Fig. 2 in Molecular detection and characterization of Leishmania infantum in free- ranging Egyptian mongoose (Herpestes ichneumon)

Fig. 2. Maximum Likelihood (ML) phylogenetic tree of 27 L. infantum nucleotide sequences (410 nt long in the final dataset, including gaps), obtained during this study (MH799321) and others available in GenBank, based on the Hasegawa-Kishino-Yano model (HKY) (Hasegawa et al., 1985). The tree with the highest log likelihood (−1026.87) is shown. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using the Maximum Composite Likelihood (MCL) approach, and then selecting the topology with superior log likelihood value. A discrete Gamma distribution was used to model evolutionary rate differences among sites (5 categories (+G, parameter = 0.3289) (HKY + G). The tree was drawn to scale, with branch lengths measured in the number of substitutions per site. Robustness of the tree nodes was assessed by bootstrapping 1000 times. The graphical edition of the phylogenetic tree was performed with tree explorer, MEGA7 software (Kumar et al., 2016). Only bootstrap (BS) values equal or greater than 70 are shown on the tree, with the exception of the MH799321 cluster wherein the Bs values, although <70, are displayed for the reader. A 2-letter code and a specific colour (Top left) was attributed to each country for better identification of the origin of each strain. Whenever possible, the host was identified by a specific shape (Top left), namely dog (Canis lupus familiaris, star), human (Homo sapiens, triangle), Egyptian mongoose (Herpestes ichneumon, square) and hoary fox (Lycalopex vetulus, diamond). Sampling dates are indicated, whenever available. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)