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Open Access Research article

Gene duplication in an African cichlid adaptive radiation

Heather E Machado1, Ginger Jui2, Domino A Joyce3, Christian RL Reilly4, David H Lunt3 and Suzy CP Renn2*

Author Affiliations

1 Department of Biology, Stanford University, Stanford, CA 94305, USA

2 Department of Biology, Reed College, Portland, OR 97202, USA

3 School of Biological Biomedical and Environmental Science, University of Hull, Hull HU6 7RX, UK

4 Santa Catalina School, Monterey, CA 93940, USA

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BMC Genomics 2014, 15:161  doi:10.1186/1471-2164-15-161

Published: 26 February 2014

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.