Supplementary files

Abstract

Fig. S1. Multilocus phylogeny of Aspergillus series Nigri based on three loci (benA, CaM and RPB2) without species A. chiangmaiensis, A. pseudopiperis and A. pseudotubingensis. Best-scoring Maximum Likelihood (ML) tree inferred in the IQ-TREE is shown; ultrafast bootstrap support values (ML bs) are appended to nodes; only support values ≥95 % are shown; the ex-type strains are designated with a bold print; the information on geographic origin and isolation source is plotted on the tree (see the legend). <br />Fig. S2. Comparison of single-gene genealogies based on the benA, CaM and RPB2 loci and created by three different phylogenetic methods (only one isolate per unique multilocus haplotype is included in each phylogeny). Best-scoring single-locus maximum likelihood (ML) trees are shown; ML ultrafast bootstrap support values (ML bs), maximum parsimony bootstrap support values (MP bs) and Bayesian inference posterior probabilities (BI pp) are appended to nodes. Only support values ≥95 %, ≥70 % and ≥0.95, respectively, are shown. A dash indicates lower statistical support for a specific node, or the absence of a node in the phylogeny, while an asterisk indicates full support. The ex-type strains are designated with a bold print. Alignment characteristics, partitioning schemes and substitution models are listed in Supplementary Table S1.<br />Fig. S3. Best scoring maximum likelihood tree inferred in IQ-TREE based on ITS rDNA region sequences of series Nigri members (Table 1). It is apparent from the tree that a limited variability present in this locus can only differentiate the three main lineages, and more detailed differentiation is not possible. The ITS sequence of the A. vadensis ex-type was excluded from the analysis because it contains numerous errors and unresolved positions (accession number AY585549). Alignment characteristics, partitioning schemes and substitution models are listed in Supplementary Table S1.<br />Table S1. Characteristics of alignments, partition-merging results and best substitution model for each partition according to the Bayesian information criterion.<br />Table S2. Assignment of strains into populations for analysis in DELINEATE based on BPP v. 4.3.<br />Table S3. Aspergillus series Nigri genomes analyzed in this study and their basic characteristics.<br />Table S4. Distribution of 200 orthologous genes into ten separate STACEY analyses.<br />Table S5. List of unique multilocus haplotypes.<br />Table S6. Maximum sequence dissimilarity between isolates of the same Aspergillus species whose species limits have been delimited using methods based on a multispecies coalescent model; only species represented by isolates from at least three countries were included.