ALBERT

Description: Cichlid fishes have evolved tremendous morphological and behavioral diversity in the waters of East Africa. Within each of the Great Lakes Tanganyika, Malawi, and Victoria, the phenomena of hybridization and retention of ancestral polymorphism explain allele sharing across species. Here, we explore the sharing of single nucleotide polymorphisms (SNPs) between the major East African cichlid assemblages. A set of approximately 200 genic and nongenic SNPs was ascertained in five Lake Malawi species and genotyped in a diverse collection of ~160 species from across Africa. We observed segregating polymorphism outside of the Malawi lineage for more than 50% of these loci; this holds similarly for genic versus nongenic SNPs, as well as for SNPs at putative CpG versus non-CpG sites. Bayesian and principal component analyses of genetic structure in the data demonstrate that the Lake Malawi endemic flock is not monophyletic and that river species have likely contributed significantly to Malawi genomes. Coalescent simulations support the hypothesis that river cichlids have transported polymorphism between lake assemblages. We observed strong genetic differentiation between Malawi lineages for approximately 8% of loci, with contributions from both genic and nongenic SNPs. Notably, more than half of these outlier loci between Malawi groups are polymorphic outside of the lake. Cichlid fishes have evolved diversity in Lake Malawi as new mutations combined with standing genetic variation shared across East Africa.

Description: 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.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4353498/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4353498/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brawand, David -- Wagner, Catherine E -- Li, Yang I -- Malinsky, Milan -- Keller, Irene -- Fan, Shaohua -- Simakov, Oleg -- Ng, Alvin Y -- Lim, Zhi Wei -- Bezault, Etienne -- Turner-Maier, Jason -- Johnson, Jeremy -- Alcazar, Rosa -- Noh, Hyun Ji -- Russell, Pamela -- Aken, Bronwen -- Alfoldi, Jessica -- Amemiya, Chris -- Azzouzi, Naoual -- Baroiller, Jean-Francois -- Barloy-Hubler, Frederique -- Berlin, Aaron -- Bloomquist, Ryan -- Carleton, Karen L -- Conte, Matthew A -- D'Cotta, Helena -- Eshel, Orly -- Gaffney, Leslie -- Galibert, Francis -- Gante, Hugo F -- Gnerre, Sante -- Greuter, Lucie -- Guyon, Richard -- Haddad, Natalie S -- Haerty, Wilfried -- Harris, Rayna M -- Hofmann, Hans A -- Hourlier, Thibaut -- Hulata, Gideon -- Jaffe, David B -- Lara, Marcia -- Lee, Alison P -- MacCallum, Iain -- Mwaiko, Salome -- Nikaido, Masato -- Nishihara, Hidenori -- Ozouf-Costaz, Catherine -- Penman, David J -- Przybylski, Dariusz -- Rakotomanga, Michaelle -- Renn, Suzy C P -- Ribeiro, Filipe J -- Ron, Micha -- Salzburger, Walter -- Sanchez-Pulido, Luis -- Santos, M Emilia -- Searle, Steve -- Sharpe, Ted -- Swofford, Ross -- Tan, Frederick J -- Williams, Louise -- Young, Sarah -- Yin, Shuangye -- Okada, Norihiro -- Kocher, Thomas D -- Miska, Eric A -- Lander, Eric S -- Venkatesh, Byrappa -- Fernald, Russell D -- Meyer, Axel -- Ponting, Chris P -- Streelman, J Todd -- Lindblad-Toh, Kerstin -- Seehausen, Ole -- Di Palma, Federica -- 2R01DE019637-04/DE/NIDCR NIH HHS/ -- F30 DE023013/DE/NIDCR NIH HHS/ -- MC_U137761446/Medical Research Council/United Kingdom -- R01 DE019637/DE/NIDCR NIH HHS/ -- R01 NS034950/NS/NINDS NIH HHS/ -- U54 HG002045/HG/NHGRI NIH HHS/ -- Wellcome Trust/United Kingdom -- England -- Nature. 2014 Sep 18;513(7518):375-81. doi: 10.1038/nature13726. Epub 2014 Sep 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK [3]. ; 1] 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]. ; 1] MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK [2]. ; 1] Gurdon Institute, Cambridge CB2 1QN, UK [2] Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK. ; Division of Aquatic Ecology, Institute of Ecology &Evolution, University of Bern, CH-3012 Bern, Switzerland. ; Department of Biology, University of Konstanz, D-78457 Konstanz, Germany. ; 1] Department of Biology, University of Konstanz, D-78457 Konstanz, Germany [2] European Molecular Biology Laboratory, 69117 Heidelberg, Germany. ; Institute of Molecular and Cell Biology, A*STAR, 138673 Singapore. ; Department of Biology, Reed College, Portland, Oregon 97202, USA. ; Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA. ; Biology Department, Stanford University, Stanford, California 94305-5020, USA. ; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA. ; Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK. ; Benaroya Research Institute at Virginia Mason, Seattle, Washington 98101, USA. ; Institut Genetique et Developpement, CNRS/University of Rennes, 35043 Rennes, France. ; CIRAD, Campus International de Baillarguet, TA B-110/A, 34398 Montpellier cedex 5, France. ; School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332-0230, USA. ; Department of Biology, University of Maryland, College Park, Maryland 20742, USA. ; Animal Genetics, Institute of Animal Science, ARO, The Volcani Center, Bet-Dagan, 50250 Israel. ; Zoological Institute, University of Basel, CH-4051 Basel, Switzerland. ; 1] 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. ; MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK. ; Department of Integrative Biology, Center for Computational Biology and Bioinformatics; The University of Texas at Austin, Austin, Texas 78712, USA. ; Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution &Biogeochemistry, CH-6047 Kastanienbaum, Switzerland. ; Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 226-8501 Yokohama, Japan. ; Systematique, Adaptation, Evolution, National Museum of Natural History, 75005 Paris, France. ; Institute of Aquaculture, University of Stirling, Stirling FK9 4LA, UK. ; Carnegie Institution of Washington, Department of Embryology, 3520 San Martin Drive Baltimore, Maryland 21218, USA. ; 1] Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 226-8501 Yokohama, Japan [2] National Cheng Kung University, Tainan City, 704 Taiwan. ; Gurdon Institute, Cambridge CB2 1QN, UK. ; 1] 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. ; 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Vertebrate and Health Genomics, The Genome Analysis Centre, Norwich NR18 7UH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25186727" target="_blank"〉PubMed〈/a〉