Fig. 2: Tree reconstruction of the Viridiplantae.

a Topological comparison between coalescent and concatenation analyses based on nuclear and plastid datasets. Support values are shown only for nodes receiving less than 95% LPP (in coalescent-based analysis) and SH-aLRT/BS (in concatenation-based analyses). Chlo Chlorodendrophyceae, core core Chlorophyta, Pico Picocystophyceae, Neph Nephroselmidophyceae, Pseu Pseudoscourfieldiales, Mami Mamiellophyceae, Pyra Pyramimonadophyceae, Stre Streptophyta, Pras Prasinodermophyta, Glau Glaucophyta, Rhodo Rhodophyta, Rhode Rhodelphidophyta. b The phylogenetic tree constructed using ASTRAL based on 557 individual gene trees with 10% BS value cutoff. Support values are shown only for nodes receiving less than 95% support from LPP analysis. The pie chart at the ancestral branch of Prasinodermophyta and Chlorophyta indicates the proportion of gene trees concordance and conflict against the coalescent species tree: blue, the proportion of gene trees supporting the species tree; green, the proportion of gene trees supporting the most common conflicting topology; red, the proportion of gene trees supporting all other conflicting topologies; dark gray, the proportion of the uninformative gene trees; light gray, the proportion of missing data. The color of circle point on each node represents two different intervals of theta values. The red asterisks in a and b indicate the ancestral branch consisting of Prasinodermophyta and Chlorophyta. c The quartet frequency (q1–q3) around the focal branch of ASTRAL tree based on the 72-taxon dataset. Each internal branch with four neighboring branches leads to three possible quartets.