Genomic exploration of the journey of Plasmodium vivax in Latin America
Fig 2
Worldwide genetic structure of P. vivax.
(a) Principal component analysis of 619 modern P. vivax strains and the Ebro ancient DNA sample from Spain, showing the first three PCs based on the genotype likelihood of 105,527 unlinked SNPs (see S2 Fig for more details). (b) Maximum likelihood (ML) tree of the 620 P. vivax individual genomes obtained with IQ-TREE [32] based on a general time reversible model of nucleotide evolution [33], as determined by ModelFinder [34]. The ML tree includes two P. vivax-like strains from African great apes indicated by an asterisk (*) used to locate the root. Note that the length of the outgroup branch was truncated. Black dots at nodes correspond to highly supported nodes (SH-aLRT ≥ 80% and UFboot ≥ 95%). The reference mark (※) highlight a Brazilian P. vivax isolate, discussed in the text. (c) Individual genetic ancestry assuming K = 4 and K = 9 distinct genetic clusters estimated using PCAngsd (see S5 Fig for the other K values). (d) Geographic distribution of the population average genetic ancestry proportions at K = 9 estimated using PCAngsd. PNG: Papua New Guinea. The base layer of the map was made with Natural Earth (naturalearthdata.com).