Figure 1

Unrooted maximum likelihood trees of DNA sequences representing three different genomes of the cryptophyte genus Cryptomonas. Figure 1A – Tree inferred from concatenated nuclear SSU rDNA, ITS2 and partial LSU rDNA sequences. Evolutionary model, GTR+I+Γ [51]; -ln L = 9254.5. Figure 1B – Nucleomorph SSU rDNA phylogeny. Evolutionary model, TVM+I+Γ [51]; -ln L = 4899.1. Figure 1C – Tree inferred from plastid-encoded rbc L genes (for a rooted tree including rbc L genes of other cryptophyte genera, see Additional file 3). Evolutionary model, GTR+I+Γ [51]; -ln L = 7857.4. Figure 1D (inlet) – Nuclear (top), nucleomorph (middle) and plastid (bottom) phylogeny scaled to the same substitution rate. Gray shaded areas in Figures 1A to C, presumed position of the root. In a rooted phylogeny inferred from a concatenated data set of nuclear (ITS2 excluded), nucleomorph and plastid DNA sequences with Guillardia theta as an outgroup, the root inserted between clade NoPyr and all other taxa (see Additional file 4). Evolutionary models were chosen according to the results of the Akaike information criterion in Modeltest (see Additional file 1 and Methods). Support values from left to right, maximum likelihood bootstrap/maximum parsimony bootstrap/distance (neighbor-joining) bootstrap/posterior probabilities (Figures 1A and B) or maximum likelihood bootstrap/maximum parsimony bootstrap/distance (neighbor-joining) bootstrap/logdet transformation bootstrap/posterior probabilities (Figure 1C). Cbo, Cryptomonas borealis; Ccu, C. curvata; Cgy, C. gyropyrenoidosa; Clu, C. lundii; Cma, C. marssonii; Cov, C. ovata; Cpa, C. paramaecium (colorless); Cpy, C. pyrenoidifera; Cte, C. tetrapyrenoidosa; blue, taxa of clade LB; red branches and strain designations, loss of photosynthesis; scale bars, substitutions per site.