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Rapid Evolution by Positive Selection and Gene Gain and Loss: PLA2 Venom Genes in Closely Related Sistrurus Rattlesnakes with Divergent Diets

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Abstract

Rapid evolution of snake venom genes by positive selection has been reported previously but key features of this process such as the targets of selection, rates of gene turnover, and functional diversity of toxins generated remain unclear. This is especially true for closely related species with divergent diets. We describe the evolution of PLA2 gene sequences isolated from genomic DNA from four taxa of Sistrurus rattlesnakes which feed on different prey. We identified four to seven distinct PLA2 sequences in each taxon and phylogenetic analyses suggest that these sequences represent a rapidly evolving gene family consisting of both paralogous and homologous loci with high rates of gene gain and loss. Strong positive selection was implicated as a driving force in the evolution of these protein coding sequences. Exons coding for amino acids that make up mature proteins have levels of variation two to three times greater than those of the surrounding noncoding intronic sequences. Maximum likelihood models of coding sequence evolution reveal that a high proportion (∼30%) of all codons in the mature protein fall into a class of codons with an estimated d N /d S (ω) ratio of at least 2.8. An analysis of selection on individual codons identified nine residues as being under strong (p < 0.01) positive selection, with a disproportionately high proportion of these residues found in two functional regions of the PLA2 protein (surface residues and putative anticoagulant region). This is direct evidence that diversifying selection has led to high levels of functional diversity due to structural differences in proteins among these snakes. Overall, our results demonstrate that both gene gain and loss and protein sequence evolution via positive selection are important evolutionary forces driving adaptive divergence in venom proteins in closely related species of venomous snakes.

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Acknowledgments

We thank Steve Mackessy for generously providing the S. c. edwardsii DNA sample, Jose Diaz, Giancarlo Lopez-Martinez, and David Denlinger for assistance with the lab work, Doug Wynn and Dan Harvey for help in the field, Joe Bielawski, Juan Calvete, James Cotton, Matt Dean, Brian Golding, Jeff Good, Dusan Kordis, Michael Nachman, Tom Waite, and Tom Wilson for advice and discussion, Laura Kubatko for help with the phylogenetic analyses, and the Gibbs Lab Group, Greg Booton, Brian Fry, and three anonymous reviewers for comments. Funding for this study was provided by the Columbus Zoo and Ohio State University.

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  1. Wayne Rossiter

    Present address: Department of Ecology, Evolution, & Natural Resources, Rutgers University, New Brunswick, NJ, 08901-8551, USA

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  1. Department of Evolution, Ecology and Organismal Biology, Ohio State University, 318 West 12th Avenue, Columbus, OH, 43210-1293, USA

    H. Lisle Gibbs & Wayne Rossiter

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Appendix

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Fig. A1
figure 6figure 6

Nucleotide sequences from PLA2 exons 2 (a), 3 (b), and 4 (c), which code for amino acid residues that make up the mature PLA2 venom protein. Complete genomic sequences for each sequence type have been deposited in GenBank under accession numbers EU369741–EU369759

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Gibbs, H.L., Rossiter, W. Rapid Evolution by Positive Selection and Gene Gain and Loss: PLA2 Venom Genes in Closely Related Sistrurus Rattlesnakes with Divergent Diets. J Mol Evol 66, 151–166 (2008). https://doi.org/10.1007/s00239-008-9067-7

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