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The genomic substrate for adaptive radiation in African cichlid fish
Year:
2014
Source of publication :
Nature
Authors :
Eshel, Orly
;
.
Hulata, Gideon
;
.
Ron, Micha
;
.
Volume :
513
Co-Authors:
Brawand, D., Broad Institute of MIT and Harvard, Cambridge, MA, United States, MRC Functional Genomics Unit, University of Oxford, Oxford, United Kingdom
Wagner, C.E., Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland, Division of Aquatic Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
Li, Y.I., MRC Functional Genomics Unit, University of Oxford, Oxford, United Kingdom
Malinsky, M., Gurdon Institute, Cambridge, United Kingdom, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
Keller, I., Division of Aquatic Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
Fan, S., Department of Biology, University of Konstanz, Konstanz, Germany
Simakov, O., Department of Biology, University of Konstanz, Konstanz, Germany, European Molecular Biology Laboratory, Heidelberg, Germany
Ng, A.Y., Institute of Molecular and Cell Biology, ASTAR, Singapore, Singapore
Lim, Z.W., Institute of Molecular and Cell Biology, ASTAR, Singapore, Singapore
Bezault, E., Department of Biology, Reed College, Portland, OR, United States
Turner-Maier, J., Broad Institute of MIT and Harvard, Cambridge, MA, United States
Johnson, J., Broad Institute of MIT and Harvard, Cambridge, MA, United States
Alcazar, R., Biology Department, Stanford University, Stanford, CA, United States
Noh, H.J., Broad Institute of MIT and Harvard, Cambridge, MA, United States
Russell, P., Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
Aken, B., Wellcome Trust Sanger Institute, Hinxton, United Kingdom
Alföldi, J., Broad Institute of MIT and Harvard, Cambridge, MA, United States
Amemiya, C., Benaroya Research Institute at Virginia Mason, Seattle, WA, United States
Azzouzi, N., Institut Génétique et Développement, CNRS/University of Rennes, Rennes, France
Baroiller, J.-F., CIRAD, Campus International de Baillarguet, TA B-110/A, Montpellier Cedex 5, France
Barloy-Hubler, F., Institut Génétique et Développement, CNRS/University of Rennes, Rennes, France
Berlin, A., Broad Institute of MIT and Harvard, Cambridge, MA, United States
Bloomquist, R., School of Biology, Georgia Institute of Technology, Atlanta, GA, United States
Carleton, K.L., Department of Biology, University of Maryland, College Park, MD, United States
Conte, M.A., Department of Biology, University of Maryland, College Park, MD, United States
D'Cotta, H., CIRAD, Campus International de Baillarguet, TA B-110/A, Montpellier Cedex 5, France
Eshel, O., Animal Genetics, Institute of Animal Science, Volcani Center, Bet-Dagan, Israel
Gaffney, L., Broad Institute of MIT and Harvard, Cambridge, MA, United States
Galibert, F., Institut Génétique et Développement, CNRS/University of Rennes, Rennes, France
Gante, H.F., Zoological Institute, University of Basel, Basel, Switzerland
Gnerre, S., Broad Institute of MIT and Harvard, Cambridge, MA, United States
Greuter, L., Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland, Division of Aquatic Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
Guyon, R., Institut Génétique et Développement, CNRS/University of Rennes, Rennes, France
Haddad, N.S., School of Biology, Georgia Institute of Technology, Atlanta, GA, United States
Haerty, W., MRC Functional Genomics Unit, University of Oxford, Oxford, United Kingdom
Harris, R.M., Department of Integrative Biology, Center for Computational Biology and Bioinformatics, University of Texas at Austin, Austin, TX, United States
Hofmann, H.A., Department of Integrative Biology, Center for Computational Biology and Bioinformatics, University of Texas at Austin, Austin, TX, United States
Hourlier, T., Wellcome Trust Sanger Institute, Hinxton, United Kingdom
Hulata, G., Animal Genetics, Institute of Animal Science, Volcani Center, Bet-Dagan, Israel
Jaffe, D.B., Broad Institute of MIT and Harvard, Cambridge, MA, United States
Lara, M., Broad Institute of MIT and Harvard, Cambridge, MA, United States
Lee, A.P., Institute of Molecular and Cell Biology, ASTAR, Singapore, Singapore
MacCallum, I., Broad Institute of MIT and Harvard, Cambridge, MA, United States
Mwaiko, S., Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland
Nikaido, M., Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, Yokohama, Japan
Nishihara, H., Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, Yokohama, Japan
Ozouf-Costaz, C., Systématique, Adaptation, Evolution, National Museum of Natural History, Paris, France
Penman, D.J., Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
Przybylski, D., Broad Institute of MIT and Harvard, Cambridge, MA, United States
Rakotomanga, M., Institut Génétique et Développement, CNRS/University of Rennes, Rennes, France
Renn, S.C.P., Department of Biology, Reed College, Portland, OR, United States
Ribeiro, F.J., Broad Institute of MIT and Harvard, Cambridge, MA, United States
Ron, M., Animal Genetics, Institute of Animal Science, Volcani Center, Bet-Dagan, Israel
Salzburger, W., Zoological Institute, University of Basel, Basel, Switzerland
Sanchez-Pulido, L., MRC Functional Genomics Unit, University of Oxford, Oxford, United Kingdom
Santos, M.E., Zoological Institute, University of Basel, Basel, Switzerland
Searle, S., Wellcome Trust Sanger Institute, Hinxton, United Kingdom
Sharpe, T., Broad Institute of MIT and Harvard, Cambridge, MA, United States
Swofford, R., Broad Institute of MIT and Harvard, Cambridge, MA, United States
Tan, F.J., Carnegie Institution of Washington, Department of Embryology, 3520 San Martin Drive, Baltimore, MD, United States
Williams, L., Broad Institute of MIT and Harvard, Cambridge, MA, United States
Young, S., Broad Institute of MIT and Harvard, Cambridge, MA, United States
Yin, S., Broad Institute of MIT and Harvard, Cambridge, MA, United States
Okada, N., Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, Yokohama, Japan, National Cheng Kung University, Tainan City, Taiwan
Kocher, T.D., Department of Biology, University of Maryland, College Park, MD, United States
Miska, E.A., Gurdon Institute, Cambridge, United Kingdom
Lander, E.S., Broad Institute of MIT and Harvard, Cambridge, MA, United States
Venkatesh, B., Institute of Molecular and Cell Biology, ASTAR, Singapore, Singapore
Fernald, R.D., Biology Department, Stanford University, Stanford, CA, United States
Meyer, A., Department of Biology, University of Konstanz, Konstanz, Germany
Ponting, C.P., MRC Functional Genomics Unit, University of Oxford, Oxford, United Kingdom
Streelman, J.T., School of Biology, Georgia Institute of Technology, Atlanta, GA, United States
Lindblad-Toh, K., Broad Institute of MIT and Harvard, Cambridge, MA, United States, Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
Seehausen, O., Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland, Division of Aquatic Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
Di Palma, F., Broad Institute of MIT and Harvard, Cambridge, MA, United States, Vertebrate and Health Genomics, Genome Analysis Centre, Norwich, United Kingdom
Facilitators :
From page:
375
To page:
381
(
Total pages:
7
)
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. ©2014 Macmillan Publishers Limited. All rights reserved.
Note:
Related Files :
Animal
Animals
gene expression
Genetics
Genome
genomics
Molecular Evolution
Oreochromis niloticus
phenotype
Tilapia
Show More
Related Content
More details
DOI :
10.1038/nature13726
Article number:
Affiliations:
Database:
Scopus
Publication Type:
article
;
.
Language:
English
Editors' remarks:
ID:
32792
Last updated date:
02/03/2022 17:27
Creation date:
17/04/2018 01:12
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Scientific Publication
The genomic substrate for adaptive radiation in African cichlid fish
513
Brawand, D., Broad Institute of MIT and Harvard, Cambridge, MA, United States, MRC Functional Genomics Unit, University of Oxford, Oxford, United Kingdom
Wagner, C.E., Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland, Division of Aquatic Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
Li, Y.I., MRC Functional Genomics Unit, University of Oxford, Oxford, United Kingdom
Malinsky, M., Gurdon Institute, Cambridge, United Kingdom, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
Keller, I., Division of Aquatic Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
Fan, S., Department of Biology, University of Konstanz, Konstanz, Germany
Simakov, O., Department of Biology, University of Konstanz, Konstanz, Germany, European Molecular Biology Laboratory, Heidelberg, Germany
Ng, A.Y., Institute of Molecular and Cell Biology, ASTAR, Singapore, Singapore
Lim, Z.W., Institute of Molecular and Cell Biology, ASTAR, Singapore, Singapore
Bezault, E., Department of Biology, Reed College, Portland, OR, United States
Turner-Maier, J., Broad Institute of MIT and Harvard, Cambridge, MA, United States
Johnson, J., Broad Institute of MIT and Harvard, Cambridge, MA, United States
Alcazar, R., Biology Department, Stanford University, Stanford, CA, United States
Noh, H.J., Broad Institute of MIT and Harvard, Cambridge, MA, United States
Russell, P., Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
Aken, B., Wellcome Trust Sanger Institute, Hinxton, United Kingdom
Alföldi, J., Broad Institute of MIT and Harvard, Cambridge, MA, United States
Amemiya, C., Benaroya Research Institute at Virginia Mason, Seattle, WA, United States
Azzouzi, N., Institut Génétique et Développement, CNRS/University of Rennes, Rennes, France
Baroiller, J.-F., CIRAD, Campus International de Baillarguet, TA B-110/A, Montpellier Cedex 5, France
Barloy-Hubler, F., Institut Génétique et Développement, CNRS/University of Rennes, Rennes, France
Berlin, A., Broad Institute of MIT and Harvard, Cambridge, MA, United States
Bloomquist, R., School of Biology, Georgia Institute of Technology, Atlanta, GA, United States
Carleton, K.L., Department of Biology, University of Maryland, College Park, MD, United States
Conte, M.A., Department of Biology, University of Maryland, College Park, MD, United States
D'Cotta, H., CIRAD, Campus International de Baillarguet, TA B-110/A, Montpellier Cedex 5, France
Eshel, O., Animal Genetics, Institute of Animal Science, Volcani Center, Bet-Dagan, Israel
Gaffney, L., Broad Institute of MIT and Harvard, Cambridge, MA, United States
Galibert, F., Institut Génétique et Développement, CNRS/University of Rennes, Rennes, France
Gante, H.F., Zoological Institute, University of Basel, Basel, Switzerland
Gnerre, S., Broad Institute of MIT and Harvard, Cambridge, MA, United States
Greuter, L., Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland, Division of Aquatic Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
Guyon, R., Institut Génétique et Développement, CNRS/University of Rennes, Rennes, France
Haddad, N.S., School of Biology, Georgia Institute of Technology, Atlanta, GA, United States
Haerty, W., MRC Functional Genomics Unit, University of Oxford, Oxford, United Kingdom
Harris, R.M., Department of Integrative Biology, Center for Computational Biology and Bioinformatics, University of Texas at Austin, Austin, TX, United States
Hofmann, H.A., Department of Integrative Biology, Center for Computational Biology and Bioinformatics, University of Texas at Austin, Austin, TX, United States
Hourlier, T., Wellcome Trust Sanger Institute, Hinxton, United Kingdom
Hulata, G., Animal Genetics, Institute of Animal Science, Volcani Center, Bet-Dagan, Israel
Jaffe, D.B., Broad Institute of MIT and Harvard, Cambridge, MA, United States
Lara, M., Broad Institute of MIT and Harvard, Cambridge, MA, United States
Lee, A.P., Institute of Molecular and Cell Biology, ASTAR, Singapore, Singapore
MacCallum, I., Broad Institute of MIT and Harvard, Cambridge, MA, United States
Mwaiko, S., Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland
Nikaido, M., Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, Yokohama, Japan
Nishihara, H., Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, Yokohama, Japan
Ozouf-Costaz, C., Systématique, Adaptation, Evolution, National Museum of Natural History, Paris, France
Penman, D.J., Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
Przybylski, D., Broad Institute of MIT and Harvard, Cambridge, MA, United States
Rakotomanga, M., Institut Génétique et Développement, CNRS/University of Rennes, Rennes, France
Renn, S.C.P., Department of Biology, Reed College, Portland, OR, United States
Ribeiro, F.J., Broad Institute of MIT and Harvard, Cambridge, MA, United States
Ron, M., Animal Genetics, Institute of Animal Science, Volcani Center, Bet-Dagan, Israel
Salzburger, W., Zoological Institute, University of Basel, Basel, Switzerland
Sanchez-Pulido, L., MRC Functional Genomics Unit, University of Oxford, Oxford, United Kingdom
Santos, M.E., Zoological Institute, University of Basel, Basel, Switzerland
Searle, S., Wellcome Trust Sanger Institute, Hinxton, United Kingdom
Sharpe, T., Broad Institute of MIT and Harvard, Cambridge, MA, United States
Swofford, R., Broad Institute of MIT and Harvard, Cambridge, MA, United States
Tan, F.J., Carnegie Institution of Washington, Department of Embryology, 3520 San Martin Drive, Baltimore, MD, United States
Williams, L., Broad Institute of MIT and Harvard, Cambridge, MA, United States
Young, S., Broad Institute of MIT and Harvard, Cambridge, MA, United States
Yin, S., Broad Institute of MIT and Harvard, Cambridge, MA, United States
Okada, N., Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, Yokohama, Japan, National Cheng Kung University, Tainan City, Taiwan
Kocher, T.D., Department of Biology, University of Maryland, College Park, MD, United States
Miska, E.A., Gurdon Institute, Cambridge, United Kingdom
Lander, E.S., Broad Institute of MIT and Harvard, Cambridge, MA, United States
Venkatesh, B., Institute of Molecular and Cell Biology, ASTAR, Singapore, Singapore
Fernald, R.D., Biology Department, Stanford University, Stanford, CA, United States
Meyer, A., Department of Biology, University of Konstanz, Konstanz, Germany
Ponting, C.P., MRC Functional Genomics Unit, University of Oxford, Oxford, United Kingdom
Streelman, J.T., School of Biology, Georgia Institute of Technology, Atlanta, GA, United States
Lindblad-Toh, K., Broad Institute of MIT and Harvard, Cambridge, MA, United States, Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
Seehausen, O., Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland, Division of Aquatic Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
Di Palma, F., Broad Institute of MIT and Harvard, Cambridge, MA, United States, Vertebrate and Health Genomics, Genome Analysis Centre, Norwich, United Kingdom
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 (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 Macmillan Publishers Limited. All rights reserved.
Scientific Publication
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