Discussion

New World leishmaniasis is caused by parasites that show an extensive phenotypic diversity in terms of evolution, ecology and clinical outcome. The two main Leishmania species encountered in Peru illustrate this diversity and present an ideal study system for a better understanding of speciation in the Neotropics, the most-species rich region in the world. Here we sequenced 116 L. braziliensis and L. peruviana clinical isolates that were collected in Peru and Bolivia. SNP calling revealed 237,721 variable sites in L. braziliensis, while only 32,110 variable sites were detected in L. peruviana. The genomes of L. peruviana were almost devoid of heterozygous sites, resulting in long tracts of homozygosity. Phylogenomic and population genomic analyses revealed strong population substructure in L. peruviana that matched biogeographical regions present along the Western slopes of the Andes. We found that the most northern L. peruviana population diverged firstly from L. braziliensis, followed by a southbound colonization of L. peruviana into each biogeographical region. Altogether, these results suggest an allopatric speciation of L. peruviana following colonization of the Western slopes of the Andes through the Porculla pass in the North of Peru, resulting in serious founder effects. Further work is ongoing to study the evolutionary history of these parasites based on genome structural variations.