{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T06:14:45Z","timestamp":1772172885464,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1008949","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2021,9,23]],"date-time":"2021-09-23T00:00:00Z","timestamp":1632355200000}}],"reference-count":27,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2021,9,13]],"date-time":"2021-09-13T00:00:00Z","timestamp":1631491200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000923","name":"Australian Research Council","doi-asserted-by":"crossref","award":["DP160103474"],"award-info":[{"award-number":["DP160103474"]}],"id":[{"id":"10.13039\/501100000923","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31501879"],"award-info":[{"award-number":["31501879"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>A current strategy for obtaining haplotype information from several individuals involves short-read sequencing of pooled amplicons, where fragments from each individual is identified by a unique DNA barcode. In this paper, we report a new method to recover the phylogeny of haplotypes from short-read sequences obtained using pooled amplicons from a mixture of individuals, without barcoding. The method, AFPhyloMix, accepts an alignment of the mixture of reads against a reference sequence, obtains the single-nucleotide-polymorphisms (SNP) patterns along the alignment, and constructs the phylogenetic tree according to the SNP patterns. AFPhyloMix adopts a Bayesian inference model to estimate the phylogeny of the haplotypes and their relative abundances, given that the number of haplotypes is known. In our simulations, AFPhyloMix achieved at least 80% accuracy at recovering the phylogenies and relative abundances of the constituent haplotypes, for mixtures with up to 15 haplotypes. AFPhyloMix also worked well on a real data set of kangaroo mitochondrial DNA sequences.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1008949","type":"journal-article","created":{"date-parts":[[2021,9,13]],"date-time":"2021-09-13T13:31:37Z","timestamp":1631539897000},"page":"e1008949","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes"],"prefix":"10.1371","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0580-6324","authenticated-orcid":true,"given":"Thomas K. F.","family":"Wong","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3224-0477","authenticated-orcid":true,"given":"Teng","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7622-4823","authenticated-orcid":true,"given":"Louis","family":"Ranjard","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7685-8009","authenticated-orcid":true,"given":"Steven H.","family":"Wu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9222-9608","authenticated-orcid":true,"given":"Jeet","family":"Sukumaran","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8327-7317","authenticated-orcid":true,"given":"Allen G.","family":"Rodrigo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2021,9,13]]},"reference":[{"issue":"7","key":"pcbi.1008949.ref001","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1016\/S0169-5347(01)02161-9","article-title":"Phylogenetics and speciation","volume":"16","author":"TG Barraclough","year":"2001","journal-title":"Trends in Ecology & Evolution"},{"issue":"5","key":"pcbi.1008949.ref002","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1038\/nrg3186","article-title":"Molecular phylogenetics: principles and practice","volume":"13","author":"Z Yang","year":"2012","journal-title":"Nature Reviews Genetics"},{"issue":"17","key":"pcbi.1008949.ref003","doi-asserted-by":"crossref","first-page":"9241","DOI":"10.1073\/pnas.2004999117","article-title":"Phylogenetic network analysis of SARS-CoV-2 genomes","volume":"117","author":"P Forster","year":"2020","journal-title":"PNAS; Proceedings of the National Academy of Sciences"},{"issue":"14","key":"pcbi.1008949.ref004","doi-asserted-by":"crossref","first-page":"3059","DOI":"10.1093\/nar\/gkf436","article-title":"MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform","volume":"30","author":"K Katoh","year":"2002","journal-title":"Nucleic Acids Research"},{"issue":"1","key":"pcbi.1008949.ref005","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies","volume":"32","author":"LT Nguyen","year":"2014","journal-title":"Molecular Biology and Evolution"},{"issue":"6","key":"pcbi.1008949.ref006","doi-asserted-by":"crossref","first-page":"344","DOI":"10.1038\/nrg3903","article-title":"Haplotype-resolved genome sequencing: experimental methods and applications","volume":"16","author":"MW Snyder","year":"2015","journal-title":"Nature Reviews Genetics"},{"issue":"4","key":"pcbi.1008949.ref007","doi-asserted-by":"crossref","first-page":"893","DOI":"10.1093\/genetics\/61.4.893","article-title":"The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations","volume":"61","author":"M Kimura","year":"1969","journal-title":"Genetics"},{"issue":"4","key":"pcbi.1008949.ref008","doi-asserted-by":"crossref","first-page":"346","DOI":"10.1016\/j.tpb.2009.04.003","article-title":"Site frequency spectra from genomic SNP surveys","volume":"75","author":"G Ganapathy","year":"2009","journal-title":"Theoretical Population Biology"},{"issue":"4","key":"pcbi.1008949.ref009","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","year":"2011","journal-title":"Bioinformatics"},{"issue":"8","key":"pcbi.1008949.ref010","doi-asserted-by":"crossref","first-page":"1879","DOI":"10.1093\/molbev\/msp098","article-title":"INDELible: A Flexible Simulator of Biological Sequence Evolution","volume":"26","author":"W Fletcher","year":"2009","journal-title":"Molecular Biology and Evolution"},{"key":"pcbi.1008949.ref011","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1016\/B978-1-4832-3211-9.50009-7","volume-title":"Mammalian Protein Metabolism","author":"TH Jukes","year":"1969"},{"issue":"2","key":"pcbi.1008949.ref012","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1016\/S0092-8240(77)80002-5","article-title":"On the compatibility of binary qualitative taxonomic characters","volume":"39","author":"FR McMorris","year":"1977","journal-title":"Bulletin of Mathematical Biology"},{"issue":"6","key":"pcbi.1008949.ref013","doi-asserted-by":"crossref","first-page":"1087","DOI":"10.1063\/1.1699114","article-title":"Equation of State Calculations by Fast Computing Machines","volume":"21","author":"N Metropolis","year":"1953","journal-title":"The Journal of Chemical Physics"},{"issue":"1","key":"pcbi.1008949.ref014","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1093\/biomet\/57.1.97","article-title":"Monte Carlo sampling methods using Markov chains and their applications","volume":"57","author":"WK Hastings","year":"1970","journal-title":"Biometrika"},{"issue":"8","key":"pcbi.1008949.ref015","doi-asserted-by":"crossref","first-page":"754","DOI":"10.1093\/bioinformatics\/17.8.754","article-title":"MRBAYES: Bayesian inference of phylogenetic trees","volume":"17","author":"JP Huelsenbeck","year":"2001","journal-title":"Bioinformatics"},{"issue":"1","key":"pcbi.1008949.ref016","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1186\/1471-2148-7-214","article-title":"BEAST: Bayesian evolutionary analysis by sampling trees","volume":"7","author":"AJ Drummond","year":"2007","journal-title":"BMC Evolutionary Biology"},{"key":"pcbi.1008949.ref017","unstructured":"Geyer CJ. Markov chain Monte Carlo maximum likelihood. In: Keramidas EM, editor. Computing Science and Statistics: Proceedings of the 23rd Symposium on the Interface. Fairfax, VA: Interface Foundation; 1991. p. 156\u2013163."},{"issue":"5550","key":"pcbi.1008949.ref018","doi-asserted-by":"crossref","first-page":"2310","DOI":"10.1126\/science.1065889","article-title":"Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology","volume":"294","author":"JP Huelsenbeck","year":"2001","journal-title":"Science"},{"issue":"5","key":"pcbi.1008949.ref019","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1093\/bioinformatics\/13.5.555","article-title":"PAML: a program package for phylogenetic analysis by maximum likelihood","volume":"13","author":"Z Yang","year":"1997","journal-title":"Bioinformatics"},{"issue":"8","key":"pcbi.1008949.ref020","doi-asserted-by":"crossref","first-page":"1586","DOI":"10.1093\/molbev\/msm088","article-title":"PAML 4: Phylogenetic Analysis by Maximum Likelihood","volume":"24","author":"Z Yang","year":"2007","journal-title":"Molecular Biology and Evolution"},{"key":"pcbi.1008949.ref021","unstructured":"Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM; 2013."},{"key":"pcbi.1008949.ref022","unstructured":"State of New South Wales and Office of Environment and Heritage. New South Wales Commercial Kangaroo Harvest Management Plan 2017-21; 2017."},{"issue":"0","key":"pcbi.1008949.ref023","doi-asserted-by":"crossref","first-page":"S3","DOI":"10.1007\/s00239-003-0001-8","article-title":"Radiation of Extant Marsupials After the K\/T Boundary: Evidence from Complete Mitochondrial Genomes","volume":"57","author":"MA Nilsson","year":"2003","journal-title":"Journal of Molecular Evolution"},{"issue":"12","key":"pcbi.1008949.ref024","doi-asserted-by":"crossref","first-page":"1660","DOI":"10.1093\/bioinformatics\/btu077","article-title":"SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads","volume":"30","author":"Y Xie","year":"2014","journal-title":"Bioinformatics"},{"issue":"12","key":"pcbi.1008949.ref025","doi-asserted-by":"crossref","first-page":"1647","DOI":"10.1093\/bioinformatics\/bts199","article-title":"Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data","volume":"28","author":"M Kearse","year":"2012","journal-title":"Bioinformatics"},{"issue":"6","key":"pcbi.1008949.ref026","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1038\/nmeth.4285","article-title":"ModelFinder: fast model selection for accurate phylogenetic estimates","volume":"14","author":"S Kalyaanamoorthy","year":"2017","journal-title":"Nature Methods"},{"issue":"15","key":"pcbi.1008949.ref027","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"AM Bolger","year":"2014","journal-title":"Bioinformatics"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1008949","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2021,9,23]],"date-time":"2021-09-23T00:00:00Z","timestamp":1632355200000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1008949","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,24]],"date-time":"2021-09-24T10:51:36Z","timestamp":1632480696000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1008949"}},"subtitle":[],"editor":[{"given":"Joel O.","family":"Wertheim","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2021,9,13]]},"references-count":27,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2021,9,13]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1008949","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2021.04.09.439138","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,9,13]]}}}