Data from: Dissecting signal and noise in diatom chloroplast protein encoding genes with phylogenetic information profiling

Theriot EC, Ashworth MP, Nakov T, Ruck E, Jansen RK

Date Published: July 1, 2016

DOI: http://dx.doi.org/10.5061/dryad.610md

 

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Title Theriot et al., diatom, 7 gene dataset, with all charsets defined
Downloaded 8 times
Description Nexus DNA sequence file of aligned sequences. 208 taxa (207 diatoms, 1 outgroup). 9349 bases. 7 genes. In order: nuclearly-encoded SSU, chloroplast encoded atpB, psaA, psaB, psbA, psbC,rbcL. Ends trimmed for each gene so that at least 50% of individual sequences have a base. Character set information included, identifying genes, inferred paired and unpaired sites for SSU, and codon positions. Each protein encoding gene further trimmed so that each begins with a first codon position.
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Title Fig.S1.SaturationPlot.psaA3
Downloaded 7 times
Description Plot of transitions and transversions from F84 distances as calculated in DAMBE5, for diatom plus Bolidomonas psaA 3rd codon position.
Download Fig.S1.SaturationPlot.psaA3.pdf (532.9 Kb)
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Title Fig.S2.7gene.full
Downloaded 73 times
Description Maximum likelihood tree with all terminals identified, from analysis of 7 genes (SSU, atpB, psaA, psaB, psbA, psbC, rbcL) for 207 diatoms and Bolidomonas pacifica (outgroup).
Download Fig.S2.7gene.full.pdf (25.56 Kb)
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Title Fig.S3.cplastonly
Downloaded 9 times
Description Maximum likelihood tree with all terminals identified, from analysis of 6 genes (atpB, psaA, psaB, psbA, psbC, rbcL) for 207 diatoms and Bolidomonas pacifica (outgroup).
Download Fig.S3.cplastonly.pdf (22.47 Kb)
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Title Fig.S4.ssuonly
Downloaded 23 times
Description Maximum likelihood tree with all terminals identified, from analysis of SSU for 207 diatoms and Bolidomonas pacifica (outgroup).
Download Fig.S4.ssuonly.pdf (22.25 Kb)
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Title Table.S1.Taxa.GenbankNumbers
Downloaded 11 times
Description Taxa, authorities, sources, and Genbank accession numbers for 7 gene dataset on diatoms submitted by Theriot et al.
Download Table.S1.Taxa.GenbankNumbers.xlsx (171.0 Kb)
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Title Table.S2.PrimerTable
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Description Table of primers used for DNA sequencing for dataset submitted by Theriot et al. (7 genes, diatoms).
Download Table.S2.PrimerTable.docx (24.78 Kb)
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Title Table.S3.EntropyTest
Downloaded 2 times
Description Results of Entropy Analysis for substitutional saturation conducted in DAMBE5 on 7 gene diatom dataset submitted by Theriot et al.
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Title Table.S4.CDCSummary
Description Results of Codon Deviation Coefficient analysis conducted on protein encoding genes of diatoms.
Download Table.S4.CDCSummary.docx (12.72 Kb)
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Title Table.S5.pC.pI.pP.byGene.v2
Downloaded 3 times
Description Probability of correct (C),and incorrect (I) parsimony informative character patterns at select nodes in the diatom tree (Figure 1 in manuscript), Probability of non-parsimony informative character pattern or polytomy (P) at select nodes. Probability of C minus I at select nodes. For each gene individually, for all 6 chloroplast genes concatenated and for all 7 genes (SSU plus chloroplast genes) concatenated.
Download Table.S5.pC.pI.pP.byGene.v2.docx (18.85 Kb)
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Title Table.S6.pC.pI.pP.byPosition
Downloaded 1 time
Description Probability of correct (C),and incorrect (I) parsimony informative character patterns at select nodes in the diatom tree (Figure 1 in manuscript), Probability of non-parsimony informative character pattern or polytomy (P) at select nodes. Probability of C minus I at select nodes. For each of 5 selected partitions (SSU paired sites, SSU unpaired sites, all 1st codon positions aggregated, all 2nd codon positions aggregated, and all 3rd codon positions aggregated.)
Download Table.S6.pC.pI.pP.byPosition.docx (15.85 Kb)
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When using this data, please cite the original publication:

Theriot EC, Ashworth MP, Nakov T, Ruck E, Jansen RK (2015) Dissecting signal and noise in diatom chloroplast protein encoding genes with phylogenetic information profiling. Molecular Phylogenetics and Evolution 89: 28-36. http://dx.doi.org/10.1016/j.ympev.2015.03.012

Additionally, please cite the Dryad data package:

Theriot EC, Ashworth MP, Nakov T, Ruck E, Jansen RK (2015) Data from: Dissecting signal and noise in diatom chloroplast protein encoding genes with phylogenetic information profiling. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.610md
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