Fig 1.
Map of study sample collection sites in the Great Mekong Subregion.
Specific collection sites and sample sizes for SNP barcode analysis are represented by landmarks with different colors. The map was generated using the online tool available at https://pixelmap.amcharts.com/. The license information can be accessed at https://www.amcharts.com/licenses/amcharts-20240401/.
Fig 2.
The total minor allele frequency (MAF) of 42 SNPs.
The location of the 42 SNPs is illustrated on the 14 chromosomes of the P. vivax genome. SNPs were colored by total MAF. 17 SNPs had 0.3 ≤ MAF < 0.5, 15 SNPs had 0.2 ≤ MAF < 0.3, 4 SNPs had 0.1 ≤ MAF < 0.2, 3 SNP had 0.05 ≤ MAF < 0.1, 3 SNPs had MAF < 0.05.
Fig 3.
Complexity of infection in different P. vivax populations in the GMS.
(A) Monoclonal and polyclonal infections were calculated using genotypes at the initially targeted SNPs, with samples carring a single allele at all positions being classified as monoclonal infections. (B) The most likely number of clones was estimated using the COIL web-based tool. Numbers within the bars indicate the sampling size for each category. The estimated numbers of polyclonal/monoclonal samples differ between the two methods.
Table 1.
Genetic diversity of P. vivax populations in the GMS.
Table 2.
Effective population size (Ne) of the P. vivax populations was estimated using the SMM and IAM models.
Fig 4.
Pairwise comparison of FST among P. vivax populations in the GMS.
Red, blue and black points represent high (FST ≥ 0.25), moderate (0.15 < FST < 0.25), and low genetic differentiation (FST ≤ 0.15), respectively.
Fig 5.
Clustering patterns of P. vivax isolates collected from the GMS.
(A) Principal component analysis of the GMS samples. (B) Phylogenetic analysis of P. vivax isolates based on neighbor-joining method. (C) ADMIXTURE analysis for K = 2. Vertical bars indicate individual P. vivax haplotypes, and colors represent individual assignments to inferred clusters.