Sequences of five plastid genes, psaB, psbA, psbB, atpA, and rbcL, from the transcriptome of B. solaris were aligned with a selected dataset of other eukaryotic sequences using the E-INSI algorithm in MAFFT (Multiple Alignment using Fast Fourier Transform) (43). In addition, rbcL sequences of the kleptoplasts from B. solaris and P. paranygulgus and a representative set of diatoms were also aligned. The alignments were trimmed and translated into amino acids to check for inconsistencies and remove large gaps in Geneious. A concatenated dataset was created from the five eukaryote alignments.

Best-fit partitioning schemes and models of molecular evolution (table S2) were recovered in PartitionFinder v1.1.0 based on a greedy search with PhyML and the Akaike information criterion (44). These partitions and models of evolution were subsequently used in the RAxML v8.2.11 maximum likelihood analyses (45) and MrBayes v3.2.6 Bayesian analyses (46) on the concatenated dataset and separate gene datasets, respectively. RAxML was run in Geneious, performing a best-scoring tree search and nonparametric bootstrapping (1000 pseudoreplicates). Bayesian analyses were run on XSEDE in the CIPRES Science Gateway (www.phylo.org), using default prior and MCMC settings, in two independent simultaneous runs for 100 million generations. Trees were sampled every 1000th generation after a 25% burnin. Convergence was determined on the basis of the logL values and the average deviation of split frequencies. For each Bayesian analysis, the resulting 75,000 trees were summarized in a 50% majority-rule consensus tree. We considered a 70% bootstrap and 0.95 posterior probabilities as threshold values for branch support (47).

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