The SYNERGY algorithm [27, 28] was applied to the 31 genomes in Table 1 . SYNERGY organizes groups of genes across organisms into orthogroups, or groups of orthologs and paralogs, which consist of all the genes descended from a single ancestral gene in the species' last common ancestor. SYNERGY also associates orthogroups with a gene tree, from which we can derive an "extended phylogenetic profile", showing the gene copy number in each extant organism and at each ancestral node. Importantly, by reconciling an organism tree with each gene tree, SYNERGY provides an evolutionary scenario for each gene tree predicting where all losses, gains, and duplications occurred in its evolution. These lists of losses, gains, and duplications contain actual evolutionary events, as well as artifacts caused by genes that could not be properly categorized by SYNERGY. However, we observe that SYNERGY is effective at properly categorizing genes into orthogroups, and the SYNERGY orthogroups were very useful in our analysis. Analysis of the 31 genomes resulted in a total of 32,505 orthogroups, including those containing single genes from only a single genome (below). There were 177 "uniform" (1:1:1:1...) orthogroups representative of some of the most conserved and indispensible housekeeping genes. Additional file 4: Figure S3 summarizes the SYNERGY orthogroups.