The Continuing Debate on Deep Molluscan Phylogeny: Evidence for Serialia (Mollusca, Monoplacophora + Polyplacophora)

Table 1

Preanalyses comparing different taxon sampling and masking strategies; Mafft [30] and RNAsalsa [18] are alignment methods; Aliscore [17, 31] and Gblocks [35] are masking methods.

Dataset	Alignment treatment	Alignment length (bp)	Major changes in tree topology, compared to main topology (Figure 2, Supplementary Figure 1)
Total set (158 taxa)	Mafft-cut and paste inconsistent blocks in 18S and 28S fragments-Aliscore	10318	Annelida s.l. sister to Mollusca; Aplacophora monophyletic (Caudofoveata sister to Solenogastres); Patellogastropoda clusters with Cephalopoda
Total set (158 taxa)	Mafft-RNAsalsa-Aliscore	7597	Mollusca non-monophyletic; Caudofoveata, Solenogastres, Cephalopoda, and Scaphopoda cluster with Annelida s.l.; Neritimorpha basal sister to remaining Gastropoda; Patellogastropoda sister to partial Vetigastropoda (Lepetelloida + Vetigastropoda s.s.)
Total set (158 taxa)	Mafft-RNAsalsa-Gblocks	4083	Nemertea + Entoprocta + Cycliophora is sister to Mollusca; Heterobranchia is sister to remaining Mollusca; Patellogastropoda clusters with Solenogastres and Cephalopoda
Large set (142 taxa, excluding Patellogastropoda)	Mafft-Gblocks	5550	Annelida s.l. + Entoprocta + Cycliophora is sister to Mollusca
Large set (142 taxa, excluding Patellogastropoda)	Mafft-Aliscore	8721	Main analyses (Figure 2, Supplementary Figure 1)