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Additional file 3:. Note. The reason for using the ML tree from the 180s77Gaa dataset under a gene partitioning scheme as the reference tree.

Additional file 2: Fig. S1. The maximum likelihood tree estimated from the 77G180saa based on the gene partition models used as a reference to evaluate conflict and concordance among the 19 plastid datasets trees (Table 2). Pie charts depict conflict amongst the input trees, with the blue, green, red, and gray slices representing, respectively, the proportion of input bipartitions concordant, conflicting (supporting a single main alternative topology), conflicting (supporting various alternative topologies), and uninformative (BS < 80) at each node. The numbers below each branch are ICA values. Fig. S2. The maximum likelihood tree estimated from the SNP-ash dataset used as a reference to evaluate conflict and concordance among the six SNP gene trees (Table 2). Pie charts depict conflict amongst the input trees, with the blue, green, red, and gray slices representing, respectively, the proportion of input bipartitions concordant, conflicting (supporting a single main alternative topology), conflicting (supporting various alternative topologies), and uninformative (BS < 80) at each node. The numbers below each branch are ICA values. Fig. S3. The maximum likelihood tree estimated from the SNP-ash dataset used as a reference to evaluate conflict and concordance among the 41 gene trees using the dividing methods. Pie charts depict conflict amongst the input trees, with the blue, green, red, and gray slices representing, respectively, the proportion of input bipartitions concordant, conflicting (supporting a single main alternative topology), conflicting (supporting various alternative topologies), and uninformative (BS < 80) at each node. The numbers below each branch are ICA values. Fig. S4. The maximum likelihood tree estimated from the 77G180saa based on the gene partition models used as a reference to evaluate conflict and concordance among the 24 trees (plastid datasets and SNP datasets, Table 2). Pie charts depict conflict amongst the input trees, with the blue, green, red, and gray slices representing, respectively, the proportion of input bipartitions concordant, conflicting (supporting a single main alternative topology), conflicting (supporting various alternative topologies), and uninformative (BS < 80) at each node. The numbers below each branch are ICA values. Fig. S5. The divergence time of Oleaceae was estimated by BEAST according to age calibrations of four nodes based on the concatenated 76-coding gene dataset.

Additional file 5: Figure S4. Molecular phylogeny of Lagerstroemia resulting from ML (maximum likelihood) and BI (Bayesian inference) analyses using SSC regions (dataset-6). Maximum likelihood bootstrap values (BS) and posterior probabilities (PP) are shown at nodes. Branches with * indicate 100 % BS and a PP of 1.0.

Additional file 3: Figure S2. Molecular phylogeny of Lagerstroemia resulting from ML (maximum likelihood) and BI (Bayesian inference) analyses using LSC regions (dataset-4). Maximum likelihood bootstrap values (BS) and posterior probabilities (PP) are shown at nodes. Branches with * indicate 100 % BS and a PP of 1.0.

Additional file 4: Figure S3. Molecular phylogeny of Lagerstroemia resulting from ML (maximum likelihood) and BI (Bayesian inference) analyses using IR regions (dataset-5). Maximum likelihood bootstrap values (BS) and posterior probabilities (PP) are shown at nodes. Branches with * indicate 100 % BS and a PP of 1.0.

Additional file 2: Figure S1. ML tree for Lagerstroemia using combined three universal plant DNA barcodes and four highly variable regions.