On the Origin of Species, 1859. ,
Tempo and Mode in Evolution, 1944. ,
Adaptive evolution and explosive speciation: the cichlid fish model, Nature Reviews Genetics, vol.10, issue.4, pp.288-298, 2004. ,
DOI : 10.1098/rspb.2002.2153
Ecological opportunity and sexual selection together predict adaptive radiation, Nature, vol.33, issue.7407, pp.366-369, 2012. ,
DOI : 10.1093/sysbio/syp074
: Alternative adaptations and ontogenetic changes in shape, Journal of Zoology, vol.32, issue.No. 1, pp.237-260, 1990. ,
DOI : 10.1111/j.1469-7998.1990.tb03994.x
Estimating the age of formation of lakes: An example from Lake Tanganyika, East African Rift system, Geology, vol.21, issue.6, pp.511-514, 1993. ,
DOI : 10.1130/0091-7613(1993)021<0511:ETAOFO>2.3.CO;2
How Fast is Speciation: Molecular, Geological and Phylogenetic Evidences from Adaptive Radiations of Fish pp, pp.585-610, 1997. ,
Repeated colonization and hybridization in Lake Malawi cichlids, Current Biology, vol.21, issue.3, pp.108-109, 2011. ,
DOI : 10.1016/j.cub.2010.11.029
Origins of Shared Genetic Variation in African Cichlids, Molecular Biology and Evolution, vol.30, issue.4, pp.906-917, 2013. ,
DOI : 10.1093/molbev/mss326
From The Cover: Integration and evolution of the cichlid mandible: The molecular basis of alternate feeding strategies, Proc. Natl Acad. Sci. USA, pp.16287-16292, 2005. ,
DOI : 10.1073/pnas.0506649102
Adaptive phenotypic plasticity in the Midas cichlid fish pharyngeal jaw and its relevance in adaptive radiation, BMC Evolutionary Biology, vol.11, issue.1, p.116, 2011. ,
DOI : 10.1111/j.1755-0998.2010.02924.x
Vision and behavior in an african cichlid fish, Am. Sci, vol.72, pp.58-65, 1984. ,
The Eyes Have It: Regulatory and Structural Changes Both Underlie Cichlid Visual Pigment Diversity, PLoS Biology, vol.25, issue.12, p.1000266, 2009. ,
DOI : 10.1371/journal.pbio.1000266.s013
Intraspecific sexual selection on a speciation trait, male coloration, in the Lake Victoria cichlid Pundamilia nyererei, Proceedings of the Royal Society B: Biological Sciences, vol.271, issue.1556, pp.2445-2452, 2004. ,
DOI : 10.1098/rspb.2004.2911
Genetic interactions controlling sex and color establish the potential for sexual conflict in Lake Malawi cichlid fishes, Heredity, vol.18, issue.3, pp.239-246, 2013. ,
DOI : 10.1371/journal.pgen.1002203
Sexual Conflict Resolved by Invasion of a Novel Sex Determiner in Lake Malawi Cichlid Fishes, Science, vol.326, issue.5955, pp.998-1001, 2009. ,
DOI : 10.1126/science.1174705
Microhabitat Use, Trophic Patterns, and the Evolution of Brain Structure in African Cichlids, Brain, Behavior and Evolution, vol.50, issue.3, pp.167-182, 1997. ,
DOI : 10.1159/000113330
Competing signals drive telencephalon diversity, Nature Communications, vol.5, p.1745, 2013. ,
DOI : 10.1038/ncomms2753
The genomic basis of adaptive evolution in threespine sticklebacks, Nature, vol.279, issue.7392, pp.55-61, 2012. ,
DOI : 10.1038/nature10944
Positive Darwinian Selection Drives the Evolution of the Morphology-Related Gene, EPCAM, in Particularly Species-Rich Lineages of African Cichlid Fishes, Journal of Molecular Evolution, vol.22, issue.1-2, pp.1-9, 2011. ,
DOI : 10.1007/s00239-011-9452-5
The Evolution of the Pro-Domain of Bone Morphogenetic Protein 4 (Bmp4) in an Explosively Speciated Lineage of East African Cichlid Fishes, Molecular Biology and Evolution, vol.19, issue.9, pp.1628-1632, 2002. ,
DOI : 10.1093/oxfordjournals.molbev.a004225
Mutational Analysis of Endothelin Receptor b1 (rose) during Neural Crest and Pigment Pattern Development in the Zebrafish Danio rerio, Developmental Biology, vol.227, issue.2, pp.294-306, 2000. ,
DOI : 10.1006/dbio.2000.9899
The Evolutionary Fate and Consequences of Duplicate Genes, Science, vol.290, issue.5494, pp.1151-1155, 2000. ,
DOI : 10.1126/science.290.5494.1151
Female preference for conspecific males based on olfactory cues in a Lake Malawi cichlid fish, Biology Letters, vol.10, issue.3, pp.411-414, 2005. ,
DOI : 10.1126/science.277.5333.1808
Genome Duplication, a Trait Shared by 22,000 Species of Ray-Finned Fish, Genome Research, vol.13, issue.3, pp.382-390, 2003. ,
DOI : 10.1101/gr.640303
Genome duplication, divergent resolution and speciation, Trends in Genetics, vol.17, issue.6, pp.299-301, 2001. ,
DOI : 10.1016/S0168-9525(01)02318-6
URL : http://nbn-resolving.de/urn:nbn:de:bsz:352-opus-34937
Retroelement Distributions in the Human Genome: Variations Associated With Age and Proximity to Genes, Genome Research, vol.12, issue.10 ,
DOI : 10.1101/gr.388902
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes, Genome Research, vol.15, issue.8, pp.1034-1050, 2005. ,
DOI : 10.1101/gr.3715005
Evolution of microRNA diversity and regulation in animals, Nature Reviews Genetics, vol.9, issue.12, pp.846-860, 2011. ,
DOI : 10.1038/nrg3079
Tissue-dependent paired expression of miRNAs, Nucleic Acids Research, vol.35, issue.17, pp.5944-5953, 2007. ,
DOI : 10.1093/nar/gkm641
Phylogeny of the Lake Tanganyika Cichlid Species Flock and Its Relationship to the Central and East African Haplochromine Cichlid Fish Faunas, Systematic Biology, vol.51, issue.1, pp.113-135, 2002. ,
DOI : 10.1080/106351502753475907
Age of Cichlids: New Dates for Ancient Lake Fish Radiations, Molecular Biology and Evolution, vol.24, issue.5, pp.1269-1282, 2007. ,
DOI : 10.1093/molbev/msm050
Insights into hominid evolution from the gorilla genome sequence, Nature, vol.105, issue.7388, pp.169-175, 2012. ,
DOI : 10.1038/nature10842
Late Pleistocene Desiccation of Lake Victoria and Rapid Evolution of Cichlid Fishes, Science, vol.273, issue.5278, pp.1091-1093, 1996. ,
DOI : 10.1126/science.273.5278.1091
Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation, Molecular Ecology, vol.60, issue.3, pp.787-798, 2012. ,
DOI : 10.1111/mec.12023
Adaptation from standing genetic variation, Trends in Ecology & Evolution, vol.23, issue.1, pp.38-44, 2008. ,
DOI : 10.1016/j.tree.2007.09.008
THE LOCI OF EVOLUTION: HOW PREDICTABLE IS GENETIC EVOLUTION?, Evolution, vol.30, issue.256, pp.2155-2177, 2008. ,
DOI : 10.1111/j.1558-5646.2008.00450.x
Molecular genetics of steroid 5 alpha-reductase 2 deficiency., Journal of Clinical Investigation, vol.90, issue.3, pp.799-809, 1992. ,
DOI : 10.1172/JCI115954
Evolutionary divergence in replicate pairs of ecotypes of Lake Victoria cichlid fish, Evol. Ecol. Res, vol.14, pp.381-401, 2012. ,
MicroRNA sequencing and annotation was supported by ERC Starting Grant to E.A.M.; M.M. was supported by a fellowship from the Wellcome Trust. MicroRNA and target in situ hybridization was supported by grant 2R01DE019637-04 to J.T.S. Population genomics analyses were supported by Swiss National Science Foundation grants, pp.31003-118293 ,
revised, planned and oversaw the genome projectH. provided tissues and RNAs for sequencing. C.A. prepared the high molecular weight tilapia DNA. M.L. extracted genomic DNA for sequencing. L.W. prepared 40-kb libraries (Fossils) for Illumina sequencing. R.S. performed quality control of RNA oversaw the sequencing and assembly of genomes and transcriptomes as well as submissions of data, performed quality control of assemblies and alignments of genomes. J.M.T. performed de novo assembly of transcriptomes ,
contributed to the tilapia radiation hybrid map annotated the tilapia genome. D.B. and Y.I.L. annotated the N. brichardi and the lake cichlids. D.B. performed gene expression, genome evolution, gene duplication and TE insertion analyses. Y.I.L. and L. S.-P. performed quality control of RNA-seq data and assemblies, gene evolution, incomplete lineage sorting and ancient variant analyses analysed the TE landscape of cichlid genomes performed the TE burst history analysis and analysed copy number variants using read depthV. performed conserved CNE analysis and functional assays of cichlid CNEs. M.M. and E.M. performed microRNA sequencing and annotation from embryos of cichlid species as well as target identificationS. performed microRNA and target gene in situ hybridization. O.S. designed and oversaw the population genomics data analysis from Lake Victoria species, analysed duplications by comparative genomic hybridization (aCGH). H.A.H. and R.M.H. performed PCR to validate the transcriptomeS. wrote the manuscript with input from D.B., C.E.W. and Y.I.L., I.K., J.T.S., W.H., C.P.P. as well as additional authors. L.G. assisted with figure preparation and coordination ,
The First Inner Loop of Endothelin Receptor Type B Is Necessary for Specific Coupling to Galpha 13, Journal of Biological Chemistry, vol.278, issue.4, pp.2384-2387, 2003. ,
DOI : 10.1074/jbc.M208683200
Palmitoylation of Human EndothelinB: ITS CRITICAL ROLE IN G PROTEIN COUPLING AND A DIFFERENTIAL REQUIREMENT FOR THE CYTOPLASMIC TAIL BY G PROTEIN SUBTYPES, Journal of Biological Chemistry, vol.272, issue.34, pp.21589-21596, 1997. ,
DOI : 10.1074/jbc.272.34.21589
A Melanocortin 1 Receptor Allele Suggests Varying Pigmentation Among Neanderthals, Science, vol.318, issue.5855, pp.1453-1455, 2007. ,
DOI : 10.1126/science.1147417
URL : https://hal.archives-ouvertes.fr/halshs-00305688