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Open Access Highly Accessed Research article

Application of community phylogenetic approaches to understand gene expression: differential exploration of venom gene space in predatory marine gastropods

Dan Chang124* and Thomas F Duda13

Author Affiliations

1 Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI, USA

2 Department of Statistics, University of Michigan, Ann Arbor, MI, USA

3 Smithsonian Tropical Research Institute, Ancόn, Balboa, Republic of Panama

4 Current address: 1156 High Street- mail stop EEBiology, Santa Cruz, CA 95064, USA

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BMC Evolutionary Biology 2014, 14:123  doi:10.1186/1471-2148-14-123

Published: 5 June 2014

Abstract

Background

Predatory marine gastropods of the genus Conus exhibit substantial variation in venom composition both within and among species. Apart from mechanisms associated with extensive turnover of gene families and rapid evolution of genes that encode venom components (‘conotoxins’), the evolution of distinct conotoxin expression patterns is an additional source of variation that may drive interspecific differences in the utilization of species’ ‘venom gene space’. To determine the evolution of expression patterns of venom genes of Conus species, we evaluated the expression of A-superfamily conotoxin genes of a set of closely related Conus species by comparing recovered transcripts of A-superfamily genes that were previously identified from the genomes of these species. We modified community phylogenetics approaches to incorporate phylogenetic history and disparity of genes and their expression profiles to determine patterns of venom gene space utilization.

Results

Less than half of the A-superfamily gene repertoire of these species is expressed, and only a few orthologous genes are coexpressed among species. Species exhibit substantially distinct expression strategies, with some expressing sets of closely related loci (‘under-dispersed’ expression of available genes) while others express sets of more disparate genes (‘over-dispersed’ expression). In addition, expressed genes show higher dN/dS values than either unexpressed or ancestral genes; this implies that expression exposes genes to selection and facilitates rapid evolution of these genes. Few recent lineage-specific gene duplicates are expressed simultaneously, suggesting that expression divergence among redundant gene copies may be established shortly after gene duplication.

Conclusions

Our study demonstrates that venom gene space is explored differentially by Conus species, a process that effectively permits the independent and rapid evolution of venoms in these species.