Can Sequence Phylogenies Safely Infer the Origin of the Global Virome?

Edward C Holmes^{1

2

3}, Sebastián Duchêne⁴

Affiliations

¹ Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia edward.holmes@sydney.edu.au.
² Charles Perkins Centre, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia.
³ Sydney Medical School, The University of Sydney, Sydney, NSW, Australia.
⁴ Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia.

PMID: 30992348
PMCID: PMC6469966
DOI: 10.1128/mBio.00289-19

Comment

Can Sequence Phylogenies Safely Infer the Origin of the Global Virome?

Edward C Holmes et al. mBio. 2019.

. 2019 Apr 16;10(2):e00289-19.

doi: 10.1128/mBio.00289-19.

Authors

Edward C Holmes^{1

2

3}, Sebastián Duchêne⁴

Affiliations

¹ Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia edward.holmes@sydney.edu.au.
² Charles Perkins Centre, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia.
³ Sydney Medical School, The University of Sydney, Sydney, NSW, Australia.
⁴ Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia.

PMID: 30992348
PMCID: PMC6469966
DOI: 10.1128/mBio.00289-19

No abstract available

Keywords: RNA polymerase; evolution; phylogeny; virus.

PubMed Disclaimer

Comment in

Reply to Holmes and Duchêne, "Can Sequence Phylogenies Safely Infer the Origin of the Global Virome?": Deep Phylogenetic Analysis of RNA Viruses Is Highly Challenging but Not Meaningless.
Wolf YI, Kazlauskas D, Iranzo J, Lucía-Sanz A, Kuhn JH, Krupovic M, Dolja VV, Koonin EV. Wolf YI, et al. mBio. 2019 Apr 16;10(2):e00542-19. doi: 10.1128/mBio.00542-19. mBio. 2019. PMID: 30992352 Free PMC article. No abstract available.

Comment on

Origins and Evolution of the Global RNA Virome.
Wolf YI, Kazlauskas D, Iranzo J, Lucía-Sanz A, Kuhn JH, Krupovic M, Dolja VV, Koonin EV. Wolf YI, et al. mBio. 2018 Nov 27;9(6):e02329-18. doi: 10.1128/mBio.02329-18. mBio. 2018. PMID: 30482837 Free PMC article.

References

1. Zanotto PMDA, Gibbs MJ, Gould EA, Holmes EC. 1996. A reevaluation of the higher taxonomy of viruses based on RNA polymerases. J Virol 70:6083–6096. - PMC - PubMed
1. Wolf YI, Kazlauskas D, Iranzo J, Lucía-Sanz A, Kuhn JH, Krupovic M, Dolja VV, Koonin EV. 2018. Origins and evolution of the global RNA virome. mBio 9:e02329-18. doi:10.1128/mBio.02329-18. - DOI - PMC - PubMed
1. Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. Mol Biol Evol 32:268–274. doi:10.1093/molbev/msu300. - DOI - PMC - PubMed
1. Talavera G, Castresana J. 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 56:564–577. doi:10.1080/10635150701472164. - DOI - PubMed
1. Capella-Gutiérrez S, Ailla-Martínez TM, Gabaldón T. 2009. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25:1972–1973. doi:10.1093/bioinformatics/btp348. - DOI - PMC - PubMed

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Can Sequence Phylogenies Safely Infer the Origin of the Global Virome?

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Can Sequence Phylogenies Safely Infer the Origin of the Global Virome?

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