Accounting for the biological complexity of pathogenic fungi in phylogenetic dating

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Title: Accounting for the biological complexity of pathogenic fungi in phylogenetic dating
Authors: Edwards, H
Rhodes, J
Item Type: Journal Article
Abstract: In the study of pathogen evolution, temporal dating of phylogenies provides information on when species and lineages may have diverged in the past. When combined with spatial and epidemiological data in phylodynamic models, these dated phylogenies can also help infer where and when outbreaks occurred, how pathogens may have spread to new geographic locations and/or niches, and how virulence or drug resistance has developed over time. Although widely applied to viruses and, increasingly, to bacterial pathogen outbreaks, phylogenetic dating is yet to be widely used in the study of pathogenic fungi. Fungi are complex organisms with several biological processes that could present issues with appropriate inference of phylogenies, clock rates, and divergence times, including high levels of recombination and slower mutation rates although with potentially high levels of mutation rate variation. Here, we discuss some of the key methodological challenges in accurate phylogeny reconstruction for fungi in the context of the temporal analyses conducted to date and make recommendations for future dating studies to aid development of a best practices roadmap in light of the increasing threat of fungal outbreaks and antifungal drug resistance worldwide.
Issue Date: 14-Aug-2021
Date of Acceptance: 11-Aug-2021
DOI: 10.3390/jof7080661
ISSN: 2309-608X
Publisher: MDPI
Journal / Book Title: Journal of Fungi
Volume: 7
Issue: 8
Copyright Statement: © 2021 by the authors.Licensee MDPI, Basel, Switzerland.This article is an open access articledistributed under the terms andconditions of the Creative CommonsAttribution (CC BY) license (
Publication Status: Published
Article Number: ARTN 661
Appears in Collections:Faculty of Medicine
School of Public Health

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