CA evolution reconciled with three phylogentic hypotheses. (a) Three different phylogentic hypotheses for the relationships of non-bilaterian phyla used for tree-reconcilation. The number of inferred ortholog origins (corresponds to ‘co-speciation’ in the JANE software), gene duplications and gene losses are presented for each evolutionary scenario. Note that the numbers are similar regardless the underliyng phylogeny of phyla. (b) CA-evolution in Porifera as obtained under all three phylogenetic hypotheses presented in (a). Accordingly, eight CAs occurred in the last common ancestor of Porifera, of which several were lost in the different sponge lineages, followed by lineage-specific duplications. Three CA forms are in the last common ancestor gave rise to the three CA clades of Calcarea (CAL1-III, Figure 2). sclCA1 and L-CAs are recovered as orthologs in S. cilatum and L. complicata. A possible origin of ancestral scl-CA2 is indicated (orange). The monophyletic clades of demosponge and hexactinellid CAs (clade DEM and HEX, repectively in Figure 2) appears to be the result of substantial gene loss, followed by several duplications.