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Brawand D, Wagner CE, Li YI, Malinsky M, Keller I, Fan S, Simakov O, Ng AY, Lim ZW, Bezault E, Turner-Maier J, Johnson J, Alcazar R, Noh HJ, Russell P, Aken B, Alföldi J, Amemiya C, Azzouzi N, Baroiller JF, Barloy-Hubler F, Berlin A, Bloomquist R, Carleton KL, Conte MA, D'Cotta H, Eshel O, Gaffney L, Galibert F, Gante HF, Gnerre S, Greuter L, Guyon R, Haddad NS, Haerty W, Harris RM, Hofmann HA, Hourlier T, Hulata G, Jaffe DB, Lara M, Lee AP, MacCallum I, Mwaiko S, Nikaido M, Nishihara H, Ozouf-Costaz C, Penman DJ, Przybylski D, Rakotomanga M, Renn SCP, Ribeiro FJ, Ron M, Salzburger W, Sanchez-Pulido L, Santos ME, Searle S, Sharpe T, Swofford R, Tan FJ, Williams L, Young S, Yin S, Okada N, Kocher TD, Miska EA, Lander ES, Venkatesh B, Fernald RD, Meyer A, Ponting CP, Streelman JT, Lindblad-Toh K, Seehausen O, Di Palma F. The genomic substrate for adaptive radiation in African cichlid fish. Nature 2014; 513:375-381. [PMID: 25186727 PMCID: PMC4353498 DOI: 10.1038/nature13726] [Citation(s) in RCA: 616] [Impact Index Per Article: 61.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 08/01/2014] [Indexed: 01/15/2023]
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.
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Affiliation(s)
- David Brawand
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK
| | - Catherine E Wagner
- Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution & Biogeochemistry, CH-6047 Kastanienbaum, Switzerland
- Division of Aquatic Ecology, Institute of Ecology & Evolution, University of Bern, CH-3012 Bern, Switzerland
| | - Yang I Li
- MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK
| | - Milan Malinsky
- Gurdon Institute, Cambridge CB2 1QN, UK
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Irene Keller
- Division of Aquatic Ecology, Institute of Ecology & Evolution, University of Bern, CH-3012 Bern, Switzerland
| | - Shaohua Fan
- Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Oleg Simakov
- Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Alvin Y Ng
- Institute of Molecular and Cell Biology, ASTAR, 138673 Singapore
| | - Zhi Wei Lim
- Institute of Molecular and Cell Biology, ASTAR, 138673 Singapore
| | - Etienne Bezault
- Department of Biology, Reed College, Portland, Oregon 97202, USA
| | | | - Jeremy Johnson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Rosa Alcazar
- Biology Department, Stanford University, Stanford, California 94305-5020, USA
| | - Hyun Ji Noh
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Pamela Russell
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Bronwen Aken
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Jessica Alföldi
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Chris Amemiya
- Benaroya Research Institute at Virginia Mason, Seattle, Washington 98101, USA
| | - Naoual Azzouzi
- Institut Génétique et Développement, CNRS/University of Rennes, 35043 Rennes, France
| | | | | | - Aaron Berlin
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Ryan Bloomquist
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332-0230, USA
| | - Karen L Carleton
- Department of Biology, University of Maryland, College Park, Maryland 20742, USA
| | - Matthew A Conte
- Department of Biology, University of Maryland, College Park, Maryland 20742, USA
| | - Helena D'Cotta
- CIRAD, Campus International de Baillarguet, TA B-110/A, 34398 Montpellier cedex 5, France
| | - Orly Eshel
- Animal Genetics, Institute of Animal Science, ARO, The Volcani Center, Bet-Dagan, 50250 Israel
| | - Leslie Gaffney
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Francis Galibert
- Institut Génétique et Développement, CNRS/University of Rennes, 35043 Rennes, France
| | - Hugo F Gante
- Zoological Institute, University of Basel, CH-4051 Basel, Switzerland
| | - Sante Gnerre
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Lucie Greuter
- Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution & Biogeochemistry, CH-6047 Kastanienbaum, Switzerland
- Division of Aquatic Ecology, Institute of Ecology & Evolution, University of Bern, CH-3012 Bern, Switzerland
| | - Richard Guyon
- Institut Génétique et Développement, CNRS/University of Rennes, 35043 Rennes, France
| | - Natalie S Haddad
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332-0230, USA
| | - Wilfried Haerty
- MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK
| | - Rayna M Harris
- Department of Integrative Biology, Center for Computational Biology and Bioinformatics; The University of Texas at Austin, Austin, Texas 78712, USA
| | - Hans A Hofmann
- Department of Integrative Biology, Center for Computational Biology and Bioinformatics; The University of Texas at Austin, Austin, Texas 78712, USA
| | | | - Gideon Hulata
- Animal Genetics, Institute of Animal Science, ARO, The Volcani Center, Bet-Dagan, 50250 Israel
| | - David B Jaffe
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Marcia Lara
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Alison P Lee
- Institute of Molecular and Cell Biology, ASTAR, 138673 Singapore
| | - Iain MacCallum
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Salome Mwaiko
- Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution & Biogeochemistry, CH-6047 Kastanienbaum, Switzerland
| | - Masato Nikaido
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 226-8501 Yokohama, Japan
| | - Hidenori Nishihara
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 226-8501 Yokohama, Japan
| | - Catherine Ozouf-Costaz
- Systématique, Adaptation, Evolution, National Museum of Natural History, 75005 Paris, France
| | - David J Penman
- Institute of Aquaculture, University of Stirling, Stirling FK9 4LA, UK
| | | | - Michaelle Rakotomanga
- Institut Génétique et Développement, CNRS/University of Rennes, 35043 Rennes, France
| | - Suzy C P Renn
- Department of Biology, Reed College, Portland, Oregon 97202, USA
| | - Filipe J Ribeiro
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Micha Ron
- Animal Genetics, Institute of Animal Science, ARO, The Volcani Center, Bet-Dagan, 50250 Israel
| | - Walter Salzburger
- Zoological Institute, University of Basel, CH-4051 Basel, Switzerland
| | | | - M Emilia Santos
- Zoological Institute, University of Basel, CH-4051 Basel, Switzerland
| | - Steve Searle
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Ted Sharpe
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Ross Swofford
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Frederick J Tan
- Carnegie Institution of Washington, Department of Embryology, 3520 San Martin Drive Baltimore, Maryland 21218, USA
| | - Louise Williams
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Sarah Young
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Shuangye Yin
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Norihiro Okada
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 226-8501 Yokohama, Japan
- National Cheng Kung University, Tainan City, 704 Taiwan
| | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, Maryland 20742, USA
| | | | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | | | - Russell D Fernald
- Biology Department, Stanford University, Stanford, California 94305-5020, USA
| | - Axel Meyer
- Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Chris P Ponting
- MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK
| | - J Todd Streelman
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332-0230, USA
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
| | - Ole Seehausen
- Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution & Biogeochemistry, CH-6047 Kastanienbaum, Switzerland
- Division of Aquatic Ecology, Institute of Ecology & Evolution, University of Bern, CH-3012 Bern, Switzerland
| | - Federica Di Palma
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Vertebrate and Health Genomics, The Genome Analysis Centre, Norwich NR18 7UH, UK
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Fan S, Meyer A. Evolution of genomic structural variation and genomic architecture in the adaptive radiations of African cichlid fishes. Front Genet 2014; 5:163. [PMID: 24917883 PMCID: PMC4042683 DOI: 10.3389/fgene.2014.00163] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 05/15/2014] [Indexed: 12/30/2022] Open
Abstract
African cichlid fishes are an ideal system for studying explosive rates of speciation and the origin of diversity in adaptive radiation. Within the last few million years, more than 2000 species have evolved in the Great Lakes of East Africa, the largest adaptive radiation in vertebrates. These young species show spectacular diversity in their coloration, morphology and behavior. However, little is known about the genomic basis of this astonishing diversity. Recently, five African cichlid genomes were sequenced, including that of the Nile Tilapia (Oreochromis niloticus), a basal and only relatively moderately diversified lineage, and the genomes of four representative endemic species of the adaptive radiations, Neolamprologus brichardi, Astatotilapia burtoni, Metriaclima zebra, and Pundamila nyererei. Using the Tilapia genome as a reference genome, we generated a high-resolution genomic variation map, consisting of single nucleotide polymorphisms (SNPs), short insertions and deletions (indels), inversions and deletions. In total, around 18.8, 17.7, 17.0, and 17.0 million SNPs, 2.3, 2.2, 1.4, and 1.9 million indels, 262, 306, 162, and 154 inversions, and 3509, 2705, 2710, and 2634 deletions were inferred to have evolved in N. brichardi, A. burtoni, P. nyererei, and M. zebra, respectively. Many of these variations affected the annotated gene regions in the genome. Different patterns of genetic variation were detected during the adaptive radiation of African cichlid fishes. For SNPs, the highest rate of evolution was detected in the common ancestor of N. brichardi, A. burtoni, P. nyererei, and M. zebra. However, for the evolution of inversions and deletions, we found that the rates at the terminal taxa are substantially higher than the rates at the ancestral lineages. The high-resolution map provides an ideal opportunity to understand the genomic bases of the adaptive radiation of African cichlid fishes.
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Affiliation(s)
- Shaohua Fan
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz Konstanz, Germany
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz Konstanz, Germany
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Nikaido M, Ota T, Hirata T, Suzuki H, Satta Y, Aibara M, Mzighani SI, Sturmbauer C, Hagino-Yamagishi K, Okada N. Multiple episodic evolution events in V1R receptor genes of East-African cichlids. Genome Biol Evol 2014; 6:1135-44. [PMID: 24803573 PMCID: PMC4040994 DOI: 10.1093/gbe/evu086] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Fish use olfaction to detect a variety of nonvolatile chemical signals, and thus, this sense is key to survival and communication. However, the contribution of the olfactory sense to social—especially reproductive—interactions in cichlids is still controversial. To obtain insights into this issue, we investigated the genes encoding V1Rs—possible candidates for reproductive pheromone receptors—among East-African cichlids. Interestingly, we found an excess of nonsynonymous over synonymous substitutions in four of six V1R genes in multiple cichlid lineages. First, we found that highly dimorphic V1R2 allele groups were shared among the cichlids inhabiting all East-African Great Lakes emerged through the episodic accumulation of the nonsynonymous substitutions prior to the radiation of the Lake Tanganyika species flock. We further detected such episodic events in V1R1 of the tribe Tropheini, and in V1R3 and V1R6 of the tribe Trematocarini. The excess of nonsynonymous substitutions in these examples were indicated as dN/dS > 1, which were all statistically significant by Fisher’s exact test. Furthermore, we speculate that the amino acid changes in these episodic events are likely functional switch because they occurred in the putative ligand-binding pocket. Our finding of the occurrence of multiple episodic events and the unexpected gene diversity in one unique gene family is suggestive of the contribution of the V1R to the species diversification and the social interaction in cichlids.
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Affiliation(s)
- Masato Nikaido
- Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
| | - Tomoki Ota
- Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
| | - Tadashi Hirata
- Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
| | - Hikoyu Suzuki
- Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
| | - Yoko Satta
- Department of Biosystems Science, School of Advanced Sciences, The Graduate University for Advanced Studies (Sokendai), Hayama, Japan
| | - Mitsuto Aibara
- Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, JapanFoundation for Advancement of International Science, Tsukuba, Japan
| | - Semvua I Mzighani
- Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, JapanTanzania Fisheries Research Institute, Dar es Salaam, Tanzania
| | | | - Kimiko Hagino-Yamagishi
- Department of Dementia and Higher Brain Function, Integrated Neuroscience Research Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Norihiro Okada
- Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, JapanFoundation for Advancement of International Science, Tsukuba, JapanDepartment of Life Sciences, National Cheng Kung University, Tainan, Taiwan
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