The genomic substrate for adaptive radiation in African cichlid fish
David Brawand
(1, 2)
,
Catherine E. Wagner
(3)
,
Yang I. Li
(1)
,
Milan Malinsky
(4, 5)
,
Irene Keller
(6)
,
Shaohua Fan
(7)
,
Oleg Simakov
(8, 7)
,
Alvin Y. Ng
(9)
,
Zhi Wei Lim
(9)
,
Etienne Bezault
(10)
,
Jason Turner-Maier
(2)
,
Jeremy Johnson
(2)
,
Rosa Alcazar
(11)
,
Hyun Ji Noh
(2)
,
Pamela Russell
(12)
,
Bronwen Aken
(4)
,
Jessica Alföldi
(2)
,
Chris Amemiya
(13)
,
Naoual Azzouzi
(14)
,
Jean-François Baroiller
(15)
,
Frederique Barloy-Hubler
(14)
,
Aaron Berlin
(2)
,
Ryan Bloomquist
(16)
,
Karen L. Carleton
(17)
,
Matthew A. Conte
(17)
,
Helena d'Cotta
(15)
,
Orly Eshel
(18)
,
Leslie Gaffney
(2)
,
Francis Galibert
(14)
,
Hugo F. Gante
(19)
,
Sante Gnerre
(2)
,
Lucie Greuter
(3)
,
Richard Guyon
(14)
,
Natalie S. Haddad
(16)
,
Wilfried Haerty
(1)
,
Rayna M. Harris
(20)
,
Hans A. Hofmann
(20)
,
Thibaut Hourlier
(4)
,
Gideon Hulata
(18)
,
David B. Jaffe
(2)
,
Marcia Lara
(2)
,
Alison P. Lee
(9)
,
Iain Maccallum
(2)
,
Salome Mwaiko
(3)
,
Masato Nikaido
(21)
,
Hidenori Nishihara
(21)
,
Catherine Ozouf-Costaz
(22)
,
David J. Penman
(23)
,
Dariusz Przybylski
(2)
,
Michaelle Rakotomanga
(14)
,
Suzy C. P. Renn
(10)
,
Filipe J. Ribeiro
(2)
,
Micha Ron
(18)
,
Walter Salzburger
(19)
,
Luis Sanchez-Pulido
(1)
,
M. Emilia Santos
(19)
,
Steve Searle
(4)
,
Ted Sharpe
(2)
,
Ross Swofford
(2)
,
Frederick J. Tan
(24)
,
Louise Williams
(2)
,
Sarah Young
(2)
,
Shuangye Yin
(25)
,
Norihiro Okada
(26, 21)
,
Thomas D. Kocher
(17)
,
Eric A. Miska
(5)
,
Eric S. Lander
(2)
,
Byrappa Venkatesh
(9)
,
Russell D. Fernald
(11)
,
Axel Meyer
(7)
,
Chris P. Ponting
(1)
,
J. Todd Streelman
(16)
,
Kerstin Lindblad-Toh
(2, 25)
,
Ole Seehausen
(3, 6)
,
Federica Di Palma
(27, 2)
1
University of Oxford
2 BROAD INSTITUTE - Broad Institute of MIT and Harvard
3 Centre of Ecology, Evolution and Biogeochemistry, Department of Fish Ecology and Evolution
4 Sanger Institute
5 Wellcome Trust/Cancer Research UK Gurdon Institute
6 Institute of Zoology, University of Bern
7 Zoology and Evolutionary Biology, Department of Biology
8 EMBL Heidelberg
9 Institute of Molecular and Cell Biology
10 Department of Biology, Reed college, Portland, OR, USA
11 Stanford University
12 CALTECH - California Institute of Technology
13 BRI - Benaroya Research Institute [Seattle]
14 IGDR - Institut de Génétique et Développement de Rennes
15 UMR INTREPID - Intensification raisonnée et écologique pour une pisciculture durable
16 Georgia Institute of Technology [Atlanta]
17 University of Maryland [College Park]
18 The Volcani Center
19 Unibas - Université de Bâle = University of Basel = Basel Universität
20 University of Texas at Austin [Austin]
21 Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku
22 MNHN - Muséum national d'Histoire naturelle
23 University of Stirling
24 Carnegie Institution for Science
25 Science for Life Laboratory
26 NCKU - National Cheng Kung University
27 TGAC - The Genome Analysis Centre
2 BROAD INSTITUTE - Broad Institute of MIT and Harvard
3 Centre of Ecology, Evolution and Biogeochemistry, Department of Fish Ecology and Evolution
4 Sanger Institute
5 Wellcome Trust/Cancer Research UK Gurdon Institute
6 Institute of Zoology, University of Bern
7 Zoology and Evolutionary Biology, Department of Biology
8 EMBL Heidelberg
9 Institute of Molecular and Cell Biology
10 Department of Biology, Reed college, Portland, OR, USA
11 Stanford University
12 CALTECH - California Institute of Technology
13 BRI - Benaroya Research Institute [Seattle]
14 IGDR - Institut de Génétique et Développement de Rennes
15 UMR INTREPID - Intensification raisonnée et écologique pour une pisciculture durable
16 Georgia Institute of Technology [Atlanta]
17 University of Maryland [College Park]
18 The Volcani Center
19 Unibas - Université de Bâle = University of Basel = Basel Universität
20 University of Texas at Austin [Austin]
21 Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku
22 MNHN - Muséum national d'Histoire naturelle
23 University of Stirling
24 Carnegie Institution for Science
25 Science for Life Laboratory
26 NCKU - National Cheng Kung University
27 TGAC - The Genome Analysis Centre
Milan Malinsky
- Fonction : Auteur
Oleg Simakov
- Fonction : Auteur
- PersonId : 763112
- ORCID : 0000-0002-3585-4511
Etienne Bezault
- Fonction : Auteur
- PersonId : 17051
- IdHAL : etiennebezault
- ORCID : 0000-0001-7172-6480
- IdRef : 107978172
Naoual Azzouzi
- Fonction : Auteur
- PersonId : 761713
- IdRef : 178168955
Frederique Barloy-Hubler
- Fonction : Auteur
- PersonId : 739315
- IdHAL : frederique-barloy-hubler
- ORCID : 0000-0002-8277-6034
- IdRef : 120734125
Helena d'Cotta
- Fonction : Auteur
- PersonId : 1250768
- ORCID : 0000-0003-2739-3476
- IdRef : 151786216
Sarah Young
- Fonction : Auteur
- PersonId : 763962
- ORCID : 0000-0003-3862-3863
Résumé
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.
Origine : Publication financée par une institution
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