Figure 2.

Spirogyra SSU rRNA phylogeny: Unrooted molecular phylogeny of Spirogyra based on SSU alignment. Individual clades are highlighted in white boxes; group with secondary loss of group I IC1 intron highlighted by light green-box. The phylogenetic tree was inferred by maximum likelihood analyses of 1645 aligned positions of 55 taxa using PAUP* 4.0b10. GTR+G+I was chosen as best evolutionary model (base frequencies: A 0.23, C 0.24, G 0.29, T 0.24; rate matrix: A-C 1.4341, A-G 2.6641, A-T 1.2357, C-G 1.6993, C-T 5.2526, G-T 1.0000) with the proportion of invariable sites (I= 0.6009) and gamma distribution parameter (G= 0.6856). Posterior Probabilities (>95%; bold; calculated by MrBayes 3.1.2 using the covariation settings (2 million generations, trees from 11070 – 20000)) as well as bootstrap values (>50%) of the maximum likelihood (100 replicates; bold italic), neighbor-joining (1000 replicates; italic), and maximum parsimony (1000 replicates; not bold) are given in the tree (PP/ML/NJ/MP). No outgroup was used, tree was rooted using clade A.

Chen et al. BMC Evolutionary Biology 2012 12:77   doi:10.1186/1471-2148-12-77
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