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Most population genetic studies in\n                    <jats:italic>P<\/jats:italic>\n                    .\n                    <jats:italic>falciparum<\/jats:italic>\n                    focus on regions of high transmission where parasite populations are large and genetically diverse, such as sub-Saharan Africa. Understanding population dynamics in low transmission settings, however, is of particular importance as these are often where drug resistance first evolves. Here, we use the Pacific Coast of Colombia and Ecuador as a model for understanding the population structure and evolution of\n                    <jats:italic>Plasmodium<\/jats:italic>\n                    parasites in small populations harboring less genetic diversity. The combination of low transmission and a high proportion of monoclonal infections means there are few outcrossing events and clonal lineages persist for long periods of time. Yet despite this, the population is evolutionarily labile and has successfully adapted to changes in drug regime. Using newly sequenced whole genomes, we measure relatedness between 166 parasites, calculated as identity by descent (IBD), and find 17 distinct but highly related clonal lineages, six of which have persisted in the region for at least a decade. This inbred population structure is captured in more detail with IBD than with other common population structure analyses like PCA, ADMIXTURE, and distance-based trees. We additionally use patterns of intra-chromosomal IBD and an analysis of haplotypic variation to explore past selection events in the region. Two genes associated with chloroquine resistance,\n                    <jats:italic>crt<\/jats:italic>\n                    and\n                    <jats:italic>aat1<\/jats:italic>\n                    , show evidence of hard selective sweeps, while selection appears soft and\/or incomplete at three other key resistance loci (\n                    <jats:italic>dhps<\/jats:italic>\n                    ,\n                    <jats:italic>mdr1<\/jats:italic>\n                    , and\n                    <jats:italic>dhfr<\/jats:italic>\n                    ). Overall, this work highlights the strength of IBD analyses for studying parasite population structure and resistance evolution in regions of low transmission, and emphasizes that drug resistance can evolve and spread in small populations, as will occur in any region nearing malaria elimination.\n                  <\/jats:p>","DOI":"10.1371\/journal.ppat.1010993","type":"journal-article","created":{"date-parts":[[2022,12,21]],"date-time":"2022-12-21T13:32:35Z","timestamp":1671629555000},"page":"e1010993","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":38,"title":["Resolving drug selection and migration in an inbred South American Plasmodium falciparum population with identity-by-descent analysis"],"prefix":"10.1371","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7953-4376","authenticated-orcid":true,"given":"Manuela","family":"Carrasquilla","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Angela M.","family":"Early","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aimee R.","family":"Taylor","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ang\u00e9lica","family":"Knudson Ospina","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Diego F.","family":"Echeverry","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timothy J. C.","family":"Anderson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elvira","family":"Mancilla","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samanda","family":"Aponte","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pablo","family":"C\u00e1rdenas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Caroline O.","family":"Buckee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julian C.","family":"Rayner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fabi\u00e1n E.","family":"S\u00e1enz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel E.","family":"Neafsey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vladimir","family":"Corredor","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2022,12,21]]},"reference":[{"key":"ppat.1010993.ref001","unstructured":"WHO. 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dynamics of Plasmodium falciparum transmission within a spatial unit on the Colombian Pacific Coast","volume":"10","author":"A Knudson","year":"2020","journal-title":"Sci Rep"},{"key":"ppat.1010993.ref020","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1038\/nrg2526","article-title":"Fundamental concepts in genetics: effective population size and patterns of molecular evolution and variation","volume":"10","author":"B. 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Malaria y espacio en el Ecuador del verde de Par\u00eds a la eliminaci\u00f3n de la enfermedad. 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World Medical Association Declaration of Helsinki: ethical principles for medical research involving human subjects. General Assembly of the World Medical Association and others. https:\/\/www.wma.net\/wp-content\/uploads\/2016\/11\/DoH-Oct2008.pdf"},{"key":"ppat.1010993.ref074","unstructured":"Presidencia de la Rep\u00fablica de Colombia. Codigo del menor. Decreto 2737 de 1989. Presidencia, Rep\u00fablica de Colombia. 1989;9. https:\/\/www.oas.org\/dil\/esp\/decreto_2737_de_1989_colombia.pdf"},{"key":"ppat.1010993.ref075","unstructured":"Ministerio de Salud y Protecci\u00f3n Social. Scientific, technical and administrative guidelines for health research. Resolution 8430 from 1993. 1993;19. https:\/\/www.animallaw.info\/sites\/default\/files\/RESOLUCION-8430-DE-1993.PDF"},{"key":"ppat.1010993.ref076","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1126\/science.781840","article-title":"Human malaria parasites in continuous culture","volume":"193","author":"W Trager","year":"1976","journal-title":"Science"},{"key":"ppat.1010993.ref077","unstructured":"Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv [q-bio.GN]. 2013. http:\/\/arxiv.org\/abs\/1303.3997"},{"key":"ppat.1010993.ref078","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data","volume":"20","author":"A McKenna","year":"2010","journal-title":"Genome Res"},{"key":"ppat.1010993.ref079","doi-asserted-by":"crossref","first-page":"1288","DOI":"10.1101\/gr.203711.115","article-title":"Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum","volume":"26","author":"A Miles","year":"2016","journal-title":"Genome Res"},{"key":"ppat.1010993.ref080","doi-asserted-by":"crossref","first-page":"e1005348","DOI":"10.1371\/journal.pcbi.1005348","article-title":"THE REAL McCOIL: A method for the concurrent estimation of the complexity of infection and SNP allele frequency for malaria parasites","volume":"13","author":"H-H Chang","year":"2017","journal-title":"PLoS Comput Biol"},{"key":"ppat.1010993.ref081","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1086\/519795","article-title":"PLINK: a tool set for whole-genome association and population-based linkage analyses","volume":"81","author":"S Purcell","year":"2007","journal-title":"Am J Hum Genet"},{"key":"ppat.1010993.ref082","doi-asserted-by":"crossref","first-page":"2156","DOI":"10.1093\/bioinformatics\/btr330","article-title":"The variant call format and VCFtools","volume":"27","author":"P Danecek","year":"2011","journal-title":"Bioinformatics"},{"key":"ppat.1010993.ref083","doi-asserted-by":"crossref","first-page":"e2122165119","DOI":"10.1073\/pnas.2122165119","article-title":"Declines in prevalence alter the optimal level of sexual investment for the malaria parasite Plasmodium falciparum","volume":"199","author":"AM Early","year":"2022","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ppat.1010993.ref084","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1186\/s12936-018-2349-7","article-title":"hmmIBD: software to infer pairwise identity by descent between haploid genotypes","volume":"17","author":"SF Schaffner","year":"2018","journal-title":"Malar J"},{"key":"ppat.1010993.ref085","first-page":"1","article-title":"The igraph software package for complex network research","volume":"1695","author":"G Csardi","year":"2006","journal-title":"InterJournal, complex systems"},{"key":"ppat.1010993.ref086","doi-asserted-by":"crossref","first-page":"D581","DOI":"10.1093\/nar\/gkw1105","article-title":"EuPathDB: the eukaryotic pathogen genomics database resource","volume":"45","author":"C Aurrecoechea","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"ppat.1010993.ref087","doi-asserted-by":"crossref","first-page":"D898","DOI":"10.1093\/nar\/gkab929","article-title":"VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center","volume":"50","author":"B Amos","year":"2022","journal-title":"Nucleic Acids Res"}],"updated-by":[{"DOI":"10.1371\/journal.ppat.1010993","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,1,5]],"date-time":"2023-01-05T00:00:00Z","timestamp":1672876800000}}],"container-title":["PLOS Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1010993","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,5]],"date-time":"2023-01-05T14:10:50Z","timestamp":1672927850000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1010993"}},"subtitle":[],"editor":[{"given":"Alyssa","family":"Barry","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2022,12,21]]},"references-count":87,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2022,12,21]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.ppat.1010993","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2022.02.18.480973","asserted-by":"object"}]},"ISSN":["1553-7374"],"issn-type":[{"value":"1553-7374","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,12,21]]}}}