{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T20:48:01Z","timestamp":1792788481483,"version":"4.5.0"},"update-to":[{"DOI":"10.1371\/journal.pgen.1007279","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2018,6,5]],"date-time":"2018-06-05T00:00:00Z","timestamp":1528156800000}}],"reference-count":57,"publisher":"Public Library of Science (PLoS)","issue":"5","license":[{"start":{"date-parts":[[2018,5,23]],"date-time":"2018-05-23T00:00:00Z","timestamp":1527033600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","award":["APP1054618"],"award-info":[{"award-number":["APP1054618"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","award":["1002098"],"award-info":[{"award-number":["1002098"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","award":["APP1027108"],"award-info":[{"award-number":["APP1027108"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Australian Postgraduate Award"},{"name":"Australian Postgraduate Award"},{"name":"John and Patricia Farrant Scholarship"}],"content-domain":{"domain":["www.plosgenetics.org"],"crossmark-restriction":false},"short-container-title":["PLoS Genet"],"DOI":"10.1371\/journal.pgen.1007279","type":"journal-article","created":{"date-parts":[[2018,5,23]],"date-time":"2018-05-23T13:46:04Z","timestamp":1527083164000},"page":"e1007279","update-policy":"https:\/\/doi.org\/10.1371\/journal.pgen.corrections_policy","source":"Crossref","is-referenced-by-count":136,"title":["Identity-by-descent analyses for measuring population dynamics and selection in recombining pathogens"],"prefix":"10.1371","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5541-7637","authenticated-orcid":true,"given":"Lyndal","family":"Henden","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1179-8436","authenticated-orcid":true,"given":"Stuart","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ivo","family":"Mueller","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1189-2310","authenticated-orcid":true,"given":"Alyssa","family":"Barry","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Melanie","family":"Bahlo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2018,5,23]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"617","DOI":"10.1146\/annurev-genet-110711-155534","article-title":"Identity by descent between distant relatives: detection and applications","volume":"46","author":"S Browning","year":"2012","journal-title":"Annu Rev Genet"},{"issue":"2","key":"ref2","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1534\/genetics.112.148825","article-title":"Identity by descent: variation in meiosis, across genomes, and in populations","volume":"194","author":"E Thompson","year":"2013","journal-title":"Genetics"},{"issue":"3","key":"ref3","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1002\/gepi.20378","article-title":"Relatedness mapping and tracts of relatedness for genome-wide data in the presence of linkage disequilibrium","volume":"33","author":"A Albrechtsen","year":"2009","journal-title":"Genet Epidemiol"},{"issue":"4","key":"ref4","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1016\/j.ajhg.2010.08.014","article-title":"Inference of unexpected genetic relatedness among individuals in HapMap Phase III","volume":"87","author":"TJ Pemberton","year":"2010","journal-title":"Am J Hum Genet"},{"issue":"1","key":"ref5","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1534\/genetics.110.113977","article-title":"Natural selection and the distribution of identity-by-descent in the human genome","volume":"186","author":"A Albrechtsen","year":"2010","journal-title":"Genetics"},{"issue":"2","key":"ref6","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1038\/ejhg.2012.148","article-title":"Using identity by descent estimation with dense genotype data to detect positive selection","volume":"21","author":"L Han","year":"2013","journal-title":"Eur J Hum Genet"},{"issue":"15","key":"ref7","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":"1","key":"ref8","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1186\/s13073-017-0398-0","article-title":"Genetic relatedness analysis reveals the cotransmission of genetically related Plasmodium falciparum parasites in Thi\u00e8s, Senegal","volume":"9","author":"W Wong","year":"2017","journal-title":"Genome Medicine"},{"issue":"22","key":"ref9","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":"Proc Natl Acad Sci U S A"},{"issue":"6","key":"ref10","doi-asserted-by":"crossref","first-page":"e1003521","DOI":"10.1371\/journal.pgen.1003521","article-title":"Inferring demographic history from a spectrum of shared haplotype length","volume":"9","author":"K Harris","year":"2013","journal-title":"PLoS Genet"},{"issue":"6909","key":"ref11","doi-asserted-by":"crossref","first-page":"832","DOI":"10.1038\/nature01140","article-title":"Detecting recent positive selection in the human genome from haplotype structure","volume":"419","author":"PC Sabeti","year":"2002","journal-title":"Nature"},{"issue":"1","key":"ref12","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":"D Lawson","year":"2012","journal-title":"PLoS Genet"},{"key":"ref13","doi-asserted-by":"crossref","DOI":"10.1101\/188078","article-title":"hmmIBD: software to infer pairwise identity by descent between haploid genotypes","author":"SF Schaffner","year":"2017"},{"key":"ref14","article-title":"Genomic epidemiology of artemisinin resistant malaria","volume":"5","year":"2016","journal-title":"Elife"},{"issue":"9","key":"ref15","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"},{"issue":"7407","key":"ref16","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":"3","key":"ref17","doi-asserted-by":"crossref","first-page":"e72","DOI":"10.1371\/journal.pbio.0040072","article-title":"A map of recent positive selection in the human genome","volume":"4","author":"BF Voight","year":"2006","journal-title":"PLoS Biol"},{"issue":"6","key":"ref18","doi-asserted-by":"crossref","first-page":"866","DOI":"10.1016\/j.ajhg.2013.04.021","article-title":"Detecting and characterizing genomic signatures of positive selection in global populations","volume":"92","author":"X Liu","year":"2013","journal-title":"Am J Hum Genet"},{"issue":"7164","key":"ref19","doi-asserted-by":"crossref","first-page":"913","DOI":"10.1038\/nature06250","article-title":"Genome-wide detection and characterization of positive selection in human populations","volume":"449","author":"PC Sabeti","year":"2007","journal-title":"Nature"},{"issue":"1478","key":"ref20","doi-asserted-by":"crossref","first-page":"1855","DOI":"10.1098\/rspb.2001.1759","article-title":"Very large long-term effective population size in the virulent human malaria parasite Plasmodium falciparum","volume":"268","author":"AL Hughes","year":"2001","journal-title":"Proc Biol Sci"},{"issue":"8","key":"ref21","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1016\/0169-4758(87)90147-5","article-title":"Spread of chloroquine resistance in Plasmodium falciparum","volume":"3","author":"D Payne","year":"1987","journal-title":"Parasitol Today"},{"issue":"10","key":"ref22","doi-asserted-by":"crossref","first-page":"1467","DOI":"10.1093\/oxfordjournals.molbev.a026247","article-title":"Microsatellite markers reveal a spectrum of population structures in the malaria parasite Plasmodium falciparum","volume":"17","author":"TJ Anderson","year":"2000","journal-title":"Mol Biol Evol"},{"issue":"10","key":"ref23","doi-asserted-by":"crossref","first-page":"e335","DOI":"10.1371\/journal.pbio.0030335","article-title":"Recombination hotspots and population structure in Plasmodium falciparum","volume":"3","author":"J Mu","year":"2005","journal-title":"PLoS Biol"},{"issue":"19","key":"ref24","doi-asserted-by":"crossref","first-page":"1959","DOI":"10.1056\/NEJMoa062032","article-title":"Return of chloroquine antimalarial efficacy in Malawi","volume":"355","author":"MK Laufer","year":"2006","journal-title":"N Engl J Med"},{"issue":"22","key":"ref25","doi-asserted-by":"crossref","first-page":"12689","DOI":"10.1073\/pnas.221440898","article-title":"Evolution of a unique Plasmodium falciparum chloroquine-resistance phenotype in association with pfcrt polymorphism in Papua New Guinea and South America","volume":"98","author":"RK Mehlotra","year":"2001","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"6895","key":"ref26","doi-asserted-by":"crossref","first-page":"320","DOI":"10.1038\/nature00813","article-title":"Genetic diversity and chloroquine selective sweeps in Plasmodium falciparum","volume":"418","author":"JC Wootton","year":"2002","journal-title":"Nature"},{"issue":"6","key":"ref27","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":"Nat Genet"},{"issue":"7481","key":"ref28","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1038\/nature12876","article-title":"A molecular marker of artemisinin-resistant Plasmodium falciparum malaria","volume":"505","author":"F Ariey","year":"2014","journal-title":"Nature"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1186\/1475-2875-13-385","article-title":"Spatial and temporal epidemiology of clinical malaria in Cambodia 2004\u20132013","volume":"13","author":"RJ Maude","year":"2014","journal-title":"Malar J"},{"issue":"5","key":"ref30","doi-asserted-by":"crossref","first-page":"670","DOI":"10.1093\/infdis\/jiu491","article-title":"Independent emergence of artemisinin resistance mutations among Plasmodium falciparum in Southeast Asia","volume":"211","author":"S Takala-Harrison","year":"2015","journal-title":"J Infect Dis"},{"issue":"32","key":"ref31","doi-asserted-by":"crossref","first-page":"13052","DOI":"10.1073\/pnas.1210585109","article-title":"Sequence-based association and selection scans identify drug resistance loci in the Plasmodium falciparum malaria parasite","volume":"109","author":"DJ Park","year":"2012","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"1","key":"ref32","doi-asserted-by":"crossref","first-page":"515","DOI":"10.1186\/s12936-016-1560-7","article-title":"Exceptionally long-range haplotypes in Plasmodium falciparum chromosome 6 maintained in an endemic African population","volume":"15","author":"A Amambua-Ngwa","year":"2016","journal-title":"Malar J"},{"issue":"11","key":"ref33","doi-asserted-by":"crossref","first-page":"3249","DOI":"10.1093\/molbev\/mss151","article-title":"SNP genotyping identifies new signatures of selection in a deep sample of West African Plasmodium falciparum malaria parasites","volume":"29","author":"A Amambua-Ngwa","year":"2012","journal-title":"Mol Biol Evol"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1126\/science.aan4472","article-title":"Mapping the malaria parasite druggable genome by using in vitro evolution and chemogenomics","volume":"359","author":"AN Cowell","year":"2018","journal-title":"Science"},{"issue":"1","key":"ref35","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1186\/s12936-016-1634-6","article-title":"Characterizing the impact of sustained sulfadoxine\/pyrimethamine use upon the Plasmodium falciparum population in Malawi","volume":"15","author":"M Ravenhall","year":"2016","journal-title":"Malar J"},{"issue":"6","key":"ref36","doi-asserted-by":"crossref","first-page":"e57","DOI":"10.1371\/journal.ppat.0020057","article-title":"A systematic map of genetic variation in Plasmodium falciparum","volume":"2","author":"C Kidgell","year":"2006","journal-title":"PLoS Pathog"},{"issue":"10","key":"ref37","doi-asserted-by":"crossref","first-page":"e1000243","DOI":"10.1371\/journal.pgen.1000243","article-title":"Adaptive Copy Number Evolution in Malaria Parasites","volume":"4","author":"S Nair","year":"2008","journal-title":"PLoS Genet"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"11553","DOI":"10.1038\/ncomms11553","article-title":"Globally prevalent PfMDR1 mutations modulate Plasmodium falciparum susceptibility to artemisinin-based combination therapies","volume":"7","author":"MI Veiga","year":"2016","journal-title":"Nat Commun"},{"issue":"4","key":"ref39","doi-asserted-by":"crossref","first-page":"e1001383","DOI":"10.1371\/journal.pgen.1001383","article-title":"Identification and functional validation of the novel antimalarial resistance locus PF10_0355 in Plasmodium falciparum","volume":"7","author":"D Van Tyne","year":"2011","journal-title":"PLoS Genet"},{"issue":"7","key":"ref40","doi-asserted-by":"crossref","first-page":"2937","DOI":"10.1128\/AAC.02574-12","article-title":"Modulation of PF10_0355 (MSPDBL2) alters Plasmodium falciparum response to antimalarial drugs","volume":"57","author":"D Van Tyne","year":"2013","journal-title":"Antimicrob Agents Chemother"},{"issue":"btx530","key":"ref41","article-title":"Deconvolution of multiple infections in Plasmodium falciparum from high throughput sequencing data","author":"SJ Zhu","year":"2017","journal-title":"Bioinformatics"},{"issue":"3","key":"ref42","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1016\/j.ygeno.2007.05.011","article-title":"Estimating genotyping error rates from Mendelian errors in SNP array genotypes and their impact on inference","volume":"90","author":"I Saunders","year":"2007","journal-title":"Genomics"},{"issue":"7214","key":"ref43","doi-asserted-by":"crossref","first-page":"757","DOI":"10.1038\/nature07327","article-title":"Comparative genomics of the neglected human malaria parasite Plasmodium vivax","volume":"455","author":"JM Carlton","year":"2008","journal-title":"Nature"},{"issue":"1","key":"ref44","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1073\/pnas.98.1.182","article-title":"Recombination within natural populations of pathogenic bacteria: short-term empirical estimates and long-term phylogenetic consequences","volume":"98","author":"EJ Feil","year":"2001","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"5","key":"ref45","doi-asserted-by":"crossref","first-page":"1198","DOI":"10.1086\/301844","article-title":"Multipoint quantitative-trait linkage analysis in general pedigrees","volume":"62","author":"L Almasy","year":"1998","journal-title":"Am J Hum Genet"},{"issue":"5","key":"ref46","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1038\/ng.806","article-title":"A framework for variation discovery and genotyping using next-generation DNA sequencing data","volume":"43","author":"MA DePristo","year":"2011","journal-title":"Nat Genet"},{"issue":"4","key":"ref47","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1093\/bioinformatics\/btr708","article-title":"ART: a next-generation sequencing read simulator","volume":"28","author":"W Huang","journal-title":"Bioinformatics"},{"issue":"4","key":"ref48","doi-asserted-by":"crossref","first-page":"1037","DOI":"10.1534\/genetics.113.152181","article-title":"SLiM: simulating evolution with selection and linkage","volume":"194","author":"PW Messer","year":"2013","journal-title":"Genetics"},{"issue":"2","key":"ref49","doi-asserted-by":"crossref","first-page":"e1003293","DOI":"10.1371\/journal.pgen.1003293","article-title":"Mitotic evolution of Plasmodium falciparum shows a stable core genome but recombination in antigen families","volume":"9","author":"SE Bopp","year":"2013","journal-title":"PLoS Genet"},{"key":"ref50","article-title":"moimix: an R package for assessing clonality in high-throughput sequencing data","author":"S Lee","year":"2016"},{"issue":"5","key":"ref51","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1038\/nrg3187","article-title":"Harnessing genomics and genome biology to understand malaria biology","volume":"13","author":"SK Volkman","year":"2012","journal-title":"Nat Rev Genet"},{"issue":"12","key":"ref52","doi-asserted-by":"crossref","first-page":"R171","DOI":"10.1186\/gb-2008-9-12-r171","article-title":"Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence","volume":"9","author":"DE Neafsey","year":"2008","journal-title":"Genome Biol"},{"key":"ref53","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":"8","key":"ref54","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":"Nat Genet"},{"key":"ref55","unstructured":"Miles A, Harding N. scikit-allel. v0.20.3 ed2016."},{"key":"ref56","unstructured":"Python Foundation Software. Python Language Reference version 2.7."},{"key":"ref57","article-title":"The igraph software package for complex network research","author":"G Csardi","year":"2006","journal-title":"InterJournal"}],"updated-by":[{"DOI":"10.1371\/journal.pgen.1007279","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2018,6,5]],"date-time":"2018-06-05T00:00:00Z","timestamp":1528156800000}}],"container-title":["PLOS Genetics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pgen.1007279","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,8]],"date-time":"2020-05-08T18:53:34Z","timestamp":1588964014000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgen.1007279"}},"subtitle":[],"editor":[{"given":"Xavier","family":"Didelot","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2018,5,23]]},"references-count":57,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2018,5,23]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pgen.1007279","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/088039","asserted-by":"object"}]},"ISSN":["1553-7404"],"issn-type":[{"value":"1553-7404","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,5,23]]}}}