Gene flow across LAM
The connectivity between P. vivax populations in Latin American countries was assessed by measuring to what extent the parasite populations are genetically related. Pairwise IBD between all samples within and between countries was used as a measure of connectivity and parasite gene flow. From the 93528 possible pairwise combinations of the 399 isolates from LAM, 1812 pairs of isolates (1.9%) had moderate-to-high relatedness (sharing 10-100% of their genome IBD). Among those, 638 pairs had high relatedness (more than 50% IBD,i.e. sibling or clonal pairs).
As expected, the majority of the related pairs (sharing 10-100% of their genome IBD) were observed within country (Figure 4 and Table 1), with observed relatedness between the different ancestral populations previously identified in Brazil (K1, K9 and K10) and Peru (K2, K8, K11) (supplementary figure 4).
A small number of related pairs (sharing 10-50% of their genome IBD) was also observed between countries: between Brazil and Peru (K10-K2) and between Colombia and Panama (K4 and K5; Figure 4). This indicates connectivity and gene flow between the different ancestral clusters within and between countries in LAM.
To simplify subsequent analysis, parasites from Guyana are grouped with Brazil due to the low number of samples (n=3) and assignment to the same population as samples from Brazil in the admixture analysis (Figure 3).