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Review

Accounting for the Biological Complexity of Pathogenic Fungi in Phylogenetic Dating

MRC Centre for Global Infectious Disease Analysis, Imperial College School of Public Health, Imperial College London, Norfolk Place, London W2 1PG, UK
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Author to whom correspondence should be addressed.
Academic Editor: David S. Perlin
J. Fungi 2021, 7(8), 661; https://doi.org/10.3390/jof7080661
Received: 4 July 2021 / Revised: 11 August 2021 / Accepted: 11 August 2021 / Published: 14 August 2021
(This article belongs to the Special Issue Fungal Pathogens and Human Health)
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. View Full-Text
Keywords: evolution; methodology; mutation rates; phylogenomics; recombination evolution; methodology; mutation rates; phylogenomics; recombination
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MDPI and ACS Style

Edwards, H.M.; Rhodes, J. Accounting for the Biological Complexity of Pathogenic Fungi in Phylogenetic Dating. J. Fungi 2021, 7, 661. https://doi.org/10.3390/jof7080661

AMA Style

Edwards HM, Rhodes J. Accounting for the Biological Complexity of Pathogenic Fungi in Phylogenetic Dating. Journal of Fungi. 2021; 7(8):661. https://doi.org/10.3390/jof7080661

Chicago/Turabian Style

Edwards, Hannah M., and Johanna Rhodes. 2021. "Accounting for the Biological Complexity of Pathogenic Fungi in Phylogenetic Dating" Journal of Fungi 7, no. 8: 661. https://doi.org/10.3390/jof7080661

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