ArticleNature2014
The genomic substrate for adaptive radiation in African cichlid fish.
Open access · hybridAbstract read
In one paragraph
Article in Nature, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 419 papers, 1 of them a synthesis that pooled it.
0numbers the graph read from it
0cells of the map it votes in
419citing papers in PubMed, 1 pooled it
189.0field-weighted citation impact, top 1% of its field
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
419 citing papers in PubMed, 1 synthesis or guideline pooled it, 1,044 citations in OpenAlex.
- Evolutionary dynamics of pre- and postzygotic reproductive isolation in cichlid fishes.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2020Pooled it
- Near-complete genomes for nine haplochromine cichlid fishes reveal a novel centromeric satellite structure organised around a pair of inverted elements.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2026Article
- Genome-Wide Evolution of Lineage-Specific Chromatin Accessibility Links Regulatory Changes to Cichlid Phenotypic Diversity.Genome biology and evolution · 2026Article
- Transposable elements as evolutionary catalysts of ant macrodiversity.Science advances · 2026Article
- Article
- Physiology mediates transcontinental radiations of freshwater fishes.bioRxiv : the preprint server for biology · 2026Article
- Transposons drove the evolution of a male sex-determining gene from a female gene with deep introgression across cichlids.Science advances · 2026Article
- Ancestral splice variation is a key substrate for rapid diversification in African cichlids.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Article
- Tetraopes Milkweed Beetle Genomes Elucidate the Adaptive Basis of a Temperate Coevolutionary Radiation.Molecular ecology resources · 2026Article
- Divergence at the IRX gene cluster underlies extreme trophic polymorphism in a cichlid fish (Herichthys minckleyi).Communications biology · 2026Article
- Stable genome structures in living fossil fishes.Genome research · 2026Article
- Evolution's hidden architecture: a non-lipschitz theory of creation and catastrophe.BMC ecology and evolution · 2025Article
- Genome-Wide Identification of the Transient Receptor Potential Channel Family in Nile Tilapia and Expression Analysis in Response to Cold Stress.Animals : an open access journal from MDPI · 2025Article
- DNA methylation of the endothelin receptor B makes blue fish yellow.Nature communications · 2025Article
- Phylogenomic and Population Genomic Analyses of Ultraconserved Elements Reveal Deep Coalescence and Introgression Shaped Diversification Patterns in Lamprologine Cichlids of the Congo River.Systematic biology · 2025Article
- Structural Rearrangements and Selection Promote Phenotypic Evolution in Anolis Lizards.Genome biology and evolution · 2025Article
- Genomic Data Reveals Cryptic Diversity in the Soda Lake CichlidEcology and evolution · 2025Article
- Bdh1l Gene Expression Is a Potential Molecular Factor in the Evolution of Carotenoid-Based Colour Diversity of Cichlid Fishes.Molecular ecology · 2025Article
- Recent rapid radiation of apex predators suggests dramatic biodiversity turnover in an ancient lake.bioRxiv : the preprint server for biology · 2025Article
359 more citing papers are in PubMed but not listed here.
Corrections and comments
- Commented on by
- Commented on by
Authors and funding
75 authors at 20 institutions in 9 countries.
David Brawand *Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
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.
Yang I Li *MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK.
Milan MalinskyGurdon Institute, Cambridge CB2 1QN, UK.
Irene KellerDivision of Aquatic Ecology, Institute of Ecology & Evolution, University of Bern, CH-3012 Bern, Switzerland.
Shaohua FanDepartment of Biology, University of Konstanz, D-78457 Konstanz, Germany.
Oleg SimakovDepartment of Biology, University of Konstanz, D-78457 Konstanz, Germany.
Alvin Y NgInstitute of Molecular and Cell Biology, ASTAR, 138673 Singapore.
Zhi Wei LimInstitute of Molecular and Cell Biology, ASTAR, 138673 Singapore.
Etienne BezaultDepartment of Biology, Reed College, Portland, Oregon 97202, USA.
Jason Turner-MaierBroad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
Jeremy JohnsonBroad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
Rosa AlcazarBiology Department, Stanford University, Stanford, California 94305-5020, USA.
Hyun Ji NohBroad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
Pamela RussellDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA.
Bronwen AkenWellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.
Jessica AlföldiBroad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
Chris AmemiyaBenaroya Research Institute at Virginia Mason, Seattle, Washington 98101, USA.
Naoual AzzouziInstitut Génétique et Développement, CNRS/University of Rennes, 35043 Rennes, France.
Jean-François BaroillerCIRAD, Campus International de Baillarguet, TA B-110/A, 34398 Montpellier cedex 5, France.
Frederique Barloy-HublerInstitut Génétique et Développement, CNRS/University of Rennes, 35043 Rennes, France.
Aaron BerlinBroad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
Ryan BloomquistSchool of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332-0230, USA.
Karen L CarletonDepartment of Biology, University of Maryland, College Park, Maryland 20742, USA.
Matthew A ConteDepartment of Biology, University of Maryland, College Park, Maryland 20742, USA.
Helena D'CottaCIRAD, Campus International de Baillarguet, TA B-110/A, 34398 Montpellier cedex 5, France.
Orly EshelAnimal Genetics, Institute of Animal Science, ARO, The Volcani Center, Bet-Dagan, 50250 Israel.
Leslie GaffneyBroad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
Francis GalibertInstitut Génétique et Développement, CNRS/University of Rennes, 35043 Rennes, France.
Hugo F GanteZoological Institute, University of Basel, CH-4051 Basel, Switzerland.
Sante GnerreBroad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
Lucie GreuterDepartment of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution & Biogeochemistry, CH-6047 Kastanienbaum, Switzerland.
Richard GuyonInstitut Génétique et Développement, CNRS/University of Rennes, 35043 Rennes, France.
Natalie S HaddadSchool of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332-0230, USA.
Wilfried HaertyMRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK.
Rayna M HarrisDepartment of Integrative Biology, Center for Computational Biology and Bioinformatics; The University of Texas at Austin, Austin, Texas 78712, USA.
Hans A HofmannDepartment of Integrative Biology, Center for Computational Biology and Bioinformatics; The University of Texas at Austin, Austin, Texas 78712, USA.
Thibaut HourlierWellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.
Gideon HulataAnimal Genetics, Institute of Animal Science, ARO, The Volcani Center, Bet-Dagan, 50250 Israel.
David B JaffeBroad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
Marcia LaraBroad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
Alison P LeeInstitute of Molecular and Cell Biology, ASTAR, 138673 Singapore.
Iain MacCallumBroad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
Salome MwaikoDepartment of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution & Biogeochemistry, CH-6047 Kastanienbaum, Switzerland.
Masato NikaidoDepartment of Biological Sciences, Tokyo Institute of Technology, Tokyo, 226-8501 Yokohama, Japan.
Hidenori NishiharaDepartment of Biological Sciences, Tokyo Institute of Technology, Tokyo, 226-8501 Yokohama, Japan.
Catherine Ozouf-CostazSystématique, Adaptation, Evolution, National Museum of Natural History, 75005 Paris, France.
David J PenmanInstitute of Aquaculture, University of Stirling, Stirling FK9 4LA, UK.
Dariusz PrzybylskiBroad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
Michaelle RakotomangaInstitut Génétique et Développement, CNRS/University of Rennes, 35043 Rennes, France.
Suzy C P RennDepartment of Biology, Reed College, Portland, Oregon 97202, USA.
Filipe J RibeiroBroad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
Micha RonAnimal Genetics, Institute of Animal Science, ARO, The Volcani Center, Bet-Dagan, 50250 Israel.
Walter SalzburgerZoological Institute, University of Basel, CH-4051 Basel, Switzerland.
Luis Sanchez-PulidoMRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK.
M Emilia SantosZoological Institute, University of Basel, CH-4051 Basel, Switzerland.
Steve SearleWellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.
Ted SharpeBroad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
Ross SwoffordBroad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
Frederick J TanCarnegie Institution of Washington, Department of Embryology, 3520 San Martin Drive Baltimore, Maryland 21218, USA.
Louise WilliamsBroad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
Sarah YoungBroad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
Shuangye YinBroad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
Norihiro OkadaDepartment of Biological Sciences, Tokyo Institute of Technology, Tokyo, 226-8501 Yokohama, Japan.
Thomas D KocherDepartment of Biology, University of Maryland, College Park, Maryland 20742, USA.
Eric A MiskaGurdon Institute, Cambridge CB2 1QN, UK.
Eric S LanderBroad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
Byrappa VenkateshInstitute of Molecular and Cell Biology, ASTAR, 138673 Singapore.
Russell D FernaldBiology Department, Stanford University, Stanford, California 94305-5020, USA.
Axel MeyerDepartment of Biology, University of Konstanz, D-78457 Konstanz, Germany.
Chris P PontingMRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK.
J Todd StreelmanSchool of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332-0230, USA.
Kerstin Lindblad-TohBroad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
Ole SeehausenDepartment of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution & Biogeochemistry, CH-6047 Kastanienbaum, Switzerland.
Federica Di PalmaBroad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
Broad Institute · USUniversity of Oxford · GBWellcome Sanger Institute · GBAgricultural Research Organization · ILGeorgia Institute of Technology · USInstitute of Molecular and Cell Biology · SGTokyo Institute of Technology · JPUniversity of Basel · CHUniversity of Bern · CHUniversity of Maryland, College Park · USCentre de Coopération Internationale en Recherche Agronomique pour le Développement · FRCentre National de la Recherche Scientifique · FRReed College · USStanford University · USSwiss Federal Institute of Aquatic Science and Technology · CHUniversité de Rennes · FRUniversity of Konstanz · DEAgency for Science, Technology and Research · SGBenaroya Research InstituteCalifornia Institute of Technology · US
Funding
Large Scale Sequencing and Analysis of GenomesU54HG003067 · NHGRI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI GABRIEL, STACEY, LANDER, ERIC S · 2004 to 2015
$568.6MCENTER FOR GENOME RESEARCHU54HG002045 · NHGRI · WHITEHEAD INSTITUTE FOR BIOMEDICAL RES · PI LANDER, ERIC S · 1999 to 2003
$242.3MPatterning the Vertebrate Dentition Through Replacement and RepairR01DE019637 · NIDCR · GEORGIA INSTITUTE OF TECHNOLOGY · PI STREELMAN, JEFFERY TODD · 2010 to 2022
$4.5MSOCIAL AND PHYSIOLOGICAL REGULATION OF MATURATIONR01NS034950 · NINDS · STANFORD UNIVERSITY · PI HELLER, H CRAIG · 1995 to 2017
$3.8MEast African Cichlids: A Natural Model for Dental RegenerationF30DE023013 · NIDCR · GEORGIA INSTITUTE OF TECHNOLOGY · PI BLOOMQUIST, RYAN FREDRIC · 2013 to 2016
$144kCancer Research UK 11832Medical Research Council MC_U137761446Medical Research Council MC_UU_12021/1NHGRI NIH HHS U54 HG002045NHGRI NIH HHS U54 HG003067NIDCR NIH HHS 2R01DE019637-04NIDCR NIH HHS F30 DE023013NIDCR NIH HHS R01 DE019637NINDS NIH HHS R01 NS034950Wellcome Trust
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.
Indexed as
Evolution, MolecularGenetic SpeciationAfrica, EasternAnimalsCichlidsDNA Transposable ElementsGene DuplicationGene Expression RegulationGenomeGenomicsLakesMicroRNAsPhylogenyPolymorphism, GeneticDNA Transposable ElementsMicroRNAs
Identifiers
What OpenQuestion holds
Textmetadata
LicenceCC BY-NC-SA
Read underepoch 390
Registered trials
None linked
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.