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Nature. 2014 Sep 18;513(7518):375-81. doi: 10.1038/nature13726. Epub 2014 Sep 3.

The genomic substrate for adaptive radiation in African cichlid fish.

Author information

  • 11] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK [3].
  • 21] Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution &Biogeochemistry, CH-6047 Kastanienbaum, Switzerland [2] Division of Aquatic Ecology, Institute of Ecology &Evolution, University of Bern, CH-3012 Bern, Switzerland [3].
  • 31] MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK [2].
  • 41] Gurdon Institute, Cambridge CB2 1QN, UK [2] Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.
  • 5Division of Aquatic Ecology, Institute of Ecology &Evolution, University of Bern, CH-3012 Bern, Switzerland.
  • 6Department of Biology, University of Konstanz, D-78457 Konstanz, Germany.
  • 71] Department of Biology, University of Konstanz, D-78457 Konstanz, Germany [2] European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
  • 8Institute of Molecular and Cell Biology, A*STAR, 138673 Singapore.
  • 9Department of Biology, Reed College, Portland, Oregon 97202, USA.
  • 10Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
  • 11Biology Department, Stanford University, Stanford, California 94305-5020, USA.
  • 12Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA.
  • 13Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.
  • 14Benaroya Research Institute at Virginia Mason, Seattle, Washington 98101, USA.
  • 15Institut Génétique et Développement, CNRS/University of Rennes, 35043 Rennes, France.
  • 16CIRAD, Campus International de Baillarguet, TA B-110/A, 34398 Montpellier cedex 5, France.
  • 17School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332-0230, USA.
  • 18Department of Biology, University of Maryland, College Park, Maryland 20742, USA.
  • 19Animal Genetics, Institute of Animal Science, ARO, The Volcani Center, Bet-Dagan, 50250 Israel.
  • 20Zoological Institute, University of Basel, CH-4051 Basel, Switzerland.
  • 211] Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution &Biogeochemistry, CH-6047 Kastanienbaum, Switzerland [2] Division of Aquatic Ecology, Institute of Ecology &Evolution, University of Bern, CH-3012 Bern, Switzerland.
  • 22MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK.
  • 23Department of Integrative Biology, Center for Computational Biology and Bioinformatics; The University of Texas at Austin, Austin, Texas 78712, USA.
  • 24Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution &Biogeochemistry, CH-6047 Kastanienbaum, Switzerland.
  • 25Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 226-8501 Yokohama, Japan.
  • 26Systématique, Adaptation, Evolution, National Museum of Natural History, 75005 Paris, France.
  • 27Institute of Aquaculture, University of Stirling, Stirling FK9 4LA, UK.
  • 28Carnegie Institution of Washington, Department of Embryology, 3520 San Martin Drive Baltimore, Maryland 21218, USA.
  • 291] Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 226-8501 Yokohama, Japan [2] National Cheng Kung University, Tainan City, 704 Taiwan.
  • 30Gurdon Institute, Cambridge CB2 1QN, UK.
  • 311] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden.
  • 321] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Vertebrate and Health Genomics, The Genome Analysis Centre, Norwich NR18 7UH, UK.

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.

PMID:
25186727
[PubMed - indexed for MEDLINE]
PMCID:
PMC4353498
Free PMC Article
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