We present the most comprehensive and robust phylogeny of PPN, including representatives from all major groups, based on multiple nuclear protein-encoding genes.
This is the first study to include all hexapod orders in a phylogenetic analysis using multiple nuclear protein-coding genes to investigate the phylogeny of Hexapoda, with an emphasis on Entognatha.
Monophyly of Aplacophora is indicated by all recent studies using multiple nuclear protein coding genes and phylogenomic data sets ([ 5, 7, 8]; Figure 1(b)) but not neuroanatomy [ 106].
These analyses rely on a spectrum of molecular data ranging from rDNA sequences [ 6- 16], mitochondrial protein sequences [ 17- 19], single nuclear protein-encoding genes [ 20, 21], Hox genes [ 22, 23], multiple nuclear protein-encoding sequences [ 24, 25] and phylogenomic approaches [ 26- 34].
Still, the monophyly of Brachiozoa (=Phoronozoa) including brachiopods and phoronids was later independently corroborated by analyses based on rDNA [ 7, 8, 12, 13, 38- 41] and sodium-potassium ATPase α-subunit sequences [ 15], multiple nuclear protein-encoding sequences [ 26, 42], total evidence analyses [ 9, 39, 43] and phylogenomic approaches [ 30, 35].
Whereas some rDNA analyses indicate that brachiopods are paraphyletic and phoronids are the sister group of inarticulate brachiopods [ 38, 40, 41, 44], brachiopods come out as monophyletic in analyses of morphological data [ 2, 4, 9, 39, 43, 45- 47], of multiple nuclear protein-encoding sequences [ 42], and of phylogenomic datasets [ 30, 35].
Secondly, DamID experiments to map lamina chromatin interactions performed in the absence of cross-linking using multiple nuclear lamina proteins (lamin B1 and emerin) show a large degree of overlap in the set of interacting genes (de Wit and van Steensel 2009; Peric-Hupkes et al. 2010).
We therefore decided to reanalyse this important question by applying the powerful simultaneous analysis of multiple orthologous nuclear protein-coding genes [13] and using up-to-date tree reconstruction methods in order to enhance the phylogenetic signal [14].
This also explains well why Euglenida and Heterolobosea are robustly separated in the gnd phylogeny (Fig. 1) despite the close relatedness of these two lineages based on SSU rRNA gene phylogeny [ 35] and multiple nuclear-encoded protein phylogenies [ 36, 37].
