hans A.
Hourlier, Thibaut
Hulata, Gideon
Jaffe, David B.
Lara, Marcia
Lee, Alison P.
MacCallum, Iain
Mwaiko, Salome
Nikaido, Masato
Nishihara, Hidenori
Ozouf-Costaz, Catherine
Penman, David J.
Przybylski, Dariusz
Rakotomanga, Michaelle
Renn, Suzy C. P.
Ribeiro, Filipe J.
Ron, Micha
Salzburger, Walter
Sanchez-Pulido, Luis
Santos, M. Emilia
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, Byrappa
Fernald, Russell D.
Meyer, Axel
Ponting, Chris P.
Streelman, J. Todd
Lindblad-Toh, Kerstin
Seehausen, Ole
Di Palma, Federica
author_facet Brawand, David
Wagner, Catherine E.
Li, 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
Russell, Pamela
Aken, Bronwen
Alföldi, Jessica
Amemiya, Chris
Azzouzi, Naoual
Baroiller, Jean-François
Barloy-Hubler, Frederique
Berlin, Aaron
Bloomquist, Ryan
Carleton, Karen L.
Conte, Matthew A.
D'Cotta, Helena
Eshel, Orly
Gaffney, Leslie
Galibert, Francis
Gante, Hugo F.
Gnerre, Sante
Greuter, Lucie
Guyon, Richard
Haddad, Natalie S.
Haerty, Wilfried
Harris, Rayna M.
Hofmann, Hans A.
Hourlier, Thibaut
Hulata, Gideon
Jaffe, David B.
Lara, Marcia
Lee, Alison P.
MacCallum, Iain
Mwaiko, Salome
Nikaido, Masato
Nishihara, Hidenori
Ozouf-Costaz, Catherine
Penman, David J.
Przybylski, Dariusz
Rakotomanga, Michaelle
Renn, Suzy C. P.
Ribeiro, Filipe J.
Ron, Micha
Salzburger, Walter
Sanchez-Pulido, Luis
Santos, M. Emilia
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, Byrappa
Fernald, Russell D.
Meyer, Axel
Ponting, Chris P.
Streelman, J. Todd
Lindblad-Toh, Kerstin
Seehausen, Ole
Di Palma, Federica
author_sort Brawand, David
collection PubMed
description 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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spelling pubmed-43534982015-03-18 The genomic substrate for adaptive radiation in African cichlid fish Brawand, David Wagner, Catherine E. Li, 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 Russell, Pamela Aken, Bronwen Alföldi, Jessica Amemiya, Chris Azzouzi, Naoual Baroiller, Jean-François Barloy-Hubler, Frederique Berlin, Aaron Bloomquist, Ryan Carleton, Karen L. Conte, Matthew A. D'Cotta, Helena Eshel, Orly Gaffney, Leslie Galibert, Francis Gante, Hugo F. Gnerre, Sante Greuter, Lucie Guyon, Richard Haddad, Natalie S. Haerty, Wilfried Harris, Rayna M. Hofmann, Hans A. Hourlier, Thibaut Hulata, Gideon Jaffe, David B. Lara, Marcia Lee, Alison P. MacCallum, Iain Mwaiko, Salome Nikaido, Masato Nishihara, Hidenori Ozouf-Costaz, Catherine Penman, David J. Przybylski, Dariusz Rakotomanga, Michaelle Renn, Suzy C. P. Ribeiro, Filipe J. Ron, Micha Salzburger, Walter Sanchez-Pulido, Luis Santos, M. Emilia 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, Byrappa Fernald, Russell D. Meyer, Axel Ponting, Chris P. Streelman, J. Todd Lindblad-Toh, Kerstin Seehausen, Ole Di Palma, Federica Nature Article 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. 2014-09-03 2014-09-18 /pmc/articles/PMC4353498/ /pubmed/25186727 http://dx.doi.org/10.1038/nature13726 Text en 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 Reprints and permissions information is available at www.nature.com/reprints (http://www.nature.com/reprints) .
spellingShingle Article
Brawand, David
Wagner, Catherine E.
Li, 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
Russell, Pamela
Aken, Bronwen
Alföldi, Jessica
Amemiya, Chris
Azzouzi, Naoual
Baroiller, Jean-François
Barloy-Hubler, Frederique
Berlin, Aaron
Bloomquist, Ryan
Carleton, Karen L.
Conte, Matthew A.
D'Cotta, Helena
Eshel, Orly
Gaffney, Leslie
Galibert, Francis
Gante, Hugo F.
Gnerre, Sante
Greuter, Lucie
Guyon, Richard
Haddad, Natalie S.
Haerty, Wilfried
Harris, Rayna M.
Hofmann, Hans A.
Hourlier, Thibaut
Hulata, Gideon
Jaffe, David B.
Lara, Marcia
Lee, Alison P.
MacCallum, Iain
Mwaiko, Salome
Nikaido, Masato
Nishihara, Hidenori
Ozouf-Costaz, Catherine
Penman, David J.
Przybylski, Dariusz
Rakotomanga, Michaelle
Renn, Suzy C. P.
Ribeiro, Filipe J.
Ron, Micha
Salzburger, Walter
Sanchez-Pulido, Luis
Santos, M. Emilia
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, Byrappa
Fernald, Russell D.
Meyer, Axel
Ponting, Chris P.
Streelman, J. Todd
Lindblad-Toh, Kerstin
Seehausen, Ole
Di Palma, Federica
The genomic substrate for adaptive radiation in African cichlid fish
title The genomic substrate for adaptive radiation in African cichlid fish
title_full The genomic substrate for adaptive radiation in African cichlid fish
title_fullStr The genomic substrate for adaptive radiation in African cichlid fish
title_full_unstemmed The genomic substrate for adaptive radiation in African cichlid fish
title_short The genomic substrate for adaptive radiation in African cichlid fish
title_sort genomic substrate for adaptive radiation in african cichlid fish
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4353498/
https://www.ncbi.nlm.nih.gov/pubmed/25186727
http://dx.doi.org/10.1038/nature13726
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