PMC

Analysis of rearranged plastid trees using the TLDB test. (A) The distribution of suboptimal ME-gtr bootstrap trees. The area shown in light gray falls outside the 95th quantile (ME score_0.05 = 4.73), whereas the darker area defines the region outside the 99th quantile (P ≤ 0.01). The score for the best ME-gtr tree is shown, as are the scores for the rearranged trees. (B) Schematic drawings of tree rearrangements used to test Chromist plastid monophyly. The “Best” ME-gtr is shown, as are trees 1, 2, and 3, in which the cryptophytes, haptophytes, and stramenopiles, respectively, are placed within the derived red algae (see arrow). Trees 4 and 5 test cryptophyte–stramenopiles and Chromista–Cyanidiales monophyly, respectively.

Phylogenetic relationships of red algal (shown in red typeface) and chromist (shown in black typeface) plastids inferred from a minimum evolution analysis of the combined DNA sequences of 16S rRNA, psaA, psbA, rbcL, and tufA. Results of a ME-gtr bootstrap analysis are shown above the branches, and bootstrap values from a ME-ld analysis are shown below the branches in italics. This tree is rooted on the branch leading to the Cyanophora paradoxa sequence. The branch lengths are proportional to the number of substitutions per site (see scale in figure). The filled circles indicate nodes that were constrained for molecular clock analyses (gray = 1,576 Ma; green = 1,174–1,222 Ma; blue = 550–590 Ma). The estimated nodes are indicated by the diamond (1,342 ± 22 Ma) and the asterisk (1,261 ± 28 Ma).