The most likely tree was transformed into a chronogram using the first records of stylasterids, 65 mya, as calibrations for the two most basal stylasterid nodes (marked with red dots in Figure 2) in r8s [40] (see Table S2 for a list of stylasterid fossils), following deletion of the most distant outgroup, Bougainvillia sp., as required by r8s [40].
Phylogenetic analysis of the PYD protein sequences indicates that in the most distant outgroup represented (mouse and rat), the only POP2-related gene is Nlrp2.
In contrast, under the CAT model (figure 2), both nematodes and platyhelminths keep their sister-group relationship with arthropods in all cases, even with the most distant outgroup.
For phylogenetic tree analysis, we allowed a maximum of 10 missing genotypes at a given SNP position and included only P. hanceana as the most distant outgroup, resulting in a set of 26,846 SNPs passing cutoffs (see File S1).
Pairwise differences were, however, only significant between the coastal T. ferreri and the most distant outgroup species tested (M. infernus), not between the coastal and Pyrenean species of Troglocharinus.
We only considered the case of the nematodes, using the most distant outgroup (fungi), and performed the test under fixed topology, which we successively set to the Coelomata tree favored by WAG, and to the Ecdysozoa topology preferred by CAT.
Where multiple outgroups were present, it was assumed that the primates and/or rodent sequences comprised the most distant outgroups, followed by the bats and then the ungulates (following [ 34]).
We calculated "similarity" values between the amino acid sequences of F. candida and three well-represented species (C. elegans (most-distant outgroup), Daphnia magna and A. mellifera).
The most distant out-group was Priapulida (2 spp).
The tree was rooted at the most phylogenetic distant outgroup species, Struthio camelus.
The most distant sequence is used as outgroup.
