Phylogenomic Testing of Root Hypotheses

Abstract

17The determination of the last common ancestor (LCA) of a group of species plays a 18 vital role in evolutionary theory. Traditionally, an LCA is inferred by the rooting of a fully 19 resolved species tree. From a theoretical perspective, however, inference of the LCA 20 amounts to the reconstruction of just one branch -the root branch -of the true unrooted 21 species tree, and should therefore be a much easier task than the full resolution of the 22 a chemolithoautotrophic and anaerobic life-style. Our inference is based on data comprising 33 between 43% (opisthokonta) and 86% (proteobacteria) of all gene families. Approaching 34 LCA inference within a statistical framework thus renders the phylogenomic inference 35 powerful and robust. 36 37

Pseudogenes in plasmid genomes reveal past transitions in plasmid mobility

“…4A). To reconstruct the ancestral mobility state of PTU-FS plasmids, we inferred the root of PTU-FS using a phylogenomic rooting approach (30). The phylogenetic inference revealed a root neighborhood in the deepest split between plasmid clusters FS A and FS B that includes branches leading to several conjugating plasmids of cluster FS A (Fig.…”

“…The reconstruction of the phylogenetic trees for plasmids was based on nucleotide sequences of complete single-copy genes (see Supplementary Table S7 & S8) applying IQ-TREE 2 ((68), v.2.2.2.7) with a transition model (with parameter -m TIM -B 1000, (69)). A rooting position for the plasmid trees was inferred by applying phylogenomic rooting using nucleotide sequences from plasmid cluster gene families ((30), Supplementary Table S7 & S8). Obtained phylogenetic trees were visualized and annotated using iTOL ((70), v.6.8) or SplitsTree4 ((71), v.4.17.0).…”