Figure 2. Genealogical history of L. donovani from the ISC.

(a) Maximum-likelihood tree based on SNPs called for 191 strains (see Figure 2—figure supplement 1) from the core population in the Indian subcontinent. Samples are coloured by population assignment, with putative hybrid strains not clustered in the main groups in black. Further analysis confirms the hybrid ancestry of some of these isolates (Figure 2—figure supplement 2). (b) Unrooted phylogenetic network of the L. donovani complex based on split decomposition of maximum-likelihood distances between isolates described here, reference genome isolates and two published Sri Lankan isolates (Zhang et al., 2014). (c) Model-based clustering of 191 isolates from the core population reveals six discrete monophyletic groups, and some groups and other samples of less certain ancestry. Coloured bars show the fraction of ancestry per strain assigned to a given cluster, with colours assigned to the population most closely related to each cluster. More detailed population clustering analysis shows largely congruent results (Figure 2—figure supplements 3 and 4).

DOI: http://dx.doi.org/10.7554/eLife.12613.006

Figure 2—figure supplement 1. Flowchart of SNP detection using COCALL.

Overview of the SNP detection method COCALL (COnsensus of SNP CALL). COCALL finds genetic variants that show a concordant signal over five different SNP callers (Cortex, Freebayes, GATK, Samtools Mpileup and Pileup). See supplementary methods for details.

DOI: http://dx.doi.org/10.7554/eLife.12613.007

Figure 2—figure supplement 2. Haplotype networks for core population isolates.

Haplotype networks indicate putative hybrids as isolates with ancestry from multiple distinct populations. Chromosomal haplotype neighbour-joining networks of the phased data for the core population were constructed using the R ape package. Each node represents one haplotype variant for (a) chromosome 32 and (b) chromosome 35, coloured by group. Black lines are network edges and red lines connect haplotype variants from the same isolate for selected isolates where haplotypes appear in different parts of the network (with isolate names shown). Six ungrouped isolates (BHU815/0, BHU764/0cl1, BHU274/0, BHU574cl4, BHU581cl2, BHU572cl3) have mixed ancestry from ISC5 and other groups, and two (BHU744/0 and BHU774/0) have a mix of ISC6/7/8/9/10 haplotypes. No mixing among ISC2/3/4 was evident.

DOI: http://dx.doi.org/10.7554/eLife.12613.008

Figure 2—figure supplement 3. Haplotype similarity for core population isolates.

Heatmap showing the mean expected number of haplotypes shared between pairs of core population isolates. Samples listed on the y-axis are haplotype donors to those on the x-axis. 18,747 phased genotypes at 2397 SNPs sites were computed with Chromopainter v0.0.2 using recombination rates from PHASE for 79 haplotype chunks with c=0.00054 effective chunks. This image confirms six discrete populations ISC2-7 and illustrates complex ancestry in certain samples not belonging to these groups.

DOI: http://dx.doi.org/10.7554/eLife.12613.009

Figure 2—figure supplement 4. Mosaic ancestry patterns in eight putative hybrid L. donovani isolates.

Representative samples from three potentially parental groups (BPK282/0cl4, ISC6; BHU200/0, ISC7; BPK275/0cl18, ISC5) were compared to eight putative hybrid samples (BHU815/0, BHU764/0cl1, BHU274/0, BHU574cl4, BHU581cl2, BHU572cl3, BHU744/0 and BHU774/0). To the left is a maximum-likelihood tree constructed with RAxML showing the evolutionary history of the aligned haplotypes. The table shows a set of SNPs for which ChromoPainter assigned ancestry probability values >0.4 in any of these eight hybrids. Individual SNPs are coloured if the sample had an ancestry probability >0.4: uncoloured ones represent those observed in multiple ISC populations. All isolates have mixed ancestry from the two groups, but four isolates (BHU574cl4, BHU764/0cl1, BHU815/0 and BHU274/0) have haplotypes that appear to have a more complex origin.

DOI: http://dx.doi.org/10.7554/eLife.12613.010