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. 2002 Mar;68(3):1180–1191. doi: 10.1128/AEM.68.3.1180-1191.2002

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Copyright © 2002, American Society for Microbiology

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FIG. 4. — (A) Evolutionary relationships of Prochlorococcus and Synechococcus isolates and environmental sequences from Monterey Bay inferred using 233 positions of the 16S-23S rDNA spacer. The tree shown was inferred by maximum likelihood (−ln likelihood = 2,364.57) using the HKY85 model of nucleotide substitution with rate heterogeneity (gamma shape parameter = 0.383), empirical nucleotide frequencies, and a transition-transversion ratio of 1.156. The tree shown was not significantly worse (as determined by the Kishino-Hasegawa test) than the best tree found by likelihood (−ln likelihood = 2,362.09) in which the Prochlorococcus low-B/A clade I was not monophyletic. The Prochlorococcus low-B/A clade I was monophyletic in the best trees inferred using HKY85 or paralinear (logdet) distances and minimum evolution as the objective function. The tree is rooted with Cyanobium cluster Synechococcus sp. strain PCC 6307. Bootstrap values from distance/maximum-parsimony/maximum-likelihood analyses are as follows, with values less than 50 indicated by dashes: A, 79/72/81; B, 100/100/100; C, 100/100/99; D, 100/99/51; E, 64/51/—; F, 100/88/78; G, 100/98/93; H, 97/95/80; I, 100/69/—; J, 90/93/71; K, 55/—/—; L, 60/52/57; M, 100/99/99; N, 99/99/82; and O, 91/87/83. (B) Evolutionary relationships of marine Synechococcus isolates inferred using 434 positions of the 16S-23S rDNA spacer. Two strains of high-B/A Prochlorococcus and three environmental sequences from Monterey Bay were also included. Asterisks denote clades which are congruent with those identified using rpoC1. The phylogenetic framework was determined using paralinear distances (logdet) and minimum evolution as the objective function. Trees inferred using HKY85 distances resulted in identical clades with essentially similar branching orders. Bootstrap values from distance/maximum-parsimony/maximum-likelihood analyses are listed to the left of each node, with values less than 50 indicated by dashes. The tree is rooted with Cyanobium cluster Synechococcus sp. strain PCC 6307.

FIG. 4. — (A) Evolutionary relationships of Prochlorococcus and Synechococcus isolates and environmental sequences from Monterey Bay inferred using 233 positions of the 16S-23S rDNA spacer. The tree shown was inferred by maximum likelihood (−ln likelihood = 2,364.57) using the HKY85 model of nucleotide substitution with rate heterogeneity (gamma shape parameter = 0.383), empirical nucleotide frequencies, and a transition-transversion ratio of 1.156. The tree shown was not significantly worse (as determined by the Kishino-Hasegawa test) than the best tree found by likelihood (−ln likelihood = 2,362.09) in which the Prochlorococcus low-B/A clade I was not monophyletic. The Prochlorococcus low-B/A clade I was monophyletic in the best trees inferred using HKY85 or paralinear (logdet) distances and minimum evolution as the objective function. The tree is rooted with Cyanobium cluster Synechococcus sp. strain PCC 6307. Bootstrap values from distance/maximum-parsimony/maximum-likelihood analyses are as follows, with values less than 50 indicated by dashes: A, 79/72/81; B, 100/100/100; C, 100/100/99; D, 100/99/51; E, 64/51/—; F, 100/88/78; G, 100/98/93; H, 97/95/80; I, 100/69/—; J, 90/93/71; K, 55/—/—; L, 60/52/57; M, 100/99/99; N, 99/99/82; and O, 91/87/83. (B) Evolutionary relationships of marine Synechococcus isolates inferred using 434 positions of the 16S-23S rDNA spacer. Two strains of high-B/A Prochlorococcus and three environmental sequences from Monterey Bay were also included. Asterisks denote clades which are congruent with those identified using rpoC1. The phylogenetic framework was determined using paralinear distances (logdet) and minimum evolution as the objective function. Trees inferred using HKY85 distances resulted in identical clades with essentially similar branching orders. Bootstrap values from distance/maximum-parsimony/maximum-likelihood analyses are listed to the left of each node, with values less than 50 indicated by dashes. The tree is rooted with Cyanobium cluster Synechococcus sp. strain PCC 6307.