Table 1.
Characteristics of the two alignments used for phylogenetic inference.
Fig 1.
Plastome phylogeny inferred from the maximum likelihood analysis of the alignment version 1.
The dataset was untrimmed except for removal of autapomorphies (columns where more than 99% of the samples had a gap). Support values are 100% unless otherwise indicated (in green). Values (in black) indicate the proportion of the 1000 simulated plastome trees (x2 scalar/x4 scalar) supporting the observed plastome relationship. Red branches indicate supported (≥95%) topological conflict with the nuclear coalescent-based and/or concatenation-based tree(s) in Thureborn et al. [36]. Inset branch lengths indicate the number of expected substitutions per site.
Fig 2.
Plastome phylogeny inferred from the maximum likelihood analysis of the alignment version 2.
The dataset was trimmed using trimAl. Support values are 100% unless otherwise indicated (in green). Values (in black) indicate the proportion of the 1000 simulated plastome trees (x2 scalar/x4 scalar) supporting the observed plastome relationship. Red branches indicate supported (≥95%) topological conflict with the nuclear coalescent-based and/or concatenation-based tree(s) in Thureborn et al. [36]. Inset branch lengths indicate the number of expected substitutions per site.
Fig 3.
The four species with identified rearrangements as well as Payera decaryi, which was set as reference (all with one IR only, indicated with pink boxes). Blocks in the same color connected by lines denote locally collinear blocks (LCBs), which represent presumably homologous regions. The LCBs are positioned laterally as they appear in the corresponding plastome. Sunken blocks have an inverted orientation relative to the reference.