We started running SYNERGY using an initial phylogenetic tree generated using orthologs based on bidirectional best BLAST hits. The list of uniform orthogroups from the first SYNERGY run was used to construct a refined phylogenetic tree. SYNERGY was then re-run using the refined phylogenetic trees. To generate our final phylogenetic tree, the final set of 177 31-way orthologs (31-way uniform orthogroups from the SYNERGY analysis) were aligned according to their nucleotide sequences with CLUSTALW [88] and concatenated, distances were computed with Phylip's DNADIST algorithm [89] , and Phylip's FITCH algorithm was used to create the tree.