Figure legends

Figure 1. Origin of P. vivax genomes per country included in the analysis. Size of the dots are proportional to the number of samples in the genome dataset, and the colours indicate the country. Dots are plotted at the centre of the country (as defined by the ggmap package in R).
Figure 2 : Global P. vivax phylogeny, admixture and population structure. (A) Principal Component analysis based on the LD-pruned biallelic SNPs using PLINK2, showing the first two principal components. The samples (dots) are coloured according to the originating population (here region). (B) Phylogenetic tree based on the LD- pruned biallelic SNPs using RAxML. (C) Admixture proportions for K=10 populations using the ADMIXTURE software, with in the small bar on top the region of origin, (AFR = Africa, ESEA= Eastern South East Asia, LAM=Latin America, MSEA= Middle South East Asia, OCE= Oceania, WAS= Western Asia).
Figure 3. Spatio-temporal population dynamics in Latin America.Admixture analysis of P. vivax samples from LAM, using K=11 populations.(A) Bar plot with admixture proportions of each sample for each ancestry cluster, with in the small bar on top the country of origin for each sample. (B) Each sample is assigned to one ancestry cluster based on the highest membership probability to that population in the admixture analysis. Pie charts represent the number of samples from each cluster in that country and year.
Figure 4. P. vivax IBD-based connectivity between countries in Latin America. Connectivity network of inferred IBD between P. vivax samples from Latin American countries. Edges connecting parasite pairs indicate that at least 10% of their genomes descended from a common ancestor without intervening recombination, indicating distant to close relatedness. Node colours indicate the country of origin of the P. vivax genomes, and nodes were plotted on the map with known latitude and longitude of collection sites by district or if unknown in the respective country’s capital (for example in Guyana).
Figure 5. Molecular markers for transmission intensity. From the studied countries, the number of P. vivax cases (A) has been highest in Brazil in all years (2010-2021), data extracted from the World Malaria report 2022 . (B) Violin plot of nucleotide diversity (pi) measured across the genome in 5000 bp windows(C) Violin plot of within-host infection complexity assessed using within sample F statistic (FWS). FWS ≥ 0.95 was considered a proxy for a monoclonal infection.
Figure 6 Pairwise IBD between isolates across the 5 populations in LAM. (A) Line plot of median IBD shared between pairs of P. vivax samples along the chromosomes. IBD segments with highly significant IBD are indicated in orange and annotated genes of interest at peaks of IBD-sharing are labelled. The top genes that share significant IBD in the populations are listed in Supplementary table 2. Labelled dots in red indicate the positions and level of IBD sharing of putative drug resistant associated genes (list from ). (B)Heatmap of significant pairwise IBD between populations in LAM are clustered on rows for similar patterns between populations. Low to high -log10 p-values indicating significance levels of IBD sharing are colour graded from blue to yellow. Significant IBD-sharing is seen at a -log10 p-value greater than 1.3 (i.e. p<0.05), and a threshold of -log10 p-value >10 was used to identify highly significant areas of IBD-sharing.