{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T07:06:57Z","timestamp":1772176017056,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pgen.1009037","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2020,10,21]],"date-time":"2020-10-21T00:00:00Z","timestamp":1603238400000}}],"reference-count":54,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2020,10,9]],"date-time":"2020-10-09T00:00:00Z","timestamp":1602201600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosgenetics.org"],"crossmark-restriction":false},"short-container-title":["PLoS Genet"],"DOI":"10.1371\/journal.pgen.1009037","type":"journal-article","created":{"date-parts":[[2020,10,9]],"date-time":"2020-10-09T13:35:45Z","timestamp":1602250545000},"page":"e1009037","update-policy":"https:\/\/doi.org\/10.1371\/journal.pgen.corrections_policy","source":"Crossref","is-referenced-by-count":6,"title":["A cautionary note on the use of unsupervised machine learning algorithms to characterise malaria parasite population structure from genetic distance matrices"],"prefix":"10.1371","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5524-0325","authenticated-orcid":true,"given":"James A.","family":"Watson","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2337-8992","authenticated-orcid":true,"given":"Aimee R.","family":"Taylor","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7620-4822","authenticated-orcid":true,"given":"Elizabeth A.","family":"Ashley","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5190-2395","authenticated-orcid":true,"given":"Arjen","family":"Dondorp","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Caroline O.","family":"Buckee","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1897-1978","authenticated-orcid":true,"given":"Nicholas J.","family":"White","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6667-4943","authenticated-orcid":true,"given":"Chris C.","family":"Holmes","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2020,10,9]]},"reference":[{"issue":"1","key":"pgen.1009037.ref001","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1186\/s12916-018-1181-9","article-title":"Mapping malaria by combining parasite genomic and epidemiologic data","volume":"16","author":"A Wesolowski","year":"2018","journal-title":"BMC Medicine"},{"issue":"8","key":"pgen.1009037.ref002","doi-asserted-by":"crossref","first-page":"904","DOI":"10.1038\/ng1847","article-title":"Principal components analysis corrects for stratification in genome-wide association studies","volume":"38","author":"AL Price","year":"2006","journal-title":"Nature Genetics"},{"issue":"3","key":"pgen.1009037.ref003","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1006\/tpbi.1996.0034","article-title":"Statistics for microsatellite variation based on coalescence","volume":"50","author":"JK Pritchard","year":"1996","journal-title":"Theoretical Population Biology"},{"issue":"1","key":"pgen.1009037.ref004","doi-asserted-by":"crossref","first-page":"e1002453","DOI":"10.1371\/journal.pgen.1002453","article-title":"Inference of Population Structure using Dense Haplotype Data","volume":"8","author":"DJ Lawson","year":"2012","journal-title":"PLoS Genetics"},{"issue":"9","key":"pgen.1009037.ref005","doi-asserted-by":"crossref","first-page":"1655","DOI":"10.1101\/gr.094052.109","article-title":"Fast model-based estimation of ancestry in unrelated individuals","volume":"19","author":"DH Alexander","year":"2009","journal-title":"Genome Research"},{"issue":"12","key":"pgen.1009037.ref006","first-page":"573","article-title":"Spreading the seeds of million-murdering death: metamorphoses of malaria in the mosquito","volume":"21","author":"LA Baton","year":"2005","journal-title":"Trends in Parasitology"},{"key":"pgen.1009037.ref007","doi-asserted-by":"crossref","first-page":"e40845","DOI":"10.7554\/eLife.40845","article-title":"The origins and relatedness structure of mixed infections vary with local prevalence of P. falciparum malaria","volume":"8","author":"SJ Zhu","year":"2019","journal-title":"Elife"},{"issue":"6","key":"pgen.1009037.ref008","doi-asserted-by":"crossref","first-page":"648","DOI":"10.1038\/ng.2624","article-title":"Multiple populations of artemisinin-resistant Plasmodium falciparum in Cambodia","volume":"45","author":"O Miotto","year":"2013","journal-title":"Nature Genetics"},{"issue":"3","key":"pgen.1009037.ref009","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1016\/S1473-3099(18)30068-9","article-title":"Origins of the current outbreak of multidrug-resistant malaria in southeast Asia: a retrospective genetic study","volume":"18","author":"R Amato","year":"2018","journal-title":"Lancet Infectious Diseases"},{"issue":"0","key":"pgen.1009037.ref010","article-title":"Evolution and expansion of multidrug-resistant malaria in southeast Asia: a genomic epidemiology study","volume":"0","author":"WL Hamilton","year":"2019","journal-title":"Lancet Infectious diseases"},{"issue":"10","key":"pgen.1009037.ref011","doi-asserted-by":"crossref","first-page":"e1000686","DOI":"10.1371\/journal.pgen.1000686","article-title":"A genealogical interpretation of principal components analysis","volume":"5","author":"G McVean","year":"2009","journal-title":"PLoS Genetics"},{"key":"pgen.1009037.ref012","article-title":"Estimating relatedness between malaria parasites","author":"AR Taylor","year":"2019","journal-title":"Genetics"},{"issue":"1","key":"pgen.1009037.ref013","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-020-15779-8","article-title":"The impact of antimalarial resistance on the genetic structure of Plasmodium falciparum in the DRC","volume":"11","author":"R Verity","year":"2020","journal-title":"Nature Communications"},{"issue":"5","key":"pgen.1009037.ref014","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1056\/NEJMoa1314981","article-title":"Spread of artemisinin resistance in Plasmodium falciparum malaria","volume":"371","author":"EA Ashley","year":"2014","journal-title":"New England Journal of Medicine"},{"issue":"3","key":"pgen.1009037.ref015","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1038\/ng.3189","article-title":"Genetic architecture of artemisinin-resistant Plasmodium falciparum","volume":"47","author":"O Miotto","year":"2015","journal-title":"Nature Genetics"},{"issue":"5","key":"pgen.1009037.ref016","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1016\/S1473-3099(17)30048-8","article-title":"The spread of artemisinin-resistant Plasmodium falciparum in the Greater Mekong subregion: a molecular epidemiology observational study","volume":"17","author":"M Imwong","year":"2017","journal-title":"Lancet Infectious Diseases"},{"issue":"10","key":"pgen.1009037.ref017","doi-asserted-by":"crossref","first-page":"1022","DOI":"10.1016\/S1473-3099(17)30524-8","article-title":"Spread of a single multidrug resistant malaria parasite lineage (PfPailin) to Vietnam","volume":"17","author":"M Imwong","year":"2017","journal-title":"Lancet Infectious Diseases"},{"issue":"9","key":"pgen.1009037.ref018","doi-asserted-by":"crossref","first-page":"952","DOI":"10.1016\/S1473-3099(19)30391-3","article-title":"Determinants of dihydroartemisinin-piperaquine treatment failure in Plasmodium falciparum malaria in Cambodia, Thailand, and Vietnam: a prospective clinical, pharmacological, and genetic study","volume":"19","author":"RW van der Pluijm","year":"2019","journal-title":"Lancet Infectious Diseases"},{"key":"pgen.1009037.ref019","unstructured":"World Health Organization. Guidelines for the treatment of malaria. 2015."},{"issue":"13","key":"pgen.1009037.ref020","doi-asserted-by":"crossref","first-page":"i248","DOI":"10.1093\/bioinformatics\/btr210","article-title":"Tanglegrams for rooted phylogenetic trees and networks","volume":"27","author":"C Scornavacca","year":"2011","journal-title":"Bioinformatics"},{"issue":"1","key":"pgen.1009037.ref021","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1093\/molbev\/msy196","article-title":"Tanglegrams are misleading for visual evaluation of tree congruence","volume":"36","author":"DM De Vienne","year":"2019","journal-title":"Molecular Biology and Evolution"},{"issue":"18","key":"pgen.1009037.ref022","doi-asserted-by":"crossref","first-page":"9787","DOI":"10.1073\/pnas.1912957117","article-title":"Testing for dependence on tree structures","volume":"117","author":"M Behr","year":"2020","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"4","key":"pgen.1009037.ref023","doi-asserted-by":"crossref","first-page":"293","DOI":"10.2307\/276978","article-title":"A Method for Chronologically Ordering Archaeological Deposits","volume":"16","author":"WS Robinson","year":"1951","journal-title":"American Antiquity"},{"issue":"3","key":"pgen.1009037.ref024","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v025.i03","article-title":"Getting things in order: an introduction to the R package seriation","volume":"25","author":"M Hahsler","year":"2008","journal-title":"Journal of Statistical Software"},{"issue":"1","key":"pgen.1009037.ref025","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":"Malaria Journal"},{"issue":"5","key":"pgen.1009037.ref026","doi-asserted-by":"crossref","first-page":"e1007279","DOI":"10.1371\/journal.pgen.1007279","article-title":"Identity-by-descent analyses for measuring population dynamics and selection in recombining pathogens","volume":"14","author":"L Henden","year":"2018","journal-title":"PLoS genetics"},{"issue":"1","key":"pgen.1009037.ref027","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-018-04965-4","article-title":"Genomic analysis of a pre-elimination Malaysian Plasmodium vivax population reveals selective pressures and changing transmission dynamics","volume":"9","author":"S Auburn","year":"2018","journal-title":"Nature Communications"},{"issue":"7543","key":"pgen.1009037.ref028","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1038\/nature14230","article-title":"The fine-scale genetic structure of the British population","volume":"519","author":"S Leslie","year":"2015","journal-title":"Nature"},{"issue":"10","key":"pgen.1009037.ref029","doi-asserted-by":"crossref","first-page":"e1007065","DOI":"10.1371\/journal.pgen.1007065","article-title":"Quantifying connectivity between local Plasmodium falciparum malaria parasite populations using identity by descent","volume":"13","author":"AR Taylor","year":"2017","journal-title":"PLoS Genetics"},{"key":"pgen.1009037.ref030","article-title":"Identity-by-descent relatedness estimates with uncertainty characterise departure from isolation-by-distance between Plasmodium falciparum populations on the Colombian-Pacific coast","author":"AR Taylor","year":"2020","journal-title":"bioRxiv"},{"issue":"9","key":"pgen.1009037.ref031","doi-asserted-by":"crossref","first-page":"1321","DOI":"10.1038\/s41588-019-0484-x","article-title":"A method for genome-wide genealogy estimation for thousands of samples","volume":"51","author":"L Speidel","year":"2019","journal-title":"Nature Genetics"},{"issue":"6","key":"pgen.1009037.ref032","doi-asserted-by":"crossref","first-page":"1219","DOI":"10.1111\/j.1755-0998.2008.02355.x","article-title":"The influence of family groups on inferences made with the program Structure","volume":"8","author":"E Anderson","year":"2008","journal-title":"Molecular Ecology Resources"},{"issue":"1","key":"pgen.1009037.ref033","doi-asserted-by":"crossref","first-page":"3258","DOI":"10.1038\/s41467-018-05257-7","article-title":"A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots","volume":"9","author":"DJ Lawson","year":"2018","journal-title":"Nature Communications"},{"issue":"1","key":"pgen.1009037.ref034","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1186\/s12936-020-03247-z","article-title":"Malaria in Venezuela: changes in the complexity of infection reflects the increment in transmission intensity","volume":"19","author":"MA Pacheco","year":"2020","journal-title":"Malaria Journal"},{"issue":"23","key":"pgen.1009037.ref035","doi-asserted-by":"crossref","first-page":"12518","DOI":"10.1073\/pnas.2007062117","article-title":"Median-joining network analysis of SARS-CoV-2 genomes is neither phylogenetic nor evolutionary","volume":"117","author":"SJ S\u00e1nchez-Pacheco","year":"2020","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"pgen.1009037.ref036","volume-title":"\u201cSurely you\u2019re joking, Mr. Feynman!\u201d: adventures of a curious character","author":"RP Feynman","year":"1992"},{"issue":"4","key":"pgen.1009037.ref037","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1111\/j.1740-9713.2018.01174.x","article-title":"Cargo-cult statistics and scientific crisis","volume":"15","author":"PB Stark","year":"2018","journal-title":"Significance"},{"issue":"1","key":"pgen.1009037.ref038","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-019-11865-8","article-title":"A short comment on statistical versus mathematical modelling","volume":"10","author":"A Saltelli","year":"2019","journal-title":"Nature Communications"},{"issue":"7407","key":"pgen.1009037.ref039","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1038\/nature11174","article-title":"Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing","volume":"487","author":"M Manske","year":"2012","journal-title":"Nature"},{"issue":"7","key":"pgen.1009037.ref040","doi-asserted-by":"crossref","first-page":"1678","DOI":"10.1093\/molbev\/msy059","article-title":"De novo mutations resolve disease transmission pathways in clonal malaria","volume":"35","author":"SN Redmond","year":"2018","journal-title":"Molecular Biology and Evolution"},{"key":"pgen.1009037.ref041","doi-asserted-by":"crossref","first-page":"e08714","DOI":"10.7554\/eLife.08714","article-title":"Genomic epidemiology of artemisinin resistant malaria","volume":"5","author":"MalariaGEN Plasmodium falciparum Community Project","year":"2016","journal-title":"eLife"},{"issue":"6455","key":"pgen.1009037.ref042","doi-asserted-by":"crossref","first-page":"813","DOI":"10.1126\/science.aav5427","article-title":"Major subpopulations of Plasmodium falciparum in sub-Saharan Africa","volume":"365","author":"A Amambua-Ngwa","year":"2019","journal-title":"Science"},{"issue":"Nov","key":"pgen.1009037.ref043","first-page":"2579","article-title":"Visualizing data using t-SNE","volume":"9","author":"Lvd Maaten","year":"2008","journal-title":"Journal of Machine Learning Research"},{"issue":"4","key":"pgen.1009037.ref044","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1016\/j.tig.2017.12.005","article-title":"Supervised Machine Learning for Population Genetics: A New Paradigm","volume":"34","author":"DR Schrider","year":"2018","journal-title":"Trends in Genetics"},{"issue":"12","key":"pgen.1009037.ref045","doi-asserted-by":"crossref","first-page":"e190","DOI":"10.1371\/journal.pgen.0020190","article-title":"Population structure and eigenanalysis","volume":"2","author":"N Patterson","year":"2006","journal-title":"PLoS Genetics"},{"issue":"6","key":"pgen.1009037.ref046","doi-asserted-by":"crossref","first-page":"e1006907","DOI":"10.1371\/journal.pcbi.1006907","article-title":"Ten quick tips for effective dimensionality reduction","volume":"15","author":"LH Nguyen","year":"2019","journal-title":"PLoS Computational Biology"},{"issue":"4","key":"pgen.1009037.ref047","first-page":"406","article-title":"The neighbor-joining method: a new method for reconstructing phylogenetic trees","volume":"4","author":"N Saitou","year":"1987","journal-title":"Molecular Biology and Evolution"},{"issue":"6","key":"pgen.1009037.ref048","doi-asserted-by":"crossref","first-page":"691","DOI":"10.1111\/cla.12147","article-title":"On the use of median-joining networks in evolutionary biology","volume":"32","author":"S Kong","year":"2016","journal-title":"Cladistics"},{"key":"pgen.1009037.ref049","unstructured":"R Core Team. R: A Language and Environment for Statistical Computing; 2019. Available from: https:\/\/www.R-project.org\/."},{"issue":"9","key":"pgen.1009037.ref050","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v053.i09","article-title":"fastcluster: Fast Hierarchical, Agglomerative Clustering Routines for R and Python","volume":"53","author":"D M\u00fcllner","year":"2013","journal-title":"Journal of Statistical Software"},{"key":"pgen.1009037.ref051","article-title":"dendextend: an R package for visualizing, adjusting, and comparing trees of hierarchical clustering","author":"T Galili","year":"2015","journal-title":"Bioinformatics"},{"issue":"15","key":"pgen.1009037.ref052","doi-asserted-by":"crossref","first-page":"2389","DOI":"10.1093\/bioinformatics\/btw124","article-title":"XIBD: software for inferring pairwise identity by descent on the X chromosome","volume":"32","author":"L Henden","year":"2016","journal-title":"Bioinformatics"},{"issue":"2","key":"pgen.1009037.ref053","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1109\/5.18626","article-title":"A tutorial on hidden Markov models and selected applications in speech recognition","volume":"77","author":"LR Rabiner","year":"1989","journal-title":"Proceedings of the IEEE"},{"issue":"22","key":"pgen.1009037.ref054","doi-asserted-by":"crossref","first-page":"7067","DOI":"10.1073\/pnas.1505691112","article-title":"Modeling malaria genomics reveals transmission decline and rebound in Senegal","volume":"112","author":"RF Daniels","year":"2015","journal-title":"Proceedings of the National Academy of Sciences"}],"updated-by":[{"DOI":"10.1371\/journal.pgen.1009037","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2020,10,21]],"date-time":"2020-10-21T00:00:00Z","timestamp":1603238400000}}],"container-title":["PLOS Genetics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgen.1009037","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,10,21]],"date-time":"2020-10-21T13:41:21Z","timestamp":1603287681000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgen.1009037"}},"subtitle":[],"editor":[{"given":"Giorgio","family":"Sirugo","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2020,10,9]]},"references-count":54,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2020,10,9]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pgen.1009037","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.03.23.004598","asserted-by":"object"}]},"ISSN":["1553-7404"],"issn-type":[{"value":"1553-7404","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,10,9]]}}}