Haplotype rarefaction curves for the Cambodian cohort.

<p>Calculated rarefaction curves are depicted by solid blue (<i>pvmsp-1</i>) and red (<i>pvcsp</i>) lines. Dotted lines represent rarefaction values extrapolated according to the methods of Cowell, et al. The 95% CIs of rarefaction estimates for <i>pvmsp-1</i> and <i>pvcsp</i> are demarked by light blue and light red shaded areas, respectively.</p

Jackknifed consensus trees demonstrate reproducible geographic clustering in <i>pvcsp</i> VK210 and VK247 isolates, but not <i>pvmsp-1</i>.

<p>The reproducibility of population clustering was assessed using 1000 jackknifed phylogenies. Individual populations clustered together or apart in each of the 1000 jackknifed phylogenies, and the frequency of a split between any two populations was quantified. Populations with grey bars (<50% splits) were genetically similar, while populations with red bars (>99.9% splits) were highly genetically distinct. Phylogenies were built from the <i>pvmsp-1</i> 42 kDa region (<b>A</b>), the <i>pvcsp</i> VK210 central repeat (<b>B</b>), and <i>pvcsp</i> VK247 central repeat (<b>C</b>).</p

McDonald-Kreitman test for selection in <i>pvmsp-1</i>.

<p>Evidence for long-term selective pressure on the <i>pvmsp-1</i> 42 kDa region and the 42 kDa intervening region was assessed with the McDonald-Kreitman test, using <i>P. knowlesi msp1</i> as the outgroup comparator. A Fisher's exact test (two tailed) was used to determine significance.</p

Protein domains and immunologically-relevant regions of <i>pvmsp-1</i> 42 kDa region and <i>pvcsp</i>.

<p>For both genes, numbers indicate coordinates according to the Sal1 reference genes. Sequences for <i>pvmsp-1</i> (PVX_099980) and pvcsp (PVX_119355) were accessed August 14, 2012 from PlasmoDB.org. (<b>A</b>) The <i>pvmsp-1</i> 42 kDa region is composed of two primary subunits – a 33 kDa and a 19 kDa subunit. Other sub-regions, including the 20 kDa and 14 kDa HARBs have been previously defined and studied. Here, we define the region between the HARBs as the “intervening region.” (<b>B</b>) The <i>pvcsp</i> gene is composed of three regions – an N-terminal non-repeat region, a central repeat region, and a C-terminal non-repeat region. The central repeat region consists of two major nonapeptide repeat types, termed VK210 and VK247. Approximate locations of <i>pvcsp</i> regions I and II are noted with horizontal lines in the N- and C-terminal non-repeat regions, respectively.</p

S_nn statistics for the <i>pvmsp-1</i> 42 kDa region and the <i>pvcsp</i> central repeat region.

<p>S_nn values approaching 1 indicate genetic isolation while values near 0.5 indicate that two geographically disparate populations may approximate panmixia. Global and pairwise S_nn values show stronger geographic clustering among <i>pvcsp</i> VK210 and VK247 repeats than among <i>pvmsp-1</i> 42 kDa regions.</p><p>* indicates significance to (<i>p</i>≤0.05) after Bonferroni correction for multiple comparisons.</p

Median-joining network of diverse <i>pvmsp-1</i> populations proposes multiple mutational paths between geographically diverse populations.

<p>286 <i>pvmsp-1</i> 42 kDa sequences from diverse geographical regions were used as input to create an unrooted median-joining network. This network is a visual representation of the mutational paths that may explain the observed sequence diversity. Each node represents an allele, node size represents the frequency of that allele (range n = 1 to n = 54), and node color corresponds to country of origin. Cycles within the diagram represent alternative evolutionary pathways. Corners represent obligate intermediate sequences that were not observed among the sampled alleles. Line length is not proportional to genetic distance.</p

Neighbor-joining tree of <i>pvcsp</i> VK210 repeat arrays.

<p>All unique repeat array haplotypes from each <i>pvcsp</i> VK210 population set were plotted on a single unrooted, neighbor-joining phylogenetic tree. Visual inspection reveals strong geographic clustering by region and country. Latin American sequences are in shades of red, South East Asian sequences are in shades of blue, and South and Central Asian sequences are in shades of green.</p

Summary population genetic data for <i>Plasmodium vivax</i> antigens.

<p>This table includes all population sequence sets which contained sufficient numbers to perform allele-based tests of neutrality. Population sets which included sequence data only for <i>pvcsp</i> repeat regions alone are not summarized here.</p><p>*<i>p</i><0.05;</p>1<p>number of haplotypes;</p>2<p>within-population variant sites;</p>3<p>average number of nucleotide differences;</p>4<p>nucleotide diversity;</p>5<p>number of haplotypes;</p>6<p>haplotype diversity.</p

Neighbor-joining tree of 42 kDa regions from <i>pvmsp-1</i> isolates.

<p>All unique 42<i>pvmsp-1</i> population set with n>25 were plotted on a single unrooted, neighbor-joining phylogenetic tree. The Sal1 reference sequence is marked in grey.</p

Use of amphotericin B.

<p>Amphotericin B formulation trends over time. Annual percentage of patients receiving lipid formulation amphotericin B (LF AmpB) or deoxycholate amphotericin B (AmpBd) for initial therapy (N = 132).</p