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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Reconstructing Colonization Dynamics of the Human Parasite <italic>Schistosoma mansoni</italic> following Anthropogenic Environmental Changes in Northwest Senegal</title><author><name sortKey="Van Den Broeck, Frederik" sort="Van Den Broeck, Frederik" uniqKey="Van Den Broeck F" first="Frederik" last="Van Den Broeck">Frederik Van Den Broeck</name><affiliation><nlm:aff id="aff001"><addr-line>Department of Biology, University of Leuven, Leuven, Belgium</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff002"><addr-line>Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium</addr-line></nlm:aff></affiliation></author><author><name sortKey="Maes, Gregory E" sort="Maes, Gregory E" uniqKey="Maes G" first="Gregory E." last="Maes">Gregory E. Maes</name><affiliation><nlm:aff id="aff001"><addr-line>Department of Biology, University of Leuven, Leuven, Belgium</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff003"><addr-line>College of Marine and Environmental Sciences, James Cook University, Townsville, Australia</addr-line></nlm:aff></affiliation></author><author><name sortKey="Larmuseau, Maarten H D" sort="Larmuseau, Maarten H D" uniqKey="Larmuseau M" first="Maarten H. D." last="Larmuseau">Maarten H. D. Larmuseau</name><affiliation><nlm:aff id="aff001"><addr-line>Department of Biology, University of Leuven, Leuven, Belgium</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff004"><addr-line>Department of Imaging and Pathology, University of Leuven, Leuven, Belgium</addr-line></nlm:aff></affiliation></author><author><name sortKey="Rollinson, David" sort="Rollinson, David" uniqKey="Rollinson D" first="David" last="Rollinson">David Rollinson</name><affiliation><nlm:aff id="aff005"><addr-line>Division of Life Sciences, Natural History Museum, London, United Kingdom</addr-line></nlm:aff></affiliation></author><author><name sortKey="Sy, Ibrahima" sort="Sy, Ibrahima" uniqKey="Sy I" first="Ibrahima" last="Sy">Ibrahima Sy</name><affiliation><nlm:aff id="aff006"><addr-line>UFR Pharmacy, University of Caen Basse-Normandie, Caen, France</addr-line></nlm:aff></affiliation></author><author><name sortKey="Faye, Djibril" sort="Faye, Djibril" uniqKey="Faye D" first="Djibril" last="Faye">Djibril Faye</name><affiliation><nlm:aff id="aff007"><addr-line>Santé Plus, Dakar, Senegal</addr-line></nlm:aff></affiliation></author><author><name sortKey="Volckaert, Filip A M" sort="Volckaert, Filip A M" uniqKey="Volckaert F" first="Filip A. M." last="Volckaert">Filip A. M. Volckaert</name><affiliation><nlm:aff id="aff001"><addr-line>Department of Biology, University of Leuven, Leuven, Belgium</addr-line></nlm:aff></affiliation></author><author><name sortKey="Polman, Katja" sort="Polman, Katja" uniqKey="Polman K" first="Katja" last="Polman">Katja Polman</name><affiliation><nlm:aff id="aff002"><addr-line>Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium</addr-line></nlm:aff></affiliation></author><author><name sortKey="Huyse, Tine" sort="Huyse, Tine" uniqKey="Huyse T" first="Tine" last="Huyse">Tine Huyse</name><affiliation><nlm:aff id="aff001"><addr-line>Department of Biology, University of Leuven, Leuven, Belgium</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff002"><addr-line>Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff008"><addr-line>Department of Biology, Royal Museum for Central Africa, Tervuren, Belgium</addr-line></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26275049</idno><idno type="pmc">4537236</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4537236</idno><idno type="RBID">PMC:4537236</idno><idno type="doi">10.1371/journal.pntd.0003998</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">002911</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">002911</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Reconstructing Colonization Dynamics of the Human Parasite <italic>Schistosoma mansoni</italic> following Anthropogenic Environmental Changes in Northwest Senegal</title><author><name sortKey="Van Den Broeck, Frederik" sort="Van Den Broeck, Frederik" uniqKey="Van Den Broeck F" first="Frederik" last="Van Den Broeck">Frederik Van Den Broeck</name><affiliation><nlm:aff id="aff001"><addr-line>Department of Biology, University of Leuven, Leuven, Belgium</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff002"><addr-line>Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium</addr-line></nlm:aff></affiliation></author><author><name sortKey="Maes, Gregory E" sort="Maes, Gregory E" uniqKey="Maes G" first="Gregory E." last="Maes">Gregory E. Maes</name><affiliation><nlm:aff id="aff001"><addr-line>Department of Biology, University of Leuven, Leuven, Belgium</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff003"><addr-line>College of Marine and Environmental Sciences, James Cook University, Townsville, Australia</addr-line></nlm:aff></affiliation></author><author><name sortKey="Larmuseau, Maarten H D" sort="Larmuseau, Maarten H D" uniqKey="Larmuseau M" first="Maarten H. D." last="Larmuseau">Maarten H. D. Larmuseau</name><affiliation><nlm:aff id="aff001"><addr-line>Department of Biology, University of Leuven, Leuven, Belgium</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff004"><addr-line>Department of Imaging and Pathology, University of Leuven, Leuven, Belgium</addr-line></nlm:aff></affiliation></author><author><name sortKey="Rollinson, David" sort="Rollinson, David" uniqKey="Rollinson D" first="David" last="Rollinson">David Rollinson</name><affiliation><nlm:aff id="aff005"><addr-line>Division of Life Sciences, Natural History Museum, London, United Kingdom</addr-line></nlm:aff></affiliation></author><author><name sortKey="Sy, Ibrahima" sort="Sy, Ibrahima" uniqKey="Sy I" first="Ibrahima" last="Sy">Ibrahima Sy</name><affiliation><nlm:aff id="aff006"><addr-line>UFR Pharmacy, University of Caen Basse-Normandie, Caen, France</addr-line></nlm:aff></affiliation></author><author><name sortKey="Faye, Djibril" sort="Faye, Djibril" uniqKey="Faye D" first="Djibril" last="Faye">Djibril Faye</name><affiliation><nlm:aff id="aff007"><addr-line>Santé Plus, Dakar, Senegal</addr-line></nlm:aff></affiliation></author><author><name sortKey="Volckaert, Filip A M" sort="Volckaert, Filip A M" uniqKey="Volckaert F" first="Filip A. M." last="Volckaert">Filip A. M. Volckaert</name><affiliation><nlm:aff id="aff001"><addr-line>Department of Biology, University of Leuven, Leuven, Belgium</addr-line></nlm:aff></affiliation></author><author><name sortKey="Polman, Katja" sort="Polman, Katja" uniqKey="Polman K" first="Katja" last="Polman">Katja Polman</name><affiliation><nlm:aff id="aff002"><addr-line>Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium</addr-line></nlm:aff></affiliation></author><author><name sortKey="Huyse, Tine" sort="Huyse, Tine" uniqKey="Huyse T" first="Tine" last="Huyse">Tine Huyse</name><affiliation><nlm:aff id="aff001"><addr-line>Department of Biology, University of Leuven, Leuven, Belgium</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff002"><addr-line>Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff008"><addr-line>Department of Biology, Royal Museum for Central Africa, Tervuren, Belgium</addr-line></nlm:aff></affiliation></author></analytic><series><title level="j">PLoS Neglected Tropical Diseases</title><idno type="ISSN">1935-2727</idno><idno type="eISSN">1935-2735</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec id="sec001"><title>Background</title><p>Anthropogenic environmental changes may lead to ecosystem destabilization and the unintentional colonization of new habitats by parasite populations. A remarkable example is the outbreak of intestinal schistosomiasis in Northwest Senegal following the construction of two dams in the ‘80s. While many studies have investigated the epidemiological, immunological and geographical patterns of <italic>Schistosoma mansoni</italic> infections in this region, little is known about its colonization history.</p></sec><sec id="sec002"><title>Methodology/Principal Findings</title><p>Parasites were collected at several time points after the disease outbreak and genotyped using a 420 bp fragment of the mitochondrial cytochrome c oxidase subunit 1 gene (<italic>cox</italic>1) and nine nuclear DNA microsatellite markers. Phylogeographic and population genetic analyses revealed the presence of (i) many genetically different haplotypes at the non-recombining mitochondrial marker and (ii) one homogenous <italic>S</italic>. <italic>mansoni</italic> genetic group at the recombining microsatellite markers. These results suggest that the <italic>S</italic>. <italic>mansoni</italic> population in Northwest Senegal was triggered by intraspecific hybridization (i.e. admixture) between parasites that were introduced from different regions. This would comply with the extensive immigration of infected seasonal agricultural workers from neighboring regions in Senegal, Mauritania and Mali. The spatial and temporal stability of the established <italic>S</italic>. <italic>mansoni</italic> population suggests a swift local adaptation of the parasite to the local intermediate snail host <italic>Biomphalaria pfeifferi</italic> at the onset of the epidemic.</p></sec><sec id="sec003"><title>Conclusions/Significance</title><p>Our results show that <italic>S</italic>. <italic>mansoni</italic> parasites are very successful in colonizing new areas without significant loss of genetic diversity. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS Negl Trop Dis</journal-id><journal-id journal-id-type="iso-abbrev">PLoS Negl Trop Dis</journal-id><journal-id journal-id-type="publisher-id">plos</journal-id><journal-id journal-id-type="pmc">plosntds</journal-id><journal-title-group><journal-title>PLoS Neglected Tropical Diseases</journal-title></journal-title-group><issn pub-type="ppub">1935-2727</issn><issn pub-type="epub">1935-2735</issn><publisher><publisher-name>Public Library of Science</publisher-name><publisher-loc>San Francisco, CA USA</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">26275049</article-id><article-id pub-id-type="pmc">4537236</article-id><article-id pub-id-type="doi">10.1371/journal.pntd.0003998</article-id><article-id pub-id-type="publisher-id">PNTD-D-15-00375</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group></article-categories><title-group><article-title>Reconstructing Colonization Dynamics of the Human Parasite <italic>Schistosoma mansoni</italic> following Anthropogenic Environmental Changes in Northwest Senegal</article-title><alt-title alt-title-type="running-head">Invasion Genetics of <italic>S</italic>. <italic>mansoni</italic> in Senegal</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Van den Broeck</surname><given-names>Frederik</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref><xref ref-type="aff" rid="aff002"><sup>2</sup></xref><xref rid="cor001" ref-type="corresp">*</xref></contrib><contrib contrib-type="author"><name><surname>Maes</surname><given-names>Gregory E.</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref><xref ref-type="aff" rid="aff003"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Larmuseau</surname><given-names>Maarten H. D.</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref><xref ref-type="aff" rid="aff004"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Rollinson</surname><given-names>David</given-names></name><xref ref-type="aff" rid="aff005"><sup>5</sup></xref></contrib><contrib contrib-type="author"><name><surname>Sy</surname><given-names>Ibrahima</given-names></name><xref ref-type="aff" rid="aff006"><sup>6</sup></xref></contrib><contrib contrib-type="author"><name><surname>Faye</surname><given-names>Djibril</given-names></name><xref ref-type="aff" rid="aff007"><sup>7</sup></xref></contrib><contrib contrib-type="author"><name><surname>Volckaert</surname><given-names>Filip A. M.</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Polman</surname><given-names>Katja</given-names></name><xref ref-type="aff" rid="aff002"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Huyse</surname><given-names>Tine</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref><xref ref-type="aff" rid="aff002"><sup>2</sup></xref><xref ref-type="aff" rid="aff008"><sup>8</sup></xref></contrib></contrib-group><aff id="aff001"><label>1</label><addr-line>Department of Biology, University of Leuven, Leuven, Belgium</addr-line></aff><aff id="aff002"><label>2</label><addr-line>Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium</addr-line></aff><aff id="aff003"><label>3</label><addr-line>College of Marine and Environmental Sciences, James Cook University, Townsville, Australia</addr-line></aff><aff id="aff004"><label>4</label><addr-line>Department of Imaging and Pathology, University of Leuven, Leuven, Belgium</addr-line></aff><aff id="aff005"><label>5</label><addr-line>Division of Life Sciences, Natural History Museum, London, United Kingdom</addr-line></aff><aff id="aff006"><label>6</label><addr-line>UFR Pharmacy, University of Caen Basse-Normandie, Caen, France</addr-line></aff><aff id="aff007"><label>7</label><addr-line>Santé Plus, Dakar, Senegal</addr-line></aff><aff id="aff008"><label>8</label><addr-line>Department of Biology, Royal Museum for Central Africa, Tervuren, Belgium</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Correa-Oliveira</surname><given-names>Rodrigo</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1"><addr-line>René Rachou Research Center, BRAZIL</addr-line></aff><author-notes><fn fn-type="COI-statement" id="coi001"><p>The authors have read the journal’s policy and have the following conflicts: DF was employed by Santé Plus at the time of this work. All other authors have declared that no competing interests exist. This does not alter our adherence to all PLOS NTDs policies on sharing data and materials.</p></fn><fn fn-type="con" id="contrib001"><p>Conceived and designed the experiments: TH GEM KP DR. Performed the experiments: FVdB TH IS DF. Analyzed the data: FVdB GEM. Contributed reagents/materials/analysis tools: FVdB TH IS DF. Wrote the paper: FVdB TH KP FAMV MHDL GEM DR.</p></fn><corresp id="cor001">* E-mail: <email>fvandenbroeck@gmail.com</email></corresp></author-notes><pub-date pub-type="epub"><day>14</day><month>8</month><year>2015</year></pub-date><pub-date pub-type="collection"><month>8</month><year>2015</year></pub-date><volume>9</volume><issue>8</issue><elocation-id>e0003998</elocation-id><history><date date-type="received"><day>9</day><month>3</month><year>2015</year></date><date date-type="accepted"><day>20</day><month>7</month><year>2015</year></date></history><permissions><copyright-statement>© 2015 Van den Broeck et al</copyright-statement><copyright-year>2015</copyright-year><copyright-holder>Van den Broeck et al</copyright-holder><license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.</license-p></license></permissions><self-uri content-type="pdf" xlink:type="simple" xlink:href="pntd.0003998.pdf"></self-uri><abstract><sec id="sec001"><title>Background</title><p>Anthropogenic environmental changes may lead to ecosystem destabilization and the unintentional colonization of new habitats by parasite populations. A remarkable example is the outbreak of intestinal schistosomiasis in Northwest Senegal following the construction of two dams in the ‘80s. While many studies have investigated the epidemiological, immunological and geographical patterns of <italic>Schistosoma mansoni</italic> infections in this region, little is known about its colonization history.</p></sec><sec id="sec002"><title>Methodology/Principal Findings</title><p>Parasites were collected at several time points after the disease outbreak and genotyped using a 420 bp fragment of the mitochondrial cytochrome c oxidase subunit 1 gene (<italic>cox</italic>1) and nine nuclear DNA microsatellite markers. Phylogeographic and population genetic analyses revealed the presence of (i) many genetically different haplotypes at the non-recombining mitochondrial marker and (ii) one homogenous <italic>S</italic>. <italic>mansoni</italic> genetic group at the recombining microsatellite markers. These results suggest that the <italic>S</italic>. <italic>mansoni</italic> population in Northwest Senegal was triggered by intraspecific hybridization (i.e. admixture) between parasites that were introduced from different regions. This would comply with the extensive immigration of infected seasonal agricultural workers from neighboring regions in Senegal, Mauritania and Mali. The spatial and temporal stability of the established <italic>S</italic>. <italic>mansoni</italic> population suggests a swift local adaptation of the parasite to the local intermediate snail host <italic>Biomphalaria pfeifferi</italic> at the onset of the epidemic.</p></sec><sec id="sec003"><title>Conclusions/Significance</title><p>Our results show that <italic>S</italic>. <italic>mansoni</italic> parasites are very successful in colonizing new areas without significant loss of genetic diversity. Maintaining high levels of diversity guarantees the adaptive potential of these parasites to cope with selective pressures such as drug treatment, which might complicate efforts to control the disease.</p></sec></abstract><abstract abstract-type="summary"><title>Author Summary</title><p><italic>Schistosoma</italic> parasites successfully colonize new regions following the construction of water schemes for power production or agricultural purposes. Here we investigated the colonization history of the human parasite <italic>Schistosoma mansoni</italic> in Northwest Senegal following the construction of two dams in the ‘80s. Parasites were collected at several time points following the disease outbreak and their genetic profile was characterized using molecular markers. Our results showed that many genetically different parasites must have been introduced at the onset of the epidemic, which complies with the extensive immigration of infected seasonal agricultural workers from neighboring regions in Senegal, Mauritania and Mali. Furthermore, we showed that parasite transmission occurred over a large geographic distance, which implies that new alleles, like resistance alleles, could spread rapidly in this system. These new insights demonstrate how colonization following anthropogenic environmental changes may lead to genetically diverse parasite populations within a short time span. High genetic diversity is often linked with a stronger potential to cope with selective pressures such as drug treatment, which may complicate efforts to control the disease.</p></abstract><funding-group><funding-statement>FVdB benefited from a doctoral fellowship (grant number VLADOC2010-07) from the Flemish Interuniversity Council (VLIR-UOS; <ext-link ext-link-type="uri" xlink:href="http://www.vliruos.be">www.vliruos.be</ext-link>). TH and MHDL benefited from a postdoctoral fellowship (grant numbers 1.2.668.11.N.01 and 12E2315N resp.) from the Research Foundation-Flanders (FWO Vlaanderen; <ext-link ext-link-type="uri" xlink:href="http://www.fwo.be">www.fwo.be</ext-link>). Research benefited from a Research Grant (grant number G.0552.10) of the Research Foundation - Flanders to TH, FAMV and KP. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</funding-statement></funding-group><counts><fig-count count="4"></fig-count><table-count count="4"></table-count><page-count count="21"></page-count></counts><custom-meta-group><custom-meta id="data-availability"><meta-name>Data Availability</meta-name><meta-value>All mitochondrial DNA sequences are available from the NCBI database (accession numbers KP343641-KP343672). All microsatellite genotypes are available as Supporting Information.</meta-value></custom-meta></custom-meta-group></article-meta><notes><title>Data Availability</title><p>All mitochondrial DNA sequences are available from the NCBI database (accession numbers KP343641-KP343672). All microsatellite genotypes are available as Supporting Information.</p></notes></front><body><sec sec-type="intro" id="sec004"><title>Introduction</title><p>Environmental change and increasing movements of people, plants and animals have led to species introductions and proliferations into new areas. The colonization, establishment and success of introduced species depend on various biotic and abiotic factors [<xref rid="pntd.0003998.ref001" ref-type="bibr">1</xref>–<xref rid="pntd.0003998.ref004" ref-type="bibr">4</xref>]. In the case of parasitic organisms, the life cycle is paramount in determining the success of colonization [<xref rid="pntd.0003998.ref005" ref-type="bibr">5</xref>]. Parasites with a direct life cycle (when a single host species is involved) can readily invade new areas together with their host [<xref rid="pntd.0003998.ref006" ref-type="bibr">6</xref>], while parasites with a complex life cycle need the presence of one or more intermediate host species in order to establish successfully [<xref rid="pntd.0003998.ref007" ref-type="bibr">7</xref>,<xref rid="pntd.0003998.ref008" ref-type="bibr">8</xref>].</p><p>The epidemic outbreak of human intestinal schistosomiasis in Northwest Senegal represents a suitable case study to investigate the evolutionary dynamics of an invasive species. This debilitating disease is caused by the flatworm <italic>Schistosoma mansoni</italic> that per generation cycles through a human final host and a snail intermediate host of the species <italic>Biomphalaria pfeifferi</italic> [<xref rid="pntd.0003998.ref009" ref-type="bibr">9</xref>]. As the Senegal River Basin (SRB) suffered from severe droughts during the 1970s and 1980s [<xref rid="pntd.0003998.ref010" ref-type="bibr">10</xref>], two dams were built to improve the agricultural conditions for rice production: the Diama dam near the mouth of the Senegal River in 1985 and the Manantali dam upstream in Mali on the Bafing River in 1989 [<xref rid="pntd.0003998.ref011" ref-type="bibr">11</xref>]. Subsequent agricultural and hydrological changes were accompanied by 1) strong agro-industrial developments in the village of Richard Toll, resulting in a massive immigration of agricultural workers from neighboring regions in Senegal, Mali and Mauritania [<xref rid="pntd.0003998.ref012" ref-type="bibr">12</xref>,<xref rid="pntd.0003998.ref013" ref-type="bibr">13</xref>], and 2) major ecological changes such as reduced salinity levels and the formation of open and permanent water bodies and irrigation canals, favoring the growth and spreading of <italic>B</italic>. <italic>pfeifferi</italic> snails [<xref rid="pntd.0003998.ref014" ref-type="bibr">14</xref>]. These factors promoted the introduction and successful establishment of <italic>S</italic>. <italic>mansoni</italic> followed by one of the most severe outbreaks of intestinal schistosomiasis ever described [<xref rid="pntd.0003998.ref011" ref-type="bibr">11</xref>,<xref rid="pntd.0003998.ref013" ref-type="bibr">13</xref>,<xref rid="pntd.0003998.ref015" ref-type="bibr">15</xref>–<xref rid="pntd.0003998.ref018" ref-type="bibr">18</xref>].</p><p>Before the construction of the two dams, human population densities were relatively low in the Delta of the SRB and they were concentrated around Saint-Louis, Ross Béthio and Richard Toll. There were no reports of <italic>S</italic>. <italic>mansoni</italic> and the intermediate snail host <italic>B</italic>. <italic>pfeifferi</italic> was only reported at low densities (< 1% of all collected snails) in the city of Saint-Louis, Lake Guiers and the village Pakh [<xref rid="pntd.0003998.ref019" ref-type="bibr">19</xref>]. The first human cases of <italic>Schistosoma mansoni</italic> were reported in 1988 in Richard Toll, the epicenter of the disease outbreak [<xref rid="pntd.0003998.ref013" ref-type="bibr">13</xref>]. About 70% of all collected snails were identified as <italic>B</italic>. <italic>pfeifferi</italic> with 44% of them infected with <italic>S</italic>. <italic>mansoni</italic> [<xref rid="pntd.0003998.ref020" ref-type="bibr">20</xref>]. The number of cases of intestinal schistosomiasis increased rapidly to epidemic proportions [<xref rid="pntd.0003998.ref015" ref-type="bibr">15</xref>,<xref rid="pntd.0003998.ref021" ref-type="bibr">21</xref>], and soon after <italic>S</italic>. <italic>mansoni</italic> colonized much of the Delta and part of the Middle Valley of the SRB [<xref rid="pntd.0003998.ref018" ref-type="bibr">18</xref>]. Many studies investigated the epidemiological, immunological and geographical patterns of <italic>S</italic>. <italic>mansoni</italic> infections in the SRB, either in single or in mixed infections with <italic>S</italic>. <italic>haematobium</italic> [<xref rid="pntd.0003998.ref013" ref-type="bibr">13</xref>,<xref rid="pntd.0003998.ref015" ref-type="bibr">15</xref>,<xref rid="pntd.0003998.ref016" ref-type="bibr">16</xref>,<xref rid="pntd.0003998.ref018" ref-type="bibr">18</xref>,<xref rid="pntd.0003998.ref022" ref-type="bibr">22</xref>–<xref rid="pntd.0003998.ref029" ref-type="bibr">29</xref>]. A few studies used molecular tools to investigate the distribution of <italic>S</italic>. <italic>mansoni</italic> among hosts [<xref rid="pntd.0003998.ref030" ref-type="bibr">30</xref>] and in response to praziquantel drug treatment [<xref rid="pntd.0003998.ref031" ref-type="bibr">31</xref>], both on a small geographic scale. However, no study looked at the phylogeography and population genetic structure of <italic>S</italic>. <italic>mansoni</italic> in Senegal at a larger scale and over time.</p><p>Here we investigated the evolutionary consequences of the anthropogenic introduction of <italic>S</italic>. <italic>mansoni</italic> in Northwest Senegal since 1988. This is a retrospective study incorporating samples collected at several time points following parasite introduction. In order to understand the dynamics of such a rapid colonization we aimed to reconstruct the epidemic by using nine microsatellite markers and sequences of the mitochondrial cytochrome c oxidase subunit 1 gene (<italic>cox</italic>1). More specifically, we wanted to test whether the current <italic>S</italic>. <italic>mansoni</italic> population was founded by a small number of strains or by multiple introductions from disparate source populations. In the first case, we expected very low levels of genetic diversity and high genetic structure due to genetic drift (e.g. [<xref rid="pntd.0003998.ref032" ref-type="bibr">32</xref>,<xref rid="pntd.0003998.ref033" ref-type="bibr">33</xref>]). In the second case, we expected average or high levels of genetic diversity, with various potential outcomes of genetic structure depending on the amount of gene flow among the introduced parasite populations (e.g. [<xref rid="pntd.0003998.ref034" ref-type="bibr">34</xref>,<xref rid="pntd.0003998.ref035" ref-type="bibr">35</xref>]).</p></sec><sec id="sec005"><title>Material & Methods</title><sec id="sec006"><title>Ethics statement</title><p>This study is part of a larger investigation on the epidemiology and control of schistosomiasis in Senegal, for which approval was obtained from ‘Le Comité National d'Ethique de la Recherche en Santé’ in Dakar (Senegal), the review board of the Institute of Tropical Medicine Antwerp (Belgium) and the ethical committee of the Antwerp University Hospital (Belgium). Before the start of the study, the respective health authorities, village leaders and school staff of the selected villages were informed about the objectives of the study. These meetings were held in the local language to ensure full comprehension. Informed consent was obtained from teachers and parents or guardians for each participating child. For the village Assoni visited in 2011 in Southwest Senegal, written informed consent was given. For the villages visited in 2006 and 2007 in Northwest Senegal, oral informed consent was given and recorded on paper by assigning ID numbers, name, age, gender and village of residence to those for whom consent was obtained. The data were anonymized prior to analyses. All schistosomiasis positive children were treated with a single dose of praziquantel at 40 mg/kg bodyweight. In schools or classes where the percentage of <italic>Schistosoma</italic> infections was more than 50%, mass treatment of all children was carried out at the end of the study according to WHO guidelines [<xref rid="pntd.0003998.ref036" ref-type="bibr">36</xref>].</p></sec><sec id="sec007"><title>Parasite collection and epidemiological background</title><p>Three genetic datasets were prepared (<xref rid="pntd.0003998.t001" ref-type="table">Table 1</xref>). The first genetic dataset, hereafter referred to as DSEQ, comprised the <italic>cox</italic>1 sequences that were generated in this study from the villages Richard Toll (1993 and 1994), Ndombo (1997 and 2006), Assoni (2011) and the villages Wayowayanko and Farako in Southwest Mali (1993) (<xref rid="pntd.0003998.t001" ref-type="table">Table 1</xref>) (see section ‘Molecular analyses’ for details on sequencing). Miracidia from the village Assoni were collected within the framework of this study (see below), while all other samples were adult worms provided by the Schistosomiasis Collection at the Natural History Museum in London (SCAN) [<xref rid="pntd.0003998.ref037" ref-type="bibr">37</xref>] (SCAN numbers: 2800, 2916, 2953, 3108, 3109, 3421, 3445, 3464, 3465, 3815, 4580). Note that sequences could not be generated for miracidia sampled in 2007 in Northwest Senegal as there was insufficient DNA. Our sequence data were therefore complemented with previously published GenBank sequences from miracidia obtained from Northwest Senegal in the villages Temey and Nder in 2007, from Southeast Senegal in the village Kolda in 2009, and from seven other countries in Africa (<xref rid="pntd.0003998.g001" ref-type="fig">Fig 1a</xref> and <xref rid="pntd.0003998.t001" ref-type="table">Table 1</xref>) [<xref rid="pntd.0003998.ref038" ref-type="bibr">38</xref>]. Sequences of cercariae and adults worms from Webster and colleagues [<xref rid="pntd.0003998.ref038" ref-type="bibr">38</xref>] were not included here as they might be clones from each other, possibly introducing a bias in estimates of diversity. In contrast, sequences generated from worms in this study were included because the microsatellite genotyping allowed us to identify and exclude clones (see below).</p><table-wrap id="pntd.0003998.t001" orientation="portrait" position="float"><object-id pub-id-type="doi">10.1371/journal.pntd.0003998.t001</object-id><label>Table 1</label><caption><title>Details of the three genetic datasets that were used in this study.</title><p>Collection of microsatellite genotypes and cytochrome <italic>c</italic> oxidase subunit 1 sequences that were obtained from <italic>Schistosoma mansoni</italic> samples during this study or during previous studies [<xref rid="pntd.0003998.ref038" ref-type="bibr">38</xref>,<xref rid="pntd.0003998.ref042" ref-type="bibr">42</xref>]. 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></caption><alternatives><graphic id="pntd.0003998.t001g" xlink:href="pntd.0003998.t001"></graphic><table frame="hsides" rules="groups"><colgroup span="1"><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col></colgroup><thead><tr><th align="center" rowspan="1" colspan="1">Region</th><th align="center" rowspan="1" colspan="1">Water course</th><th align="center" rowspan="1" colspan="1">Village</th><th align="center" rowspan="1" colspan="1">GPS</th><th align="center" rowspan="1" colspan="1">Year</th><th align="center" rowspan="1" colspan="1">Type</th><th align="center" rowspan="1" colspan="1">DMS1</th><th align="center" rowspan="1" colspan="1">DMS2</th><th align="center" rowspan="1" colspan="1">DSEQ</th><th align="center" rowspan="1" colspan="1">AC DSEQ</th><th align="center" rowspan="1" colspan="1">Reference</th></tr></thead><tbody><tr><td align="center" rowspan="1" colspan="1">Northwest Senegal</td><td align="center" rowspan="1" colspan="1">Senegal River</td><td align="center" rowspan="1" colspan="1">Rhonne</td><td align="center" rowspan="1" colspan="1">16°20'01"N 16°17'46"W</td><td align="center" rowspan="1" colspan="1">2007</td><td align="center" rowspan="1" colspan="1">Miracidia</td><td align="center" rowspan="1" colspan="1">98</td><td align="center" rowspan="1" colspan="1">121</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">This study</td></tr><tr><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1">Diadiam</td><td align="center" rowspan="1" colspan="1">16°30'24"N 16°12'04"W</td><td align="center" rowspan="1" colspan="1">2007</td><td align="center" rowspan="1" colspan="1">Miracidia</td><td align="center" rowspan="1" colspan="1">6</td><td align="center" rowspan="1" colspan="1">8</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">This study</td></tr><tr><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1">Richard Toll</td><td align="center" rowspan="1" colspan="1">16°28'08"N 15°41'09"W</td><td align="center" rowspan="1" colspan="1">1993</td><td align="center" rowspan="1" colspan="1">Worms<sup>SCAN</sup></td><td align="center" rowspan="1" colspan="1">7</td><td align="center" rowspan="1" colspan="1">7</td><td align="center" rowspan="1" colspan="1">8</td><td align="center" rowspan="1" colspan="1">KP343660-65</td><td align="center" rowspan="1" colspan="1">This study</td></tr><tr><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1">1994</td><td align="center" rowspan="1" colspan="1">Worms<sup>SCAN</sup></td><td align="center" rowspan="1" colspan="1">12</td><td align="center" rowspan="1" colspan="1">22</td><td align="center" rowspan="1" colspan="1">30</td><td align="center" rowspan="1" colspan="1">KP343666-72</td><td align="center" rowspan="1" colspan="1">This study</td></tr><tr><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1">2007</td><td align="center" rowspan="1" colspan="1">Miracidia</td><td align="center" rowspan="1" colspan="1">11</td><td align="center" rowspan="1" colspan="1">14</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">This study</td></tr><tr><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1">Canal de Taouey</td><td align="center" rowspan="1" colspan="1">Ndombo</td><td align="center" rowspan="1" colspan="1">16°26'23"N 15°41'54"W</td><td align="center" rowspan="1" colspan="1">1997</td><td align="center" rowspan="1" colspan="1">Worms<sup>SCAN</sup></td><td align="center" rowspan="1" colspan="1">53</td><td align="center" rowspan="1" colspan="1">62</td><td align="center" rowspan="1" colspan="1">46</td><td align="center" rowspan="1" colspan="1">KP343653-59</td><td align="center" rowspan="1" colspan="1">This study</td></tr><tr><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1">2006</td><td align="center" rowspan="1" colspan="1">Worms<sup>SCAN</sup></td><td align="center" rowspan="1" colspan="1">5</td><td align="center" rowspan="1" colspan="1">7</td><td align="center" rowspan="1" colspan="1">7</td><td align="center" rowspan="1" colspan="1">KP343650-52</td><td align="center" rowspan="1" colspan="1">This study</td></tr><tr><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1">Lake Guiers</td><td align="center" rowspan="1" colspan="1">Temey</td><td align="center" rowspan="1" colspan="1">16°19'46"N 15°46'04"W</td><td align="center" rowspan="1" colspan="1">2007</td><td align="center" rowspan="1" colspan="1">Miracidia</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">69</td><td align="center" rowspan="1" colspan="1">JQ289678-87</td><td align="center" rowspan="1" colspan="1">[<xref rid="pntd.0003998.ref038" ref-type="bibr">38</xref>]</td></tr><tr><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1">Theuss</td><td align="center" rowspan="1" colspan="1">16°14'19"N 15°52'04"W</td><td align="center" rowspan="1" colspan="1">2006</td><td align="center" rowspan="1" colspan="1">Miracidia</td><td align="center" rowspan="1" colspan="1">7</td><td align="center" rowspan="1" colspan="1">18</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">This study</td></tr><tr><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1">2007</td><td align="center" rowspan="1" colspan="1">Miracidia</td><td align="center" rowspan="1" colspan="1">67</td><td align="center" rowspan="1" colspan="1">68</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">This study</td></tr><tr><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1">Nder</td><td align="center" rowspan="1" colspan="1">16°16'00"N 15°52'28"W</td><td align="center" rowspan="1" colspan="1">2007</td><td align="center" rowspan="1" colspan="1">Miracidia</td><td align="center" rowspan="1" colspan="1">89</td><td align="center" rowspan="1" colspan="1">152</td><td align="center" rowspan="1" colspan="1">81</td><td align="center" rowspan="1" colspan="1">JQ289655-73</td><td align="center" rowspan="1" colspan="1">[<xref rid="pntd.0003998.ref038" ref-type="bibr">38</xref>]</td></tr><tr><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1">Ndieumeul</td><td align="center" rowspan="1" colspan="1">16°13'12"N 15°51'36"W</td><td align="center" rowspan="1" colspan="1">2007</td><td align="center" rowspan="1" colspan="1">Miracidia</td><td align="center" rowspan="1" colspan="1">15</td><td align="center" rowspan="1" colspan="1">17</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">This study</td></tr><tr><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1">Lampsar River</td><td align="center" rowspan="1" colspan="1">Mbodjene</td><td align="center" rowspan="1" colspan="1">16°13'06"N 16°14'57"W</td><td align="center" rowspan="1" colspan="1">2007</td><td align="center" rowspan="1" colspan="1">Miracidia</td><td align="center" rowspan="1" colspan="1">18</td><td align="center" rowspan="1" colspan="1">21</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">This study</td></tr><tr><td align="center" rowspan="1" colspan="1">Southeast Senegal</td><td align="center" rowspan="1" colspan="1">Gambia River</td><td align="center" rowspan="1" colspan="1">Assoni</td><td align="center" rowspan="1" colspan="1">12°36'28"N 12°30'07"W</td><td align="center" rowspan="1" colspan="1">2011</td><td align="center" rowspan="1" colspan="1">Miracidia</td><td align="center" rowspan="1" colspan="1">154</td><td align="center" rowspan="1" colspan="1">168</td><td align="center" rowspan="1" colspan="1">27</td><td align="center" rowspan="1" colspan="1">KP343641-46</td><td align="center" rowspan="1" colspan="1">This study</td></tr><tr><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1">Gambia River</td><td align="center" rowspan="1" colspan="1">Kolda</td><td align="center" rowspan="1" colspan="1">12°53'22"N 14°56'31"W</td><td align="center" rowspan="1" colspan="1">2009</td><td align="center" rowspan="1" colspan="1">Miracidia</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">4</td><td align="center" rowspan="1" colspan="1">JQ289688-90</td><td align="center" rowspan="1" colspan="1">[<xref rid="pntd.0003998.ref038" ref-type="bibr">38</xref>]</td></tr><tr><td align="center" rowspan="1" colspan="1">Southwest Mali</td><td align="center" rowspan="1" colspan="1">Niger River</td><td align="center" rowspan="1" colspan="1">Wayowayanko</td><td align="center" rowspan="1" colspan="1">12°36'46"N 8°02'50"W</td><td align="center" rowspan="1" colspan="1">1993</td><td align="center" rowspan="1" colspan="1">Worms<sup>SCAN</sup></td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">2</td><td align="center" rowspan="1" colspan="1">KP343647-48</td><td align="center" rowspan="1" colspan="1">This study</td></tr><tr><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1">Niger River</td><td align="center" rowspan="1" colspan="1">Farako</td><td align="center" rowspan="1" colspan="1">13°24'36"N 6°23'11"W</td><td align="center" rowspan="1" colspan="1">1993</td><td align="center" rowspan="1" colspan="1">Worms<sup>SCAN</sup></td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">1</td><td align="center" rowspan="1" colspan="1">KP343649</td><td align="center" rowspan="1" colspan="1">This study</td></tr><tr><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1">Niger River</td><td align="center" rowspan="1" colspan="1">Kokry-Bozo</td><td align="center" rowspan="1" colspan="1">13°57'36"N 5°30'36"W</td><td align="center" rowspan="1" colspan="1">2007</td><td align="center" rowspan="1" colspan="1">Miracidia</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">73</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">[<xref rid="pntd.0003998.ref042" ref-type="bibr">42</xref>]</td></tr><tr><td align="center" rowspan="1" colspan="1">Cameroon</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">Bessoum</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">2007</td><td align="center" rowspan="1" colspan="1">Miracidia</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">11</td><td align="center" rowspan="1" colspan="1">JQ289588-95</td><td align="center" rowspan="1" colspan="1">[<xref rid="pntd.0003998.ref038" ref-type="bibr">38</xref>]</td></tr><tr><td align="center" rowspan="1" colspan="1">Coastal Kenya</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">Rekeke</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">2007</td><td align="center" rowspan="1" colspan="1">Miracidia</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">85</td><td align="center" rowspan="1" colspan="1">JQ289596-617</td><td align="center" rowspan="1" colspan="1">[<xref rid="pntd.0003998.ref038" ref-type="bibr">38</xref>]</td></tr><tr><td align="center" rowspan="1" colspan="1">Niger</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">Namarigoungou</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">2007</td><td align="center" rowspan="1" colspan="1">Miracidia</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">133</td><td align="center" rowspan="1" colspan="1">JQ289624-40</td><td align="center" rowspan="1" colspan="1">[<xref rid="pntd.0003998.ref038" ref-type="bibr">38</xref>]</td></tr><tr><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">Diambala</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">2007</td><td align="center" rowspan="1" colspan="1">Miracidia</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">27</td><td align="center" rowspan="1" colspan="1">JQ289643-50</td><td align="center" rowspan="1" colspan="1">[<xref rid="pntd.0003998.ref038" ref-type="bibr">38</xref>]</td></tr><tr><td align="center" rowspan="1" colspan="1">Nigeria</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">Nebbi</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">2003</td><td align="center" rowspan="1" colspan="1">Miracidia</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">5</td><td align="center" rowspan="1" colspan="1">JQ28962-3</td><td align="center" rowspan="1" colspan="1">[<xref rid="pntd.0003998.ref038" ref-type="bibr">38</xref>]</td></tr><tr><td align="center" rowspan="1" colspan="1">Uganda</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">Tonya</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">2007</td><td align="center" rowspan="1" colspan="1">Miracidia</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">16</td><td align="center" rowspan="1" colspan="1">JQ289711</td><td align="center" rowspan="1" colspan="1">[<xref rid="pntd.0003998.ref038" ref-type="bibr">38</xref>]</td></tr><tr><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">Bugoto</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">2009</td><td align="center" rowspan="1" colspan="1">Miracidia</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">5</td><td align="center" rowspan="1" colspan="1">JQ289712-15</td><td align="center" rowspan="1" colspan="1">[<xref rid="pntd.0003998.ref038" ref-type="bibr">38</xref>]</td></tr><tr><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">Walakuba</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">2008</td><td align="center" rowspan="1" colspan="1">Miracidia</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">10</td><td align="center" rowspan="1" colspan="1">JQ289721-26</td><td align="center" rowspan="1" colspan="1">[<xref rid="pntd.0003998.ref038" ref-type="bibr">38</xref>]</td></tr><tr><td align="center" rowspan="1" colspan="1">Tanzania</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">Humayebe</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">2008</td><td align="center" rowspan="1" colspan="1">Miracidia</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">44</td><td align="center" rowspan="1" colspan="1">JQ289691-710</td><td align="center" rowspan="1" colspan="1">[<xref rid="pntd.0003998.ref038" ref-type="bibr">38</xref>]</td></tr><tr><td align="center" rowspan="1" colspan="1">Zambia</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">Kaunga</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">2008</td><td align="center" rowspan="1" colspan="1">Miracidia</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">40</td><td align="center" rowspan="1" colspan="1">JQ289727-38</td><td align="center" rowspan="1" colspan="1">[<xref rid="pntd.0003998.ref038" ref-type="bibr">38</xref>]</td></tr><tr><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">Siamikobo</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">2008</td><td align="center" rowspan="1" colspan="1">Miracidia</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">6</td><td align="center" rowspan="1" colspan="1">JQ289739-41</td><td align="center" rowspan="1" colspan="1">[<xref rid="pntd.0003998.ref038" ref-type="bibr">38</xref>]</td></tr><tr><td align="center" rowspan="1" colspan="1"><bold>Total</bold></td><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1"><bold>542</bold></td><td align="center" rowspan="1" colspan="1"><bold>758</bold></td><td align="center" rowspan="1" colspan="1"><bold>657</bold></td><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1"></td></tr></tbody></table></alternatives><table-wrap-foot><fn id="t001fn001"><p>Worms<sup>SCAN</sup>: worms obtained from the Schistosomiasis Collection at the Natural History Museum in London [<xref rid="pntd.0003998.ref037" ref-type="bibr">37</xref>]. DMS1: microsatellite dataset 1. DMS2: microsatellite dataset 2. DSEQ: <italic>cox</italic>1 dataset. AC DSEQ = accession number of <italic>cox</italic>1 sequences from Genbank; only unique sequences (haplotypes) were submitted to GenBank.</p></fn></table-wrap-foot></table-wrap><fig id="pntd.0003998.g001" orientation="portrait" position="float"><object-id pub-id-type="doi">10.1371/journal.pntd.0003998.g001</object-id><label>Fig 1</label><caption><title>Geographic location of <italic>Schistosoma mansoni</italic> samples.</title><p>Panel (a) shows the African countries (shaded areas) for which sequence data was generated in this study or obtained from previous studies [<xref rid="pntd.0003998.ref038" ref-type="bibr">38</xref>]. Panel (b) and (c) show the location of the villages in Mali and Senegal for which microsatellite data was generated in this study or obtained from previous studies [<xref rid="pntd.0003998.ref042" ref-type="bibr">42</xref>]. Panel (c) shows a detailed map of the lower valley of the Senegal River Basin with sampling locations. Detailed information about all samples used in this study are listed in <xref rid="pntd.0003998.t001" ref-type="table">Table 1</xref>.</p></caption><graphic xlink:href="pntd.0003998.g001"></graphic></fig><p>The second genetic dataset, hereafter referred to as DMS1, comprised parasites that were genotyped at nine microsatellite markers (see section ‘Molecular analyses’ for details on microsatellite genotyping), and that were either miracidia collected within the framework of this study or adult worms provided by SCAN [<xref rid="pntd.0003998.ref037" ref-type="bibr">37</xref>] (see <xref rid="pntd.0003998.t001" ref-type="table">Table 1</xref> for details on sample origin and sample type). These parasites originated from eight villages in Northwest Senegal and from one village in Southeast Senegal. There are three major water bodies in Northwest Senegal: the Senegal River, the Lampsar River and Lake Guiers, each with their tributaries (<xref rid="pntd.0003998.g001" ref-type="fig">Fig 1c</xref>). The Senegal River and Lake Guiers are connected in Richard Toll through the Canal of Taouey (<xref rid="pntd.0003998.g001" ref-type="fig">Fig 1c</xref>). The respective villages enrolled in this study along the Senegal River are Rhonne (2007), Diadiam (2007), Richard Toll (1993, 1994, 2007) and Ndombo (1997, 2006). Note that Ndombo lies near the Canal of Taouey within one-kilometer distance from Richard Toll. Hence, samples from Richard Toll and Ndombo combined (1993–2007) are representative for the epicenter of the disease outbreak. Near Lake Guiers, the following villages were enrolled: Theuss (2006, 2007), Nder (2007) and Ndieumeul (2007). Near the Lampsar River only one village was enrolled, namely Mbodjene (2007). To our knowledge, there were treatments in most of the villages around Lake Guiers in March and April 2006. Detailed information on the treatment history for all villages enrolled in this study is however lacking. In each village, about 75 schoolchildren aged 7 to 14 were selected randomly. From each child one stool sample was collected and examined by Kato Katz (2 slides of 25mg) [<xref rid="pntd.0003998.ref039" ref-type="bibr">39</xref>]. Eggs from positive stool samples were isolated after filtration, hatched and miracidia were individually pipetted onto Whatman FTA indicator cards in a volume of 3μl of water as described in [<xref rid="pntd.0003998.ref040" ref-type="bibr">40</xref>]. Adult worms, provided by SCAN [<xref rid="pntd.0003998.ref037" ref-type="bibr">37</xref>], were obtained after one laboratory passage of naturally collected miracidia and/or cercariae (<xref rid="pntd.0003998.t001" ref-type="table">Table 1</xref>). As adult worms may be genetically identical (i.e. clones), microsatellite genotypes obtained from worms were visually inspected to identify identical multilocus genotypes. When such identical genotypes were found within a sample, all but one were removed from the dataset. In addition, miracidia were collected within the framework of this study from eight children aged 5–14 in 2011 in the village Assoni in the Region of Kédougou (Southeast Senegal) (<xref rid="pntd.0003998.g001" ref-type="fig">Fig 1b</xref>). Six of these children were treated eight months prior to this study. The village is situated near tributaries of the Tiokaye River, itself a tributary of the Gambia River. Assoni was enrolled as pilot village in the national control program of Senegal, namely ‘le Programme National de Lutte contre les bilharzioses’ (PNLB) [<xref rid="pntd.0003998.ref041" ref-type="bibr">41</xref>]. The prevalence of <italic>S</italic>. <italic>mansoni</italic> infection in Assoni among children aged 6–14 years was initially 100% in 2006 (i.e. before treatment), but decreased to 50% in 2013 after three treatment rounds (2008, 2010, 2012) with praziquantel to those children that were diagnosed positively for <italic>S</italic>. <italic>mansoni</italic> infection [<xref rid="pntd.0003998.ref041" ref-type="bibr">41</xref>]. Similar to above, eggs from positive stool samples were isolated after filtration, hatched and miracidia were individually pipetted onto Whatman FTA indicator cards in a volume of 3 μl of water [<xref rid="pntd.0003998.ref040" ref-type="bibr">40</xref>].</p><p>The third genetic dataset, hereafter referred to as DMS2, includes the same genotypes as DMS1, but complemented with previously published <italic>S</italic>. <italic>mansoni</italic> genotypes from miracidia that were collected in the village Kokry-Bozo in 2007 in Southwest Mali within the framework of the study of Gower and colleagues [<xref rid="pntd.0003998.ref042" ref-type="bibr">42</xref>]. Main local watercourses are irrigation channels fed by the Niger River. The prevalence of <italic>S</italic>. <italic>mansoni</italic> infection in Kokry-Bozo at the time of sampling was 88% [<xref rid="pntd.0003998.ref042" ref-type="bibr">42</xref>]. Samples were obtained from children that had not been treated previously and miracidia were genotyped at the Department of Infectious Disease Epidemiology (Faculty of Medicine, Imperial College London) [<xref rid="pntd.0003998.ref042" ref-type="bibr">42</xref>]. The genetic data of 104 miracidia were provided as raw genotyping chromatogram files that were scored within our lab using GENEMAPPER v4.0 (Applied Biosystems). Six microsatellite markers (<italic>CA11-1</italic>, <italic>S9-1</italic>, <italic>SMD25</italic>, <italic>SMD28</italic>, <italic>SMD89</italic>, <italic>SMDA28</italic>) were shared among the study of Gower and colleagues [<xref rid="pntd.0003998.ref042" ref-type="bibr">42</xref>] and our study (see section ‘Molecular analyses’); hence DMS2 only contained six loci. All genotypes were imported into ALLEOGRAM v2.2 [<xref rid="pntd.0003998.ref043" ref-type="bibr">43</xref>] for binning of allele lengths. Note that only those samples that were successfully typed at all markers (nine for DMS1 and six for DMS2) were included in the analyses.</p></sec><sec id="sec008"><title>Molecular analyses</title><p>Genomic DNA extractions of lab-derived adult worms and naturally collected miracidia were performed with the Nucleospin Tissue kit (Macherey Nagel) following the manufacturer’s instructions. For miracidia, 3 mm discs containing the whole miracidium were excised from the FTA cards and for worms the whole sample was used as DNA source [<xref rid="pntd.0003998.ref040" ref-type="bibr">40</xref>].</p><p>Sequences of the mitochondrial <italic>cox</italic>1 gene (450 bp) were obtained using primers Asmit-1 and Schisto-3' [<xref rid="pntd.0003998.ref044" ref-type="bibr">44</xref>,<xref rid="pntd.0003998.ref045" ref-type="bibr">45</xref>] in 25μl PCR reactions, each containing 2 μl of DNA template, 0.5 units of Platinum Taq DNA polymerase (Life Technologies), 1x reaction buffer (Life Technologies), 2 mM MgCl<sub>2</sub>, 0.2 mM dNTPs and 0.8 μM of each primer. PCR conditions were the following: denaturation for 3 min at 95°C, followed by 35 cycles of 45 s at 94°C, 45 s at 49°C, 45 s at 72°C with a final extension of 10 min at 72°C. PCR products were visualized on a 1% agarose gel to check for amplicons, and subsequently purified and sequenced using a Big Dye Chemistry Cycle Sequencing Kit v1.1 in a 3130 Genetic Analyser (Applied Biosystems). The forward primer Asmit-1 was used and complemented with sequencing reverse primer Schisto-3' when sequence quality was poor.</p><p>All individual <italic>S</italic>. <italic>mansoni</italic> parasites (both naturally obtained miracidia and lab-derived worms) were genotyped using nine microsatellite loci in a single multiplex reaction (<italic>L46951</italic>, <italic>SMD11</italic>, <italic>S9-1</italic>, <italic>CA11-1</italic>, <italic>SMD25</italic>, <italic>SMD28</italic>, <italic>SMD43</italic>, <italic>SMD89</italic>, <italic>SMDA28</italic> [<xref rid="pntd.0003998.ref046" ref-type="bibr">46</xref>–<xref rid="pntd.0003998.ref048" ref-type="bibr">48</xref>]) as described in [<xref rid="pntd.0003998.ref040" ref-type="bibr">40</xref>]. All PCR products were analyzed using an ABI 3130 Genetic Analyser (Applied Biosystems) and GeneScan 500 LIZ as Size Standard. Allele sizes were manually verified using GENEMAPPER v4.0 (Applied Biosystems).</p></sec><sec id="sec009"><title>Phylogeographic analyses using partial <italic>cox</italic>1 sequences (DSEQ)</title><p>All <italic>cox</italic>1 sequences were manually edited and aligned using MUSCLE [<xref rid="pntd.0003998.ref049" ref-type="bibr">49</xref>] as implemented in Geneious R6 (<ext-link ext-link-type="uri" xlink:href="http://www.geneious.com/">http://www.geneious.com/</ext-link>). Species identity was confirmed using BLAST (<ext-link ext-link-type="uri" xlink:href="http://blast.ncbi.nlm.nih.gov/">http://blast.ncbi.nlm.nih.gov/</ext-link>).</p><p>Genetic diversity at the <italic>cox</italic>1 fragment (DSEQ) was quantified per region, per village and per year in DNA-SP v5.10.1 [<xref rid="pntd.0003998.ref050" ref-type="bibr">50</xref>] by estimating the number of haplotypes (i.e. unique sequences), the haplotype diversity <italic>h</italic> [<xref rid="pntd.0003998.ref051" ref-type="bibr">51</xref>], the number of polymorphic sites and the average number of nucleotide differences per site between two randomly chosen DNA sequences (i.e. nucleotide diversity <italic>Π</italic>). Based on the commonly used mutation rate of 10<sup>−8</sup> mutations per site per year for mitochondrial DNA [<xref rid="pntd.0003998.ref052" ref-type="bibr">52</xref>], we assume that the time frame (~ 30 years) is too short to generate new mtDNA lineages, and that mutation will therefore not have affected mtDNA diversity.</p><p>Genealogical relationships between all sequences were explored by constructing two haplotype networks based on statistical parsimony [<xref rid="pntd.0003998.ref053" ref-type="bibr">53</xref>] in the package ‘pegas’ [<xref rid="pntd.0003998.ref054" ref-type="bibr">54</xref>] as implemented in the R software [<xref rid="pntd.0003998.ref055" ref-type="bibr">55</xref>]. Haplotypes were first identified using the function <italic>haplotype</italic> and used to construct a network with the function <italic>haploNet</italic>. The number of sequences that represented a given haplotype was logarithmically transformed to narrow high and small values, and used to determine the size of its corresponding pie diagram. A first network included all sequences from the DSEQ dataset. A second network included only sequences from Senegal and Mali.</p></sec><sec id="sec010"><title>Population genetic analyses using microsatellite markers (DMS1 and DMS2)</title><p>First, the genetic diversity of parasite populations was quantified by estimating the proportion of heterozygous individuals (i.e. observed heterozygosity, Ho), the expected proportion of heterozygous individuals assuming Hardy-Weinberg Equilibrium (unbiased expected heterozygosity, Hs) and the number of alleles corrected for sample size (allelic richness, AR). Ho and Hs were estimated in GENETIX v4.05 [<xref rid="pntd.0003998.ref056" ref-type="bibr">56</xref>] while AR was estimated in the R package ‘hierfstat’ [<xref rid="pntd.0003998.ref057" ref-type="bibr">57</xref>]. The inbreeding coefficient <italic>F</italic><sub>IS</sub> was estimated by <italic>f</italic> [<xref rid="pntd.0003998.ref058" ref-type="bibr">58</xref>] in GENETIX; the significance of <italic>f</italic> was tested using 10,000 permutations and corrected for multiple testing using Bonferroni corrections. Analyses were done per village, year and region.</p><p>Second, the ancestry of individual parasites was inferred using a Bayesian Markov Chain Monte Carlo (MCMC) clustering analysis as implemented in STRUCTURE v2.2.3 [<xref rid="pntd.0003998.ref059" ref-type="bibr">59</xref>]. The program assigns individuals to <italic>K</italic> populations that are each characterized by a set of allele frequencies. Individuals could be assigned to two or more populations if their genotypes indicate that they are admixed. As <italic>K</italic> is unknown, the model is run multiple times, each time with a different <italic>K-</italic>value (from 1–10). Sampling locations (i.e. village) were included in the model as a prior (LOCPRIOR = 1), as they can assist clustering when the amount of genetic markers is low [<xref rid="pntd.0003998.ref060" ref-type="bibr">60</xref>]. Note that the LOCPRIOR model will not falsely identify genetic structure when there is none and will ignore sampling information when the ancestry of individuals is uncorrelated with sampling locations [<xref rid="pntd.0003998.ref060" ref-type="bibr">60</xref>]. Five replicate runs were initiated assuming the admixture model and correlated allele frequencies for datasets DMS1 and DMS2; each run consisted of 10<sup>6</sup> MCMC chains, initiated by 10<sup>5</sup> burn-in steps. All jobs were run parallel on multiple cores using the R package ‘ParallelStructure’ [<xref rid="pntd.0003998.ref061" ref-type="bibr">61</xref>]. The optimal <italic>K</italic> value was identified by the maximum LnP(D), which is the log likelihood of the observed genotype distribution in <italic>K</italic> clusters.</p><p>Third, population genetic structure was visualized by exploring the distribution of genotypes of DMS1 and DMS2 in hyperspace using a Factorial Correspondence Analysis (FCA) as implemented in GENETIX and results were visualized using the R software. FCA visualizes genotypic (dis)-similarities among individual parasites.</p><p>Fourth, genotypic (dis)-similarities were studied among groups of parasites by estimating the <italic>F</italic><sub>ST</sub> analogue <italic>θ</italic> [<xref rid="pntd.0003998.ref058" ref-type="bibr">58</xref>]. This was done pairwise between regions and villages in GENETIX for DMS1 and DMS2. Significant population differentiation was tested for all estimates by 1,000 permutations of individuals among localities, and Bonferroni correction was applied for multiple testing. Pairwise estimates of <italic>θ</italic> between villages were visualized with classical multidimensional scaling (CMDS) plots using the R software. Only populations with at least 10 genotypes were kept in order to minimize bias due to low sample size.</p></sec></sec><sec sec-type="results" id="sec011"><title>Results</title><sec id="sec012"><title>Characteristics of the datasets</title><p>The DSEQ dataset comprised a total of 657 <italic>cox</italic>1 sequences of which 121 were generated in this study (<xref rid="pntd.0003998.t001" ref-type="table">Table 1</xref>). After alignment and trimming, sequence fragments of 420 bp long were retained for further analyses.</p><p>The DMS1 dataset comprised a total of 542 <italic>S</italic>. <italic>mansoni</italic> parasites that were successfully genotyped for all nine microsatellite loci, among which 154 originated from the village Assoni in Southeast Senegal and 388 from several villages across Northwest Senegal (<xref rid="pntd.0003998.t001" ref-type="table">Table 1</xref>). Sample sizes for Northwest Senegal ranged from five genotypes in Ndombo in 2006 to 98 genotypes in Rhonne in 2007 (<xref rid="pntd.0003998.t001" ref-type="table">Table 1</xref>).</p><p>The DMS2 dataset comprised a total of 758 <italic>S</italic>. <italic>mansoni</italic> parasites that were successfully genotyped for all six microsatellite loci. A total of 73 out of 104 genotypes were successfully scored for the Kokry-Bozo sample from Southwest Mali. Sample sizes for Northwest Senegal ranged from seven in Diadiam and Ndombo (2006) to 152 in Nder (<xref rid="pntd.0003998.t001" ref-type="table">Table 1</xref>).</p></sec><sec id="sec013"><title>Phylogeographic analyses</title><p>Twenty unique <italic>cox</italic>1 haplotypes were found in Northwest Senegal (<xref rid="pntd.0003998.t002" ref-type="table">Table 2</xref>), which is currently about one fifth of the total number of haplotypes observed so far in Africa (i.e. 103). Almost all of the haplotypes found in Northwest Senegal were also found within the village Nder (i.e. 19 out of 20). A total of six haplotypes were identified within a single village (Assoni) in Southeast Senegal, of which three haplotypes were unique to this village; the other three haplotypes were shared with Northwest Senegal. In Kolda in Southeast Senegal, three <italic>cox</italic>1 haplotypes were identified of which one was unique to that village, while the other two haplotypes were also found in Northwest Senegal. The three sequences from Wayowayanko and Farako (Southwest Mali) differed from each other but were in common with Northwest Senegal, of which one was also found in Assoni (Southeast Senegal). Haplotype diversity of all parasites found in Northwest Senegal (<italic>h</italic> = 0.847; N = 241) was high compared to other regions in Africa, ranging from 0.543 in Niger (N = 160) to 0.927 in Tanzania (N = 44). Haplotype diversity was 1.000 in Mali, but the sample size was very low (N = 3). In Richard Toll, haplotype diversity in 1993 (N = 8) and 1994 (N = 30) was equal to 0.929 and 0.772 respectively, comparable to other regions in Africa (<xref rid="pntd.0003998.t002" ref-type="table">Table 2</xref>). Similarly, nucleotide diversity of all parasites sampled in Northwest Senegal (<italic>Π</italic> = 0.0081) was similar to other populations in Africa. Only parasites sampled in Zambia and Coastal Kenya showed higher levels of nucleotide diversity (<xref rid="pntd.0003998.t002" ref-type="table">Table 2</xref>).</p><table-wrap id="pntd.0003998.t002" orientation="portrait" position="float"><object-id pub-id-type="doi">10.1371/journal.pntd.0003998.t002</object-id><label>Table 2</label><caption><title><italic>Schistosoma mansoni</italic> genetic diversity as estimated at a partial fragment of the cytochrome c oxidase subunit 1 gene.</title><p>Genetic diversity was estimated for samples obtained from Senegal and eight other African countries (see <xref rid="pntd.0003998.t001" ref-type="table">Table 1</xref> for details on data collection). Sequences that were sampled in other countries than Senegal were pooled per country.</p></caption><alternatives><graphic id="pntd.0003998.t002g" xlink:href="pntd.0003998.t002"></graphic><table frame="hsides" rules="groups"><colgroup span="1"><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col></colgroup><thead><tr><th align="justify" rowspan="1" colspan="1">Region</th><th align="justify" rowspan="1" colspan="1">Village(s)</th><th align="justify" rowspan="1" colspan="1">Year(s)</th><th align="justify" rowspan="1" colspan="1">N<sub>seq</sub></th><th align="justify" rowspan="1" colspan="1">N<sub>hap</sub></th><th align="justify" rowspan="1" colspan="1">N<sub>pol</sub></th><th align="justify" rowspan="1" colspan="1"><italic>h</italic> (SD)</th><th align="justify" rowspan="1" colspan="1"><italic>Π</italic> (SD)</th></tr></thead><tbody><tr><td align="justify" rowspan="1" colspan="1">Northwest Senegal</td><td align="justify" rowspan="1" colspan="1"></td><td align="justify" rowspan="1" colspan="1"></td><td align="justify" rowspan="1" colspan="1">241</td><td align="justify" rowspan="1" colspan="1">20</td><td align="justify" rowspan="1" colspan="1">23</td><td align="justify" rowspan="1" colspan="1">0.847 (0.012)</td><td align="justify" rowspan="1" colspan="1">0.0081 (0.0001)</td></tr><tr><td align="justify" rowspan="1" colspan="1"></td><td align="justify" rowspan="1" colspan="1">Richard Toll</td><td align="justify" rowspan="1" colspan="1">1993</td><td align="justify" rowspan="1" colspan="1">8</td><td align="justify" rowspan="1" colspan="1">6</td><td align="justify" rowspan="1" colspan="1">9</td><td align="justify" rowspan="1" colspan="1">0.929 (0.084)</td><td align="justify" rowspan="1" colspan="1">0.0079 (0.0017)</td></tr><tr><td align="justify" rowspan="1" colspan="1"></td><td align="justify" rowspan="1" colspan="1"></td><td align="justify" rowspan="1" colspan="1">1994</td><td align="justify" rowspan="1" colspan="1">30</td><td align="justify" rowspan="1" colspan="1">7</td><td align="justify" rowspan="1" colspan="1">10</td><td align="justify" rowspan="1" colspan="1">0.772 (0.003)</td><td align="justify" rowspan="1" colspan="1">0.0060 (0.0009)</td></tr><tr><td align="justify" rowspan="1" colspan="1"></td><td align="justify" rowspan="1" colspan="1">Ndombo</td><td align="justify" rowspan="1" colspan="1">1997</td><td align="justify" rowspan="1" colspan="1">46</td><td align="justify" rowspan="1" colspan="1">7</td><td align="justify" rowspan="1" colspan="1">12</td><td align="justify" rowspan="1" colspan="1">0.563 (0.007)</td><td align="justify" rowspan="1" colspan="1">0.0054 (0.0010)</td></tr><tr><td align="justify" rowspan="1" colspan="1"></td><td align="justify" rowspan="1" colspan="1"></td><td align="justify" rowspan="1" colspan="1">2006</td><td align="justify" rowspan="1" colspan="1">7</td><td align="justify" rowspan="1" colspan="1">3</td><td align="justify" rowspan="1" colspan="1">4</td><td align="justify" rowspan="1" colspan="1">0.667 (0.160)</td><td align="justify" rowspan="1" colspan="1">0.0032 (0.0014)</td></tr><tr><td align="justify" rowspan="1" colspan="1"></td><td align="justify" rowspan="1" colspan="1">Nder</td><td align="justify" rowspan="1" colspan="1">2007</td><td align="justify" rowspan="1" colspan="1">81</td><td align="justify" rowspan="1" colspan="1">19</td><td align="justify" rowspan="1" colspan="1">22</td><td align="justify" rowspan="1" colspan="1">0.906 (0.014)</td><td align="justify" rowspan="1" colspan="1">0.0087 (0.0005)</td></tr><tr><td align="justify" rowspan="1" colspan="1"></td><td align="justify" rowspan="1" colspan="1">Temey</td><td align="justify" rowspan="1" colspan="1">2007</td><td align="justify" rowspan="1" colspan="1">69</td><td align="justify" rowspan="1" colspan="1">10</td><td align="justify" rowspan="1" colspan="1">14</td><td align="justify" rowspan="1" colspan="1">0.679 (0.059)</td><td align="justify" rowspan="1" colspan="1">0.0078 (0.0007)</td></tr><tr><td align="justify" rowspan="1" colspan="1">Southeast Senegal</td><td align="justify" rowspan="1" colspan="1"></td><td align="justify" rowspan="1" colspan="1"></td><td align="justify" rowspan="1" colspan="1">31</td><td align="justify" rowspan="1" colspan="1">8</td><td align="justify" rowspan="1" colspan="1">12</td><td align="justify" rowspan="1" colspan="1">0.705 (0.060)</td><td align="justify" rowspan="1" colspan="1">0.0045 (0.0012)</td></tr><tr><td align="justify" rowspan="1" colspan="1"></td><td align="justify" rowspan="1" colspan="1">Assoni</td><td align="justify" rowspan="1" colspan="1">2011</td><td align="justify" rowspan="1" colspan="1">27</td><td align="justify" rowspan="1" colspan="1">6</td><td align="justify" rowspan="1" colspan="1">7</td><td align="justify" rowspan="1" colspan="1">0.638 (0.068)</td><td align="justify" rowspan="1" colspan="1">0.0025 (0.0007)</td></tr><tr><td align="justify" rowspan="1" colspan="1"></td><td align="justify" rowspan="1" colspan="1">Kolda</td><td align="justify" rowspan="1" colspan="1">2009</td><td align="justify" rowspan="1" colspan="1">4</td><td align="justify" rowspan="1" colspan="1">3</td><td align="justify" rowspan="1" colspan="1">9</td><td align="justify" rowspan="1" colspan="1">0.833 (0.222)</td><td align="justify" rowspan="1" colspan="1">0.0127 (0.0034)</td></tr><tr><td align="justify" rowspan="1" colspan="1">Southwest Mali</td><td align="justify" rowspan="1" colspan="1">Wayowayanko-Farako</td><td align="justify" rowspan="1" colspan="1">1993</td><td align="justify" rowspan="1" colspan="1">3</td><td align="justify" rowspan="1" colspan="1">3</td><td align="justify" rowspan="1" colspan="1">4</td><td align="justify" rowspan="1" colspan="1">1.000 (0.074)</td><td align="justify" rowspan="1" colspan="1">0.0064 (0.0024)</td></tr><tr><td align="justify" rowspan="1" colspan="1">Cameroon</td><td align="justify" rowspan="1" colspan="1">Bessoum</td><td align="justify" rowspan="1" colspan="1">2007</td><td align="justify" rowspan="1" colspan="1">11</td><td align="justify" rowspan="1" colspan="1">7</td><td align="justify" rowspan="1" colspan="1">9</td><td align="justify" rowspan="1" colspan="1">0.873 (0.089)</td><td align="justify" rowspan="1" colspan="1">0.0074 (0.0010)</td></tr><tr><td align="justify" rowspan="1" colspan="1">Coastal Kenya</td><td align="justify" rowspan="1" colspan="1">Rekeke</td><td align="justify" rowspan="1" colspan="1">2007</td><td align="justify" rowspan="1" colspan="1">85</td><td align="justify" rowspan="1" colspan="1">18</td><td align="justify" rowspan="1" colspan="1">32</td><td align="justify" rowspan="1" colspan="1">0.860 (0.029)</td><td align="justify" rowspan="1" colspan="1">0.0234 (0.0008)</td></tr><tr><td align="justify" rowspan="1" colspan="1">Nigeria</td><td align="justify" rowspan="1" colspan="1">Nebbi</td><td align="justify" rowspan="1" colspan="1">2003</td><td align="justify" rowspan="1" colspan="1">5</td><td align="justify" rowspan="1" colspan="1">2</td><td align="justify" rowspan="1" colspan="1">6</td><td align="justify" rowspan="1" colspan="1">0.600 (0.175)</td><td align="justify" rowspan="1" colspan="1">0.0086 (0.0025)</td></tr><tr><td align="justify" rowspan="1" colspan="1">Niger</td><td align="justify" rowspan="1" colspan="1">Namarigoungou-Diambala</td><td align="justify" rowspan="1" colspan="1">2007</td><td align="justify" rowspan="1" colspan="1">160</td><td align="justify" rowspan="1" colspan="1">18</td><td align="justify" rowspan="1" colspan="1">28</td><td align="justify" rowspan="1" colspan="1">0.543 (0.047)</td><td align="justify" rowspan="1" colspan="1">0.0056 (0.0009)</td></tr><tr><td align="justify" rowspan="1" colspan="1">Uganda</td><td align="justify" rowspan="1" colspan="1">Bugoto-Walakuba</td><td align="justify" rowspan="1" colspan="1">2008–2009</td><td align="justify" rowspan="1" colspan="1">31</td><td align="justify" rowspan="1" colspan="1">10</td><td align="justify" rowspan="1" colspan="1">19</td><td align="justify" rowspan="1" colspan="1">0.716 (0.080)</td><td align="justify" rowspan="1" colspan="1">0.0052 (0.0012)</td></tr><tr><td align="justify" rowspan="1" colspan="1">Tanzania</td><td align="justify" rowspan="1" colspan="1">Humayebe</td><td align="justify" rowspan="1" colspan="1">2008</td><td align="justify" rowspan="1" colspan="1">44</td><td align="justify" rowspan="1" colspan="1">20</td><td align="justify" rowspan="1" colspan="1">24</td><td align="justify" rowspan="1" colspan="1">0.927 (0.021)</td><td align="justify" rowspan="1" colspan="1">0.0073 (0.0009)</td></tr><tr><td align="justify" rowspan="1" colspan="1">Zambia</td><td align="justify" rowspan="1" colspan="1">Kaunga-Siamikobo</td><td align="justify" rowspan="1" colspan="1">2008</td><td align="justify" rowspan="1" colspan="1">46</td><td align="justify" rowspan="1" colspan="1">14</td><td align="justify" rowspan="1" colspan="1">44</td><td align="justify" rowspan="1" colspan="1">0.884 (0.025)</td><td align="justify" rowspan="1" colspan="1">0.0321 (0.0043)</td></tr></tbody></table></alternatives><table-wrap-foot><fn id="t002fn001"><p>N<sub>seq</sub>: number of sequences. N<sub>hap</sub>: number of unique haplotypes. N<sub>pol</sub>: number of polymorphic sites. <italic>h</italic>: haplotype diversity. <italic>Π</italic>: nucleotide diversity. SD: standard deviation.</p></fn></table-wrap-foot></table-wrap><p>The statistical parsimony network showed that sequences from Northwest Senegal clustered together with haplotypes found in Southeast Senegal, Southwest Mali and some from Niger, and the corresponding haplotype diversity was 0.860 (SD = 0.010) (<xref rid="pntd.0003998.g002" ref-type="fig">Fig 2a</xref>). Parasites from other regions in Africa were grouped into divergent phylogeographic clades, which were separated from the ‘West-African’ clade by many unsampled or extinct haplotypes (<xref rid="pntd.0003998.g002" ref-type="fig">Fig 2a</xref>). Haplotype diversity was highest in the ‘East-African’ phylogeographic clade (<italic>h</italic> = 0.907; SD = 0.015) containing parasites from Coastal Kenya, Tanzania and Uganda (<xref rid="pntd.0003998.g002" ref-type="fig">Fig 2a</xref>). The second network revealed the diversity found in Northwest Senegal, showing many divergent haplotypes that did not cluster according to village or year of sampling (<xref rid="pntd.0003998.g002" ref-type="fig">Fig 2b</xref>).</p><fig id="pntd.0003998.g002" orientation="portrait" position="float"><object-id pub-id-type="doi">10.1371/journal.pntd.0003998.g002</object-id><label>Fig 2</label><caption><title>Haplotype networks based on statistical parsimony using partial cytochrome <italic>c</italic> oxidase subunit 1 sequences.</title><p>The network above (a) comprises all sequences from nine African countries obtained during this study or a previous study [<xref rid="pntd.0003998.ref038" ref-type="bibr">38</xref>]. For each phylogeographic group, the number of sequences (Nseq), the number of haplotypes (Nhap), the nucleotide diversity (<italic>Π</italic>) and the haplotype diversity (<italic>h</italic>) 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></caption><graphic xlink:href="pntd.0003998.g002"></graphic></fig></sec><sec id="sec014"><title>Population genetic analyses</title><p>Parasite population genetic diversity as estimated by unbiased expected heterozygosity (Hs), observed heterozygosity (Ho) and allelic richness (AR) was rather uniform across all villages sampled in Northwest Senegal (<xref rid="pntd.0003998.t003" ref-type="table">Table 3</xref>), with the exception of Ndombo (2006) that showed lower values of genetic diversity. The diversity levels of <italic>S</italic>. <italic>mansoni</italic> in Northwest Senegal (Hs = 0.38; Ho = 0.36; AR = 2.90) were similar to the diversity in Assoni in Southeast Senegal (Hs = 0.35; Ho = 0.32; AR = 2.85), but slightly lower compared to Kokry-Bozo in Southwest Mali (Hs = 0.45; Ho = 0.42; AR = 3.31) (<xref rid="pntd.0003998.t003" ref-type="table">Table 3</xref>).</p><table-wrap id="pntd.0003998.t003" orientation="portrait" position="float"><object-id pub-id-type="doi">10.1371/journal.pntd.0003998.t003</object-id><label>Table 3</label><caption><title><italic>Schistosoma mansoni</italic> genetic diversity estimated from microsatellite markers.</title><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 <xref rid="pntd.0003998.t001" ref-type="table">Table 1</xref> for details on data collection).</p></caption><alternatives><graphic id="pntd.0003998.t003g" xlink:href="pntd.0003998.t003"></graphic><table frame="hsides" rules="groups"><colgroup span="1"><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col></colgroup><thead><tr><th align="center" rowspan="1" colspan="1"></th><th align="center" rowspan="1" colspan="1"></th><th align="center" rowspan="1" colspan="1"></th><th align="center" rowspan="1" colspan="1">DMS1</th><th align="center" rowspan="1" colspan="1"></th><th align="center" rowspan="1" colspan="1"></th><th align="center" rowspan="1" colspan="1"></th><th align="center" rowspan="1" colspan="1"></th><th align="center" rowspan="1" colspan="1">DMS2</th><th align="center" rowspan="1" colspan="1"></th><th align="center" rowspan="1" colspan="1"></th><th align="center" rowspan="1" colspan="1"></th><th align="center" rowspan="1" colspan="1"></th></tr><tr><th align="center" rowspan="1" colspan="1">Region</th><th align="center" rowspan="1" colspan="1">Village</th><th align="center" rowspan="1" colspan="1">Year</th><th align="center" rowspan="1" colspan="1">N<sub><italic>μ</italic>sat</sub></th><th align="center" rowspan="1" colspan="1">Hs</th><th align="center" rowspan="1" colspan="1">Ho</th><th align="center" rowspan="1" colspan="1">AR<xref rid="t003fn002" ref-type="table-fn"><sup>#</sup></xref></th><th align="center" rowspan="1" colspan="1"><italic>F</italic><sub>IS</sub></th><th align="center" rowspan="1" colspan="1">N<sub><italic>μ</italic>sat</sub></th><th align="center" rowspan="1" colspan="1">Hs</th><th align="center" rowspan="1" colspan="1">Ho</th><th align="center" rowspan="1" colspan="1">AR<xref rid="t003fn003" ref-type="table-fn"><sup>##</sup></xref></th><th align="center" rowspan="1" colspan="1"><italic>F</italic><sub>IS</sub></th></tr></thead><tbody><tr><td align="center" rowspan="1" colspan="1">Northwest Senegal</td><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1">388</td><td align="char" char="." rowspan="1" colspan="1">0.54</td><td align="char" char="." rowspan="1" colspan="1">0.52</td><td align="char" char="." rowspan="1" colspan="1">3.74</td><td align="char" char="." rowspan="1" colspan="1">0.04**</td><td align="center" rowspan="1" colspan="1">517</td><td align="char" char="." rowspan="1" colspan="1">0.38</td><td align="char" char="." rowspan="1" colspan="1">0.36</td><td align="char" char="." rowspan="1" colspan="1">2.90</td><td align="char" char="." rowspan="1" colspan="1">0.05**</td></tr><tr><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1">Rhonne</td><td align="center" rowspan="1" colspan="1">2007</td><td align="center" rowspan="1" colspan="1">98</td><td align="char" char="." rowspan="1" colspan="1">0.55</td><td align="char" char="." rowspan="1" colspan="1">0.50</td><td align="char" char="." rowspan="1" colspan="1">3.74</td><td align="char" char="." rowspan="1" colspan="1">0.06**</td><td align="center" rowspan="1" colspan="1">121</td><td align="char" char="." rowspan="1" colspan="1">0.38</td><td align="char" char="." rowspan="1" colspan="1">0.35</td><td align="char" char="." rowspan="1" colspan="1">2.90</td><td align="char" char="." rowspan="1" colspan="1">0.07*</td></tr><tr><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1">Diadiam</td><td align="center" rowspan="1" colspan="1">2007</td><td align="center" rowspan="1" colspan="1">6</td><td align="char" char="." rowspan="1" colspan="1">0.55</td><td align="char" char="." rowspan="1" colspan="1">0.52</td><td align="char" char="." rowspan="1" colspan="1">3.73</td><td align="char" char="." rowspan="1" colspan="1">0.06</td><td align="center" rowspan="1" colspan="1">8</td><td align="char" char="." rowspan="1" colspan="1">0.42</td><td align="char" char="." rowspan="1" colspan="1">0.44</td><td align="char" char="." rowspan="1" colspan="1">2.93</td><td align="char" char="." rowspan="1" colspan="1">-0.05</td></tr><tr><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1">Richard Toll</td><td align="center" rowspan="1" colspan="1">1993</td><td align="center" rowspan="1" colspan="1">7</td><td align="char" char="." rowspan="1" colspan="1">0.54</td><td align="char" char="." rowspan="1" colspan="1">0.51</td><td align="char" char="." rowspan="1" colspan="1">3.83</td><td align="char" char="." rowspan="1" colspan="1">0.07</td><td align="center" rowspan="1" colspan="1">7</td><td align="char" char="." rowspan="1" colspan="1">0.37</td><td align="char" char="." rowspan="1" colspan="1">0.38</td><td align="char" char="." rowspan="1" colspan="1">2.83</td><td align="char" char="." rowspan="1" colspan="1">-0.03</td></tr><tr><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1">1994</td><td align="center" rowspan="1" colspan="1">12</td><td align="char" char="." rowspan="1" colspan="1">0.55</td><td align="char" char="." rowspan="1" colspan="1">0.56</td><td align="char" char="." rowspan="1" colspan="1">3.71</td><td align="char" char="." rowspan="1" colspan="1">0.03</td><td align="center" rowspan="1" colspan="1">22</td><td align="char" char="." rowspan="1" colspan="1">0.38</td><td align="char" char="." rowspan="1" colspan="1">0.42</td><td align="char" char="." rowspan="1" colspan="1">2.94</td><td align="char" char="." rowspan="1" colspan="1">-0.11*</td></tr><tr><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1">2007</td><td align="center" rowspan="1" colspan="1">11</td><td align="char" char="." rowspan="1" colspan="1">0.57</td><td align="char" char="." rowspan="1" colspan="1">0.60</td><td align="char" char="." rowspan="1" colspan="1">3.74</td><td align="char" char="." rowspan="1" colspan="1">0.06</td><td align="center" rowspan="1" colspan="1">14</td><td align="char" char="." rowspan="1" colspan="1">0.42</td><td align="char" char="." rowspan="1" colspan="1">0.42</td><td align="char" char="." rowspan="1" colspan="1">2.96</td><td align="char" char="." rowspan="1" colspan="1">-0.001</td></tr><tr><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1">Ndombo</td><td align="center" rowspan="1" colspan="1">1997</td><td align="center" rowspan="1" colspan="1">53</td><td align="char" char="." rowspan="1" colspan="1">0.49</td><td align="char" char="." rowspan="1" colspan="1">0.48</td><td align="char" char="." rowspan="1" colspan="1">3.41</td><td align="char" char="." rowspan="1" colspan="1">0.03</td><td align="center" rowspan="1" colspan="1">62</td><td align="char" char="." rowspan="1" colspan="1">0.35</td><td align="char" char="." rowspan="1" colspan="1">0.33</td><td align="char" char="." rowspan="1" colspan="1">2.72</td><td align="char" char="." rowspan="1" colspan="1">0.05</td></tr><tr><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1">2006</td><td align="center" rowspan="1" colspan="1">5</td><td align="char" char="." rowspan="1" colspan="1">0.46</td><td align="char" char="." rowspan="1" colspan="1">0.49</td><td align="char" char="." rowspan="1" colspan="1">3.00</td><td align="char" char="." rowspan="1" colspan="1">-0.06</td><td align="center" rowspan="1" colspan="1">7</td><td align="char" char="." rowspan="1" colspan="1">0.33</td><td align="char" char="." rowspan="1" colspan="1">0.33</td><td align="char" char="." rowspan="1" colspan="1">2.17</td><td align="char" char="." rowspan="1" colspan="1">-0.01</td></tr><tr><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1">Theuss</td><td align="center" rowspan="1" colspan="1">2006</td><td align="center" rowspan="1" colspan="1">7</td><td align="char" char="." rowspan="1" colspan="1">0.52</td><td align="char" char="." rowspan="1" colspan="1">0.44</td><td align="char" char="." rowspan="1" colspan="1">3.63</td><td align="char" char="." rowspan="1" colspan="1">0.16**</td><td align="center" rowspan="1" colspan="1">18</td><td align="char" char="." rowspan="1" colspan="1">0.37</td><td align="char" char="." rowspan="1" colspan="1">0.36</td><td align="char" char="." rowspan="1" colspan="1">2.68</td><td align="char" char="." rowspan="1" colspan="1">0.01</td></tr><tr><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1">2007</td><td align="center" rowspan="1" colspan="1">67</td><td align="char" char="." rowspan="1" colspan="1">0.54</td><td align="char" char="." rowspan="1" colspan="1">0.52</td><td align="char" char="." rowspan="1" colspan="1">3.72</td><td align="char" char="." rowspan="1" colspan="1">0.04*</td><td align="center" rowspan="1" colspan="1">68</td><td align="char" char="." rowspan="1" colspan="1">0.39</td><td align="char" char="." rowspan="1" colspan="1">0.38</td><td align="char" char="." rowspan="1" colspan="1">2.94</td><td align="char" char="." rowspan="1" colspan="1">0.03</td></tr><tr><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1">Nder</td><td align="center" rowspan="1" colspan="1">2007</td><td align="center" rowspan="1" colspan="1">89</td><td align="char" char="." rowspan="1" colspan="1">0.54</td><td align="char" char="." rowspan="1" colspan="1">0.53</td><td align="char" char="." rowspan="1" colspan="1">3.71</td><td align="char" char="." rowspan="1" colspan="1">0.01</td><td align="center" rowspan="1" colspan="1">152</td><td align="char" char="." rowspan="1" colspan="1">0.38</td><td align="char" char="." rowspan="1" colspan="1">0.36</td><td align="char" char="." rowspan="1" colspan="1">2.85</td><td align="char" char="." rowspan="1" colspan="1">0.06*</td></tr><tr><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1">Ndieumeul</td><td align="center" rowspan="1" colspan="1">2007</td><td align="center" rowspan="1" colspan="1">15</td><td align="char" char="." rowspan="1" colspan="1">0.54</td><td align="char" char="." rowspan="1" colspan="1">0.47</td><td align="char" char="." rowspan="1" colspan="1">3.77</td><td align="char" char="." rowspan="1" colspan="1">0.12*</td><td align="center" rowspan="1" colspan="1">17</td><td align="char" char="." rowspan="1" colspan="1">0.37</td><td align="char" char="." rowspan="1" colspan="1">0.33</td><td align="char" char="." rowspan="1" colspan="1">2.94</td><td align="char" char="." rowspan="1" colspan="1">0.11*</td></tr><tr><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1">Mbodjene</td><td align="center" rowspan="1" colspan="1">2007</td><td align="center" rowspan="1" colspan="1">18</td><td align="char" char="." rowspan="1" colspan="1">0.54</td><td align="char" char="." rowspan="1" colspan="1">0.60</td><td align="char" char="." rowspan="1" colspan="1">3.43</td><td align="char" char="." rowspan="1" colspan="1">-0.11*</td><td align="center" rowspan="1" colspan="1">21</td><td align="char" char="." rowspan="1" colspan="1">0.39</td><td align="char" char="." rowspan="1" colspan="1">0.44</td><td align="char" char="." rowspan="1" colspan="1">2.72</td><td align="char" char="." rowspan="1" colspan="1">-0.13*</td></tr><tr><td align="center" rowspan="1" colspan="1">Southeast Senegal</td><td align="center" rowspan="1" colspan="1">Assoni</td><td align="center" rowspan="1" colspan="1">2011</td><td align="center" rowspan="1" colspan="1">154</td><td align="char" char="." rowspan="1" colspan="1">0.50</td><td align="char" char="." rowspan="1" colspan="1">0.45</td><td align="char" char="." rowspan="1" colspan="1">3.55</td><td align="char" char="." rowspan="1" colspan="1">0.12**</td><td align="center" rowspan="1" colspan="1">168</td><td align="char" char="." rowspan="1" colspan="1">0.35</td><td align="char" char="." rowspan="1" colspan="1">0.32</td><td align="char" char="." rowspan="1" colspan="1">2.85</td><td align="char" char="." rowspan="1" colspan="1">0.09**</td></tr><tr><td align="center" rowspan="1" colspan="1">Southwest Mali</td><td align="center" rowspan="1" colspan="1">Kokry-Bozo</td><td align="center" rowspan="1" colspan="1">2007</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">/</td><td align="center" rowspan="1" colspan="1">73</td><td align="char" char="." rowspan="1" colspan="1">0.45</td><td align="char" char="." rowspan="1" colspan="1">0.42</td><td align="char" char="." rowspan="1" colspan="1">3.31</td><td align="char" char="." rowspan="1" colspan="1">0.06*</td></tr></tbody></table></alternatives><table-wrap-foot><fn id="t003fn001"><p>DMS1: microsatellite dataset 1. DMS2: microsatellite dataset 2. N<sub>μsat</sub>: number of successfully genotyped parasites. Hs: unbiased expected heterozygosity. Ho: observed heterozygosity. AR: Allelic richness.</p></fn><fn id="t003fn002"><p><sup>#</sup>: minimum of 10 alleles used for rarefaction.</p></fn><fn id="t003fn003"><p><sup>##</sup>: minimum of 14 alleles used for rarification.</p></fn><fn id="t003fn004"><p>Statistical significant <italic>F</italic><sub>IS</sub> values are given with * for the nominal level of 0.05 and with ** for the nominal level of 0.001.</p></fn></table-wrap-foot></table-wrap><p>The highest log likelihood values as estimated in STRUCTURE were found for <italic>K</italic> = 4 for DMS1 and for <italic>K</italic> = 3 for DMS2; the log likelihood decreased thereafter for larger values of <italic>K</italic>. For DMS1, parasites from almost all villages sampled in Northwest Senegal were assigned to one genetic cluster, with the exception of parasites from Ndombo (1997) and Mbodjene (2007) (<xref rid="pntd.0003998.g003" ref-type="fig">Fig 3a</xref>). In addition, parasites from Assoni were assigned to a separate genetic cluster (<xref rid="pntd.0003998.g003" ref-type="fig">Fig 3a</xref>). For DMS2, three genetic clusters were identified that were concordant with the three regions Northwest Senegal, Southeast Senegal and Southwest Mali (<xref rid="pntd.0003998.g003" ref-type="fig">Fig 3b</xref>).</p><fig id="pntd.0003998.g003" orientation="portrait" position="float"><object-id pub-id-type="doi">10.1371/journal.pntd.0003998.g003</object-id><label>Fig 3</label><caption><title>Bayesian clustering analysis with STRUCTURE using microsatellite markers.</title><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 <italic>K</italic> (<italic>K</italic> = 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 <italic>K—</italic>value (<italic>K</italic> = 4 for DMS1 and <italic>K</italic> = 3 for DMS2) was determined by the maximum LnP(D), which is the log likelihood of the observed genotype distribution in <italic>K</italic> clusters.</p></caption><graphic xlink:href="pntd.0003998.g003"></graphic></fig><p>Factorial Correspondence analysis (FCA) for DMS2 revealed that most of the parasites from Northwest Senegal sampled in several villages from 1993 to 2007 always clustered together and differed strongly from parasites sampled in Assoni in 2011 (Southeast Senegal) and Kokry-Bozo in 2007 (Southwest Mali) (<xref rid="pntd.0003998.g004" ref-type="fig">Fig 4b</xref>). For DMS1, parasites sampled in Mbodjene (2007) and Ndombo (1997) differed slightly from the remainder of Northwest Senegal, although the second axis explained only 9.84% of the total observed variation (<xref rid="pntd.0003998.g004" ref-type="fig">Fig 4a</xref>).</p><fig id="pntd.0003998.g004" orientation="portrait" position="float"><object-id pub-id-type="doi">10.1371/journal.pntd.0003998.g004</object-id><label>Fig 4</label><caption><title>Population genetic structure of <italic>Schistosoma mansoni</italic> using microsatellite markers.</title><p>Results of the Factorial Correspondence Analysis for datasets DMS1 (a) and DMS2 (b). Classical multidimensional scaling plots of pairwise <italic>F</italic><sub>ST</sub> between villages for datasets DMS1 (c) and DMS2 (d).</p></caption><graphic xlink:href="pntd.0003998.g004"></graphic></fig><p>Pairwise estimates of <italic>F</italic><sub>ST</sub> between regions for DMS2 were 0.064 (<italic>p</italic> < 0.001) between Southwest Mali and Northwest Senegal, 0.056 (<italic>p</italic> < 0.001) between Southwest Mali and Southeast Senegal and 0.044 (<italic>p</italic> < 0.001) between Northwest Senegal and Southeast Senegal. <xref rid="pntd.0003998.t004" ref-type="table">Table 4</xref> summarizes the pairwise <italic>F</italic><sub>ST</sub> between villages and shows that parasite populations from Kokry-Bozo (2007), Assoni (2011), Ndombo (1997) and Mbodjene (2007) were almost always significantly differentiated from the other samples when genotypes were permuted among villages. In contrast, genetic differentiation among the other samples in Northwest Senegal was mostly low and often insignificant (<xref rid="pntd.0003998.t004" ref-type="table">Table 4</xref>). Classical multidimensional scaling (CMDS) plots based on pairwise <italic>F</italic><sub>ST</sub> between villages visualized this pattern (<xref rid="pntd.0003998.g004" ref-type="fig">Fig 4c and 4d</xref>).</p><table-wrap id="pntd.0003998.t004" orientation="portrait" position="float"><object-id pub-id-type="doi">10.1371/journal.pntd.0003998.t004</object-id><label>Table 4</label><caption><title>Pairwise <italic>F</italic><sub>ST</sub> estimates between <italic>Schistosoma mansoni</italic> samples from Mali and Senegal.</title><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></caption><alternatives><graphic id="pntd.0003998.t004g" xlink:href="pntd.0003998.t004"></graphic><table frame="hsides" rules="groups"><colgroup span="1"><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col></colgroup><thead><tr><th align="center" rowspan="1" colspan="1"></th><th align="center" rowspan="1" colspan="1">Kokry '07</th><th align="center" rowspan="1" colspan="1">Assoni '11</th><th align="center" rowspan="1" colspan="1">Rhonne '07</th><th align="center" rowspan="1" colspan="1">Rtoll '93–94’</th><th align="center" rowspan="1" colspan="1">Rtoll '07</th><th align="center" rowspan="1" colspan="1">Ndombo '97</th><th align="center" rowspan="1" colspan="1">Theuss '06</th><th align="center" rowspan="1" colspan="1">Theuss '07</th><th align="center" rowspan="1" colspan="1">Nder '07</th><th align="center" rowspan="1" colspan="1">Ndieumeul '07</th><th align="center" rowspan="1" colspan="1">Mbodjene '07</th></tr></thead><tbody><tr><td align="center" rowspan="1" colspan="1">Kokry '07</td><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1">0.056<xref rid="t004fn003" ref-type="table-fn">**</xref></td><td align="center" rowspan="1" colspan="1">0.059<xref rid="t004fn003" ref-type="table-fn">**</xref></td><td align="center" rowspan="1" colspan="1">0.041<xref rid="t004fn003" ref-type="table-fn">**</xref></td><td align="center" rowspan="1" colspan="1">0.029<xref rid="t004fn002" ref-type="table-fn">*</xref></td><td align="center" rowspan="1" colspan="1">0.110<xref rid="t004fn003" ref-type="table-fn">**</xref></td><td align="center" rowspan="1" colspan="1">0.067<xref rid="t004fn003" ref-type="table-fn">**</xref></td><td align="char" char="." rowspan="1" colspan="1">0.050<xref rid="t004fn003" ref-type="table-fn">**</xref></td><td align="char" char="." rowspan="1" colspan="1">0.066<xref rid="t004fn003" ref-type="table-fn">**</xref></td><td align="char" char="." rowspan="1" colspan="1">0.032<xref rid="t004fn003" ref-type="table-fn">**</xref></td><td align="char" char="." rowspan="1" colspan="1">0.065<xref rid="t004fn003" ref-type="table-fn">**</xref></td></tr><tr><td align="center" rowspan="1" colspan="1">Assoni '11</td><td align="center" rowspan="1" colspan="1">na</td><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1">0.037<xref rid="t004fn003" ref-type="table-fn">**</xref></td><td align="center" rowspan="1" colspan="1">0.022<xref rid="t004fn003" ref-type="table-fn">**</xref></td><td align="center" rowspan="1" colspan="1">0.014</td><td align="center" rowspan="1" colspan="1">0.083<xref rid="t004fn003" ref-type="table-fn">**</xref></td><td align="center" rowspan="1" colspan="1">0.056<xref rid="t004fn003" ref-type="table-fn">**</xref></td><td align="char" char="." rowspan="1" colspan="1">0.045<xref rid="t004fn003" ref-type="table-fn">**</xref></td><td align="char" char="." rowspan="1" colspan="1">0.055<xref rid="t004fn003" ref-type="table-fn">**</xref></td><td align="char" char="." rowspan="1" colspan="1">0.027<xref rid="t004fn002" ref-type="table-fn">*</xref></td><td align="char" char="." rowspan="1" colspan="1">0.069<xref rid="t004fn003" ref-type="table-fn">**</xref></td></tr><tr><td align="center" rowspan="1" colspan="1">Rhonne '07</td><td align="center" rowspan="1" colspan="1">na</td><td align="center" rowspan="1" colspan="1">0.039<xref rid="t004fn003" ref-type="table-fn">**</xref></td><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1">-0.002</td><td align="center" rowspan="1" colspan="1">0.023<xref rid="t004fn002" ref-type="table-fn">*</xref></td><td align="center" rowspan="1" colspan="1">0.024<xref rid="t004fn003" ref-type="table-fn">**</xref></td><td align="center" rowspan="1" colspan="1">0.016</td><td align="char" char="." rowspan="1" colspan="1">-0.001</td><td align="char" char="." rowspan="1" colspan="1">0.001</td><td align="char" char="." rowspan="1" colspan="1">0.002</td><td align="char" char="." rowspan="1" colspan="1">0.014<xref rid="t004fn002" ref-type="table-fn">*</xref></td></tr><tr><td align="center" rowspan="1" colspan="1">Rtoll '93 –‘94</td><td align="center" rowspan="1" colspan="1">na</td><td align="center" rowspan="1" colspan="1">0.044<xref rid="t004fn003" ref-type="table-fn">**</xref></td><td align="center" rowspan="1" colspan="1">-0.001</td><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1">0.011</td><td align="center" rowspan="1" colspan="1">0.041<xref rid="t004fn003" ref-type="table-fn">**</xref></td><td align="center" rowspan="1" colspan="1">0.017<xref rid="t004fn002" ref-type="table-fn">*</xref></td><td align="char" char="." rowspan="1" colspan="1">-0.001</td><td align="char" char="." rowspan="1" colspan="1">0.007</td><td align="char" char="." rowspan="1" colspan="1">-0.001</td><td align="char" char="." rowspan="1" colspan="1">0.015</td></tr><tr><td align="center" rowspan="1" colspan="1">Rtoll '07</td><td align="center" rowspan="1" colspan="1">na</td><td align="center" rowspan="1" colspan="1">0.045<xref rid="t004fn003" ref-type="table-fn">**</xref></td><td align="center" rowspan="1" colspan="1">0.012<xref rid="t004fn002" ref-type="table-fn">*</xref></td><td align="center" rowspan="1" colspan="1">0.006</td><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1">0.053<xref rid="t004fn003" ref-type="table-fn">**</xref></td><td align="center" rowspan="1" colspan="1">0.038<xref rid="t004fn003" ref-type="table-fn">**</xref></td><td align="char" char="." rowspan="1" colspan="1">0.020<xref rid="t004fn002" ref-type="table-fn">*</xref></td><td align="char" char="." rowspan="1" colspan="1">0.033<xref rid="t004fn002" ref-type="table-fn">*</xref></td><td align="char" char="." rowspan="1" colspan="1">0.003</td><td align="char" char="." rowspan="1" colspan="1">0.051<xref rid="t004fn003" ref-type="table-fn">**</xref></td></tr><tr><td align="center" rowspan="1" colspan="1">Ndombo '97</td><td align="center" rowspan="1" colspan="1">na</td><td align="center" rowspan="1" colspan="1">0.073<xref rid="t004fn003" ref-type="table-fn">**</xref></td><td align="center" rowspan="1" colspan="1">0.021<xref rid="t004fn003" ref-type="table-fn">**</xref></td><td align="center" rowspan="1" colspan="1">0.025<xref rid="t004fn003" ref-type="table-fn">**</xref></td><td align="center" rowspan="1" colspan="1">0.038<xref rid="t004fn003" ref-type="table-fn">**</xref></td><td align="center" rowspan="1" colspan="1"></td><td align="center" rowspan="1" colspan="1">0.009</td><td align="char" char="." rowspan="1" colspan="1">0.027<xref rid="t004fn003" ref-type="table-fn">**</xref></td><td align="char" char="." rowspan="1" colspan="1">0.018<xref rid="t004fn003" ref-type="table-fn">**</xref></td><td align="char" char="." rowspan="1" colspan="1">0.012</td><td align="char" char="." rowspan="1" colspan="1">0.066<xref rid="t004fn003" ref-type="table-fn">**</xref></td></tr><tr><td align="center" rowspan="1" colspan="1">Theuss '06</td><td align="center" rowspan="1" colspan="1">na</td><td align="center" rowspan="1" colspan="1">na</td><td align="center" rowspan="1" colspan="1">na</td><td align="center" rowspan="1" colspan="1">na</td><td align="center" rowspan="1" colspan="1">na</td><td align="center" rowspan="1" colspan="1">na</td><td align="center" rowspan="1" colspan="1"></td><td align="char" char="." rowspan="1" colspan="1">0.012</td><td align="char" char="." rowspan="1" colspan="1">0.016<xref rid="t004fn002" ref-type="table-fn">*</xref></td><td align="char" char="." rowspan="1" colspan="1">-0.014</td><td align="char" char="." rowspan="1" colspan="1">0.053<xref rid="t004fn003" ref-type="table-fn">**</xref></td></tr><tr><td align="center" rowspan="1" colspan="1">Theuss '07</td><td align="center" rowspan="1" colspan="1">na</td><td align="center" rowspan="1" colspan="1">0.049<xref rid="t004fn003" ref-type="table-fn">**</xref></td><td align="center" rowspan="1" colspan="1">0.001</td><td align="center" rowspan="1" colspan="1">-0.001</td><td align="center" rowspan="1" colspan="1">0.007</td><td align="center" rowspan="1" colspan="1">0.021<xref rid="t004fn003" ref-type="table-fn">**</xref></td><td align="center" rowspan="1" colspan="1">na</td><td align="center" rowspan="1" colspan="1"></td><td align="char" char="." rowspan="1" colspan="1">0.000</td><td align="char" char="." rowspan="1" colspan="1">-0.001</td><td align="char" char="." rowspan="1" colspan="1">0.012<xref rid="t004fn002" ref-type="table-fn">*</xref></td></tr><tr><td align="center" rowspan="1" colspan="1">Nder '07</td><td align="center" rowspan="1" colspan="1">na</td><td align="center" rowspan="1" colspan="1">0.046<xref rid="t004fn003" ref-type="table-fn">**</xref></td><td align="center" rowspan="1" colspan="1">0.002</td><td align="center" rowspan="1" colspan="1">0.007</td><td align="center" rowspan="1" colspan="1">0.020<xref rid="t004fn002" ref-type="table-fn">*</xref></td><td align="center" rowspan="1" colspan="1">0.020<xref rid="t004fn003" ref-type="table-fn">**</xref></td><td align="center" rowspan="1" colspan="1">na</td><td align="char" char="." rowspan="1" colspan="1">0.003</td><td align="center" rowspan="1" colspan="1"></td><td align="char" char="." rowspan="1" colspan="1">0.003</td><td align="char" char="." rowspan="1" colspan="1">0.012</td></tr><tr><td align="center" rowspan="1" colspan="1">Ndieumeul '07</td><td align="center" rowspan="1" colspan="1">na</td><td align="center" rowspan="1" colspan="1">0.028<xref rid="t004fn003" ref-type="table-fn">**</xref></td><td align="center" rowspan="1" colspan="1">-0.001</td><td align="center" rowspan="1" colspan="1">-0.003</td><td align="center" rowspan="1" colspan="1">0.009</td><td align="center" rowspan="1" colspan="1">0.016<xref rid="t004fn002" ref-type="table-fn">*</xref></td><td align="center" rowspan="1" colspan="1">na</td><td align="char" char="." rowspan="1" colspan="1">0.001</td><td align="char" char="." rowspan="1" colspan="1">0.000</td><td align="center" rowspan="1" colspan="1"></td><td align="char" char="." rowspan="1" colspan="1">0.037<xref rid="t004fn002" ref-type="table-fn">*</xref></td></tr><tr><td align="center" rowspan="1" colspan="1">Mbodjene '07</td><td align="center" rowspan="1" colspan="1">na</td><td align="center" rowspan="1" colspan="1">0.068<xref rid="t004fn003" ref-type="table-fn">**</xref></td><td align="center" rowspan="1" colspan="1">0.013<xref rid="t004fn002" ref-type="table-fn">*</xref></td><td align="center" rowspan="1" colspan="1">0.023<xref rid="t004fn002" ref-type="table-fn">*</xref></td><td align="center" rowspan="1" colspan="1">0.029<xref rid="t004fn002" ref-type="table-fn">*</xref></td><td align="center" rowspan="1" colspan="1">0.047<xref rid="t004fn003" ref-type="table-fn">**</xref></td><td align="center" rowspan="1" colspan="1">na</td><td align="char" char="." rowspan="1" colspan="1">0.012<xref rid="t004fn002" ref-type="table-fn">*</xref></td><td align="char" char="." rowspan="1" colspan="1">0.015<xref rid="t004fn002" ref-type="table-fn">*</xref></td><td align="char" char="." rowspan="1" colspan="1">0.028<xref rid="t004fn003" ref-type="table-fn">**</xref></td><td align="center" rowspan="1" colspan="1"></td></tr></tbody></table></alternatives><table-wrap-foot><fn id="t004fn001"><p>Kokry = short for Kokry-Bozo. Rtoll = short for Richard Toll.</p></fn><fn id="t004fn002"><p>* = significant for permutation of genotypes among villages at the nominal level of 0.05.</p></fn><fn id="t004fn003"><p>** = significant for permutation of genotypes among villages at the nominal level of 0.001 (i.e. Bonferroni corrected). na = not applicable.</p></fn></table-wrap-foot></table-wrap></sec></sec><sec sec-type="conclusions" id="sec015"><title>Discussion</title><p>The construction of two dams in the 1980s within the Senegal River Basin (SRB) led to a massive outbreak of intestinal schistosomiasis, a debilitating and neglected disease that had not been reported before in the region. The rate and intensity at which the epidemic expanded over Northwest Senegal was devastating: within a few years, <italic>S</italic>. <italic>mansoni</italic> was present almost everywhere in the lower valley and prevalence reached 91% in some villages [<xref rid="pntd.0003998.ref018" ref-type="bibr">18</xref>]. Here, we investigated the level and the distribution of <italic>S</italic>. <italic>mansoni</italic> genetic diversity over a large geographic scale and wide timeframe in order to provide insight into the colonization history of this parasite in Northwest Senegal.</p><sec id="sec016"><title>Parasite genetic diversity</title><p>Our results showed that genetic diversity of <italic>S</italic>. <italic>mansoni</italic> was high, both at the mitochondrial and at the nuclear level. A total of 20 different <italic>cox</italic>1 haplotypes (out of 103 described across Africa) were identified in Northwest Senegal (<xref rid="pntd.0003998.g002" ref-type="fig">Fig 2a</xref>). Despite the fact that mitochondrial genes are particularly prone to diversity loss after colonization events due to their haploid state and uniparental inheritance [<xref rid="pntd.0003998.ref052" ref-type="bibr">52</xref>], a substantial level of nucleotide and haplotype diversity was detected, also for those parasite populations collected in 1993–1994 shortly after the onset of the epidemic (<xref rid="pntd.0003998.t002" ref-type="table">Table 2</xref>). This observation was confirmed by statistical parsimony analysis that showed a relatively wide range of haplotypes that were often separated by many mutations (<xref rid="pntd.0003998.g002" ref-type="fig">Fig 2b</xref>). These results suggest that many <italic>S</italic>. <italic>mansoni</italic> parasites were introduced from multiple source populations. Note that, based on the commonly used 2% divergence rate for mitochondrial DNA [<xref rid="pntd.0003998.ref052" ref-type="bibr">52</xref>], we expect none or only a few mutations in the 30 years since the beginning of the disease outbreak. At the nuclear level, levels of diversity in Northwest Senegal were relatively similar compared to Southeast Senegal and Southwest Mali (<xref rid="pntd.0003998.t003" ref-type="table">Table 3</xref>). These results suggest that there was no significant loss of genetic diversity upon introduction, and confirm that many parasites were probably introduced at the onset of the epidemic. An interesting finding in this respect is that <italic>S</italic>. <italic>mansoni</italic> genetic diversity in Richard Toll remained relatively stable since 1993 despite the many treatments during the course of the disease outbreak. Although treatment with praziquantel is expected to result in decreased population sizes and thus decreased genetic diversity [<xref rid="pntd.0003998.ref062" ref-type="bibr">62</xref>], field-based studies revealed only a slight [<xref rid="pntd.0003998.ref063" ref-type="bibr">63</xref>] or no decrease in diversity at all following treatment [<xref rid="pntd.0003998.ref031" ref-type="bibr">31</xref>,<xref rid="pntd.0003998.ref064" ref-type="bibr">64</xref>] suggesting that treatment may only have little effect on the genetic composition of natural <italic>S</italic>. <italic>mansoni</italic> populations. Note however that the actual diversity in 1993/1994 may have been larger than the one observed here, as parasites were passaged through mice, which may have induced a loss in genetic diversity.</p><p>These results highlight the success of this parasite in extending its geographic range without notable loss of genetic diversity. Maintaining genetic diversity allows the parasite to quickly adapt to a new environment or a new host, or to counteract selective pressures such as drug treatment [<xref rid="pntd.0003998.ref065" ref-type="bibr">65</xref>,<xref rid="pntd.0003998.ref066" ref-type="bibr">66</xref>]. Such a strong evolutionary potential could explain why <italic>Schistosoma</italic> parasites continue to (re-)emerge successfully into new regions [<xref rid="pntd.0003998.ref067" ref-type="bibr">67</xref>], and why caution is warranted in any future anthropogenic environmental changes involving creation of potential new transmission sites.</p></sec><sec id="sec017"><title>Parasite population structure</title><p>Multidimensional scaling of pairwise <italic>F</italic><sub>ST</sub>, Factorial Correspondence Analysis and STRUCTURE analysis revealed the presence of three genetic populations in Northwest Senegal: one dominant <italic>S</italic>. <italic>mansoni</italic> population that is present in almost all villages and at all times, and two smaller populations in Ndombo 1997 and in Mbodjene 2007 (Figs <xref rid="pntd.0003998.g003" ref-type="fig">3</xref> and <xref rid="pntd.0003998.g004" ref-type="fig">4</xref> and <xref rid="pntd.0003998.t004" ref-type="table">Table 4</xref>). The presence of one widespread population suggests that most <italic>S</italic>. <italic>mansoni</italic> parasites originated from one and the same source population (scenario 1), or that they are the result of intraspecific hybridization (admixture) among multiple introduced parasite populations (scenario 2). Admixture among different introductions might produce recombinant genotypes that are characterized by a unique genetic profile if these genotypes were extensively shuffled, which will furthermore erode the genetic signal of the native range [<xref rid="pntd.0003998.ref068" ref-type="bibr">68</xref>–<xref rid="pntd.0003998.ref071" ref-type="bibr">71</xref>]. We favor the second scenario of admixture among multiple introductions because of the following reasons. (i) The presence of many divergent haplotypes at the non-recombining mitochondrial marker suggests that multiple introductions likely occurred (see above). (ii) Multiple introductions could have happened due to the substantial seasonal immigration of infected agricultural workers from neighboring regions in Senegal, Mauritania and Mali [<xref rid="pntd.0003998.ref011" ref-type="bibr">11</xref>,<xref rid="pntd.0003998.ref012" ref-type="bibr">12</xref>]. (iii) There is evidence of high parasite gene flow in Northwest Senegal, which tends to homogenize populations, as 19 out of 20 identified <italic>cox</italic>1 haplotypes were found within a single village (<xref rid="pntd.0003998.t002" ref-type="table">Table 2</xref>) and pairwise <italic>F</italic><sub>ST</sub> between most villages was low and insignificant (<xref rid="pntd.0003998.t004" ref-type="table">Table 4</xref>). (iv) The presence of two divergent populations in Ndombo (1997) and Mbodjene (2007) might support the hypothesis of multiple introductions. However, population bottlenecks followed by genetic drift could also produce divergent populations [<xref rid="pntd.0003998.ref072" ref-type="bibr">72</xref>], which could apply to the sample from Ndombo that was obtained after laboratory passage [<xref rid="pntd.0003998.ref073" ref-type="bibr">73</xref>,<xref rid="pntd.0003998.ref074" ref-type="bibr">74</xref>]. Altogether, these findings support the hypothesis that the widespread dominant population of <italic>S</italic>. <italic>mansoni</italic> in Northwest Senegal is more likely the result of an admixture between multiple introductions (scenario 2) than the result of a single introduction (scenario 1). Unfortunately, our sampling in the native range is too restricted to reliably discriminate among both scenarios. Analyses of genetic structure indicated that the samples from Southeast Senegal and Southwest Mali represent separate genetic groups (<xref rid="pntd.0003998.t004" ref-type="table">Table 4</xref> and Figs <xref rid="pntd.0003998.g003" ref-type="fig">3</xref> and <xref rid="pntd.0003998.g004" ref-type="fig">4</xref>), suggesting that parasites were probably not introduced from these regions, or at least not from the villages that were sampled in these regions. Based on statistical parsimony networks it is clear that the putative source populations are within West Africa, as haplotypes sampled in Northwest Senegal clustered tightly with those from Southwest Senegal, Mali and some from Niger (<xref rid="pntd.0003998.g002" ref-type="fig">Fig 2a</xref>). Additional sampling within neighboring regions is therefore necessary, preferably from regions such as Mauritania from where agricultural workers have immigrated [<xref rid="pntd.0003998.ref012" ref-type="bibr">12</xref>] or from villages in Mali closer to the Senegalese border.</p></sec><sec id="sec018"><title>Snail population structure</title><p>In light of the dynamic nature of a disease outbreak, it is remarkable that parasite genetic diversity remained relatively stable in space and time. <italic>Schistosoma mansoni</italic> genetic diversity in 1993–1994 from Richard Toll is of the same order of magnitude as 14 years later (Tables <xref rid="pntd.0003998.t002" ref-type="table">2</xref> and <xref rid="pntd.0003998.t003" ref-type="table">3</xref>) and genetic differentiation between samples from different years (1993–1994 and 2007) and different villages was low and insignificant (<xref rid="pntd.0003998.t004" ref-type="table">Table 4</xref>). These results indicate that a successful parasite population, whether the result of a single introduction or of admixture between multiple introductions, must have established and spread quickly at the start of the epidemic. Such a colonization history could be linked to the colonization history of the intermediate snail host <italic>B</italic>. <italic>pfeifferi</italic>. Microsatellite analyses revealed that <italic>B</italic>. <italic>pfeifferi</italic> snail populations were genetically homogeneous in the region around Richard Toll, suggesting a rapid expansion of one or a few fecund lines at the expense of less fecund ones [<xref rid="pntd.0003998.ref075" ref-type="bibr">75</xref>]. Experimental infection studies revealed that <italic>B</italic>. <italic>pfeifferi</italic> from Senegal showed unusual high vectorial capacities, with higher snail longevity and higher frequency of patent infections in combination with Senegalese <italic>S</italic>. <italic>mansoni</italic> (i.e. sympatric combination) than in combination with Cameroonian <italic>S</italic>. <italic>mansoni</italic> (i.e. allopatric combination) [<xref rid="pntd.0003998.ref076" ref-type="bibr">76</xref>]. This was also evidenced from the extremely high <italic>S</italic>. <italic>mansoni</italic> prevalence (44%) in <italic>B</italic>. <italic>pfeifferi</italic> snails at the onset of the epidemic [<xref rid="pntd.0003998.ref020" ref-type="bibr">20</xref>]. Altogether these results suggest local adaptation of <italic>S</italic>. <italic>mansoni</italic> to its intermediate snail host <italic>B</italic>. <italic>pfeifferi</italic> in Northwest Senegal. This could have led to priority effects in <italic>S</italic>. <italic>mansoni</italic>, lowering the establishment success of subsequent invasions and ensuring the temporal and spatial stability of the dominant <italic>S</italic>. <italic>mansoni</italic> population in Northwest Senegal [<xref rid="pntd.0003998.ref077" ref-type="bibr">77</xref>,<xref rid="pntd.0003998.ref078" ref-type="bibr">78</xref>].</p><p>An interesting finding is that <italic>S</italic>. <italic>mansoni</italic> parasites from Mbodjene (2007) in the Lampsar region were significantly differentiated from most other samples in the vicinity of Richard Toll. Likewise, the <italic>B</italic>. <italic>pfeifferi</italic> population sampled close to this locality was genetically different from the other two populations near the Lampsar River and the populations around Richard Toll [<xref rid="pntd.0003998.ref075" ref-type="bibr">75</xref>]. This correspondence between host and parasite geographic structure further suggests that the genetic composition of the intermediate snail hosts could be an important factor determining establishment success of <italic>S</italic>. <italic>mansoni</italic> in a certain region. At the molecular level, this could comply with the hypothesis of a matching phenotype model where the interactions between parasite antigens and host immune receptors during the early stages of the infection determine the success or failure of the infection [<xref rid="pntd.0003998.ref079" ref-type="bibr">79</xref>].</p></sec><sec id="sec019"><title>Conclusions</title><p>This study is the first to reconstruct a recent epidemic of human intestinal schistosomiasis using mitochondrial and nuclear markers, revealing the evolutionary consequences of such a rapid colonization. The occurrence of many different haplotypes as revealed by the non-recombining mitochondrial marker indicated that multiple introductions occurred, while the recombining microsatellite markers pointed to the presence of mainly one widespread homogeneous population. We argue that admixture among multiple introductions generated a homogenous parasite population with a distinct genetic signature. The spatial and temporal stability of the established <italic>S</italic>. <italic>mansoni</italic> population suggest a swift local adaptation of the parasite to its intermediate snail host <italic>B</italic>. <italic>pfeifferi</italic> at the onset of the epidemic. Further research using samples from different localities in Senegal, Mali and Mauritania will help to pinpoint the putative source population(s) of this disease outbreak.</p></sec></sec><sec sec-type="supplementary-material" id="sec020"><title>Supporting Information</title><supplementary-material content-type="local-data" id="pntd.0003998.s001"><label>S1 Data</label><caption><title>This excel file contains the two microsatellite datasets that were used in this study.</title><p>DMS1 can be found in excel tab 1 and contains 542 <italic>S</italic>. <italic>mansoni</italic> samples that were genotyped at nine microsatellite markers. DMS2 can be found in excel tab 2 and contains 758 <italic>S</italic>. <italic>mansoni</italic> samples that were genotyped at six microsatellite markers. Loci are coded in 6 digits (three digits per allele).</p><p>(XLSX)</p></caption><media xlink:href="pntd.0003998.s001.xlsx"><caption><p>Click here for additional data file.</p></caption></media></supplementary-material></sec></body><back><ack><p>We thank Prof. J. Webster for access to the raw microsatellite data of Kokry-Bozo (Mali) and the Schistosomiasis Collection team at the Natural History Museum in London (SCAN) for providing <italic>S</italic>. <italic>mansoni</italic> worms. 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