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The genomic substrate for adaptive radiation in African cichlid fish.

  • Brawand D Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
  • Wagner CE Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution & Biogeochemistry, CH-6047 Kastanienbaum, Switzerland.
  • Li YI MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK.
  • Malinsky M Gurdon Institute, Cambridge CB2 1QN, UK.
  • Keller I Division of Aquatic Ecology, Institute of Ecology & Evolution, University of Bern, CH-3012 Bern, Switzerland.
  • Fan S Department of Biology, University of Konstanz, D-78457 Konstanz, Germany.
  • Simakov O Department of Biology, University of Konstanz, D-78457 Konstanz, Germany.
  • Ng AY Institute of Molecular and Cell Biology, ASTAR, 138673 Singapore.
  • Lim ZW Institute of Molecular and Cell Biology, ASTAR, 138673 Singapore.
  • Bezault E Department of Biology, Reed College, Portland, Oregon 97202, USA.
  • Turner-Maier J Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
  • Johnson J Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
  • Alcazar R Biology Department, Stanford University, Stanford, California 94305-5020, USA.
  • Noh HJ Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
  • Russell P Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA.
  • Aken B Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.
  • Alföldi J Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
  • Amemiya C Benaroya Research Institute at Virginia Mason, Seattle, Washington 98101, USA.
  • Azzouzi N Institut Génétique et Développement, CNRS/University of Rennes, 35043 Rennes, France.
  • Baroiller JF CIRAD, Campus International de Baillarguet, TA B-110/A, 34398 Montpellier cedex 5, France.
  • Barloy-Hubler F Institut Génétique et Développement, CNRS/University of Rennes, 35043 Rennes, France.
  • Berlin A Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
  • Bloomquist R School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332-0230, USA.
  • Carleton KL Department of Biology, University of Maryland, College Park, Maryland 20742, USA.
  • Conte MA Department of Biology, University of Maryland, College Park, Maryland 20742, USA.
  • D'Cotta H CIRAD, Campus International de Baillarguet, TA B-110/A, 34398 Montpellier cedex 5, France.
  • Eshel O Animal Genetics, Institute of Animal Science, ARO, The Volcani Center, Bet-Dagan, 50250 Israel.
  • Gaffney L Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
  • Galibert F Institut Génétique et Développement, CNRS/University of Rennes, 35043 Rennes, France.
  • Gante HF Zoological Institute, University of Basel, CH-4051 Basel, Switzerland.
  • Gnerre S Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
  • Greuter L Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution & Biogeochemistry, CH-6047 Kastanienbaum, Switzerland.
  • Guyon R Institut Génétique et Développement, CNRS/University of Rennes, 35043 Rennes, France.
  • Haddad NS School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332-0230, USA.
  • Haerty W MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK.
  • Harris RM Department of Integrative Biology, Center for Computational Biology and Bioinformatics; The University of Texas at Austin, Austin, Texas 78712, USA.
  • Hofmann HA Department of Integrative Biology, Center for Computational Biology and Bioinformatics; The University of Texas at Austin, Austin, Texas 78712, USA.
  • Hourlier T Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.
  • Hulata G Animal Genetics, Institute of Animal Science, ARO, The Volcani Center, Bet-Dagan, 50250 Israel.
  • Jaffe DB Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
  • Lara M Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
  • Lee AP Institute of Molecular and Cell Biology, ASTAR, 138673 Singapore.
  • MacCallum I Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
  • Mwaiko S Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution & Biogeochemistry, CH-6047 Kastanienbaum, Switzerland.
  • Nikaido M Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 226-8501 Yokohama, Japan.
  • Nishihara H Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 226-8501 Yokohama, Japan.
  • Ozouf-Costaz C Systématique, Adaptation, Evolution, National Museum of Natural History, 75005 Paris, France.
  • Penman DJ Institute of Aquaculture, University of Stirling, Stirling FK9 4LA, UK.
  • Przybylski D Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
  • Rakotomanga M Institut Génétique et Développement, CNRS/University of Rennes, 35043 Rennes, France.
  • Renn SCP Department of Biology, Reed College, Portland, Oregon 97202, USA.
  • Ribeiro FJ Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
  • Ron M Animal Genetics, Institute of Animal Science, ARO, The Volcani Center, Bet-Dagan, 50250 Israel.
  • Salzburger W Zoological Institute, University of Basel, CH-4051 Basel, Switzerland.
  • Sanchez-Pulido L MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK.
  • Santos ME Zoological Institute, University of Basel, CH-4051 Basel, Switzerland.
  • Searle S Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.
  • Sharpe T Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
  • Swofford R Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
  • Tan FJ Carnegie Institution of Washington, Department of Embryology, 3520 San Martin Drive Baltimore, Maryland 21218, USA.
  • Williams L Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
  • Young S Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
  • Yin S Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
  • Okada N Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 226-8501 Yokohama, Japan.
  • Kocher TD Department of Biology, University of Maryland, College Park, Maryland 20742, USA.
  • Miska EA Gurdon Institute, Cambridge CB2 1QN, UK.
  • Lander ES Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
  • Venkatesh B Institute of Molecular and Cell Biology, ASTAR, 138673 Singapore.
  • Fernald RD Biology Department, Stanford University, Stanford, California 94305-5020, USA.
  • Meyer A Department of Biology, University of Konstanz, D-78457 Konstanz, Germany.
  • Ponting CP MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK.
  • Streelman JT School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332-0230, USA.
  • Lindblad-Toh K Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
  • Seehausen O Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution & Biogeochemistry, CH-6047 Kastanienbaum, Switzerland.
  • Di Palma F Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
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  • 2014-09-05
Published in:
  • Nature. - 2014
Africa, Eastern
Animals
Cichlids
DNA Transposable Elements
Evolution, Molecular
Gene Duplication
Gene Expression Regulation
Genetic Speciation
Genome
Genomics
Lakes
MicroRNAs
Phylogeny
Polymorphism, Genetic
English 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.
Language
  • English
Open access status
hybrid
Identifiers
Persistent URL
https://folia.unifr.ch/global/documents/157129
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