Fig. 2.

Haplotype co-ancestry among T. cruzi I clones from southern Ecuador. The heatmap of co-ancestry is based on a sorted haplotype co-ancestry matrix x_ij, which estimates the number of discrete segments of genome i that are most closely related to the corresponding segment of genome j. These nearest-neighbor relationships from fineSTRUCTURE²⁸ analysis are sorted such that samples clustered along the diagonal are those that most share recent genealogical events, and pairwise comparisons outside of the diagonal indicate levels of genetic connectivity among these clusters. The matrix also includes ‘genomes’ of non-cloned T. cruzi cultures. Strong horizontal banding points to the accumulation of diversity from throughout the dataset in four of these original infections. Cell color represents the frequency of nearest-neighbor relationships for each sample pair, increasing from yellow (2) through red (68) and pink (134) to black (200). Four anomalous (outlier) samples are described further on in main text. Analysis uses 110,326 phased SNP sites