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

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

Authors

Joshua J Faber-Hammond

Etienne Bezault

Suzy C P Renn



Contributors

B Venkatesh
Editor

Abstract

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.

Citation

Faber-Hammond, J. J., Bezault, E., Lunt, D. H., Joyce, D. A., & 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. https://doi.org/10.1093/gbe/evz185

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 30, -0001
Journal Genome Biology and Evolution
Print ISSN 1759-6653
Publisher Oxford University Press (OUP)
Peer Reviewed Peer Reviewed
Volume 11
Issue 10
Pages 2856-2874
DOI https://doi.org/10.1093/gbe/evz185
Keywords Cichlid; Gene duplication; Genomic architecture; Adaptive radiation; Copy number variation
Public URL https://hull-repository.worktribe.com/output/3267182
Publisher URL https://academic.oup.com/gbe/article/11/10/2856/5556293

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Publisher Licence URL
https://creativecommons.org/licenses/by/4.0/

Copyright Statement
Creative Commons Licence: Attribution 4.0 International License. See: http://creativecommons.org/licenses/by/4.0/





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