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jpy12003-sup-0001-FigS1.pdfapplication/PDF99KFigure S1. Diagrammatic representation of the locations of primers designed for this study (Table 2) relative to the coding sequences of three chloroplast genes (psaA, psaB, psbC). Arrows indicate the direction of forward and reverse primers, and the locations of putative introns recovered in one or more taxon (cf. Fig. S2) are indicated by inverted triangles.
jpy12003-sup-0002-FigS2.pdfapplication/PDF110KFigure S2. Sequence completeness for taxa and genes analyzed during this study. Boxes are bounded by the length of the alignment for each gene. Gray bars indicate regions with sequence data, whereas white areas represent missing sequence data. Locations of putative introns for psaA, psaB, and psbC are indicated with heavy vertical lines.
jpy12003-sup-0003-FigS3.pdfapplication/PDF632KFigure S3. Phylogenetic trees recovered from analyses of single genes (18S, psaA, psaB, psbC, rbcL) or all genes combined except for psaB (“no psaB”). Tree topologies represent single maximum likelihood trees, with branch lengths indicated. Support values are given as likelihood bootstrap percents followed by Bayesian posterior probabilities. Values <50% or 0.50 are indicated as dashes (“—”). Heavy lines indicate branches that were supported by >95% likelihood and >0.98 Bayesian values.
jpy12003-sup-0004-FigS4.pdfapplication/PDF129KFigure S4. Relative support from single-gene analyses for major clades described in the text. Genes are ordered arbitrarily by their relative support for clades. Abbreviations: S: Sphaeropleales, V: Volvocales, SV: S + V, OCC: Oedogoniales + Chaetopeltidales + Chaetophorales.
jpy12003-sup-0005-FigS5.pdfapplication/PDF280KFigure S5. Results of Bayesian analyses that allow for trees to contain polytomies demonstrating lack of support for anomalous placements of particular taxa in maximum likelihood gene trees. Polytomy analyses were carried out using Phycas with a polytomy prior parameter C = 1.0 (i.e., flat topology prior over all tree topologies, including the star tree and other less-resolved tree topologies). (a) 18S gene tree (note position of Oedogoniales and Bracteacoccus). (b) rbcL gene tree (note position of Oltmansiellopsis).
jpy12003-sup-0006-AppendixS6.zipapplication/ZIP211KAppendix S1. Zipped directory containing python scripts, data files, and figures resulting from the Phycas polytomy analyses performed.

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