Multiple targets of balancing selection in Leishmania donovani complex parasites

The Leishmania donovani species complex are the causative agents of visceral leishmaniasis, which cause 20-40,000 fatalities a year. Here, we conduct a screen for balancing selection in this specie complex. We sequence 93 isolates of L. infantum from Brazil and used 387 publicly-available L. donovani and L. infantum genomes, to describe the global diversity of this species complex. We identify five genetically-distinct populations that are sufficiently represented by genomic data to search for signatures of selection. We show that multiple metrics identify genes with robust signatures of balancing selection. We produce a curated set of 19 genes with robust signatures, including zeta toxin, nodulin-like and flagellum attachment proteins. Candidate genes were generally not shared between populations, consistent with divergent rather than long-term balancing selection in these species. This study highlights the extent of genetic divergence between L. donovani complex parasites and provides candidate genes for further study.