Maximum likelihood (ML) tree based on phased and concatenated L. donovani haplotypes across eight coding loci (10.9 kb in total). The ML substitution model adopted was the General Time Reversible plus Gamma with Invariable sites. ML bootstrap support is given in bold. Non-bold bootstraps are derived from the distance based (F84 + Gamma model) neighbor-joining tree from the same dataset. Non-Sudanese strains are identified by country code: SD - Sudan, IN-India, KE-Kenya, ET-Ethiopia, PT-Portugal, FR-France, ES-Spain. Sudanese strains from 1997 (blue), 1998 (yellow), 1999 (orange) and 2001 (red) are labelled. Population codes on the left hand site correspond to those identified via microsatellites (Figure 1).