Bumblebee orthology with selected Hymenopterans and representative species from other insect orders. The maximum likelihood phylogenetic tree built from the concatenated alignments of 2,294 single-copy orthologs recovers the expected phylogeny rooted with the human body louse, Pediculus humanus. The tree highlights the pairs of closely-related bumblebees (Bombus terrestris and Bombus impatiens), honeybees (Apis mellifera and Apis florea), and fungus-growing ants (Atta cephalotes and Acromyrmex echinatior). It also shows slow average rates of molecular evolution in the Hymenopterans, similar to the flour beetle, Tribolium castaneum, but much slower than the silk moth, Bombyx mori, the malaria mosquito, Anopheles gambiae, and the fruit fly, Drosophila melanogaster. The bars represent the total gene counts in each species partitioned according to their homology to genes in the other species and other arthropods: from universally present single-copy orthologs (dark blue, left) to lineage-specific orthologs, and genes with no detectable orthology (gray, right). A small fraction made up of about 100 to 150 genes in each of the bee and ant species exhibit orthology only to genes from the most closely-related species (red, green, purple). The inset boxplots show the distributions of percent amino acid identities between pairs of Bombus, Apis, and Attini (ants) universal single-copy orthologs, where the identity is much higher between the bumblebee orthologs than between the honeybees or the ants.