Calcarea

The currently most comprehensive dataset from nuclear ribosomal genes is the following:

Voigt O, Wülfing E, Wörheide G (2012) Molecular phylogenetic evaluation of classification and scenarios of character evolution in calcareous sponges (Porifera, Class Calcarea). PLoS ONE 7: e33417 (open access)

See also for the mitochondrial cox3:

Voigt O, Eichmann V, Wörheide G (2012) First evaluation of mitochondrial DNA as a marker for phylogeographic studies of Calcarea: a case study from Leucetta chagosensis. Hydrobiologia 687: 101-106 (link)

At this stage, trees of the Calcarea sequences were readily taken from the following publication and will be updated until mid-January 2013:

Dohrmann M, Voigt O, Erpenbeck D, Wörheide G (2006) Non-monophyly of most supraspecific taxa of calcareous sponges (Porifera, Calcarea) revealed by increased taxon sampling and partitioned Bayesian analysis of ribosomal DNA. Molecular Phylogenetics and Evolution 40: 830-843 (link).

nuclear LSU (28S) after Dohrmann et al. 2006 (Java)

nuclear SSU (18S) after Dohrmann et al. 2006 (Java)