Research article
East African cassava mosaic-like viruses from Africa to Indian ocean islands: molecular diversity, evolutionary history and geographical dissemination of a bipartite begomovirus
- † Equal contributors
1 CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l’IRAT, Saint-Pierre, Ile de La Réunion, 97410, France
2 Université de La Réunion, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l’IRAT, Saint-Pierre, Ile de La Réunion, 97410, France
3 Service de Protection des Végétaux - Direction de l’Agriculture et de la Forêt, B.P 103, Mamoudzou, Mayotte, 97600, France
4 Institut National de Recherche pour l’Agriculture, la Pêche et l’Environnement, BP289, Moroni, Grande Comore, Union des Comores
5 South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
6 School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
7 Biomolecular interaction centre, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
8 Electron Microscope Unit, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
9 Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory 7925, Cape Town, South Africa
BMC Evolutionary Biology 2012, 12:228 doi:10.1186/1471-2148-12-228
Published: 27 November 2012Additional files
Additional file 1:
Table S1. List of the sequences used in the phylogeographic analyses. For each sequence, accession number, sampling date, source, geographical cluster and datasets including the sequence are informed. Additionally, for sequences used in the pseudo-recombination analysis, associated components are indicated.
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Additional file 2:
Figure S1. Maximum Likelihood phylogenetic tree of CMG DNA-A sequences. The robustness of each branch is assessed using approximate likelihood ratio test statistics. Different species are indicated with different colours. The tree is rooted with the Sri Lankan cassava mosaic virus (SLCMV) and Indian cassava mosaic virus (ICMV) group.
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Additional file 3:
Figure S2. Maximum Likelihood phylogenetic tree of CMG DNA-B sequences. The robustness of each branch is assessed using approximate likelihood ratio test statistics. The tree is rooted with the SLCMV/ICMV and ACMV groups.
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Additional file 4:
Figure S3. Distribution of recombination breakpoints detected within (A) DNA-A and (B) DNA-B sequences. All estimated breakpoint positions are indicated by small vertical lines at the top of the graph. A 200-nucleotide window was moved along the alignment one nucleotide at a time and the number of breakpoints detected within the window region was counted and plotted (solid line). The horizontal lines at the top of each graph indicate 99% and 95% confidence thresholds for globally significant breakpoint clusters. Light and dark grey areas respectively indicate local 99% and 95% breakpoint clustering thresholds, taking into account local regional differences in sequence diversity that influence the ability of different recombination detection methods to identify recombination breakpoints. Red areas indicate recombination hot-spots.
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Additional file 5:
Figure S4. Geographical distance based clustering of FG-A, CP and FG-B sequence datasets. Groups are indicated on the figure and were used as discrete geographical locations for phylogeographic reconstructions in BEAST.
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Additional file 6:
Figure S5. Maximum clade credibility trees constructed from the EACMV-like DNA-A Full genomes (FG-A) dataset. Branches are coloured according to the most probable location state of their descendant nodes, with black circled nodes indicating a state probability < 0.5. The time-scale of evolutionary changes represented in the tree is indicated by the scale bar below it. Whereas filled circles associated with nodes to the right of branches indicate > 95% posterior probability support for these branches, open circles indicate branches with > 70% posterior support. Nodes to the right of branches with < 70% support are left unlabelled. The bar graph on the left corner indicates the root location probabilities. Grey bars represent the probabilities obtained with randomisation of the tip locations. Probable introduction events from Africa to the SWIO islands are indicated with red arrows. Note the bicoloured branch for which uncertainty is highlighted as it is very uncertain whether the location state is East/Centre Africa or Grande Comore (an important distinction when attempting to infer the number of migrations between Africa and the SWIO islands).
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Additional File 7:
KML file of CP dataset phylogeography analysis. Lines between locations represent branches in the MCC tree along which location transition occurs. Location circle diameters are proportional to the number of MCC branches maintaining a particular location state at each time-point. The yellow-orange color gradient informs the location state probability (low-high). Altitude of each line is proportional to the time elapsed between its nodes. KML files can be visualized in Google Earth (http://www.google.com/earth/index.html webcite).
Format: KML Size: 1.9MB Download file
Additional File 8:
KML file of FG-A dataset phylogeography analysis. Lines between locations represent branches in the MCC tree along which location transition occurs. Location circle diameters are proportional to the number of MCC branches maintaining a particular location state at each time-point. The yellow-orange color gradient informs the location state probability (low-high). Altitude of each line is proportional to the time elapsed between its nodes. KML files can be visualized in Google Earth (http://www.google.com/earth/index.html webcite).
Format: KML Size: 1.9MB Download file
Additional File 9:
KML file of FG-B dataset phylogeography analysis. Lines between locations represent branches in the MCC tree along which location transition occurs. Location circle diameters are proportional to the number of MCC branches maintaining a particular location state at each time-point. The yellow-orange color gradient informs the location state probability (low-high). Altitude of each line is proportional to the time elapsed between its nodes. KML files can be visualized in Google Earth (http://www.google.com/earth/index.html webcite).
Format: KML Size: 1.5MB Download file
