Imperial College London
Alternate

DrErikVolz

Faculty of Medicine, School of Public Health

Reader in Population Biology of Infectious Diseases
 
 
 
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Contact

 

+44 (0)20 7594 1933e.volz Website

 
 
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Location

 

UG10Norfolk PlaceSt Mary's Campus

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Summary

 

Publications

Citation

BibTex format

@article{Didelot:2021:molbev/msaa193,
author = {Didelot, X and Siveroni, I and Volz, EM},
doi = {molbev/msaa193},
journal = {Molecular Biology and Evolution},
pages = {307--317},
title = {Additive uncorrelated relaxed clock models for the dating of genomic epidemiology phylogenies},
url = {http://dx.doi.org/10.1093/molbev/msaa193},
volume = {38},
year = {2021}
}
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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - Phylogenetic dating is one of the most powerful and commonly used methods of drawing epidemiological interpretations from pathogen genomic data. Building such trees requires considering a molecular clock model which represents the rate at which substitutions accumulate on genomes. When the molecular clock rate is constant throughout the tree then the clock is said to be strict, but this is often not an acceptable assumption. Alternatively, relaxed clock models consider variations in the clock rate, often based on a distribution of rates for each branch. However, we show here that the distributions of rates across branches in commonly used relaxed clock models are incompatible with the biological expectation that the sum of the numbers of substitutions on two neighbouring branches should be distributed as the substitution number on a single branch of equivalent length. We call this expectation the additivity property. We further show how assumptions of commonly used relaxed clock models can lead to estimates of evolutionary rates and dates with low precision and biased confidence intervals. We therefore propose a new additive relaxed clock model where the additivity property is satisfied. We illustrate the use of our new additive relaxed clock model on a range of simulated and real datasets, and we show that using this new model leads to more accurate estimates of mean evolutionary rates and ancestral dates.
AU  - Didelot,X
AU  - Siveroni,I
AU  - Volz,EM
DO  - molbev/msaa193
EP  - 317
PY  - 2021///
SN  - 0737-4038
SP  - 307
TI  - Additive uncorrelated relaxed clock models for the dating of genomic epidemiology phylogenies
T2  - Molecular Biology and Evolution
UR  - http://dx.doi.org/10.1093/molbev/msaa193
UR  - https://www.ncbi.nlm.nih.gov/pubmed/32722797
UR  - https://academic.oup.com/mbe/article/38/1/307/5877436
UR  - http://hdl.handle.net/10044/1/83378
VL  - 38
ER  -
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