Rectifying long-standing misconceptions about the p statistic for molecular dating

Macaulay, V. , Soares, P. and Richards, M. B. (2019) Rectifying long-standing misconceptions about the p statistic for molecular dating. PLoS ONE, 14(2), e0212311. (doi: 10.1371/journal.pone.0212311) (PMID:30779770)

Abstract

When divided by a given mutation rate, the ρ (rho) statistic provides a simple estimator of the age of a clade within a phylogenetic tree by averaging the number of mutations from each sample in the clade to its root. However, a long-standing critique of the use of ρ in genetic dating has been quite often cited. Here we show that the critique is unfounded. We demonstrate by a formal mathematical argument and illustrate with a simulation study that ρ estimates are unbiased and also that ρ and maximum likelihood estimates do not differ in any systematic fashion. We also demonstrate that the claim that the associated confidence intervals commonly estimate the uncertainty inappropriately is flawed since it relies on a means of calculating standard errors that is not used by any other researchers, whereas an established expression for the standard error is largely unproblematic. We conclude that ρ dating, alongside approaches such as maximum likelihood (ML) and Bayesian inference, remains a useful tool for genetic dating.

• Item Type: Articles
• Additional Information: P.S. and M.B.R. acknowledge FCT support through project PTDC/EPH-ARQ/4164/ 2014 partially funded by FEDER funds (COMPETE 2020 project 016899). P.S. is supported by FCT, European Social Fund, Programa Operacional Potencial Humano and the FCT Investigator Programme (IF/01641/2013) and acknowledges FCT/MEC for support to CBMA through Portuguese funds (PIDDAC)—PEst-OE/BIA/UI4050/2014. M.B. R. received support from a Leverhulme Doctoral Scholarship programme.
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Macaulay, Dr Vincent

Creator Roles

Macaulay, V.: Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Project administration, Software, Supervision, Validation, Visualization, Writing – original draft, Writing – review and editing

• Authors: Macaulay, V., Soares, P., and Richards, M. B.
• College/School: College of Science and Engineering > School of Mathematics and Statistics > Mathematics
• Journal Name: PLoS ONE
• Publisher: Public Library of Science
• ISSN: 1932-6203
• ISSN (Online): 1932-6203
• Copyright Holders: Copyright © 2019 The Authors
• First Published: First published in PLoS ONE 14(2):e0212311
• Publisher Policy: Reproduced under a Creative Commons License