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. 2011;6(7):e22252.
doi: 10.1371/journal.pone.0022252. Epub 2011 Jul 29.

Codivergence of mycoviruses with their hosts

Markus Göker  1 , Carmen Scheuner, Hans-Peter Klenk, J Benjamin Stielow, Wulf Menzel
Affiliations

Codivergence of mycoviruses with their hosts

Markus Göker et al. PLoS One. 2011.

Abstract

Background: The associations between pathogens and their hosts are complex and can result from any combination of evolutionary events such as codivergence, switching, and duplication of the pathogen. Mycoviruses are RNA viruses which infect fungi and for which natural vectors are so far unknown. Thus, lateral transfer might be improbable and codivergence their dominant mode of evolution. Accordingly, mycoviruses are a suitable target for statistical tests of virus-host codivergence, but inference of mycovirus phylogenies might be difficult because of low sequence similarity even within families.

Methodology: We analyzed here the evolutionary dynamics of all mycovirus families by comparing virus and host phylogenies. Additionally, we assessed the sensitivity of the co-phylogenetic tests to the settings for inferring virus trees from their genome sequences and approximate, taxonomy-based host trees.

Conclusions: While sequence alignment filtering modes affected branch support, the overall results of the co-phylogenetic tests were significantly influenced only by the number of viruses sampled per family. The trees of the two largest families, Partitiviridae and Totiviridae, were significantly more similar to those of their hosts than expected by chance, and most individual host-virus links had a significant positive impact on the global fit, indicating that codivergence is the dominant mode of virus diversification. However, in this regard mycoviruses did not differ from closely related viruses sampled from non-fungus hosts. The remaining virus families were either dominated by other evolutionary modes or lacked an apparent overall pattern. As this negative result might be caused by insufficient taxon sampling, the most parsimonious hypothesis still is that host-parasite evolution is basically the same in all mycovirus families. This is the first study of mycovirus-host codivergence, and the results shed light not only on how mycovirus biology affects their co-phylogenetic relationships, but also on their presumable host range itself.

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Conflict of interest statement

Competing Interests: Markus Göker, Carmen Scheuner, Hans-Peter Klenk, J. Benjamin Stielow and Wulf Menzel are employees of Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ). The DSMZ is an independent, non-profit organisation. There are no patents, products in development or marketed products to declare. The authors adhere to all the PLoS ONE policies on sharing data and materials.

Figures

Figure 1
Figure 1. Results of the cost-space exploration with TreeFitter for Chrysoviridae (upper left), Narnaviridae (upper right), Partitiviridae (lower left) and Totiviridae (lower right).
For each family, the resulting p values are plotted over the respective combination of duplication (parasite speciation on a single host) and switching (lateral transfer of the parasite) cost. Duplication and switching costs were varied between 0.0 and 10.0 in increments of 0.5. Those p values at most as large as the chosen threshold (α = 0.05) indicate a set of evolutionary event costs which explains the data significantly better than random.
Figure 2
Figure 2. Tanglegram for the Chrysoviridae and their hosts.
The parasite supermatrix was constructed using RASCAL and GBLOCKS alignment filtering, and the ‘theory’ host distances were used. All links were insignificant according to the ParaFit test, which also accepted the global null hypothesis of no correspondence between host and Chrysoviridae phylogenies. The numbers on the branches within the parasite tree are maximum-likelihood bootstrap values ≥60%. Host branches are colored according to their deep taxonomic affiliations: blue, Fungi; light blue, Ascomycota. Stars on the host branches indicate those that were obtained by randomly resolving polytomies; all other branches were derived from the host classification.
Figure 3
Figure 3. Tanglegram for the Narnaviridae and their hosts.
The parasite supermatrix was constructed using RASCAL and GBLOCKS alignment filtering, and the ‘theory’ host distances were used. All links were insignificant according to the ParaFit test, which also accepted the global null hypothesis of no correspondence between host and Narnaviridae phylogenies. The numbers on the branches within the parasite tree are maximum-likelihood bootstrap values ≥60%. Host branches are coloured according to their deep taxonomic affiliations: blue, Fungi (light blue, Ascomycota; dark blue, Basidiomycota); green, Viridiplantae.
Figure 4
Figure 4. Tanglegram for the Partitiviridae and their hosts.
The parasite supermatrix was constructed using RASCAL and GBLOCKS alignment filtering, and the ‘theory’ host distances were used. Most (69%) links were significant according to the ParaFit test, which also rejected the global null hypothesis of no correspondence between host and Partitiviridae phylogenies. The numbers on the branches within the parasite tree are maximum-likelihood bootstrap values ≥60%. ‘A’, ‘B’, ‘C’, ‘D’ and ‘E’ denote the major virus clades as discussed in the text. Host branches are colored according to their deep taxonomic affiliations: blue, Fungi (light blue, Ascomycota; dark blue, Basidiomycota); green, Viridiplantae. Stars on the host branches indicate those that were obtained by randomly resolving polytomies; all other branches were derived from the host classification.
Figure 5
Figure 5. Tanglegram for the Totiviridae and their hosts.
The parasite supermatrix was constructed using RASCAL and GBLOCKS alignment filtering, and the ‘theory’ host distances were used. Most (82%) links were significant according to the ParaFit test, which also rejected the global null hypothesis of no correspondence between host and Totiviridae phylogenies. The numbers on the branches within the parasite tree are maximum-likelihood bootstrap values ≥60%. ‘A’, ‘B’, ‘C’ and ‘D’ denote the major virus clades as discussed in the text. Host branches are colored according to their deep taxonomic affiliations: blue, Fungi (light blue, Ascomycota; dark blue, Basidiomycota); green, Viridiplantae; red, Metazoa; yellow, others. Stars on the host branches indicate those that were obtained by randomly resolving polytomies; all other branches were derived from the host classification.
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