Distribution and timing of plastid and nuclear NDH gene loss across seed plants. Representation of land plant relationships (A). Groups where photosynthetic taxa have lost/pseudogenized plastome NDH genes are indicated with red font; arrows indicate the relevant cladogram for each subgroup. (B-D) Cladograms showing divergence times and lineage specific loss of nuclear transcripts encoding NDH proteins. ‘A, lumenal and B’ refer to subunits in the NDH complex. Green shading indicates detection of the nuclear transcript for each gene. Numeric values indicate the divergence time (MYA: million year ago) for each lineage. In C, the asterisk indicates a questionable branch discussed in the text. In D, the number after the generic name indicates the number of species included in the analysis with identical patterns with regard to NDH expression. Orchid and Geraniales relationships are represented by plastid 12-gene maximum likelihood trees (see Methods); gymnosperm phylogeny is based on two plastid genes, rbcL and matK.