Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is conserved across prokaryotic genomes: influence of excluding poorly alignable sites from analysis.

Abstract

Thirty-nine proteins encoded in a large gene cluster that is well-conserved in gene content and gene order across 18 sequenced prokaryotic genomes were extracted, aligned and subjected to phylogenetic analysis. In individual analyses of the alignments, only two probable examples of lateral gene transfer between archaea and eubacteria were detected, involving the genes for ribosomal protein Rpl23 and adenylate kinase. Amino acid sequences for 35 of the 39 proteins were concatenated to yield a data set of 9087 amino acid positions per genome. Many of these proteins, 33 of which are ribosomal proteins, are not highly conserved across distantly related organisms and thus contain many regions that are difficult to align. Phylogenetic analyses were performed with subsets of the concatenated data from which the most highly variable sites had been iteratively removed, using the number of different amino acids that occur at a given site as a criterion of variability. Glycine, which has a strong influence on protein structure, tended to be more frequent at the most conserved (least polymorphic) sites. With most subsets of the data, the proteins from the cyanobacterium Synechocystis tended to branch with their homologues from Gram-positive bacteria. The results indicate that excluding only a few percentage of poorly alignable sites from phylogenetic analysis can have a severe impact upon the phylogeny inferred and that bootstrap support for branches can fluctuate substantially, depending upon which sites are excluded.

Orthologs of a novel archaeal and of the bacterial peptidyl–tRNA hydrolase are nonessential in yeast

“…Parts of the pth2 phylogeny are poorly resolved due to the sequences' short lengths and significant differences in rates of change among amino acid positions. Still, this phylogeny is compatible with phylogenies of the ribosome and other translational apparatus components (35)(36)(37). Genetic complementation and deletion experiments show that Pth and Pth2 are functionally interchangeable in E. coli and even dispensable in yeast.…”

Evolutionary analysis ofArabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus

“…The Gϩve signal in the Arabidopsis data most likely ref lects an overall similarity of many proteins in Gϩve genomes to homologues in cyanobacteria. Data from rRNA (44) and protein trees (45)(46)(47), operon organization (48), and lipoprotein components (49) phylogenetically link Gϩves and cyanobacteria. In our view, the Gϩve signal in the Arabidopsis data are most easily attributed to genes that entered the plant lineage through the ancestors of plastids, even though the gene trees recover a Gϩve branch, either because of shared ancestry or lateral transfer of Gϩve and cyanobacterial genes (17).…”

Early Microbial Evolution: The Age of Anaerobes

“…The reason is that one of us reported the first concatenated trees using that specific data set 15 years ago (Hansmann and Martin 2000), overlooked in Ciccarelli et al's (2006) "automated" procedure to produce a tree of life that found the same proteins, and it was immediately apparent that there are many, many saturated sites in the alignments of that data set, and that if we start removing the saturated sites or those lacking observable sequence conservation then we obtain different topologies. Investigators are still using such site stripping approaches today (Petitjean et al 2015;Raymann et al 2015), sometimes pruning alignments by hand (Spang et al 2015), but the problem is that there is no good justification for when to stop excluding either genes or sites, one just gets different likelihoods.…”