Sequence analyses of the distal-less homeobox gene family in East African cichlid fishes reveal signatures of positive selection

BMC Evolutionary Biology

Walter Salzburger¹  Fabienne D Kim¹  Eveline T Diepeveen¹ 

[1] Zoological Institute, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland

关键词: dN/dS;    Gene duplication;    Differential selection;    Positive selection;    Teleost fishes;    Cichlid fishes;    Molecular evolution;    Distal-less homeobox gene;   

Others  :  1086785
DOI  :  10.1186/1471-2148-13-153

 received in 2013-05-09, accepted in 2013-07-05,  发布年份 2013

【 摘 要 】

Background

Gen(om)e duplication events are hypothesized as key mechanisms underlying the origin of phenotypic diversity and evolutionary innovation. The diverse and species-rich lineage of teleost fishes is a renowned example of this scenario, because of the fish-specific genome duplication. Gene families, generated by this and other gene duplication events, have been previously found to play a role in the evolution and development of innovations in cichlid fishes - a prime model system to study the genetic basis of rapid speciation, adaptation and evolutionary innovation. The distal-less homeobox genes are particularly interesting candidate genes for evolutionary novelties, such as the pharyngeal jaw apparatus and the anal fin egg-spots. Here we study the dlx repertoire in 23 East African cichlid fishes to determine the rate of evolution and the signatures of selection pressure.

Results

Four intact dlx clusters were retrieved from cichlid draft genomes. Phylogenetic analyses of these eight dlx loci in ten teleost species, followed by an in-depth analysis of 23 East African cichlid species, show that there is disparity in the rates of evolution of the dlx paralogs. Dlx3a and dlx4b are the fastest evolving dlx genes, while dlx1a and dlx6a evolved more slowly. Subsequent analyses of the nonsynonymous-synonymous substitution rate ratios indicate that dlx3b, dlx4a and dlx5a evolved under purifying selection, while signs of positive selection were found for dlx1a, dlx2a, dlx3a and dlx4b.

Conclusions

Our results indicate that the dlx repertoire of teleost fishes and cichlid fishes in particular, is shaped by differential selection pressures and rates of evolution after gene duplication. Although the divergence of the dlx paralogs are putative signs of new or altered functions, comparisons with available expression patterns indicate that the three dlx loci under strong purifying selection, dlx3b, dlx4a and dlx5a, are transcribed at high levels in the cichlids’ pharyngeal jaw and anal fin. The dlx paralogs emerge as excellent candidate genes for the development of evolutionary innovations in cichlids, although further functional analyses are necessary to elucidate their respective contribution.

【 授权许可】

   
2013 Diepeveen et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

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