Neighbour joining tree. Phylogenetic relationship between strains of L. tropica based on the proportion of shared alleles. Bootstrap values > 50 are indicated at the nodes. Strain labels specify: the animal host or sand fly vector by their conventional four letter code; the country of origin by the conventional two letter code; and the year of isolation. The codes for sand fly vectors, animal hosts, and countries are given in Additional file 1. If not indicated otherwise, strains were from human cases. The Bikaner strains are circumscribed by a dotted line. Strains from human cases of VL from India are indicated by an asterisk. Strains of the same identity share a single label with the number of identical strains specified in parentheses. Bayesian results are indicated by colours: background colours show main populations; coloured squares, triangles and circles represent subcomponents within populations.