Gene duplication in an African cichlid adaptive radiation

Machado, Heather E; Jui, Ginger; Joyce, Domino A.; Reilly, Christian R. L.; Lunt, David H.; Renn, Suzy CP

Abstract

Background Gene duplication is a source of evolutionary innovation and can contribute to the divergence of lineages; however, the relative importance of this process remains to be determined. The explosive divergence of the African cichlid adaptive radiations provides both a model for studying the general role of gene duplication in the divergence of lineages and also an exciting foray into the identification of genomic features that underlie the dramatic phenotypic and ecological diversification in this particular lineage. We present the first genome-wide study of gene duplication in African cichlid fishes, identifying gene duplicates in three species belonging to the Lake Malawi adaptive radiation (Metriaclima estherae, Protomelas similis, Rhamphochromis “chilingali”) and one closely related species from a non-radiated riverine lineage (Astatotilapia tweddlei). Results Using Astatotilapia burtoni as reference, microarray comparative genomic hybridization analysis of 5689 genes reveals 134 duplicated genes among the four cichlid species tested. Between 51 and 55 genes were identified as duplicated in each of the three species from the Lake Malawi radiation, representing a 38%–49% increase in number of duplicated genes relative to the non-radiated lineage (37 genes). Duplicated genes include several that are involved in immune response, ATP metabolism and detoxification. Conclusions These results contribute to our understanding of the abundance and type of gene duplicates present in cichlid fish lineages. The duplicated genes identified in this study provide candidates for the analysis of functional relevance with regard to phenotype and divergence. Comparative sequence analysis of gene duplicates can address the role of positive selection and adaptive evolution by gene duplication, while further study across the phylogenetic range of cichlid radiations (and more generally in other adaptive radiations) will determine whether the patterns of gene duplication seen in this study consistently accompany rapid radiation.

Citation

Machado, H. E., Jui, G., Joyce, D. A., Reilly, C. R. L., Lunt, D. H., & Renn, S. C. (2014). Gene duplication in an African cichlid adaptive radiation. BMC Genomics, 15(1), 161. https://doi.org/10.1186/1471-2164-15-161

• Acceptance Date: Feb 19, 2014
• Publication Date: Feb 26, 2014
• Deposit Date: Mar 22, 2016
• Publicly Available Date: Mar 22, 2016
• Journal: BMC genomics
• Print ISSN: 1471-2164
• Publisher: Springer Verlag
• Peer Reviewed: Peer Reviewed
• Volume: 15
• Issue: 1
• Article Number: ARTN 161
• Pages: 161
• DOI: https://doi.org/10.1186/1471-2164-15-161
• Keywords: Cichlids; Gene duplication; Adaptive radiation
• Public URL: https://hull-repository.worktribe.com/output/433990
• Publisher URL: http://www.biomedcentral.com/1471-2164/15/161
• Additional Information: Copy of article first published in: BMC genomics, 2014, v.15, issue 1.
• Contract Date: Mar 22, 2016