<i>Pvs25</i> worldwide polymorphism by gene CDS and gene-domain.

<p><i>Pvs25</i> worldwide polymorphism by gene CDS and gene-domain.</p

<i>Pvs28</i> gene worldwide polymorphism by countries.

<p><i>Pvs28</i> gene worldwide polymorphism by countries.</p

Pairwise <i>F</i>_<i>ST</i> indices of inter-population variance for the <i>pvs28</i> gene.

<p>Pairwise <i>F</i>_<i>ST</i> indices of inter-population variance for the <i>pvs28</i> gene.</p

<i>Pvs25</i> gene worldwide polymorphism by countries.

<p><i>Pvs25</i> gene worldwide polymorphism by countries.</p

Positively selected codons detected in <i>pvs28</i> and <i>pvs25</i> using random effects likelihood (REL) method as implemented in HyPhy.

<p>The estimated dN-dS (E[dN-dS]) per codon across the <i>pvs28</i> and <i>pvs25</i> genes are depicted against their position using Salvador I as a reference (see <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004786#pntd.0004786.s001" target="_blank">S1</a> and <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004786#pntd.0004786.s002" target="_blank">S2</a> Tables). Schematic diagrams of Pvs28 and Pvs25 indicate their EGF domains. <i>Pvs28</i> codons 52, 113, and 116 yield Bayes factors (BF) of 97.69, 101.51, and 367.92 respectively, indicating that the data provided strong evidence for positive selection. Codons 52, 65, 95, 98, and 123 for Pvs28 and 35, 97, 130, 132, and 135 for <i>pvs25</i> have BF higher than 10 but lower than 50, indicating that the data provided some evidence for positive selection acting at those codons. The LCR of <i>pvs28</i> was not included in this analysis.</p

Median joining network of the <i>P</i>. <i>vivax pvs28</i> haplotypes sampled two or more times plus selected singleton haplotypes.

<p>Branch lengths are proportional to divergence; node sizes are proportional to the total haplotype frequencies. The network shows 63 haplotypes found in 284 sequences with a haplotype diversity of 0.765. The most frequent haplotypes are indicated. Every color corresponds to a different geographic origin. Lines separating haplotypes represent mutational steps.</p

Sliding window analysis of the nucleotide diversity (<i>π</i>) on the <i>pvs28</i> and <i>pvs25</i> genes.

<p>Genetic diversity (<i>π</i>) was estimated using a sliding window of 50 base pairs (bp) with a step size of 10 sites. The LCR of tandem repeats of the <i>pvs28</i> gene was not included but its location is indicated by a blue arrow.</p

<i>Pvs28</i> worldwide polymorphism by gene CDS and gene-domain.

<p><i>Pvs28</i> worldwide polymorphism by gene CDS and gene-domain.</p