Gene gains and losses preceding the origin of metazoans. Reconstruction of ancestral gene content (predicted number of ortholog clusters indicated at each node) reveals that metazoans evolved as many as 1,235 ortholog clusters since their divergence from choanoflagellates and as many as 1,995 following their divergence with fungi, off-setting the loss of 20% of the Uropisthokont gene content. In contrast, current genome data suggest that the choanoflagellate and fungal lineages were dominated by gene loss. Choanoflagellates lost 47% of the Uropisthokont gene content and 37% of the gene content present in the Urchoanimal. Similarly, the fungal linage has lost 33% of the Uropisthokont gene content. Predicted ortholog cluster gain (+) and loss (-) is indicated, respectively, above and below each branch. Colored ovals represent predicted ancestral ortholog cluster content: red, S. rosetta; purple, M. brevicollis; black, Urmetazoan; white, Urfungus; blue, Urchoanoflagellate; yellow, Urchoanimal; green, Uropisthokont (Additional files 4 and 5).