title: Removal of noisy characters from chloroplast genome-scale data suggests revision of phylogenetic placements of Amborella and Ceratophyllum.
abstract: It is widely appreciated that noisy, highly variable data can impede phylogeney reconstruction. Researchers have for a long time omitted problematic data from phylogenetic analyses, such as the third-codon positions and variable regions. In the analyses of the phylogenetic relations of the angiosperms; however, inclusion of complete gene sequences into genomic-scale alignments has become a common practice. Here we demonstrate that this practice can be misleading. We show that support of the basal-most position of Amborella trichopoda among the angiosperms in the chloroplast genomic data is based only on a tiny subset (< 1% of the total alignment length) of the most variable positions in alignment, exhibiting mean maximum likelihood (ML) distance among the angiosperm operational taxonomic units (OTUs) approximately 36 substitutions/site. Exclusion of these positions leads to disappearance of the basal Amborella branch. Likewise, the recently reported sister-group relationship of Ceratophyllum to the eudicots is based on the presence of 2% of the most variable positions in the genomic alignment, exhibiting, on average, 20 substitutions/site in comparison among the angiosperm OTUs. These observations highlight a need for excluding a certain proportion of saturated positions in alignment from phylogenomic analyses.
authors.affiliation: IASMA Research Center, Via E. Mach 1, 38010, San Michele all'Adige, TN, Italy. vadim.goremykin@iasma.it
authors.forename: Vadim V
authors.initials: VV
authors.lastname: Goremykin
authors.forename: Roberto
authors.initials: R
authors.lastname: Viola
authors.forename: Frank H
authors.initials: FH
authors.lastname: Hellwig
mesh_terms: D002736:Chloroplasts / Q000235:genetics*; D003627:Data Interpretation, Statistical; D030541:Databases, Genetic; D019143:Evolution, Molecular; D020459:Genes, rRNA; D054627:Genome, Plastid; D019684:Magnoliopsida / Q000235:genetics*; D008957:Models, Genetic; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics; D012343:RNA, Transfer / Q000235:genetics; D016415:Sequence Alignment
chemical_list: D010940:Plant Proteins; D018749:RNA, Plant; D012343:RNA, Transfer