Firth, Cadhla, Kitchen, Andrew, Shapiro, Beth, Suchard, Marc A., Holmes, Edward C., and Rambaut, Andrew (2010) Using Time-Structured Data to Estimate Evolutionary Rates of Double-Stranded DNA Viruses. Molecular Biology and Evolution, 27 (9). pp. 2038-2051.

PDF (Published Version) - Published Version Restricted to Repository staff only

Abstract

Double-stranded (ds) DNA viruses are often described as evolving through long-term codivergent associations with their hosts, a pattern that is expected to be associated with low rates of nucleotide substitution. However, the hypothesis of codivergence between dsDNA viruses and their hosts has rarely been rigorously tested, even though the vast majority of nucleotide substitution rate estimates for dsDNA viruses are based upon this assumption. It is therefore important to estimate the evolutionary rates of dsDNA viruses independent of the assumption of host-virus codivergence. Here, we explore the use of temporally structured sequence data within a Bayesian framework to estimate the evolutionary rates for seven human dsDNA viruses, including variola virus (VARV) (the causative agent of smallpox) and herpes simplex virus-1. Our analyses reveal that although the VARV genome is likely to evolve at a rate of approximately 1 × 10−5 substitutions/site/year and hence approaching that of many RNA viruses, the evolutionary rates of many other dsDNA viruses remain problematic to estimate. Synthetic data sets were constructed to inform our interpretation of the substitution rates estimated for these dsDNA viruses and the analysis of these demonstrated that given a sequence data set of appropriate length and sampling depth, it is possible to use time-structured analyses to estimate the substitution rates of many dsDNA viruses independently from the assumption of host-virus codivergence. Finally, the discovery that some dsDNA viruses may evolve at rates approaching those of RNA viruses has important implications for our understanding of the long-term evolutionary history and emergence potential of this major group of viruses.

Item ID:	59918
Item Type:	Article (Research - C1)
ISSN:	0737-4038
Copyright Information:	© The Author 2010. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved.
Date Deposited:	31 Jul 2024 23:27
FoR Codes:	06 BIOLOGICAL SCIENCES > 0603 Evolutionary Biology > 060399 Evolutionary Biology not elsewhere classified @ 50% 06 BIOLOGICAL SCIENCES > 0605 Microbiology > 060506 Virology @ 25% 06 BIOLOGICAL SCIENCES > 0605 Microbiology > 060503 Microbial Genetics @ 25%
SEO Codes:	97 EXPANDING KNOWLEDGE > 970106 Expanding Knowledge in the Biological Sciences @ 100%
	More Statistics