Fig. 12

Phylogenetic relationships within Rotifera-Acanthocephala. A) Unrooted BI tree as inferred from concatenated sequences of 100 orthologous metazoan proteins (dataset: Concat100-6OTUs). Rooting the tree with the platyhelminth S. mediterranea would invert the topology, thus suggesting a monophyletic origin of A. vaga and P. laevis in support of Lemniscea (Bdelloidea+Acanthocephala). B) Unrooted BI tree built from an alignment devoid of singleton positions and lacking the platyhelminth (Concat100-noSing-5OTUs). Here, S. nebaliae clusters with P. laevis. C) Unrooted BI tree after deletion of singleton positions, the outgroup representative and S. nebaliae strain B from the alignment (Concat100-noSing-4OTUs-A): The clustering of S. nebaliae and P. laevis is stable also when branch lengths are homogenized. The corresponding tree for Concat100-noSing-4OTUs-B showed the same topology. D) Rooted BI tree as derived from an alignment in which the platyhelminth sequence was replaced by a reconstructed sequence of the last common ancestor (LCA) of Rotifera-Acanthocephala (Concat100-6OTUs-LCA): Support for monophyletic Pararotatoria and Hemirotifera was maximal. Phylograms depicted were inferred with MrBayes v. 3.2.7a. Average deviation of split frequencies was always smaller than 0.01 in BI. Tree reconstruction with PhyML v. 3.3 led to identical topologies. Support values preceding slashes represent clade credibility values after discard of the first 25% of generations collected. Support values following slashes refer to the SH-like approximate likelihood ratio test (aLRT) in PhyML. The model of best-fit (LG + G + I + F) was determined by smart model selection (SMS)