Consensus-level substitution rates are distinct from the virion-level rate
Abstract
Estimating viral substitution rates is central to evolutionary epidemiology, and recent interest in within-host evolution has sharpened the question of what such rates measure. I distinguish two classes of evolutionary rate estimand that are rarely separated in phylogenetic analysis: the virion-level substitution rate (VLSR), a molecular quantity counting mutational events along lineages, and consensus-level substitution rates (CLSRs), population-summary quantities counting allele frequency threshold crossings from below. CLSRs are indexed by the consensus-generation rule. The VLSR and CLSRs are both biologically meaningful, but not interchangeable. Because the consensus-generation rule defines a given CLSR, it should be reported routinely. This reflection should help analysts make more informed methodological choices when working with sets of virus sequences.
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BibTeX
@misc{pascall2026consensuslevel,
title = {{Consensus-level substitution rates are distinct from the virion-level rate}},
author = {David J Pascall},
howpublished = {arXiv},
year = {2026},
month = oct,
doi = {10.48550/arxiv.2605.31305},
eprint = {2605.31305},
archivePrefix = {arXiv},
url = {https://arxiv.org/abs/2605.31305},
note = {CC BY 4.0},
}
RIS
TY - UNPB
TI - Consensus-level substitution rates are distinct from the virion-level rate
AU - David J Pascall
PY - 2026
DA - 2026/10/19
PB - arXiv
DO - 10.48550/arxiv.2605.31305
UR - https://arxiv.org/abs/2605.31305
AB - Estimating viral substitution rates is central to evolutionary epidemiology, and recent interest in within-host evolution has sharpened the question of what such rates measure. I distinguish two classes of evolutionary rate estimand that are rarely separated in phylogenetic analysis: the virion-level substitution rate (VLSR), a molecular quantity counting mutational events along lineages, and consensus-level substitution rates (CLSRs), population-summary quantities counting allele frequency threshold crossings from below. CLSRs are indexed by the consensus-generation rule. The VLSR and CLSRs are both biologically meaningful, but not interchangeable. Because the consensus-generation rule defines a given CLSR, it should be reported routinely. This reflection should help analysts make more informed methodological choices when working with sets of virus sequences.
ER -