1. IntroductionGlass sponges (Porifera, Hexactinellida) are major componentsof benthic deep-water communities, and are remarkable for theirunique tissue organization, physiology, and aesthetically appealingskeletal morphology (Leys et al., 2007). Leys et al. (2007, p. 117)reported 531 described species, but since then this number hasincreased to 550 (Lopes et al., 2007; Menshenina et al., 2007a,b;Reiswig et al., 2008; Tabachnick and Collins, 2008; Tabachnicket al., 2008), and description of many more new species and evengenera is in progress, suggesting that biodiversity of glass spongesis much higher than currently appreciated. A well-resolved phylog-eny of this important yet understudied group of sponges is highlydesirable in order to understand how this diversity evolved.The first molecular phylogeny of Hexactinellida (based on threeribosomal DNA markers) has only recently been published, andrevealed a surprisingly high level of congruence with morphol-ogy-based systems (Dohrmann et al., 2008). However, monophylyof the most species-rich order, the Lyssacinosida, remained ambig-uous, being model dependent. Furthermore, limited taxon sam-pling prevented resolution of subfamily-level relationshipsamong the Euplectellidae (the ‘venus-flower basket’ family). Final-ly, the accuracyof the placement of Farreidae(Sceptrulophora) wasalso questionable because this taxon was only represented by asingle erroneous or possibly pseudogenic 18S rDNA sequence fromGenBank (see also Voigt et al., 2008). This same sequence may alsohave had an adverse effect on the rest of the phylogeny.Here, we have addressed these issues by including 10 addi-tional species that were previously unavailable to us (i.e., Dohr-mann et al., 2008). Among them was a Farrea species thatyielded high-quality sequences of all three markers, and a repre-sentative of the most species-rich family of Sceptrulophora, theEuretidae. Whereas the position of Farrea did not change, wefind that Lyssacinosida is monophyletic but two of the threesubfamilies of Euplectellidae are not. Implications of these re-sults for evolution of morphological characters are discussed.We also elaborate further on comparison of RNA (paired-sites)substitution models (see Savill et al., 2001; Dohrmann et al.,2008) and highlight the non-trivial relationship of taxon sam-pling and model choice in deep metazoan phylogenies inferredfrom rDNA data.2. Materials and methods2.1. New specimens and sequencesTaxonomic and collection information of the new specimens,and sequence accession numbers, are given in Table 1. Full-length18S, and partial 28S and mitochondrial 16S rDNA sequences wereobtained as described, and added to the previously reported align-ments (see Dohrmann et al., 2008). A few additional sites (9 bpoverall) had to be excluded due to further ambiguities regardingpositional homology introduced by the new sequences. The finalconcatenated alignment [TreeBase (www.treebase.org) matrixaccession number M4266] consisted of 3426 bp for 60 taxa, includ-ing the 17 outgroup species (from Choanoflagellata, Demospon-giae, Homoscleromorpha, Calcarea, Placozoa, and Cnidaria) usedin our previous study (see Dohrmann et al., 2008). The totalamount of missing data decreased from 18.75% to 16.82% becauseof the morecomplete sequencingof Farrea and one Hyalonema spe-cies (see Table 1).