Additional file 1: of Risk factors for schistosomiasis in an urban area in northern Côte d’Ivoire

Multilingual abstracts in the six official working languages of the United Nations. (PDF 594 kb

Pairwise <i>F</i>_ST estimates between <i>Schistosoma mansoni</i> samples from Mali and Senegal.

<p>Kokry = short for Kokry-Bozo. Rtoll = short for Richard Toll.</p><p>* = significant for permutation of genotypes among villages at the nominal level of 0.05.</p><p>** = significant for permutation of genotypes among villages at the nominal level of 0.001 (i.e. Bonferroni corrected). na = not applicable.</p><p>Estimates were obtained for microsatellite dataset DMS1 (below diagonal) and DMS2 (above diagonal). Note that samples with less than 10 parasites were not included to avoid biased estimation, and that samples from Richard Toll from 1993 and 1994 were pooled.</p

Population genetic structure of <i>Schistosoma mansoni</i> using microsatellite markers.

<p>Results of the Factorial Correspondence Analysis for datasets DMS1 (a) and DMS2 (b). Classical multidimensional scaling plots of pairwise <i>F</i>_ST between villages for datasets DMS1 (c) and DMS2 (d).</p

Pairwise <i>F</i>_ST estimates between <i>Schistosoma mansoni</i> samples from Mali and Senegal.

<p>Kokry = short for Kokry-Bozo. Rtoll = short for Richard Toll.</p><p>* = significant for permutation of genotypes among villages at the nominal level of 0.05.</p><p>** = significant for permutation of genotypes among villages at the nominal level of 0.001 (i.e. Bonferroni corrected). na = not applicable.</p><p>Estimates were obtained for microsatellite dataset DMS1 (below diagonal) and DMS2 (above diagonal). Note that samples with less than 10 parasites were not included to avoid biased estimation, and that samples from Richard Toll from 1993 and 1994 were pooled.</p

Bayesian clustering analysis with STRUCTURE using microsatellite markers.

<p>Each barplot shows the probability on the y-axis (0.0–1.0) of an individual parasite being assigned to a given number of clusters <i>K</i> (<i>K</i> = 2, 3 or 4) for microsatellite dataset DMS1 (a) and DMS2 (b). Individual parasites are aligned along the x-axis, and grouped according to the location and year of sampling (1–14). Parasites are assigned either to one cluster (each cluster is represented by a different color) or to multiple clusters if their genotypes were admixed (indicated by multiple colors). The optimal <i>K—</i>value (<i>K</i> = 4 for DMS1 and <i>K</i> = 3 for DMS2) was determined by the maximum LnP(D), which is the log likelihood of the observed genotype distribution in <i>K</i> clusters.</p

Details of the three genetic datasets that were used in this study.

<p>Worms^SCAN: worms obtained from the Schistosomiasis Collection at the Natural History Museum in London [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003998#pntd.0003998.ref037" target="_blank">37</a>]. DMS1: microsatellite dataset 1. DMS2: microsatellite dataset 2. DSEQ: <i>cox</i>1 dataset. AC DSEQ = accession number of <i>cox</i>1 sequences from Genbank; only unique sequences (haplotypes) were submitted to GenBank.</p><p>Collection of microsatellite genotypes and cytochrome <i>c</i> oxidase subunit 1 sequences that were obtained from <i>Schistosoma mansoni</i> samples during this study or during previous studies [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003998#pntd.0003998.ref038" target="_blank">38</a>,<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003998#pntd.0003998.ref042" target="_blank">42</a>]. The region and year of sampling and the type of sample used as source for DNA template are listed for each sample. Note that the number of samples for each dataset reflects the total number of samples that were successfully genotyped for all loci.</p

<i>Schistosoma mansoni</i> genetic diversity estimated from microsatellite markers.

<p>DMS1: microsatellite dataset 1. DMS2: microsatellite dataset 2. N_μsat: number of successfully genotyped parasites. Hs: unbiased expected heterozygosity. Ho: observed heterozygosity. AR: Allelic richness.</p><p>^#: minimum of 10 alleles used for rarefaction.</p><p>^##: minimum of 14 alleles used for rarification.</p><p>Statistical significant <i>F</i>_IS values are given with * for the nominal level of 0.05 and with ** for the nominal level of 0.001.</p><p>Genetic diversity was estimated per village, per region and per year for samples typed at nine (DMS1–542 samples in total) or six (DMS2–758 samples in total) microsatellites markers (see <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003998#pntd.0003998.t001" target="_blank">Table 1</a> for details on data collection).</p

Haplotype networks based on statistical parsimony using partial cytochrome <i>c</i> oxidase subunit 1 sequences.

<p>The network above (a) comprises all sequences from nine African countries obtained during this study or a previous study [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003998#pntd.0003998.ref038" target="_blank">38</a>]. For each phylogeographic group, the number of sequences (Nseq), the number of haplotypes (Nhap), the nucleotide diversity (<i>Π</i>) and the haplotype diversity (<i>h</i>) with standard deviations (SD) are given. The network below (b) comprises sequences obtained from different villages in Northwest Senegal (1993–2007), Southeast Senegal (2011) and Southwest Mali (2007). Each pie diagram represents a haplotype (i.e. unique sequence) and dots represent haplotypes that were either not sampled or went extinct and can thus be regarded as mutational steps. The sizes of the pie diagrams are in relation to the log transformed number of sequences that represent the respective haplotypes, and the colors indicate the location or year of sampling.</p

<i>Schistosoma mansoni</i> genetic diversity as estimated at a partial fragment of the cytochrome c oxidase subunit 1 gene.

<p>N_seq: number of sequences. N_hap: number of unique haplotypes. N_pol: number of polymorphic sites. <i>h</i>: haplotype diversity. <i>Π</i>: nucleotide diversity. SD: standard deviation.</p><p>Genetic diversity was estimated for samples obtained from Senegal and eight other African countries (see <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003998#pntd.0003998.t001" target="_blank">Table 1</a> for details on data collection). Sequences that were sampled in other countries than Senegal were pooled per country.</p

Distribution of monthly malaria counts across the years 2004–2013 in Korhogo.

<p>Distribution of monthly malaria counts across the years 2004–2013 in Korhogo.</p