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).