Details der Publikation - The genomic substrate for adaptive radiation in African cichlid fish

The genomic substrate for adaptive radiation in African cichlid fish

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 a massing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification..

Medienart:	Artikel

Erscheinungsjahr:	2014
Erschienen:	2014

Enthalten in:	Zur Gesamtaufnahme - volume:513
Enthalten in:	Nature - 513(2014), 7518, Seite 375-381

Sprache:	Englisch

Beteiligte Personen:	David Brawand [VerfasserIn] Catherine E Wagner [Sonstige Person] Yang I Li [Sonstige Person] Milan Malinsky [Sonstige Person] Irene Keller [Sonstige Person] Shaohua Fan [Sonstige Person] Oleg Simakov [Sonstige Person] Alvin Y Ng [Sonstige Person] Zhi Wei Lim [Sonstige Person] Etienne Bezault [Sonstige Person] Jason Turner-Maier [Sonstige Person] Jeremy Johnson [Sonstige Person] Rosa Alcazar [Sonstige Person] Hyun Ji Noh [Sonstige Person] Pamela Russell [Sonstige Person] Bronwen Aken [Sonstige Person] Jessica Alföldi [Sonstige Person] Chris Amemiya [Sonstige Person] Naoual Azzouzi [Sonstige Person] Jean-François Baroiller [Sonstige Person] Frederique Barloy-Hubler [Sonstige Person] Aaron Berlin [Sonstige Person] Ryan Bloomquist [Sonstige Person] Karen L Carleton [Sonstige Person] Matthew A Conte [Sonstige Person] Helena D'Cotta [Sonstige Person] Orly Eshel [Sonstige Person] Leslie Gaffney [Sonstige Person] Francis Galibert [Sonstige Person] Hugo F Gante [Sonstige Person] Sante Gnerre [Sonstige Person] Lucie Greuter [Sonstige Person] Richard Guyon [Sonstige Person] Natalie S Haddad [Sonstige Person] Wilfried Haerty [Sonstige Person] Rayna M Harris [Sonstige Person] Hans A Hofmann [Sonstige Person] Thibaut Hourlier [Sonstige Person] Gideon Hulata [Sonstige Person] David B Jaffe [Sonstige Person] Marcia Lara [Sonstige Person] Alison P Lee [Sonstige Person] Iain MacCallum [Sonstige Person] Salome Mwaiko [Sonstige Person] Masato Nikaido [Sonstige Person] Hidenori Nishihara [Sonstige Person] Catherine Ozouf-Costaz [Sonstige Person] David J Penman [Sonstige Person] Dariusz Przybylski [Sonstige Person] Michaelle Rakotomanga [Sonstige Person] Suzy C P Renn [Sonstige Person] Filipe J Ribeiro [Sonstige Person] Micha Ron [Sonstige Person] Walter Salzburger [Sonstige Person] Luis Sanchez-Pulido [Sonstige Person] M Emilia Santos [Sonstige Person] Steve Searle [Sonstige Person] Ted Sharpe [Sonstige Person] Ross Swofford [Sonstige Person] Frederick J Tan [Sonstige Person] Louise Williams [Sonstige Person] Sarah Young [Sonstige Person] Shuangye Yin [Sonstige Person] Norihiro Okada [Sonstige Person] Thomas D Kocher [Sonstige Person] Eric A Miska [Sonstige Person] Eric S Lander [Sonstige Person] Byrappa Venkatesh [Sonstige Person] Russell D Fernald [Sonstige Person] Axel Meyer [Sonstige Person] Chris P Ponting [Sonstige Person] J Todd Streelman [Sonstige Person] Kerstin Lindblad-Toh [Sonstige Person] Ole Seehausen [Sonstige Person] Federica Di Palma [Sonstige Person]

Links:	Volltext www.ncbi.nlm.nih.gov search.proquest.com www.pubmedcentral.nih.gov urn.kb.se

Themen:	Adaptation (Biology) Africa, Eastern Animals Cichlidae Cichlids Cichlids - classification Cichlids - genetics DNA Transposable Elements DNA Transposable Elements - genetics Evolution Evolution, Molecular Fish Gene Duplication Gene Duplication - genetics Gene Expression Regulation Gene Expression Regulation - genetics Gene expression Genetic Speciation Genetic aspects Genetic research Genome Genome - genetics Genomes Genomics Lake Victoria Lakes MicroRNAs MicroRNAs - genetics Phylogeny Polymorphism, Genetic Polymorphism, Genetic - genetics Research Tanganyika Zebrafish

doi:	10.1038/nature13726

funding:
Förderinstitution / Projekttitel:

PPN (Katalog-ID):	OLC1962476553

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520			\|a 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 a massing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.
540			\|a Nutzungsrecht: © COPYRIGHT 2014 Nature Publishing Group
540			\|a © 2014 Macmillan Publishers Limited. All rights reserved 2014
650		4	\|a Genomes
650		4	\|a Genetic Speciation
650		4	\|a Phylogeny
650		4	\|a Gene Duplication
650		4	\|a Animals
650		4	\|a Africa, Eastern
650		4	\|a MicroRNAs
650		4	\|a Polymorphism, Genetic
650		4	\|a Genome
650		4	\|a Evolution, Molecular
650		4	\|a Zebrafish
650		4	\|a Gene expression
650		4	\|a Lakes
650		4	\|a Tanganyika
650		4	\|a Lake Victoria
650		4	\|a DNA Transposable Elements
650		4	\|a Gene Expression Regulation
650		4	\|a Fish
650		4	\|a Cichlids
650		4	\|a Evolution
650		4	\|a Genomics
650		4	\|a DNA Transposable Elements - genetics
650		4	\|a Gene Duplication - genetics
650		4	\|a MicroRNAs - genetics
650		4	\|a Genome - genetics
650		4	\|a Polymorphism, Genetic - genetics
650		4	\|a Cichlids - genetics
650		4	\|a Cichlids - classification
650		4	\|a Gene Expression Regulation - genetics
650		4	\|a Genetic research
650		4	\|a Cichlidae
650		4	\|a Research
650		4	\|a Genetic aspects
650		4	\|a Adaptation (Biology)
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The genomic substrate for adaptive radiation in African cichlid fish

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