All T. mercedesae samples were collected from capped brood cells using a soft paintbrush and soft tweezers. Reproductive mites (Rep) were collected from brood cells containing white-eyed pupae. Protonymphs (Pro) and one deutonymphs (Deu) were sampled from brood cells containing purple-eyed pupae. Adult T. mercedesae (Adu) were collected from cells close to emerge (about one day before adult bees emerge). For each group (protonymphs, deutonymphs, adults, and reproductive mites), collected mites from all 12 colonies were randomly allocated to one of three replicates (50 mg for each replicate). All samples were rinsed with PBS and air-dried to remove many contaminates that may have been attached to the cuticle, flash-frozen using liquid nitrogen, and stored at -80°C for further processing.