title: Dissecting signal and noise in diatom chloroplast protein encoding genes with phylogenetic information profiling.
abstract: 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.
authors.affiliation: Department of Integrative Biology, University of Texas, Austin, TX 78712, United States.
authors.forename: Edward C
authors.initials: EC
authors.lastname: Theriot
authors.affiliation: Plant Biology Graduate Program, University of Texas at Austin, 1 University Station (A6700), Austin, TX 78712, United States. Electronic address: mashworth@utexas.edu.
authors.forename: Matt P
authors.initials: MP
authors.lastname: Ashworth
authors.affiliation: Plant Biology Graduate Program, University of Texas at Austin, 1 University Station (A6700), Austin, TX 78712, United States.
authors.forename: Teofil
authors.initials: T
authors.lastname: Nakov
authors.affiliation: University of Arkansas, Department of Biological Sciences, 850 W Dickson St., SCEN 601, Fayetteville, AR 72701, United States.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Ruck
authors.affiliation: Department of Integrative Biology, University of Texas, Austin, TX 78712, United States; Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
authors.forename: Robert K
authors.initials: RK
authors.lastname: Jansen
mesh_terms: D060365:Chloroplast Proteins / Q000235:genetics*; D003062:Codon / Q000235:genetics; D017377:Diatoms / Q000145:classification / Q000235:genetics*; D061125:Genes, Chloroplast / Q000235:genetics*; D010802:Phylogeny; D017422:Sequence Analysis, DNA
chemical_list: D060365:Chloroplast Proteins; D003062:Codon
keywords: Chloroplast genes; Diatoms; Partitioned Bremer support; Phylogenetic information profiling; Phylogenetic signal