For each node in the phylogenetic tree, we tabulated orthogroups lost, gained, or duplicated. Using GO terms, GO Slim terms, and PFAM domain groupings with less than 500 members, we calculated over-representations within losses, gains, and duplications each of these groupings at each node using the hypergeometric test. A complete summary of gains, losses, and duplications for all nodes in the phylogenetic tree is available on our supplementary information website.