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  current news   Press   selected story    
     
  18 September 2014  
  The genomic substrate for adaptive radiation in African cichlid fish
 
 




Authors
David Brawand1,2, Catherine E. Wagner3,4, Yang I. Li,2, Milan Malinsky5,6, Irene Keller4, Shaohua Fan7, Oleg Simakov8, Alvin Y. Ng9, Zhi Wei Lim9, Etienne Bezault10, Jason Turner-Maier1, Jeremy Johnson1, Rosa Alcazar11, Hyun Ji Noh1, Pamela Russell12, Bronwen Aken6, Jessica Alföldi1, Chris Amemiya13, Naoual Azzouzi14, Jean-François Barollier15, Frederique Barloy-Hubler14, Aaron Berlin1, Ryan Bloomquist16, Karen L. Carleton17, Matthew A. Conte17, Helena D'Cotta15, Orly Eshel18, Leslie Gaffney1, Francis Galibert14, Hugo F. Gante19, Sante Gnerre1, Lucie Greuter3,4, Richard Guyon14, Natalie S. Haddad16, Wilfried Haerty2, Rayna M. Harris20, Hans A. Hofmann20, Thibaut Hourlier6, Gideon Hulata18, David B. Jaffe1, Marcia Lara1, Alison P. Lee9, Iain MacCallum1, Salome Mwaiko3, Masato Nikaido21, Hidenori Nishihara21, Catherine Ozouf-Costaz22, David J. Penman23, Dariusz Przybylski1, Michaelle Rakotomanga14, Suzy C. P. Renn10, Filipe J. Ribeiro1, Micha Ron18, Walter Salzburger19, Luis Sanchez-Pulido2, M. Emilia Santos19, Steve Searle6, Ted Sharpe1, Ross Swofford1, Frederick Tan24, Louise Williams1, Sarah Young1, Shuangye Yin1, Norihiro Okada21,25, Thomas D. Kocher17, Eric Miska5, Eric S. Lander1, Byrappa Venkatesh9, Russell Fernald11, Axel Meyer7, Chris P. Ponting2, J. Todd Streelman16, Kerstin Lindblad-Toh1,26, Ole Seehausen3,4 and Federica Di Palma1,27

1    Broad Institute of MIT and Harvard, Cambridge, MA, USA
2    MRC Functional Genomics Unit, University of Oxford, Oxford, UK 
3    Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute for Aquatic Sciences,       Center for Ecology, Evolution & Biogeochemistry, Kastanienbaum, Switzerland 
4    Division of Aquatic Ecology, Institute of Ecology & Evolution, University of Bern, Bern, Switzerland 
5    Gurdon Institute, Cambridge, UK 
6    Wellcome Trust Sanger Institute, Hinxton, UK 
7    Department of Biology, University of Konstanz, Konstanz, Germany
8    European Molecular Biology Laboratory, Heidelberg, Germany 
9    Institute of Molecular and Cell Biology, A*STAR, Singapore 
10  Department of Biology, Reed College, Portland, OR, USA 
11  Biology Department, Stanford University, Stanford, CA, USA 
12  Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA,USA 
13  Benaroya Research Institute at Virgnia Mason, Seattle, WA, USA 
14  Institut Génétique et Développement, CNRS/University of Rennes, Rennes, France 
15  Cirad, Montpellier, France 
16  School of Biology, Georgia Institute of Technology, Atlanta, GA, USA 
17  Department of Biology, University of Maryland, College Park, MD, USA 
18  Animal Genetics, Institute of Animal Science, ARO, The Volcani Center, Bet-Dagan, Israel 
19  Zoological Institute, University of Basel, Basel, Switzerland 
20  Department of Integrative Biology, Center for Computational Biology and Bioinformatics; The       University of Texas at Austin, Austin, TX, USA 
21  Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, Japan 
22  Systématique, Adaptation, Evolution, National Museum of Natural History, Paris, France 
23  Institute of Aquaculture, University of Stirling, Stirling, Scotland, UK 
24  Department of Embyology, Carnegie Institution of Washington, Washington, D.C., USA 
25  National Cheng Kung University, Tainan City, Taiwan
26  Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala       University, Uppsala, Sweden
27  Vertebrate and Health Genomics, The Genome Analysis Center, Norwich, UK

Published in Nature on 18 September 2014 (Vol 513: 375-381).

To read the Nature article, click here: http://www.nature.com/nature/journal/v513/n7518/full/nature13726.html

News & Views of this paper is published in Nature Vol 513:318-319.

Abstract

Cichlid fishes are famous for large, diverse and replicated adaptive radiations, most dramatically in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity and the stunning number of diverse species, we sequenced the genomes and transcriptomes of five distinct lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity, and four members of the East African lineage, namely Neolamprologus brichardi/pulcher (representing an older radiation in Lake Tanganyika), Metriaclima zebra (recent Lake Malawi radiation), Pundamilia nyererei (very recent Lake Victoria radiation), and Astatotilapia burtoni (a riverine species which lives around Lake Tanganyika and has not radiated). We found East African cichlids to be characterized by: (1) an excess of gene duplications compared to tilapia and other teleosts; (2) an abundance of non-coding element divergence and accelerated coding sequence evolution; (3) expression divergence associated with transposable element insertions in orthologous gene pairs; and (4) regulation by novel miRNAs. In addition, we performed re-sequencing of sixty individuals representing six very closely related species from the most recent radiation, and show that rapid cichlid speciation is associated with 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 have 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.


Figure Legend:
Rapidly evolving cis-regulatory element in a cichlid fish (identified as an accelerated conserved noncoding element or aCNE). (a) An accelerated CNE (aCNE LG18.20714) in the Pbx1a locus of an African cichlid fish (Pundamilia nyererei) from Lake Victoria. This element is highly conserved in other cichlids (M. zebra, A. burtoni, N. brichardi, O. niloticus) and medaka (O. latipes). (b) Expression pattern driven by aCNE of P. nyererei and its corresponding highly conserved CNE (hCNE) in Nile tilapia (O. niloticus) in 72 hpf G1 zebrafish embryos. The transgenic studies show that the aCNE has the potential to confer a different expression pattern to its target gene compared to its corresponding highly conserved CNEs in other fishes

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