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jpy12111-sup-0001-FigureS1a.pdfapplication/PDF373KFigure S1. Phylogenetic positioning of the primary plastids as a function of cyanobacterial taxa selection using Maximum Parsimony. Phylogenetic analyses were carried out on the (a) core cyanobacteria, (b) core cyanobacteria + Thermosynechococcus elongatus, (c) core cyanobacteria + Acaryochloris marina, (d) core cyanobacteria + the thermophilic Synechococcus, (e) core cyanobacteria + Synechococcus elongatus, and (f) core cyanobacteria + Synechococcus PCC 7335. Trees were constructed using the 31-gene Eukaryote plastid data set. Numbers above branches indicates bootstrap support. Branches with no numbers were supported 100%. Backbone topology is indicated (topology A is where chloroplasts branch sister to the cyanobacterial SPM and PNT clades, topology B is where chloroplasts branch deep in the cyanobacterial tree).
jpy12111-sup-0002-FigureS1b.pdfapplication/PDF350K 
jpy12111-sup-0003-FigureS2a.pdfapplication/PDF315KFigure S2. Phylogenetic positioning of the primary plastids as a function of cyanobacterial taxa selection using Mr. Bayes. Numbers above branches indicates posterior probability. Branches with no numbers had 100% posterior probability.
jpy12111-sup-0004-FigureS2b.pdfapplication/PDF322K 
jpy12111-sup-0005-FigureS3.pdfapplication/PDF391KFigure S3. Phylogenetic positioning of primary Viridiplantae plastids (Streptophyta and Chlorophyta) as a function of cyanobacterial taxa selection. Phylogenetic analyses were carried out on the (a) core cyanobacteria, (b) core cyanobacteria + Thermosynechococcus elongatus, (c) core cyanobacteria + Acaryochloris marina, (d) core cyanobacteria + the thermophilic Synechococcus, (e) core cyanobacteria + Synechococcus elongatus, and (f) core cyanobacteria + Synechococcus PCC 7335. Trees were constructed using the 38-gene Viridiplantae plastid data set, using MP (numbers above branches indicates bootstrap support) and MB (numbers below branches indicate posterior probability). Branches with an asterisk (*) showed no support. Backbone topology (A or B) is indicated.
jpy12111-sup-0006-FigureS4.pdfapplication/PDF346KFigure S4. Phylogenetic positioning of primary Rhodophyta and Glaucocystophyta as a function of cyanobacterial taxa selection. Phylogenetic analyses were carried out on the (a) core cyanobacteria, (b) core cyanobacteria + Thermosynechococcus elongatus, (c) core cyanobacteria + Acaryochloris marina, (d) core cyanobacteria + the thermophilic Synechococcus, (e) core cyanobacteria + Synechococcus elongatus, and (f) core cyanobacteria + Synechococcus PCC 7335. Trees were constructed using the 60-gene Rhodophyta plastid data set, using MP (numbers above branches indicates bootstrap support) and MB (numbers below branches indicate posterior probability). Branches with an asterisk (*) showed no support. Backbone topology (A or B) is indicated.
jpy12111-sup-0007-FigureS5.pdfapplication/PDF471KFigure S5. Phylogenetic relationships among Chlorophyta plastids as a function of optimality criterion. Analyses were carried out using the core cyanobacteria and either included all Chlorophyta taxa (a–d) or excluded the “problematic” Chlorophyta (e, f). Optimality criteria include (a) maximum parsimony (MP), (b) neighbor joining (NJ), (c) minimum evolution (ME), (d) Bayesian analyzing using a covarion model (COV), (e) MP and ME, and (f) COV. Bootstrap support values for panels a–d, and f are shown above the branches. Trees were constructed using the 41-gene Chlorophyta plastid data set. Boostrap support values using MP for panel e are shown above the branch, ME below the branch (branches with no values had 100% support). The “problematic” Chlorophyta taxa are indicated in red.
jpy12111-sup-0008-FigureS6.pdfapplication/PDF369KFigure S6. Phylogenetic relationships among Streptophyta plastids as a function of optimality criterion. Analyses were carried out using the core cyanobacteria and all Streptophyta taxa. Optimality criteria include (a) MP, (b) NJ and ME, and (c) COV. Bootstrap support values for panels a and c are shown above the branches. Trees were constructed using the 45-gene Streptophyta plastid data set. Bootstrap support values using NJ for panel b are shown above the branch, ME below the branch (branches with no values had 100% support). The “problematic” Streptophyta taxa are indicated in red.
jpy12111-sup-0009-FigureS7.pdfapplication/PDF453KFigure S7. Phylogenetic relationships among Rhodophyta and Glaucocystophyta plastids as a function of optimality criterion. Analyses were carried out using the core cyanobacteria and either included all Rhodophyta and Glaucocystophyta taxa (a–c) or excluded the “problematic” Rhodophyta taxa (d–f). Optimality criteria include (a) MP, (b) ME, (c) COV, (d) MP, (e) ME, and (f) COV. Trees were constructed using the 60-gene Rhodophyta plastid data set. Bootstrap support values are shown above the branches. The “problematic” Rhodophyta taxa are indicated in red.
jpy12111-sup-0010-FigureS8.pdfapplication/PDF469KFigure S8. Ancestral state reconstruction of habitat characters on genomic tree with extended taxa. Ancestral state reconstruction using maximum parsimony and ordered characters showing the parsimony inference of the habitat state at each ancestral node in the tree. A completely empty white circle at the node indicates this ancestor's most parsimonious habitat state is freshwater. A completely light blue circle indicates this ancestor's most parsimonious habitat state is brackish, a dark blue circle indicates marine habitat, and a red circle indicates hypersaline habitat. Tree was constructed using the 31 gene Eukaryote plastid data set, using the backbone constraint for the cyanobacterial relationships.
jpy12111-sup-0011-FigureS9.pdfapplication/PDF559KFigure S9. Maximum Likelihood Reconstruction of Freshwater Salinity in the Cyanobacteria, Green Algae, and Land Plants. The proportion of the filled circle corresponds to the likelihood of freshwater salinity growth at each ancestral node in the tree.
jpy12111-sup-0012-FigureS10.pdfapplication/PDF557KFigure S10. Maximum Likelihood Reconstruction of Marine/Hypersaline Salinity in the Cyanobacteria, Green Algae, and Land Plants. The proportion of the filled circle corresponds to the likelihood of marine or hypersaline salinity growth at each ancestral node in the tree.
jpy12111-sup-0013-FigureS11.pdfapplication/PDF206KFigure S11. Ancestral state Reconstruction of habitat characters on the rbcL-tufA tree. Tree was constructed using MP and 50 random addition replicates. Ancestral character state reconstructions were performed across all best trees using MP in Mesquite (see legend for key to reconstructed ancestral states). Node Absent (red) indicates that the node was absent in some of the trees. Equivocal (gray) indicates that the reconstructed ancestral state could be freshwater, brackish, or marine.
jpy12111-sup-0014-FigureS12.pdfapplication/PDF246KFigure S12. Ancestral state reconstruction of habitat characters on the rbcL-atpB tree. Tree was constructed using MP and 50 random addition replicates. Ancestral character state reconstructions were performed across all best trees using MP in Mesquite (see legend for key to reconstructed ancestral states). Node Absent (red) indicates that the node was absent in some of the trees. Equivocal (gray) indicates that the reconstructed ancestral state could be freshwater, brackish, or marine.
jpy12111-sup-0015-FigureS13.pdfapplication/PDF333KFigure S13. Ancestral state reconstruction of habitat characters on the rbcL-18S tree. Tree was constructed using MP and 50 random addition replicates. Ancestral character state reconstructions were performed across all best trees using MP in Mesquite (see legend for key to reconstructed ancestral states). Node Absent (red) indicates that the node was absent in some of the trees. Equivocal (gray) indicates that the reconstructed ancestral state could be freshwater, brackish, or marine.
jpy12111-sup-0016-TableS1.pdfapplication/PDF56KTable S1. Sequence composition of genomic data sets.
jpy12111-sup-0017-TableS2.docWord document282KTable S2. Accession numbers for rbcL-18S, rbcL-tufA, and rbcL-atpB analyses.
jpy12111-sup-0018-TableS3.pdfapplication/PDF74KTable S3. AU test output using core Cyanobacteria and plastids.

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