File S1 - Bayesian Analysis of Congruence of Core Genes in Prochlorococcus and Synechococcus and Implications on Horizontal Gene Transfer

Supplemental Information on: Complexity Hypothesis background, methods, and results; regression analysis; and supplementary figures. Included in File S1: Figure S1. Example gene trees for single-gene alignments. Figure S2. Example NMMDS plot showing the location of randomly-selected treeclouds subjected 1, 3, 6, or 28 (complete randomization) switches of labels. Figure S3. Functional Categories of HGT Candidates. Figure S4. NMMDS plots with treeclouds colored by value. Figure S5. Correlation of treelength with alignment length, unscaled RF distance to UP tree, symmetric distance to UP tree, and rescaled RF distance to UP tree. Figure S6. Negative correlation of alignment length and distance to the UP treecloud. Figure S7. Distribution of distances between treeclouds- UP tree clouds excluded. Text S1. Complexity Hypothesis background; Complexity Hypothesis: Methods and Results; Functional Categories of HGT candidates; Effect of alignment length and divergence on tree distance: Methods and Results; and Regression Analyses. (DOC)