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The Genomic Substrate for Adaptive Radiation: Copy Number Variation across 12 Tribes of African Cichlid Species

Faber-Hammond, Joshua J.; Renn, Suzy C.P.; Venkatesh, B.; Faber-Hammond, Joshua J; Bezault, Etienne; Lunt, David H.; Joyce, Domino A.; Renn, Suzy C P


Joshua J. Faber-Hammond

Suzy C.P. Renn

B. Venkatesh

Joshua J Faber-Hammond

Etienne Bezault

Suzy C P Renn


B Venkatesh


© 2019 Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution 2019. This work is written by US Government employees and is in the public domain in the US. The initial sequencing of five cichlid genomes revealed an accumulation of genetic variation, including extensive copy number variation in cichlid lineages particularly those that have undergone dramatic evolutionary radiation. Gene duplication has the potential to generate substantial molecular substrate for the origin of evolutionary novelty. We use array-based comparative heterologous genomic hybridization to identify copy number variation events (CNVEs) for 168 samples representing 53 cichlid species including the 5 species for which full genome sequence is available. We identify an average of 50-100 CNVEs per individual. For those species represented by multiple samples, we identify 150-200 total CNVEs suggesting a substantial amount of intraspecific variation. For these species, only ∼10% of the detected CNVEs are fixed. Hierarchical clustering of species according to CNVE data recapitulates phylogenetic relationships fairly well at both the tribe and radiation level. Although CNVEs are detected on all linkage groups, they tend to cluster in "hotspots" and are likely to contain and be flanked by transposable elements. Furthermore, we show that CNVEs impact functional categories of genes with potential roles in adaptive phenotypes that could reasonably promote divergence and speciation in the cichlid clade. These data contribute to a more complete understanding of the molecular basis for adaptive natural selection, speciation, and evolutionary radiation.


Faber-Hammond, J. J., Renn, S. C., Venkatesh, B., Faber-Hammond, J. J., Bezault, E., Lunt, D. H., …Renn, S. C. P. (2019). The Genomic Substrate for Adaptive Radiation: Copy Number Variation across 12 Tribes of African Cichlid Species. Genome Biology and Evolution, 11(10), 2856-2874.

Journal Article Type Article
Acceptance Date Aug 27, 2019
Online Publication Date Aug 29, 2019
Publication Date Oct 1, 2019
Deposit Date Nov 28, 2019
Publicly Available Date Nov 28, 2019
Journal Genome Biology and Evolution
Print ISSN 1759-6653
Electronic ISSN 1759-6653
Publisher Oxford University Press
Peer Reviewed Peer Reviewed
Volume 11
Issue 10
Pages 2856-2874
Keywords Cichlid; Gene duplication; Genomic architecture; Adaptive radiation; Copy number variation
Public URL
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