Table 1.
GenBank Accession Numbers and Voucher Information for Query Sequences.
Figure 1.
Modified Rand Index (MRI) plot based on the poa alignment, uncorrected distances, the globally optimal F value (1.0) and two suboptimal F values (0.0 and 0.5). Axes: x-axis, T values examined (values larger than 0.25 gave the same result because all sequences were assigned to a single cluster); y-axis, resulting MRI values for taxonomy-based optimization (thick lines) and host-based optimization (thin lines). Colours: black, F = 1.0; dark grey, F = 0.5; light grey, F = 0.0.
Figure 2.
Dependency of the number of molecular taxonomic units (TU) on T and F.
The subset of the data with correctly formatted taxon names was analysed. Axes: x-axis, T values examined (values larger than 0.25 gave the same result because all sequences were assigned to a single cluster); y-axis, natural logarithm of the resulting number of clusters (TU) for three selected values of F. Colours: black, F = 1.0; dark grey, F = 0.5; light grey, F = 0.0.
Figure 3.
Maximum-likelihood tree, bottom part.
Phylogram as inferred with RAxML and rooted with the Pseudoperonospora sequences present in the dataset. Branches are scaled in terms of the number of substitutions per site. Numbers above/below the branches are maximum likelihood and maximum parsimony bootstrap support values from 100 replicates. The sequence labels contain the “organism” entry and the accession number from the GenBank files; for the validity of these entries, the corrected “organism” names and the revised taxonomy, see supporting file S2. Taxonomic unit (TU) numbers from optimal clustering settings are provided in rectangular brackets. These numbers are only used to circumscribe the TU; they do not indicate relationships between the TU (e.g. TU 16 is not closer to TU 15 than to TU 91). Red labels denote accessions affected by type I conflicts, blue labels by type II conflicts, mauve labels by both type I and II conflicts and green labels by database errors due to incorrect data submission. The red (type I) or blue (type II) lines connect the accessions affected by the respective conflict, with the conflict subtype given to the right. Type I concern the presence of the same taxon in different clusters (TU), type II the presence of several taxa within the same cluster (TU). Subtypes: Ia, different TU correspond to different hosts; Ib-Ic, different TU correspond to the same host; Ib, different TU are effected by sequencing/alignment artefacts; Ic different TU are effected by high genetic variability; IIa different taxa within a TU occur on the same host species/genus; (IIa) different taxa within a TU occur on different host genera within the same family; IIb different taxa within a TU occur on different host families. The tree is continued in Fig. 4.
Figure 4.
Maximum-likelihood tree, central part.
Phylogram as inferred with RAxML; continuation of Fig. 3 (connections indicated by arrowheads). For a description of the sequence labels and the colouring, see legend to Fig. 3. The tree is continued in Fig. 5.
Figure 5.
Maximum-likelihood tree, top part.
Phylogram as inferred with RAxML; continuation of Fig. 4 (connections indicated by arrowheads). For a description of the sequence labels and the colouring, see legend to Fig. 3.