DOI: 10.5061/dryad.610md
title: Data from: Dissecting signal and noise in diatom chloroplast protein encoding genes with phylogenetic information profiling

description: Previous analyses of single diatom chloroplast protein-encoded genes
 recovered results highly incongruent with both traditional phylogenies and
 phylogenies derived from the nuclear encoded small subunit (SSU) gene. Our
 analysis here of six individual chloroplast genes (atpB, psaA, psaB, psbA,
 psbC and rbcL) obtained similar anomalous results. However, phylogenetic
 noise in these genes did not appear to be correlated, and their
 concatenation appeared to effectively sum their collective signal. We
 empirically demonstrated the value of combining phylogenetic information
 profiling, partitioned Bremer support and entropy analysis in examining
 the utility of various partitions in phylogenetic analysis. Noise was low
 in the 1st and 2nd codon positions, but so was signal. Conversely, high
 noise levels in the 3rd codon position was accompanied by high signal.
 Perhaps counterintuitively, simple exclusion experiments demonstrated this
 was especially true at deeper nodes where the 3rd codon position
 contributed most to a result congruent with morphology and SSU (and the
 total evidence tree here). Correlated with our empirical findings,
 probability of correct signal (derived from information profiling)
 increased and the statistical significance of substitutional saturation
 decreased as data were aggregated. In this regard, the aggregated 3rd
 codon position performed as well or better than more slowly evolving
 sites. Simply put, direct methods of noise removal (elimination of
 fast-evolving sites) disproportionately removed signal. Information
 profiling and partitioned Bremer support suggest that addition of
 chloroplast data will rapidly improve our understanding of the diatom
 phylogeny, but conversely also illustrate that some parts of the diatom
 tree are likely to remain recalcitrant to addition of molecular data. The
 methods based on information profiling have been criticized for their
 numerous assumptions and parameter estimates and the fact that they are
 based on quartets of taxa. Our empirical results support theoretical
 arguments that the simplifying assumptions made in these methods are
 robust to “real-life” situations.
description: Theriot et al., diatom,
 7 gene dataset, with all charsets definedNexus 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.Theriot.etal.July2014.diatom.7gene.data.with.all.charsets.nexFig.S1.SaturationPlot.psaA3Plot of transitions and transversions from F84 distances as calculated in DAMBE5, for diatom plus Bolidomonas psaA 3rd codon position.Fig.S2.7gene.fullMaximum 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).Fig.S3.cplastonlyMaximum likelihood tree with all terminals identified, from analysis of 6 genes (atpB, psaA, psaB, psbA, psbC, rbcL) for 207 diatoms and Bolidomonas pacifica (outgroup).Fig.S4.ssuonlyMaximum likelihood tree with all terminals identified, from analysis of SSU for 207 diatoms and Bolidomonas pacifica (outgroup).Table.S1.Taxa.GenbankNumbersTaxa, authorities, sources, and Genbank accession numbers for 7 gene dataset on diatoms submitted by Theriot et al.Table.S2.PrimerTableTable of primers used for DNA sequencing for dataset submitted by Theriot et al. (7 genes, diatoms).Table.S3.EntropyTestResults of Entropy Analysis for substitutional saturation conducted in DAMBE5 on 7 gene diatom dataset submitted by Theriot et al.Table.S4.CDCSummaryResults of Codon Deviation Coefficient analysis conducted on protein encoding genes of diatoms.Table.S5.pC.pI.pP.byGene.v2Probability 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.Table.S6.pC.pI.pP.byPositionProbability 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.)