Multiple targets of balancing selection in Leishmania donovani complex parasites

The Leishmania donovani species complex, comprising L. donovani and L. infantum, are the causative agents of visceral leishmaniasis, which cause 20-40,000 fatalities a year. Here, we conduct a screen for balancing selection in these species. 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 Betascan2 and NCD2 metrics identified multiple genes with robust signatures of balancing selection. We produce a curated set of 19 genes with the most robust signatures, including zeta toxin, nodulin-like and flagellum attachment proteins. Candidates 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 a small list of candidate genes that appear to be subject to strong diversifying selection.