Full representation of the Bayesian phylogenetic tree based on whole chloroplast genome sequences.

Phylogenetic tree derived from an alignment of whole genome chloroplast sequences via Bayesian phylogenetic inference (BI). The multiple sequence alignment comprised 183 genomes assembled in the present study and 39 genomes that were downloaded from GenBank. Brachypodium distachyon was used as outgroup taxon. The tree shown corresponds to an analysis based on the complete alignment of 123,531 base pairs (bp). Posterior probabilities (pp) for the main clades are depicted next to the nodes if they were higher then 0.75. Support values of a second BI analysis based on 114,788 bp of whole chloroplast genomes were alignment positions with more than 50% of missing data were masked are shown below the values of the corresponding nodes in the complete chloroplast analysis if the values differed between analyses. For clades comprising multiple taxa, the taxon affiliation of single accession is indicated by the same symbols behind accession and taxon name (e.g. ‘;“, *). The ploidy level is provided in brackets after the taxon label. Single accessions grouping apart from other accessions of their taxon are shown in bold. To the right the genomic groups are indicated. The red circle represents the secondary calibration point from Marcussen et al. [20] used for node calibrations in multispecies coalescent analyses (MSC). Major nodes are shown in blue and their estimated ages in million years are given in the box. Two age values for the same node correspond to the analysis with (first value) and without the inclusion of Psathyrostachys (second value). For more information on the results of the MSC analyses see Additional file 5: Fig. S2 and Additional file 6: Fig. S3. For the full representation of the tree showing the grouping of all single accessions see Additional file 4: Fig. S1. For species synonyms see Additional file 1: Table S1. Arrows with support values indicate the nodes they refer to.