Table 1.
Collections of Armillaria used in this study.
Fig 1.
Phylogenetic tree generated from the three-locus (ITS, tef1-α and β-tubulin) dataset.
The labels on the right of the phylogram indicate groups identified by phylogenetic analyses. The values of the bootstrap frequencies of ML (BP ≥ 70%), posterior probability (PP ≥ 0.95) and maximum parsimony bootstraps (PB ≥ 70%) are shown above the nodes. Thick black branches indicate high support in the analyses (ML-BP ≥ 70%, BI-PP ≥ 0.95). Green branches were concordantly supported by the majority of the loci (genealogical concordance), or were well supported by at least one locus and not contradicted by any other locus (genealogical non-concordance). Triangles at nodes indicate that all taxa united by it belong to the same phylogenetic lineage (see text for details). Taxon labels indicate strain number and geographic source. If a strain was originally identified as a CBS (Chinese biological species), the CBS taxon is listed before the strain number.
Fig 2.
Phylogenetic relationships between samples of Armillaria inferred from tef1-α sequences using ML analysis.
Branch support values are indicated by numbers above branches (ML-BP/BI-PP/MP-PB). Thick black branches received high support in the analyses (ML-BP ≥ 70%, BI-PP≥ 0.95). The accession numbers for the sequences retrieved from the GenBank database are listed in S1 Table.
Fig 3.
Phylogeny of Armillaria samples inferred from tef1-α DNA sequences using ML analysis to show the intraspecific level within Lineage 6.
Branch support values are indicated by numbers above branches (ML-BP/BI-PP/MP-PB). The nodes appearing in common between Fig 3 and Fig 2 are indicated by triangles. The species names labeled on our collections correspond to Fig 1. Seven samples with heterozygous sites (HKAS45821, HKAS51692, HKAS86558, HKAS86559, HKAS86564, HKAS85567 and HKAS85572) were analyzed using PHASE 2.0 and every isolate was divided into two haploid genotypes. The four subgroups of Lineage 6 were highlighted in different colors.
Table 2.
Support values for Armillaria lineages recognized by genealogical concordance in analyses of individual gene partitions and in the combined three-locus dataset.
Values are shown as ML-BP/Bayesian-PP. Missing values (-) apply to non-monophyly.
Fig 4.
The link between 14 CBS (Chinese Biological Species) and phylogenetic lineages identified in this study.
CBS were recognized in previous studies and phylogenetic lineages were delimited in this study. The m/n on the arrows between “CBS” and “phylogenetic lineage” means that m of n isolates of a CBS were assigned to phylogenetic lineages.