The genomic substrate for adaptive radiation in African cichlid fish
| Autor: | Alison P. Lee, Michaelle Rakotomanga, Jeremy A. Johnson, Hidenori Nishihara, Frederick J. Tan, Jessica Alföldi, Alvin Yu Jin Ng, Naoual Azzouzi, Byrappa Venkatesh, Steve Searle, Orly Eshel, Bronwen Aken, Ted Sharpe, Thomas D. Kocher, Gideon Hulata, Filipe J. Ribeiro, Eric S. Lander, Norihiro Okada, Wilfried Haerty, Thibaut Hourlier, Natalie S. Haddad, Marcia Lara, Rosa Alcazar, Karen L. Carleton, Catherine E. Wagner, Federica Di Palma, M. Emília Santos, Masato Nikaido, Eric A. Miska, Salome Mwaiko, Axel Meyer, Frédérique Barloy-Hubler, Leslie Gaffney, Sante Gnerre, David B. Jaffe, Jason Turner-Maier, David Brawand, Oleg Simakov, Lucie Greuter, Helena D'Cotta, Milan Malinsky, Iain MacCallum, Hyun Ji Noh, Shuangye Yin, Luis Sanchez-Pulido, Jean-François Baroiller, Shaohua Fan, David J. Penman, Ryan F. Bloomquist, Ross Swofford, Matthew A. Conte, Chris P. Ponting, Chris T. Amemiya, J. Todd Streelman, Richard Guyon, Hugo F. Gante, Dariusz Przybylski, Robert M Harris, Walter Salzburger, Irene Keller, Francis Galibert, Russell D. Fernald, Aaron M. Berlin, Yang I. Li, Pamela Russell, Hans A. Hofmann, Ole Seehausen, Suzy C. P. Renn, Louise Williams, Micha Ron, Kerstin Lindblad-Toh, Zhi Wei Lim, Catherine Ozouf-Costaz, Etienne Bezault, Sarah Young |
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| Přispěvatelé: | University of Oxford [Oxford], Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Centre of Ecology, Evolution and Biogeochemistry, Department of Fish Ecology and Evolution, Swiss Federal Institute for Environmental Science and Technology, Sanger Institute, Welcome Trust, Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge [UK] (CAM), Institute of Zoology, University of Bern, Université de Bern, Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, EMBL Heidelberg, Institute of Molecular and Cell Biology, Singapour, Department of Biology, Reed college, Portland, OR, USA, Stanford University, California Institute of Technology (CALTECH), Benaroya Research Institute, Virginia Mason, Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Intensification raisonnée et écologique pour une pisciculture durable (UMR INTREPID), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Georgia Institute of Technology [Atlanta], University of Maryland [College Park], University of Maryland System, The Volcani Center, University of Basel (Unibas), University of Texas at Austin [Austin], Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku, Tokyo Institute of Technology [Tokyo] (TITECH), Muséum national d'Histoire naturelle (MNHN), University of Stirling, Carnegie Institution for Science [Washington], Science for Life Laboratory, Uppsala University-Department of Medical Biochemistry and Microbiology, National Cheng Kung University (NCKU), The Genome Analysis Centre (TGAC), Sequencing, assembly, annotation and analysis by Broad Institute were supported by grants from the National Human Genome Research Institute (NHGRI). Genome evolution, duplication and TE analysis, ILS and ancient variant analyses were also supported by Swiss National Science Foundation grant PBLAP3-142774 awarded to D.B. and by University of Oxford Nuffield Department of Medicine Prize Studentship to Y.I.L. TE and copy number variation analyses were supported by the German Science Foundation (DFG), and advanced grant 29700 ('GenAdap') by the European Research Council (ERC). CNE analysis and zebrafish functional assays were supported by the Biomedical Research Council of A*STAR, Singapore. MicroRNA sequencing and annotation was supported by ERC Starting Grant to E.A.M., M.M. was supported by a fellowship from the Wellcome Trust. MicroRNA and target in situ hybridization was supported by grant 2R01DE019637-04 to J.T.S. Population genomics analyses were supported by Swiss National Science Foundation grants 31003A-118293 and 31003A-144046 to O.S., Massachusetts Institute of Technology. Department of Biology, Lander, Eric S., University of Oxford, Universität Bern [Bern] (UNIBE), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Carnegie Institution for Science, Jonchère, Laurent |
| Rok vydání: | 2014 |
| Předmět: |
Phylogénie
Astatotilapia burtoni Polymorphisme génétique Lineage (evolution) Évolution Evolutionary biology [SDV.GEN] Life Sciences [q-bio]/Genetics Eastern Nile tilapia Adaptive radiation Gene Duplication Phylogeny Multidisciplinary Genome Oreochromis niloticus Tilapia Cichlids Genomics Cichlidae Africa Eastern Oreochromis Genome evolution Evolution Comparative genomics Evolutionary biology Neolamprologus Séquence nucléotidique food.ingredient Evolution Genetic Speciation General Science & Technology 1.1 Normal biological development and functioning Cours d'eau Zoology Biology Evolution Molecular food Genetic Cichlid Underpinning research ddc:570 Genetics Animals 14. Life underwater Adaptation Polymorphism Génie génétique Lac [SDV.GEN]Life Sciences [q-bio]/Genetics Génome Polymorphism Genetic Comparative genomics Human Genome L60 - Taxonomie et géographie animales Molecular L10 - Génétique et amélioration des animaux biology.organism_classification Genome evolution M01 - Pêche et aquaculture - Considérations générales MicroRNAs Lakes Gene Expression Regulation Africa DNA Transposable Elements 570 Life sciences biology human activities |
| Zdroj: | Nature, vol 513, iss 7518 Nature Nature, Nature Publishing Group, 2014, 513 (7518), pp.375-381. ⟨10.1038/nature13726⟩ PMC Nature, 2014, 513 (7518), pp.375-381. ⟨10.1038/nature13726⟩ Brawand, David; Wagner, Catherine; 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; ... (2014). The genomic substrate for adaptive radiation in African cichlid fish. Nature, 513(7518), pp. 375-381. Macmillan Journals Ltd. 10.1038/nature13726 |
| ISSN: | 0028-0836 1476-4679 1476-4687 |
| DOI: | 10.1038/nature13726⟩ |
| Popis: | CC-BY-NC-SA; International audience; 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. |
| Databáze: | OpenAIRE |
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