The genomic substrate for adaptive radiation in African cichlid fish.

Nature
Authors
Keywords
Abstract

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.

Year of Publication
2014
Journal
Nature
Volume
513
Issue
7518
Pages
375-81
Date Published
2014 Sep 18
ISSN
1476-4687
URL
DOI
10.1038/nature13726
PubMed ID
25186727
PubMed Central ID
PMC4353498
Links
Grant list
U54 HG002045 / HG / NHGRI NIH HHS / United States
MC_U137761446 / Medical Research Council / United Kingdom
F30 DE023013 / DE / NIDCR NIH HHS / United States
R01 NS034950 / NS / NINDS NIH HHS / United States
2R01DE019637-04 / DE / NIDCR NIH HHS / United States
R01 DE019637 / DE / NIDCR NIH HHS / United States
Wellcome Trust / United Kingdom