Glossina fuscipes populations provide insights for human African trypanosomiasis transmission in Uganda.

Highlights: [•] Population genetics data offer insights with relevance for vector control programs. [•] Genetic data can help to devise control strategies to prevent reinvasion of target areas. [•] There are three (northern, southern, and western) genetically distinct clusters of Glossina fuscipes in Uganda. [•] There is apparent gene flow from southeast to northwest regions of Uganda. [•] Movement of flies from the southeast towards central Uganda may fuel new HAT foci. [•] The fly microbiome may influence parasite transmission traits. [•] Low-density infections with multiple Wolbachia strains are widely prevalent. [•] There is evidence for a high frequency of multiple matings in females. [ABSTRACT FROM AUTHOR]