Annotated list of samples and sequences used for analysis. New sequences and samples are indicated in bold.

(1)Formerly identified as Darwinella muelleri (Darwinellidae) in Sperling et al. (2007); specimen from the Gulf of Mexico.
(2)Formerly identified as Dysidea camera in Sperling et al. (2007), and as Dysidea sp. in GenBank.
(3)Formerly identified as Chondrilla sp. in Sperling et al. (2007) and as Chondrilla nucula in GenBank.
(4)Formerly labeled as Clypeatula cooperensis in Sperling et al. (2004) and Ephydatia cooperensis in GenBank, but synonomized with Ephydatia fluviatilis in WPD.
(5)Presently in WPD as Stelleta fibrosa as part of family Ancorinidae, but see Cárdenas et al. (2011) for updated classification.
(6)Formerly identified as Geodia gibberosa in Sperling et al. (2009) and in GenBank; G. tumulosa was resurected by Cárdenas et al. (2011).
(7)Characella presently classified in the WPD within Pachastrellidae, but is incertae sedis according to Cárdenas et al. (2011).
(8)Microscleroderma and its family Scleritodermidae presently classified in the WPD within Lithistida, well-known as a polyphyletic group, but is transferred to Spirophorida by Cárdenas et al. (2012).
(9)Formerly identified as Cinachyrella alloclada in Sperling et al. (2009) and in GenBank.
(10)Presently in WPD as Axinella corrugata as part of family Axinellidae within Halichondrida, but see Gazave et al. (2010) and Morrow et al. (2012), who updated its classification.
(11)Ectyoplasia and Raspailiidae presently classified in the WPD within Poecilosclerida, but was transferred to Axinellida by Morrow et al. (2012).
(12)Formerly identified as Damiria sp. in Sperling et al. (2009) and in GenBank.
(13)Formerly identified as Tethya aurantia in Sperling et al. (2009), and as Tethya actinia in GenBank.
(14)Formerly identified as Spirastrella coccinea in Sperling et al. (2009) and in GenBank.
(15)Formerly labeled as Microciona prolifera in Peterson & Butterfield (2005) and in GenBank, and as Clathria (Microciona) prolifera in Sperling et al. (2009).
(16)Derived from genomic traces, as reported in Sperling et al. (2007).
(17)Derived from genomic traces, as reported in Sperling et al. (2010).
(18)Derived from genomic traces, as reported in Sperling et al. (2009).