Figure 1. History and geography of Indian subcontinent L. donovani.
(a) Location of the patients from which the 204 L. donovani genomes were isolated, and of historical Kala-Azar outbreaks. Genetic groups of the parasite isolates are indicated by the colour of the dots representing them, matching those in Figure 2a,c. Sampling dates and locations are summarised in Figure 1—figure supplement 1, and detailed information about each strain including GPS coordinates are given in the source data file. Citations are to historical primary literature reviewed and cited in (Gibson, 1983). Posterior probability distributions of estimated ages for the oldest split in (b) the main population in Bihar and Nepal and (c) the ISC5 group associated with Sb resistance. Dark shading shows estimates under a strict molecular clock, light shading from relaxed molecular clock and lines show relaxed clock results with Bangladeshi and putative hybrid isolates included. (d) Estimated effective population size through time for ISC5 population (green) and the rest of the parasite population (black/grey). Lines show median of posterior distributions, dark and light shading cover 50% and 95% of the posterior density respectively. Dates for all splits on this phylogeny and other results of phylogeographic analysis are shown in Figure 1—figure supplement 2.
Figure 1—figure supplement 1. Sampling of genetic groups.
Figure 1—figure supplement 2. Full results of discrete-space, constant population size molecular clock Bayesian phylogeography analysis of core population.
