{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,24]],"date-time":"2026-07-24T01:43:48Z","timestamp":1784857428434,"version":"3.55.0"},"reference-count":84,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2025,4,1]],"date-time":"2025-04-01T00:00:00Z","timestamp":1743465600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000016","name":"Department of Health and Human Services","doi-asserted-by":"publisher","award":["U19Al110818"],"award-info":[{"award-number":["U19Al110818"]}],"id":[{"id":"10.13039\/100000016","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The malaria parasite Plasmodium falciparum regularly confronts orchestrated changes in frontline drug treatment that drastically alter its selection landscape. When this has occurred, the parasite has successfully adapted to new drugs through novel resistance mutations. These novel mutations, however, emerge in a genetic background already shaped by prior drug selection. In some instances, selection imposed by different drugs targets the same loci in either synergistic or antagonistic ways, which may leave genomic signatures that are hard to attribute to a specific agent. Here, we use two approaches for detecting sequential bouts of drug adaptation: haplotype-based selection testing and temporal changes in allele frequencies. Using a set of longitudinal samples from French Guiana, we determine that since the official introduction of artemisinin combination therapy in 2007 there have been rapid hard selective sweeps at both known and novel loci. At four high-profile genes with demonstrated involvement in drug resistance (pfcrt, pfmdr1, pfaat1, and pfgch1), we see selection signals both before and after drug regime change; however, selection favored different haplotypes in the two time periods. Similarly, allele frequency analysis identified coding variants whose frequency trajectory changed signs under the new drug pressure. These selected alleles were enriched for genes implicated in artemisinin or partner-drug resistance in other global populations. Overall, these results suggest that drug resistance in P. falciparum is governed by known alleles of large effect along with a polygenic architecture of potentially more subtle variants, any of which can experience fitness reversals under distinct drug regimes.<\/jats:p>","DOI":"10.1093\/molbev\/msaf075","type":"journal-article","created":{"date-parts":[[2025,3,30]],"date-time":"2025-03-30T22:07:39Z","timestamp":1743372459000},"source":"Crossref","is-referenced-by-count":2,"title":["Temporal Patterns of Haplotypic and Allelic Diversity Reflect the Changing Selection Landscape of the Malaria Parasite <i>Plasmodium falciparum<\/i>"],"prefix":"10.1093","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3169-2324","authenticated-orcid":false,"given":"Angela M","family":"Early","sequence":"first","affiliation":[{"name":"Infectious Disease and Microbiome Program, Broad Institute , Cambridge, MA 02142 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7070-2177","authenticated-orcid":false,"given":"St\u00e9phane","family":"Pelleau","sequence":"additional","affiliation":[{"name":"Infectious Diseases Epidemiology and Analytics Unit, Department of Global Health, lnstitut Pasteur, Universit\u00e9 Paris Cit\u00e9 , Paris 75015 ,","place":["France"]},{"name":"Centre National de R\u00e9f\u00e9rence du Paludisme, World Health Organization Collaborating Center for Surveillance of Antimalarial Drug Resistance, lnstitut Pasteur de la Guyane , Cayenne 97300 ,","place":["French Guiana"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0215-4110","authenticated-orcid":false,"given":"Lise","family":"Musset","sequence":"additional","affiliation":[{"name":"Centre National de R\u00e9f\u00e9rence du Paludisme, World Health Organization Collaborating Center for Surveillance of Antimalarial Drug Resistance, lnstitut Pasteur de la Guyane , Cayenne 97300 ,","place":["French Guiana"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1665-9323","authenticated-orcid":false,"given":"Daniel E","family":"Neafsey","sequence":"additional","affiliation":[{"name":"Infectious Disease and Microbiome Program, Broad Institute , Cambridge, MA 02142 ,","place":["USA"]},{"name":"Department of Immunology and Infectious Diseases, Harvard T. 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