Table 1.
Species, taxonomic classification, and sequencing coverage of mitochondrial genes.
Table 2.
Support for alternative bdelloid roots and major bdelloid and syndermate clades from various phylogenetic analyses.
Table 3.
Results from Dayhoff-recoding alignments to reduce compositional biases.
Figure 1.
Maximum Likelihood and Bayesian phylogenies reconstructed with concatenated mitochondrial proteins and rooted with Monogononta and Acanthocephala. Left and right trees represent two predominant topologies, where the root lies between Macrotrachela and the rest of the bdelloids (left) or Philodina and the rest of the bdelloids (right). The left tree represents the topology recovered from three analyses: 1) ML + JTT, 2) MrBayes + MtRev, and 3) Phylobayes with CAT + Poisson model. Bootstrap support values and posterior probabilities for the position of the root are listed in the order given above for each analysis. The right tree represents the topology recovered from six analyses: 1) ML + MtRev, 2) ML + Partitioned data (models were assigned to each partition and partitions were generated by grouping together genes that shared the same model) 3) ML + JTT on Dayhoff-recoded data, 4) Maximum Parsimony, 5) MrBayes + WAG, and 6) Phylobayes with CAT + GTR model. Bootstrap support values and posterior probabilities for the position of the root and the RHM clade (Rotaria, Habrotrocha, and Macrotrachela) are listed in the order given above for each analysis. Thicker branches indicate clades strongly supported by most analyses (bootstrap support or posterior probability >90). Red taxon labels indicate members of the family Philodinidae, green taxon labels indicate the family Habrotrochidae, and black indicates the family Adinetidae. Neither Philodinidae nor the order Philodinida is monophyletic. Line represents 0.25 amino acid substitutions per site. Summaries of strategies and support value provided in Table 2.
Table 4.
Bdelloid topology tests.
Figure 2.
Syndermate phylogenies reconstructed with ML and Bayesian analyses of concatenated mitochondrial protein alignments and rooted with Platyhelminthes or Chaetognatha. A, Acanthocephala; B, Bdelloidea; M, Monogononta; E, Eurotatoria (Bdelloidea + Monogononta); L, Lemniscea (Bdelloidea + Acanthocephala). Summaries of the two predominant topologies recovered are presented. Only support values for Eurotatoria and Lemniscea are shown as the monophylies of Bdelloidea, Monogononta, and Acanthocephala were always fully supported. All analyses performed with Platyhelminthes, except for one, produced the top phylogeny. Bootstrap support values and posterior probabilities from these analyses are listed in the following order: 1) ML + MtRev, 2) ML + JTT, 3) ML + Partitioned data (models were assigned to each partition and partitions were generated by grouping together genes that shared the same model), 4) ML + JTT on Dayhoff-recoded data, and 5) MrBayes + MtRev. All analyses performed with Chaetognatha and one Platyhelminthes analysis recovered the bottom phylogeny. The first value represents the posterior probability from a Phylobayes analysis of Syndermata + Platyhelminthes under a CAT + Poisson model. The remaining values represent results from Syndermata + Chaetognatha analyses: 1) ML + MtRev, 2) ML + JTT, 3) ML + Partitioned, 4) ML + JTT on Dayhoff-recoded data, 5) MrBayes + MtRev, and 6) Phylobayes with CAT + Poisson model. Lines represent number of amino acid substitutions per site. Summaries of strategies and support values provided in Table 2.
Figure 3.
Possible sister relationships among lineages of Syndermata and the morphological support for each.
Table 5.
Syndermate topology tests.