The phylodynamic threshold of measurably evolving populations
Abstract
The molecular clock is a fundamental tool for understanding the time and pace of evolution, requiring calibration information alongside molecular data. Sampling times are often used for calibration since some organisms accumulate enough mutations over the course of their sampling period. This practice ties together two key concepts: measurably evolving populations and the phylodynamic threshold. Our current understanding suggests that populations meeting these criteria are suitable for molecular clock calibration via sampling times. However, the definitions and implications of these concepts remain unclear. Using Hepatitis B virus-like simulations and analyses of empirical data, this study shows that determining whether a population is measurably evolving or has reached the phylodynamic threshold does not only depend on the data, but also on model assumptions and sampling strategies. In Bayesian applications, a lack of temporal signal due to a narrow sampling window results in a prior that is overly informative relative to the data, such that a prior that is potentially misleading typically requires a wider sampling window than one that is reasonable. In our analyses we demonstrate that assessing prior sensitivity is more important than the outcome of tests of temporal signal. Our results offer guidelines to improve molecular clock inferences and highlight limitations in molecular sequence sampling procedures.
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BibTeX
@article{weber2026phylodynamic,
title = {{The phylodynamic threshold of measurably evolving populations}},
author = {Ariane Weber and Julia Kende and Camila Duitama González and Sanni Översti and Sebastian Duchene},
journal = {Molecular Biology and Evolution},
year = {2026},
month = jun,
doi = {10.1093/molbev/msag133},
url = {https://pasteur.hal.science/pasteur-05646474v2},
note = {CC BY-NC 4.0},
}
RIS
TY - JOUR
TI - The phylodynamic threshold of measurably evolving populations
AU - Ariane Weber
AU - Julia Kende
AU - Camila Duitama González
AU - Sanni Översti
AU - Sebastian Duchene
PY - 2026
DA - 2026/06/03
JO - Molecular Biology and Evolution
DO - 10.1093/molbev/msag133
UR - https://pasteur.hal.science/pasteur-05646474v2
AB - The molecular clock is a fundamental tool for understanding the time and pace of evolution, requiring calibration information alongside molecular data. Sampling times are often used for calibration since some organisms accumulate enough mutations over the course of their sampling period. This practice ties together two key concepts: measurably evolving populations and the phylodynamic threshold. Our current understanding suggests that populations meeting these criteria are suitable for molecular clock calibration via sampling times. However, the definitions and implications of these concepts remain unclear. Using Hepatitis B virus-like simulations and analyses of empirical data, this study shows that determining whether a population is measurably evolving or has reached the phylodynamic threshold does not only depend on the data, but also on model assumptions and sampling strategies. In Bayesian applications, a lack of temporal signal due to a narrow sampling window results in a prior that is overly informative relative to the data, such that a prior that is potentially misleading typically requires a wider sampling window than one that is reasonable. In our analyses we demonstrate that assessing prior sensitivity is more important than the outcome of tests of temporal signal. Our results offer guidelines to improve molecular clock inferences and highlight limitations in molecular sequence sampling procedures.
SN - 0737-4038
SN - 1537-1719
ER -