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Supplemental Information

Symmetric Difference Distance between Maximum Parsinomy trees

DOI: 10.7287/peerj.preprints.2822v1/supp-2

Symmetric Difference Distance between Maximum Likelihood trees

DOI: 10.7287/peerj.preprints.2822v1/supp-3

Phylogram for MP tree build using the five loci TEF1-TUB-CAL-HIS-ITS for the 96 Diaporthe species

DOI: 10.7287/peerj.preprints.2822v1/supp-4

Phylogram for ML tree build using the five loci TEF1-TUB-CAL-HIS-ITS for the 96 Diaporthe species

DOI: 10.7287/peerj.preprints.2822v1/supp-5

Phylogram for MP tree build using the TEF1 locus for the 96 Diaporthe species

DOI: 10.7287/peerj.preprints.2822v1/supp-6

Phylogram for ML tree build using the TEF1 locus for the 96 Diaporthe species

DOI: 10.7287/peerj.preprints.2822v1/supp-7

Comparison of MP trees generated from the same alignment of 5 genes, when changing the position of the TEF sequences in that alignment

The numbers represent the bootstrap value for the branching in each tree. Red – MP tree with TEF in the first position of the alignment. Mauve – MP tree with TEF in the second position of the alignment. Green – MP tree with TEF in the third position of the alignment. Blue – MP tree with TEF in the fourth position of the alignment. Black – MP tree with TEF in the fifth position of the alignment. The only small effect of shifting the position of TEF is observed in the TEF-ITS-TUB-HIS-CAL (red) and ITS-TEF-TUB-HIS-CAL (mauve) trees. In TEF-ITS-TUB-HIS-CAL case, flipping is observed in a small number of terminal branches. That flipping does not affect the overall topology of the tree, which is identical to that of the remaining trees. These results suggest that changing the order of the genes in the alignment will have a negligible effect on the topology of the phylogenetic trees.

DOI: 10.7287/peerj.preprints.2822v1/supp-8

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Liliana Santos conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Artur Alves conceived and designed the experiments, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Rui Alves conceived and designed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Data Deposition

The following information was supplied regarding data availability:

TreeBase (Study 20343)

http://purl.org/phylo/treebase/phylows/study/TB2:S20343?x-access-code=7bc7845289824d16cadf49a198e2c723&format=html

Funding

This work was financed by European Funds through COMPETE and by National Funds through the Portuguese Foundation for Science and Technology (FCT) within project PANDORA (PTDC/AGR-FOR/3807/2012 – FCOMP-01-0124-FEDER-027979). The authors received financing from FCT to CESAM (UID/AMB/50017/2013), Artur Alves (FCT Investigator Programme – IF/00835/2013) and a post-doctoral grant to Liliana Santos (SFRH/BPD/90684/2012), grants BFU2010-17704 from Ministerio de Ciencia e Innovación, 2009SGR809 from Generalitat de Catalunya, and bridge grants from the Dean for Research and the Departament de Ciències Mèdiques Bàsiques of the University of Lleida (Spain) to Rui Alves. There was no additional external funding received for this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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