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Open Access Highly Accessed Research article

Complex patterns of divergence among green-sensitive (RH2a) African cichlid opsins revealed by Clade model analyses

Cameron J Weadick12 and Belinda SW Chang3*

Author affiliations

1 Current Affiliation: Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Spemmanstr. 37, Tuebingen, 72076, Germany

2 Department of Ecology and Evolutionary Biology, University of Toronto, 25 Harbord Ave, Toronto, Ontario, M5S 3G5, Canada

3 Department of Ecology and Evolutionary Biology, Department of Cell and Systems Biology, and Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Harbord Ave, Toronto, Ontario, M5S 3G5, Canada

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Citation and License

BMC Evolutionary Biology 2012, 12:206  doi:10.1186/1471-2148-12-206

Published: 18 October 2012

Abstract

Background

Gene duplications play an important role in the evolution of functional protein diversity. Some models of duplicate gene evolution predict complex forms of paralog divergence; orthologous proteins may diverge as well, further complicating patterns of divergence among and within gene families. Consequently, studying the link between protein sequence evolution and duplication requires the use of flexible substitution models that can accommodate multiple shifts in selection across a phylogeny. Here, we employed a variety of codon substitution models, primarily Clade models, to explore how selective constraint evolved following the duplication of a green-sensitive (RH2a) visual pigment protein (opsin) in African cichlids. Past studies have linked opsin divergence to ecological and sexual divergence within the African cichlid adaptive radiation. Furthermore, biochemical and regulatory differences between the RH2aα and RH2aβ paralogs have been documented. It thus seems likely that selection varies in complex ways throughout this gene family.

Results

Clade model analysis of African cichlid RH2a opsins revealed a large increase in the nonsynonymous-to-synonymous substitution rate ratio (ω) following the duplication, as well as an even larger increase, one consistent with positive selection, for Lake Tanganyikan cichlid RH2aβ opsins. Analysis using the popular Branch-site models, by contrast, revealed no such alteration of constraint. Several amino acid sites known to influence spectral and non-spectral aspects of opsin biochemistry were found to be evolving divergently, suggesting that orthologous RH2a opsins may vary in terms of spectral sensitivity and response kinetics. Divergence appears to be occurring despite intronic gene conversion among the tandemly-arranged duplicates.

Conclusions

Our findings indicate that variation in selective constraint is associated with both gene duplication and divergence among orthologs in African cichlid RH2a opsins. At least some of this variation may reflect an adaptive response to differences in light environment. Interestingly, these patterns only became apparent through the use of Clade models, not through the use of the more widely employed Branch-site models; we suggest that this difference stems from the increased flexibility associated with Clade models. Our results thus bear both on studies of cichlid visual system evolution and on studies of gene family evolution in general.

Keywords:
Codon substitution model; Visual pigment evolution; Nonsynonymous-to-synonymous substitution rate ratio; dN/dS; Clade model; Maximum likelihood; Gene family evolution