Fig 1.
Concise graphical illustration of the methodology and workflow used for the creation of the different datasets analysed.
Left/Blue: Genome Gene Content. “Ab initio” refers to dataset construction where the whole homo/orthogroup prediction was carried out de novo on the reduced taxon samplings, while “pruning” refers to the strategy where taxa are deleted from the full Opi homo/orthogroup data matrices which were constructed using default E (similarity) and I (inflation) values (see text for details). See data repository for the illustration of the complete steps of the gene content dataset creation; Right/Yellow: Morphology. The character list was assembled from three solid datasets that encompass the morphological disparity of the taxa in this study. Redundant characters were removed in addition to those that are not applicable to any of the terminals and historical ones that have been explicitly refuted in recent studies. The different taxon samplings mirror those of the gene content in addition to one in which the longest branches from the other morphological analyses were excluded.
Fig 2.
Reconstruction of animal phylogeny with 47 species (Opi taxon sampling) based on gene content datasets (TPCT) and morphological data.
Left: Total consensus tree of >10.5 million individual tree samples from analyses using datasets of homogroups and orthogroups of all the different E- and I-values for genome gene content (for details see Materials and Methods, see S1 File for details of analytical settings). Right: morphology-based phylogeny based on the non-additive coding scheme.Note the different positions of Ctenophora. Second to branch off in gene content and sister group to Cnidaria in morphology (i.e., Coelenterata) analyses. The monophyly of Deuterostomia is strongly supported by morphology but around 50% by gene content datasets. Posterior probabilities lower than 0.99 are indicated on both phylogenies. Statistical hypothesis tests of focal nodes: Green circle = node is strongly supported in the majority of tests conducted; Purple circle = node is not strongly supported in the majority of tests conducted (see S9, S12, and S13 Figs for details).
Fig 3.
Reconstruction of animal phylogeny with 47 species (Opi taxon sampling) based on gene content datasets constructed with the default methods settings of I-value 1.5 and E-value 1e-3.
Posterior probabilities lower than 0.99 are indicated. Note differences in branching order of closest outgroups, Ctenophora and Placozoa, as well as Schistosoma mansoni (Platyhelminthes).