The genomic substrate for adaptive radiation in African cichlid fish

By D. Brawand, C. Wagner, Yang I Li, M. Malinsky, I. Keller, Shaohua Fan, O. Simakov, A. Y. Ng, Z. Lim, Étienne Bezault and 65 more. Nature, 2014

934 citations recorded by the source corpus.

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.

Subfields: Aquatic Science, Ecology, Genetics

View Paper: https://www.semanticscholar.org/paper/04bf7c14152d8d86866c7cdd23b00b1cfda1fef2

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Citations in the corpus

Ecology and Evolution of the African Great Lakes and Their Faunas (2014, background): “…may be associated with a differential propensity to diversify: The radiating cichlid clades of the AGL show accelerated rates of molecular evolution, a greater number of duplicated genes, divergence in gene expression, and gene regulation that occurs through novel miRNAs (Brawand et al. 2014).”
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis (2018, methodology): “Whole-genome sequence data for the six 570 species have been generated by [105] and [106] and were used by [106] to generate 426 571 time-calibrated phylogenies from individual regions of the genomes; a comparison of 572 these phylogenies then supported three past hybridization events in Princess ci”
Lepbase: the Lepidopteran genome database (2016, background): “All results and datafiles are available at http://download.lepase.org”
Evolution of Ecological Niche Breadth (2017, background): “For example, a recent investigation of cichlid phenotypic diversity and adaptive radiations found support for multiple molecular mechanisms at work (Brawand et al. 2014).”
Next-Generation Sequencing — An Overview of the History, Tools, and “Omic” Applications (2016, background): “Each species contains a reservoir of mutations different from the other species [225].”
Ancient hybridization fuels rapid cichlid fish adaptive radiations (2017, positive): “Toanalyse the genomic distribution of LV outliers that are ﬁxed for alternative alleles between the Congolese and Upper Nile taxa, we used liftOver (http://genome.ucsc.edu/) with a chain ﬁle from Brawand et al. 50 to get positions on the Oreochromis niloticus genome which includes chromosomal inform”
Ecological Opportunity and Adaptive Radiation (2016, background): “…into the genomic structure of several well-studied adaptive radiations have already begun [e.g., Darwin’s finches (Almen et al. 2015), African Rift Lake cichlids (Wagner et al. 2013, Brawand et al. 2014), Heliconius butterflies (Heliconius Genome Consort. et al. 2012, Supple et al. 2013)].”
The Ensembl gene annotation system (2016, background): “1 67 May 2012 (38) Platypus Ornithorhynchus anatinus OANA5 GCF_000002275.”