The variation in coverage between chromosomes and unusual allele frequency distributions in our isolates (Figure 2—figure supplement 2) confirmed the presence of extensive aneuploidy in our samples, as observed for all Leishmania promastigote cultures investigated to date. In our study, this variation in aneuploidy between samples reflected differences in the average chromosome copy number of a population of promastigote cells grown in vitro for each isolate, and showed no apparent phylogenetic structure. We assume that this reflects the well-documented mosaic aneuploidy present across Leishmania populations (Prieto Barja et al., 2017; Lachaud et al., 2014; Sterkers et al., 2011), where aneuploidy variation is present between cells within a parasite population. This variation could be selected upon and quickly change mean observed aneuploidies in a new environment, such as in vitro culture. However, we cannot directly address aneuploidy mosaicism with our data due to pooling cells within a strain for sequencing. To address this issue in future studies and understand the dynamics of Leishmania aneuploidy in infections and in culture, single-cell approaches seem to be most promising (e.g. Dujardin et al., 2014).