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Schneider K, Adams CE, Elmer KR. Parallel selection on ecologically relevant gene functions in the transcriptomes of highly diversifying salmonids. BMC Genomics 2019; 20:1010. [PMID: 31870285 PMCID: PMC6929470 DOI: 10.1186/s12864-019-6361-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 12/01/2019] [Indexed: 12/11/2022] Open
Abstract
Background Salmonid fishes are characterised by a very high level of variation in trophic, ecological, physiological, and life history adaptations. Some salmonid taxa show exceptional potential for fast, within-lake diversification into morphologically and ecologically distinct variants, often in parallel; these are the lake-resident charr and whitefish (several species in the genera Salvelinus and Coregonus). To identify selection on genes and gene categories associated with such predictable diversifications, we analysed 2702 orthogroups (4.82 Mbp total; average 4.77 genes/orthogroup; average 1783 bp/orthogroup). We did so in two charr and two whitefish species and compared to five other salmonid lineages, which do not evolve in such ecologically predictable ways, and one non-salmonid outgroup. Results All selection analyses are based on Coregonus and Salvelinus compared to non-diversifying taxa. We found more orthogroups were affected by relaxed selection than intensified selection. Of those, 122 were under significant relaxed selection, with trends of an overrepresentation of serine family amino acid metabolism and transcriptional regulation, and significant enrichment of behaviour-associated gene functions. Seventy-eight orthogroups were under significant intensified selection and were enriched for signalling process and transcriptional regulation gene ontology terms and actin filament and lipid metabolism gene sets. Ninety-two orthogroups were under diversifying/positive selection. These were enriched for signal transduction, transmembrane transport, and pyruvate metabolism gene ontology terms and often contained genes involved in transcriptional regulation and development. Several orthogroups showed signs of multiple types of selection. For example, orthogroups under relaxed and diversifying selection contained genes such as ap1m2, involved in immunity and development, and slc6a8, playing an important role in muscle and brain creatine uptake. Orthogroups under intensified and diversifying selection were also found, such as genes syn3, with a role in neural processes, and ctsk, involved in bone remodelling. Conclusions Our approach pinpointed relevant genomic targets by distinguishing among different kinds of selection. We found that relaxed, intensified, and diversifying selection affect orthogroups and gene functions of ecological relevance in salmonids. Because they were found consistently and robustly across charr and whitefish and not other salmonid lineages, we propose these genes have a potential role in the replicated ecological diversifications.
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Affiliation(s)
- Kevin Schneider
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Colin E Adams
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.,Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Rowardennan, G63 0AW, UK
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
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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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