Population structure in Central and South America
To investigate shared ancestry of P. vivax in Latin America at a finer geographic resolution, the population genomic analyses were repeated including only isolates from this region (n= 399). Results from both the PCA and the phylogenetic tree indicated clustering on a country level (supplementary figure 3).
The high degree of admixture in LAM noted in the global comparison is confirmed in this analysis and constitutes, for a large part, admixed samples within Brazil and admixture between populations from Brazil and Peru (Figure 3A). Eleven ancestral clusters (K=11) within LAM were estimated (Figure 3A), and these populations are structured geographically by country or at specific locations within a country (supplementary figure 3). In addition, admixture is observed between isolates from Colombia, Mexico, and Panama with mixed ancestry from multiple populations across LAM. Country specific ancestral populations are seen in Mexico (K7), Panama (K6), Colombia (K5), Brazil (K1 and K9), and Peru (K3 and K11). In addition, some populations are seen in multiple countries, such as isolates from Mexico and Panama that share ancestry with a population predominantly observed in Colombia (K4). While our dataset contains isolates sampled at different time periods, and populations are seen in multiple years (Figure 3B), we observed some distinct populations at specific locations, such as the Madre de Dios population (K3) in Peru, the K5 population in Tierralta in Colombia, and isolates from Manaus in Brazil (K9) (supplementary figure 3).
Temporal analysis (Figure 3B) shows that the K10 sub-population that is predominant in Brazil across most years, is later also observed in other countries in the Amazon Basin (2018 in Guyana, and in 2019 in Peru in a region relatively close to the border with Brazil), and in two isolates in Panama from 2007 (supplementary figure 3). Two additional populations are seen in Brazil that are predominant in Peru (K2 and K8).