Gene duplication in an African cichlid adaptive radiation

Heather E Machado,Christian Rl Reilly,Suzy Cp Renn,Ginger Jui,David H Lunt,Domino A Joyce

doi:10.1186/1471-2164-15-161

Abstract

BackgroundGene 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).ResultsUsing 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.ConclusionsThese 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.

Highlights

Gene duplication is a source of evolutionary innovation and can contribute to the divergence of lineages; the relative importance of this process remains to be determined
The number of duplicated genes identified for the species from the radiated lineage represents a 38%– 49% increase relative to the number of duplicated genes identified in A. tweddlei
Only recently have studies begun to examine the patterns of gene duplication and copy number polymorphism across species in natural systems, beyond primates (e.g. [26,54,55,56])

Summary

Introduction

Gene duplication is a source of evolutionary innovation and can contribute to the divergence of lineages; the relative importance of this process remains to be determined. Differential selection in heterogeneous environments can result in adaptive radiation when there is a genetic basis for variability in organisms’ success in exploiting alternative resources [1,2,3,4,5] Examples of such radiations include the Cambrian explosion of metazoans [6], the diversification of Darwin’s finches in the Galapagos [7], variations in amphipods and cottoid fishes in Lake Baikal [8], the Caribbean anoles [9], the Hawaiian Silverswords [10] and the explosive speciation of the cichlid fishes in the African Great Lakes [11]. While cichlids can be found on several continents [12], the most dramatic radiations are those of the haplochromine cichlids in the great lakes of East Africa This speciose clade exhibits unprecedented diversity in morphological and behavioral characteristics [13] and accounts for ~10% of the world’s teleost fish. This clade includes lineages that have remained in a riverine environment and have not radiated [14]

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Conclusion