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These seven subfamilies are robustly placed into three major clades: the first clade is composed of plakophilin 1, plakophilin 2, and plakophilin 3, the second clade of δ-catenin and p0071, and the third clade of p120 and ARVCF.
Moreover, the better fitted CAT model robustly placed Gromia in a sister position to Retaria.
Three Lysmata species (L. anchisteus, L. hochi, L. lipkei) are robustly placed outside the Lysmata + Hippolysmata clade in the 16S phylogeny.
All elephant shark KCNA genes were relatively robustly placed in the phylogenetic trees, in accordance with its phylogenetic position in the species tree.
These outgroups had to be robustly placed with the ingroup, not too distant to cause inaccurate measures of genetic distance (i.e., exposure to substitution saturation), but distant enough to offer a clear comparison between members of the ingroup.
The "LG" model robustly placed Gromia as the most closely related lineage to the Foraminifera + Acantharea group (93% BP), and Phytomyxea were recovered as sister to this assemblage with 87% BP.
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One explanation for the difficulty observed in robustly placing some lineages of interest is LBA.
Their phylogenetic position was long debated but molecular phylogenies now robustly place them within the eukaryote supergroup Rhizaria, as sister group to the omnivorous vampyrellid amoebae [ 3, 4].
Although some applications of parsimony principles might suggest that the simpler, direct life cycle should be ancestral for the group, molecular phylogenetic analyses robustly place two clades of parasites (Spirurina A and B) that have complex life histories as successive sister groups, at the base of the Spirurina, to clades that include direct life cycle parasites.
Despite initial hopes, phylogenomic analyses including tens to hundreds of genes still fail to robustly place many bilaterian taxa.
Again, IRAC I could not be placed robustly in any of the two clusters within IxAC-A (bootstrap support <650/1000).
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