Figure 6.

Evolution of gene losses in the phylogenetic tree of Orchidaceae. A total of 129 taxa—124 Orchidaceae and five outgroup taxa—were the subject of tree reconstruction. The sequences of 83 protein coding genes were concatenated to a length of 87,399 bp. A maximum likelihood (ML) tree was constructed using RaxML-HPC2 with a GTR+G+I model (ML = −672774.637133 of ML optimization likelihood). All the genes were then plotted on the tree node using parsimony criteria under the condition of no parallel gains of the same gene. The species names in red indicate mycoheterotrophic orchids. (A): The basal portion of the tree showing the subfamilies Apostasioideae, Vanilloideae, Cypripedioideae, and Orchidoideae. (B): The upper portions of the tree showing the subfamily Epidendroideae.