Time Clustered Sampling Can Inflate the Inferred Substitution Rate in Foot-And- Mouth Disease Virus Analyses
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Date
2015
Journal Title
Journal ISSN
Volume Title
Publisher
PLoS ONE
Abstract
With the emergence of analytical software for the inference of viral evolution, a number of
studies have focused on estimating important parameters such as the substitution rate and
the time to the most recent common ancestor (tMRCA) for rapidly evolving viruses. Coupled
with an increasing abundance of sequence data sampled under widely different schemes,
an effort to keep results consistent and comparable is needed. This study emphasizes commonly
disregarded problems in the inference of evolutionary rates in viral sequence data
when sampling is unevenly distributed on a temporal scale through a study of the foot-andmouth
(FMD) disease virus serotypes SAT 1 and SAT 2. Our study shows that clustered
temporal sampling in phylogenetic analyses of FMD viruses will strongly bias the inferences
of substitution rates and tMRCA because the inferred rates in such data sets reflect a rate
closer to the mutation rate rather than the substitution rate. Estimating evolutionary parameters
from viral sequences should be performed with due consideration of the differences in
short-term and longer-term evolutionary processes occurring within sets of temporally sampled
viruses, and studies should carefully consider how samples are combined.
Description
Keywords
Foot-And- Mouth Disease, Virus Analyses
Citation
Pedersen C-ET, Frandsen P, Wekesa SN, Heller R, Sangula AK, Wadsworth J, et al. (2015) Time Clustered Sampling Can Inflate the Inferred Substitution Rate in Foot-And-Mouth Disease Virus Analyses. PLoS ONE 10(12): e0143605. doi:10.1371/ journal.pone.0143605