Baseline Characteristics of the Study Population.

<p>Baseline Characteristics of the Study Population.</p

Clinical features associated with death in children with SM.

<p>Odds of death and blood lactate concentration in children with SM. Data show the odds ratio (95%CI) of death in relation to increasing concentrations of blood lactate in 467 children with SM (a). Odds of death and Blantyre coma score. OR and P values are relative to BCS = 5 (b). Specificity and sensitivity of different blood lactate concentration cut-off values (c) and coma scores measured by BCS (d) to predict death. AUC =  area under the curve,* P<0.05, ***P<0.001.</p

Clinical features in Gambian children with severe malaria independently associated with a fatal outcome.

<p>The multiple logistic regression analysis included 1,931 observations with complete data (5 degrees of freedom) χ² = 180.4 (P<0.001); pseudo-R2 = 0.10; Goodness-of- fit, statistics: Hosmer-Lemeshow  = 4.47 (P = 0.61). AUC =  area under the curve.</p

Prevalence of clinical features in Gambian children admitted to hospital with severe malaria.

<p>variables were defined as follows: Prostration, inability to sit (children aged >7 months); Impaired consciousness, BCS ≤4; Coma, BCS ≤2; Repeated convulsions, >3 in 24 h; Severe anemia (with any parasite density), Hb <5 g/dL or PCV <15; Respiratory distress, abnormal respiratory pattern (respiratory pattern values > or  = 3), grunting or use of accessory muscles of respiration, or abnormally deep (acidotic) breathing; Hypoglycemia ≤2.2 mM; Hyperlactatemia, plasma lactate >5 mM; Hyperpyrexia, temp>40°C; Hyperparasitemia, <i>P. falciparum</i> parasite density >500,000 /µl; Hypotensive shock, circulatory collapse with systolic blood pressure <50 mmHg; Hepatomegaly >2 cm below right costal margin; Splenomegaly >2 cm below left costal margin.</p

Genes with estimated peak expression at the merozoite stage have highest Tajima's D values overall.

<p>Assignment of peak stage transcript expression for 2710 genes in data from microarray studies <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002992#pgen.1002992-LeRoch1" target="_blank">[37]</a> used an expression time series query implemented by PlasmoDB <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002992#pgen.1002992-Aurrecoechea1" target="_blank">[36]</a>, and are plotted against the polymorphism data from the present study. The points show the values for individual genes (and horizontal bars the medians of all genes) with estimated peak expression at each stage (ER, early ring; LR, late ring; ET, early trophozoite; LT, late trophozoite; ES, early schizont; LS, late schizont; M, merozoite; G, gametocyte). The proportions of genes with values above zero are shown at the top (this is highest for merozoite-stage genes, with 72/404 or 17.8%, p<0.0001 compared with all other genes). Asterisks indicate p values for Mann-Whitney tests on the comparisons of distributions between pairs of stages (* p<0.01, *** p<0.0001).</p

25 genes with ≥10 SNPs showing highest values of Tajima's D index in a genome-wide analysis of sequences of 65 Gambian <i>P. falciparum</i> isolates.

<p>N, number of aligned nucleotide positions analysed; % CDS, percentage of the complete gene coding sequence analysed; S, number of polymorphic sites analysed per gene; π, pairwise nucleotide diversity index; peak expression, as determined by previous microarray transcriptome analyses; dN/dS, Nei & Gojobori ratio of pairwise nucleotide diversity at nonsynonymous sites compared with synonymous sites. <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002992#s2" target="_blank">Results</a> for all 2853 genes with 3 or more SNPs are given in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002992#pgen.1002992.s005" target="_blank">Table S2</a>.</p

Tajima's and Fu & Li's summary indices of nucleotide site frequency spectrum for each of 2,853 <i>P. falciparum</i> genes with 3 or more SNPs in the Gambian population.

<p>A. Frequency distribution histograms for the individual gene values for Tajima's D, Fu & Li's F* and Fu & Li's D* respectively. B. Two-dimensional plot of Tajima's D and Fu & Li's F* values for each of the 2853 genes (<i>r</i> = 0.67; correlation between Fu & Li's F* and D* indices is stronger, <i>r</i> = 0.96; correlation between Tajima's D and Fu & Li's D* is less, <i>r</i> = 0.50; P<0.001 for all correlations). Those in the top right tail of the distribution with high indices of both are considered further as genes with candidate signatures of balancing selection.</p

Distribution of Tajima's D values in members of different gene families and groups of genes defined by expression location.

<p>For each, plots show the mean (mid-line), one standard deviation (boxes), and 2 standard deviations (whiskers) with any individual outlier genes as points. The proportions of genes with values above zero and the numbers of genes analysed in each gene family are shown above the plot.</p

Distribution of numbers of SNPs per gene for 5,056 <i>P. falciparum</i> genes analyzed with a population sample of 65 Gambian clinical isolates.

<p>Distribution of numbers of SNPs per gene for 5,056 <i>P. falciparum</i> genes analyzed with a population sample of 65 Gambian clinical isolates.</p

Mapping signatures to particular regions within genes.

<p>A. Plots of linkage disequilibrium (<i>r</i>²) with distance between polymorphic nucleotides within genes each containing 10 or more SNPs. Nine genes are illustrated: left hand column shows genes with data on SNPs covering <500 bp, middle column 500–1000 bp, and right hand column >1000 bp, each column plotted with a different x-axis scale. Decline of LD with distance is evident in most genes, although the bottom plots show examples with some extended LD over most of the sequence analysed. B. Sliding window analysis identifies regions of genes with candidate signatures of balancing selection: top plot shows a <i>PHISTa</i> gene (PFL2555w) with high Tajima's D values in the 5′-region; middle plot shows the strongest signature on a <i>clag</i>-like gene (MAL7P1.229) is in the 3′-region; bottom plot for PF10_0355 shows the signature in the middle of the sequence. Window size of 100 bp was applied with step size of 25 bp.</p