{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,22]],"date-time":"2026-07-22T23:06:04Z","timestamp":1784761564121,"version":"3.55.0"},"reference-count":56,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,4,24]],"date-time":"2026-04-24T00:00:00Z","timestamp":1776988800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2026,7,23]],"date-time":"2026-07-23T00:00:00Z","timestamp":1784764800000},"content-version":"vor","delay-in-days":90,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"name":"Belgium Development Cooperation","award":["FA4 Peru (2017 \u2013 2021) and FA5 Peru (2022 \u2013 2026)"],"award-info":[{"award-number":["FA4 Peru (2017 \u2013 2021) and FA5 Peru (2022 \u2013 2026)"]}]},{"name":"Belgium Development Cooperation","award":["FA4 Peru (2017 \u2013 2021) and FA5 Peru (2022 \u2013 2026)"],"award-info":[{"award-number":["FA4 Peru (2017 \u2013 2021) and FA5 Peru (2022 \u2013 2026)"]}]},{"name":"Belgium Development Cooperation","award":["FA4 Peru (2017 \u2013 2021) and FA5 Peru (2022 \u2013 2026)"],"award-info":[{"award-number":["FA4 Peru (2017 \u2013 2021) and FA5 Peru (2022 \u2013 2026)"]}]},{"name":"Belgium Development Cooperation","award":["FA4 Peru (2017 \u2013 2021) and FA5 Peru (2022 \u2013 2026)"],"award-info":[{"award-number":["FA4 Peru (2017 \u2013 2021) and FA5 Peru (2022 \u2013 2026)"]}]},{"name":"Armed Forces Health Surveillance Division (AFHSD), Global Emerging Infections Surveillance Branch","award":["ProMIS ID P0146_25_N6"],"award-info":[{"award-number":["ProMIS ID P0146_25_N6"]}]},{"name":"VLIR-UOS JOINT","award":["PE2019JOI018A102"],"award-info":[{"award-number":["PE2019JOI018A102"]}]},{"name":"VLIR-UOS JOINT","award":["PE2019JOI018A102"],"award-info":[{"award-number":["PE2019JOI018A102"]}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["U19AI089681"],"award-info":[{"award-number":["U19AI089681"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"DOI":"10.1038\/s41598-026-48246-3","type":"journal-article","created":{"date-parts":[[2026,4,24]],"date-time":"2026-04-24T06:33:50Z","timestamp":1777012430000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Parasite population dynamics shaped P. falciparum pfhrp2 and pfhrp3 deletion expansion in the Peruvian Amazon"],"prefix":"10.1038","volume":"16","author":[{"given":"Erick","family":"Figueroa-Ildefonso","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luis","family":"Cabrera-Sosa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Johanna H.","family":"Kattenberg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hugo O.","family":"Valdivia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher","family":"Delgado-Ratto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna","family":"Rosanas-Urgell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dionicia","family":"Gamboa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,4,24]]},"reference":[{"key":"48246_CR1","unstructured":"Ministerio de Salud. N\u00famero de casos de malaria, Per\u00fa 2020\u20132025, (2025). https:\/\/www.dge.gob.pe\/portal\/docs\/vigilancia\/sala\/2025\/SE52\/malaria.pdf"},{"key":"48246_CR2","unstructured":"Organismo Andino de Salud - Convenio Hip\u00f3lito Unanue. Reporte de Resultados Fase II PAMAFRO & < (2009). https:\/\/www.orasconhu.org\/documentos\/1PAMAFRO%20Reporte%20Resultados%20No%207.pdf"},{"key":"48246_CR3","unstructured":"Ministerio de Salud. Documento T\u00e9cnico: Plan Malaria Cero Periodo 2017\u20132021, (2017). https:\/\/cdn.www.gob.pe\/uploads\/document\/file\/190350\/189846_RM_244-2017-MINSA.PDF20180823-24725-1yk3i0y.PDF?v=1593748780"},{"key":"48246_CR4","doi-asserted-by":"publisher","first-page":"e0096022","DOI":"10.1128\/spectrum.00960-22","volume":"11","author":"JH Kattenberg","year":"2023","unstructured":"Kattenberg, J. H. et al. Malaria Molecular Surveillance in the Peruvian Amazon with a Novel Highly Multiplexed Plasmodium falciparum AmpliSeq Assay. Microbiol. Spectr. 11, e0096022. https:\/\/doi.org\/10.1128\/spectrum.00960-22 (2023).","journal-title":"Microbiol. Spectr."},{"key":"48246_CR5","doi-asserted-by":"publisher","first-page":"19845","DOI":"10.1038\/s41598-022-23881-8","volume":"12","author":"HO Valdivia","year":"2022","unstructured":"Valdivia, H. O. et al. Spatiotemporal dynamics of Plasmodium falciparum histidine-rich protein 2 and 3 deletions in Peru. Sci. Rep. 12, 19845. https:\/\/doi.org\/10.1038\/s41598-022-23881-8 (2022).","journal-title":"Sci. Rep."},{"key":"48246_CR6","doi-asserted-by":"publisher","first-page":"21212","DOI":"10.1038\/s41598-021-00806-5","volume":"11","author":"FE Villena","year":"2021","unstructured":"Villena, F. E., Lizewski, S. E., Joya, C. A. & Valdivia, H. O. Population genomics and evidence of clonal replacement of Plasmodium falciparum in the Peruvian Amazon. Sci. Rep. 11, 21212. https:\/\/doi.org\/10.1038\/s41598-021-00806-5 (2021).","journal-title":"Sci. Rep."},{"key":"48246_CR7","doi-asserted-by":"publisher","first-page":"797","DOI":"10.3201\/eid2105.141427","volume":"21","author":"GC Baldeviano","year":"2015","unstructured":"Baldeviano, G. C. et al. Molecular Epidemiology of Plasmodium falciparum Malaria Outbreak, Tumbes, Peru, 2010\u20132012. Emerg. Infect. Dis. 21, 797\u2013803. https:\/\/doi.org\/10.3201\/eid2105.141427 (2015).","journal-title":"Emerg. Infect. Dis."},{"key":"48246_CR8","doi-asserted-by":"publisher","first-page":"128","DOI":"10.4269\/ajtmh.15-0442","volume":"94","author":"SA Okoth","year":"2016","unstructured":"Okoth, S. A. et al. Molecular Investigation into a Malaria Outbreak in Cusco, Peru: Plasmodium falciparum BV1 Lineage is Linked to a Second Outbreak in Recent Times. Am. J. Trop. Med. Hyg. 94, 128\u2013131. https:\/\/doi.org\/10.4269\/ajtmh.15-0442 (2016).","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"48246_CR9","doi-asserted-by":"publisher","first-page":"112","DOI":"10.1016\/j.pt.2019.12.004","volume":"36","author":"KE Poti","year":"2020","unstructured":"Poti, K. E., Sullivan, D. J., Dondorp, A. M. & Woodrow, C. J. HRP2: Transforming Malaria Diagnosis, but with Caveats. Trends Parasitol. 36, 112\u2013126. https:\/\/doi.org\/10.1016\/j.pt.2019.12.004 (2020).","journal-title":"Trends Parasitol."},{"key":"48246_CR10","doi-asserted-by":"publisher","first-page":"e8091","DOI":"10.1371\/journal.pone.0008091","volume":"5","author":"D Gamboa","year":"2010","unstructured":"Gamboa, D. et al. A large proportion of P. falciparum isolates in the Amazon region of Peru lack pfhrp2 and pfhrp3: implications for malaria rapid diagnostic tests. PLoS One. 5, e8091. https:\/\/doi.org\/10.1371\/journal.pone.0008091 (2010).","journal-title":"PLoS One"},{"key":"48246_CR11","doi-asserted-by":"publisher","first-page":"e0273872","DOI":"10.1371\/journal.pone.0273872","volume":"17","author":"J Bendezu","year":"2022","unstructured":"Bendezu, J. et al. Geographical distribution and genetic characterization of pfhrp2 negative Plasmodium falciparum parasites in the Peruvian Amazon. PLoS One. 17, e0273872. https:\/\/doi.org\/10.1371\/journal.pone.0273872 (2022).","journal-title":"PLoS One"},{"key":"48246_CR12","doi-asserted-by":"publisher","first-page":"2797","DOI":"10.1038\/srep02797","volume":"3","author":"S Akinyi","year":"2013","unstructured":"Akinyi, S. et al. Multiple genetic origins of histidine-rich protein 2 gene deletion in Plasmodium falciparum parasites from Peru. Sci. Rep. 3, 2797. https:\/\/doi.org\/10.1038\/srep02797 (2013).","journal-title":"Sci. Rep."},{"key":"48246_CR13","unstructured":"Quispe-Carbajal, M. An\u00e1lisis de la diversidad gen\u00e9tica y estructura gen\u00e9tica poblacional de Plasmodium falciparum con deleciones en los genes PFHRP2 y PFHRP3 en tres comunidades de la Amazon\u00eda Peruana Master in Biochemistry and Molecular Biology thesis, Universidad Peruana Cayetano Heredia, (2017)."},{"key":"48246_CR14","doi-asserted-by":"publisher","first-page":"16291","DOI":"10.1038\/s41598-024-66925-x","volume":"14","author":"L Cabrera-Sosa","year":"2024","unstructured":"Cabrera-Sosa, L. et al. Genomic surveillance of malaria parasites in an indigenous community in the Peruvian Amazon. Sci. Rep. 14, 16291. https:\/\/doi.org\/10.1038\/s41598-024-66925-x (2024).","journal-title":"Sci. Rep."},{"key":"48246_CR15","doi-asserted-by":"publisher","first-page":"e0163137","DOI":"10.1371\/journal.pone.0163137","volume":"11","author":"EJ Dorado","year":"2016","unstructured":"Dorado, E. J. et al. Genetic Characterisation of Plasmodium falciparum Isolates with Deletion of the pfhrp2 and\/or pfhrp3 Genes in Colombia: The Amazon Region, a Challenge for Malaria Diagnosis and Control. PLoS One. 11, e0163137. https:\/\/doi.org\/10.1371\/journal.pone.0163137 (2016).","journal-title":"PLoS One"},{"key":"48246_CR16","doi-asserted-by":"publisher","unstructured":"Goes, L. et al. Evaluation of Histidine-Rich Proteins 2 and 3 Gene Deletions in Plasmodium falciparum in Endemic Areas of the Brazilian Amazon. Int. J. Environ. Res. Public. Health. 18 https:\/\/doi.org\/10.3390\/ijerph18010123 (2020).","DOI":"10.3390\/ijerph18010123"},{"key":"48246_CR17","doi-asserted-by":"publisher","first-page":"471","DOI":"10.3201\/eid2702.191410","volume":"27","author":"C Prosser","year":"2021","unstructured":"Prosser, C. et al. Plasmodium falciparum Histidine-Rich Protein 2 and 3 Gene Deletions in Strains from Nigeria, Sudan, and South Sudan. Emerg. Infect. Dis. 27, 471\u2013479. https:\/\/doi.org\/10.3201\/eid2702.191410 (2021).","journal-title":"Emerg. Infect. Dis."},{"key":"48246_CR18","doi-asserted-by":"publisher","first-page":"108","DOI":"10.1186\/s12936-024-04904-3","volume":"23","author":"B Mekonen","year":"2024","unstructured":"Mekonen, B. et al. Widespread pfhrp2\/3 deletions and HRP2-based false-negative results in southern Ethiopia. Malar. J. 23, 108. https:\/\/doi.org\/10.1186\/s12936-024-04904-3 (2024).","journal-title":"Malar. J."},{"key":"48246_CR19","doi-asserted-by":"publisher","first-page":"1289","DOI":"10.1038\/s41564-021-00962-4","volume":"6","author":"SM Feleke","year":"2021","unstructured":"Feleke, S. M. et al. Plasmodium falciparum is evolving to escape malaria rapid diagnostic tests in Ethiopia. Nat. Microbiol. 6, 1289\u20131299. https:\/\/doi.org\/10.1038\/s41564-021-00962-4 (2021).","journal-title":"Nat. Microbiol."},{"key":"48246_CR20","doi-asserted-by":"publisher","unstructured":"Watson, O. J. et al. Modelling the drivers of the spread of Plasmodium falciparum hrp2 gene deletions in sub-Saharan Africa. Elife 6 https:\/\/doi.org\/10.7554\/eLife.25008 (2017).","DOI":"10.7554\/eLife.25008"},{"key":"48246_CR21","unstructured":"Ministerio de Salud. Documento T\u00e9cnico: Plan hacia la Eliminaci\u00f3n de la Malaria 2022\u20132030, (2022). https:\/\/bvs.minsa.gob.pe\/local\/fi-admin\/RM-034-2022%20MINSA.pdf"},{"key":"48246_CR22","doi-asserted-by":"publisher","first-page":"42","DOI":"10.12688\/wellcomeopenres.16168.2","volume":"6","author":"MalariaGen","year":"2021","unstructured":"MalariaGen et al. An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples. Wellcome Open. Res. 6, 42. https:\/\/doi.org\/10.12688\/wellcomeopenres.16168.2 (2021).","journal-title":"Wellcome Open. Res."},{"key":"48246_CR23","doi-asserted-by":"publisher","first-page":"2435","DOI":"10.1128\/JCM.43.5.2435-2440.2005","volume":"43","author":"KA Mangold","year":"2005","unstructured":"Mangold, K. A. et al. Real-time PCR for detection and identification of Plasmodium spp. J. Clin. Microbiol. 43, 2435\u20132440. https:\/\/doi.org\/10.1128\/JCM.43.5.2435-2440.2005 (2005).","journal-title":"J. Clin. Microbiol."},{"key":"48246_CR24","doi-asserted-by":"publisher","first-page":"369","DOI":"10.1016\/s0035-9203(99)90120-7","volume":"93","author":"G Snounou","year":"1999","unstructured":"Snounou, G. et al. Biased distribution of msp1 and msp2 allelic variants in Plasmodium falciparum populations in Thailand. Trans. R Soc. Trop. Med. Hyg. 93, 369\u2013374. https:\/\/doi.org\/10.1016\/s0035-9203(99)90120-7 (1999).","journal-title":"Trans. R Soc. Trop. Med. Hyg."},{"key":"48246_CR25","doi-asserted-by":"publisher","first-page":"11078","DOI":"10.1038\/ncomms11078","volume":"7","author":"SA Sundararaman","year":"2016","unstructured":"Sundararaman, S. A. et al. Genomes of cryptic chimpanzee Plasmodium species reveal key evolutionary events leading to human malaria. Nat. Commun. 7, 11078. https:\/\/doi.org\/10.1038\/ncomms11078 (2016).","journal-title":"Nat. Commun."},{"key":"48246_CR26","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","volume":"30","author":"AM Bolger","year":"2014","unstructured":"Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114\u20132120. https:\/\/doi.org\/10.1093\/bioinformatics\/btu170 (2014).","journal-title":"Bioinformatics"},{"key":"48246_CR27","doi-asserted-by":"publisher","first-page":"589","DOI":"10.1093\/bioinformatics\/btp698","volume":"26","author":"H Li","year":"2010","unstructured":"Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26, 589\u2013595. https:\/\/doi.org\/10.1093\/bioinformatics\/btp698 (2010).","journal-title":"Bioinformatics"},{"key":"48246_CR28","doi-asserted-by":"publisher","first-page":"1297","DOI":"10.1101\/gr.107524.110","volume":"20","author":"A McKenna","year":"2010","unstructured":"McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297\u20131303. https:\/\/doi.org\/10.1101\/gr.107524.110 (2010).","journal-title":"Genome Res."},{"key":"48246_CR29","doi-asserted-by":"publisher","first-page":"52","DOI":"10.12688\/wellcomeopenres.14571.1","volume":"3","author":"TD Otto","year":"2018","unstructured":"Otto, T. D. et al. Long read assemblies of geographically dispersed Plasmodium falciparum isolates reveal highly structured subtelomeres. Wellcome Open. Res. 3, 52. https:\/\/doi.org\/10.12688\/wellcomeopenres.14571.1 (2018).","journal-title":"Wellcome Open. Res."},{"key":"48246_CR30","doi-asserted-by":"publisher","first-page":"2156","DOI":"10.1093\/bioinformatics\/btr330","volume":"27","author":"P Danecek","year":"2011","unstructured":"Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156\u20132158. https:\/\/doi.org\/10.1093\/bioinformatics\/btr330 (2011).","journal-title":"Bioinformatics"},{"key":"48246_CR31","unstructured":"Lee, S. & Bahlo, M. moimix: an R package for assessing clonality in high-throughput sequencing data, (2016). https:\/\/zenodo.org\/record\/58257"},{"key":"48246_CR32","doi-asserted-by":"publisher","first-page":"e32891","DOI":"10.1371\/journal.pone.0032891","volume":"7","author":"S Auburn","year":"2012","unstructured":"Auburn, S. et al. Characterization of within-host Plasmodium falciparum diversity using next-generation sequence data. PLoS One. 7, e32891. https:\/\/doi.org\/10.1371\/journal.pone.0032891 (2012).","journal-title":"PLoS One"},{"key":"48246_CR33","doi-asserted-by":"publisher","first-page":"559","DOI":"10.1086\/519795","volume":"81","author":"S Purcell","year":"2007","unstructured":"Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559\u2013575. https:\/\/doi.org\/10.1086\/519795 (2007).","journal-title":"Am. J. Hum. Genet."},{"key":"48246_CR34","doi-asserted-by":"publisher","first-page":"1655","DOI":"10.1101\/gr.094052.109","volume":"19","author":"DH Alexander","year":"2009","unstructured":"Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655\u20131664. https:\/\/doi.org\/10.1101\/gr.094052.109 (2009).","journal-title":"Genome Res."},{"key":"48246_CR35","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1111\/1755-0998.12509","volume":"17","author":"RM Francis","year":"2017","unstructured":"Francis, R. M. pophelper: an R package and web app to analyse and visualize population structure. Mol. Ecol. Resour. 17, 27\u201332. https:\/\/doi.org\/10.1111\/1755-0998.12509 (2017).","journal-title":"Mol. Ecol. Resour."},{"key":"48246_CR36","doi-asserted-by":"publisher","first-page":"e1007279","DOI":"10.1371\/journal.pgen.1007279","volume":"14","author":"L Henden","year":"2018","unstructured":"Henden, L., Lee, S., Mueller, I., Barry, A. & Bahlo, M. Identity-by-descent analyses for measuring population dynamics and selection in recombining pathogens. PLoS Genet. 14, e1007279. https:\/\/doi.org\/10.1371\/journal.pgen.1007279 (2018).","journal-title":"PLoS Genet."},{"key":"48246_CR37","doi-asserted-by":"publisher","first-page":"1478706","DOI":"10.3389\/fgene.2024.1478706","volume":"15","author":"JH Kattenberg","year":"2024","unstructured":"Kattenberg, J. H. et al. Genetic surveillance shows spread of ACT resistance during period of malaria decline in Vietnam (2018\u20132020). Front. Genet. 15, 1478706. https:\/\/doi.org\/10.3389\/fgene.2024.1478706 (2024).","journal-title":"Front. Genet."},{"key":"48246_CR38","first-page":"1","volume":"1695","author":"G Csardi","year":"2006","unstructured":"Csardi, G. & Nepusz, T. The Igraph Software Package for Complex Network Research. InterJournal Complex. Syst. 1695, 1\u20139 (2006).","journal-title":"InterJournal Complex. Syst."},{"key":"48246_CR39","doi-asserted-by":"publisher","first-page":"4725","DOI":"10.1111\/mec.14782","volume":"27","author":"S Liu","year":"2018","unstructured":"Liu, S., Ferchaud, A. L., Gronkjaer, P., Nygaard, R. & Hansen, M. M. Genomic parallelism and lack thereof in contrasting systems of three-spined sticklebacks. Mol. Ecol. 27, 4725\u20134743. https:\/\/doi.org\/10.1111\/mec.14782 (2018).","journal-title":"Mol. Ecol."},{"key":"48246_CR40","unstructured":"cggh\/scikit-allel: v1.3.13. Zenodo, (2024)."},{"key":"48246_CR41","doi-asserted-by":"publisher","first-page":"447","DOI":"10.4310\/SII.2015.v8.n4.a4","volume":"8","author":"Q Zhang","year":"2015","unstructured":"Zhang, Q., Tyler-Smith, C. & Long, Q. An extended Tajima\u2019s D neutrality test incorporating SNP calling and imputation uncertainties. Stat. Interface. 8, 447\u2013456. https:\/\/doi.org\/10.4310\/SII.2015.v8.n4.a4 (2015).","journal-title":"Stat. Interface"},{"key":"48246_CR42","doi-asserted-by":"publisher","first-page":"817","DOI":"10.1038\/ng.3583","volume":"48","author":"J O\u2019Connell","year":"2016","unstructured":"O\u2019Connell, J. et al. Haplotype estimation for biobank-scale data sets. Nat. Genet. 48, 817\u2013820. https:\/\/doi.org\/10.1038\/ng.3583 (2016).","journal-title":"Nat. Genet."},{"key":"48246_CR43","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1111\/1755-0998.12634","volume":"17","author":"M Gautier","year":"2017","unstructured":"Gautier, M., Klassmann, A. & Vitalis, R. rehh 2.0: a reimplementation of the R package rehh to detect positive selection from haplotype structure. Mol. Ecol. Resour. 17, 78\u201390. https:\/\/doi.org\/10.1111\/1755-0998.12634 (2017).","journal-title":"Mol. Ecol. Resour."},{"key":"48246_CR44","doi-asserted-by":"publisher","first-page":"e1000695","DOI":"10.1371\/journal.pgen.1000695","volume":"5","author":"RN Gutenkunst","year":"2009","unstructured":"Gutenkunst, R. N., Hernandez, R. D., Williamson, S. H. & Bustamante, C. D. Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet. 5, e1000695. https:\/\/doi.org\/10.1371\/journal.pgen.1000695 (2009).","journal-title":"PLoS Genet."},{"key":"48246_CR45","doi-asserted-by":"publisher","first-page":"100477","DOI":"10.1016\/j.lana.2023.100477","volume":"20","author":"MM Janko","year":"2023","unstructured":"Janko, M. M. et al. The impact of sustained malaria control in the Loreto region of Peru: a retrospective, observational, spatially-varying interrupted time series analysis of the PAMAFRO program. Lancet Reg. Health Am. 20, 100477. https:\/\/doi.org\/10.1016\/j.lana.2023.100477 (2023).","journal-title":"Lancet Reg. Health Am."},{"key":"48246_CR46","doi-asserted-by":"publisher","first-page":"R837","DOI":"10.1016\/j.cub.2011.08.007","volume":"21","author":"J Masel","year":"2011","unstructured":"Masel, J. Genetic drift. Curr. Biol. 21, R837\u2013838. https:\/\/doi.org\/10.1016\/j.cub.2011.08.007 (2011).","journal-title":"Curr. Biol."},{"key":"48246_CR47","doi-asserted-by":"publisher","first-page":"e23486","DOI":"10.1371\/journal.pone.0023486","volume":"6","author":"SM Griffing","year":"2011","unstructured":"Griffing, S. M. et al. South American Plasmodium falciparum after the malaria eradication era: clonal population expansion and survival of the fittest hybrids. PLoS One. 6, e23486. https:\/\/doi.org\/10.1371\/journal.pone.0023486 (2011).","journal-title":"PLoS One"},{"key":"48246_CR48","doi-asserted-by":"publisher","first-page":"16474","DOI":"10.1038\/s41598-022-21028-3","volume":"12","author":"FE Villena","year":"2022","unstructured":"Villena, F. E. et al. Drug resistance and population structure of Plasmodium falciparum and Plasmodium vivax in the Peruvian Amazon. Sci. Rep. 12, 16474. https:\/\/doi.org\/10.1038\/s41598-022-21028-3 (2022).","journal-title":"Sci. Rep."},{"key":"48246_CR49","doi-asserted-by":"publisher","unstructured":"Soni, V. & Jensen, J. D. Temporal challenges in detecting balancing selection from population genomic data. G3 (Bethesda). 14. https:\/\/doi.org\/10.1093\/g3journal\/jkae069 (2024).","DOI":"10.1093\/g3journal\/jkae069"},{"key":"48246_CR50","doi-asserted-by":"publisher","first-page":"471","DOI":"10.1016\/j.pt.2025.04.010","volume":"41","author":"KP Day","year":"2025","unstructured":"Day, K. P. et al. Var genes, strain hyperdiversity, and malaria transmission dynamics. Trends Parasitol. 41, 471\u2013485. https:\/\/doi.org\/10.1016\/j.pt.2025.04.010 (2025).","journal-title":"Trends Parasitol."},{"key":"48246_CR51","doi-asserted-by":"publisher","first-page":"105725","DOI":"10.1016\/j.meegid.2025.105725","volume":"129","author":"JG Lawton","year":"2025","unstructured":"Lawton, J. G. et al. Diamonds in the rif: Alignment-free comparative genomics analysis reveals strain-transcendent Plasmodium falciparum antigens amidst extensive genetic diversity. Infect. Genet. Evol. 129, 105725. https:\/\/doi.org\/10.1016\/j.meegid.2025.105725 (2025).","journal-title":"Infect. Genet. Evol."},{"key":"48246_CR52","doi-asserted-by":"publisher","first-page":"959","DOI":"10.1038\/ng.3599","volume":"48","author":"RD Pearson","year":"2016","unstructured":"Pearson, R. D. et al. Genomic analysis of local variation and recent evolution in Plasmodium vivax. Nat. Genet. 48, 959\u2013964. https:\/\/doi.org\/10.1038\/ng.3599 (2016).","journal-title":"Nat. Genet."},{"key":"48246_CR53","doi-asserted-by":"publisher","first-page":"4089","DOI":"10.1128\/AAC.00623-08","volume":"52","author":"AM McCollum","year":"2008","unstructured":"McCollum, A. M., Basco, L. K., Tahar, R., Udhayakumar, V. & Escalante, A. A. Hitchhiking and selective sweeps of Plasmodium falciparum sulfadoxine and pyrimethamine resistance alleles in a population from central Africa. Antimicrob. Agents Chemother. 52, 4089\u20134097. https:\/\/doi.org\/10.1128\/AAC.00623-08 (2008).","journal-title":"Antimicrob. Agents Chemother."},{"issue":"Suppl 1","key":"48246_CR54","doi-asserted-by":"publisher","first-page":"S98","DOI":"10.1017\/S0031182014000067","volume":"142","author":"HH Chang","year":"2015","unstructured":"Chang, H. H. & Hartl, D. L. Recurrent bottlenecks in the malaria life cycle obscure signals of positive selection. Parasitology 142 (Suppl 1), S98\u2013S107. https:\/\/doi.org\/10.1017\/S0031182014000067 (2015).","journal-title":"Parasitology"},{"key":"48246_CR55","doi-asserted-by":"publisher","first-page":"2001","DOI":"10.1093\/genetics\/144.4.2001","volume":"144","author":"JM Cornuet","year":"1996","unstructured":"Cornuet, J. M. & Luikart, G. Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144, 2001\u20132014. https:\/\/doi.org\/10.1093\/genetics\/144.4.2001 (1996).","journal-title":"Genetics"},{"key":"48246_CR56","doi-asserted-by":"publisher","first-page":"215","DOI":"10.12688\/wellcomeopenres.19092.1","volume":"9","author":"D Kwiatkowski","year":"2024","unstructured":"Kwiatkowski, D. Modelling transmission dynamics and genomic diversity in a recombining parasite population. Wellcome Open. Res. 9, 215. https:\/\/doi.org\/10.12688\/wellcomeopenres.19092.1 (2024).","journal-title":"Wellcome Open. Res."}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41598-026-48246-3","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-026-48246-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-026-48246-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,22]],"date-time":"2026-07-22T22:50:40Z","timestamp":1784760640000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41598-026-48246-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,4,24]]},"references-count":56,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["48246"],"URL":"https:\/\/doi.org\/10.1038\/s41598-026-48246-3","relation":{"has-preprint":[{"id-type":"doi","id":"10.21203\/rs.3.rs-7255462\/v1","asserted-by":"object"}]},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,4,24]]},"assertion":[{"value":"30 July 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"7 April 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"24 April 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Declarations"}}],"article-number":"23001"}}