{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,11]],"date-time":"2026-04-11T23:04:48Z","timestamp":1775948688416,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1008380","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2021,9,16]],"date-time":"2021-09-16T00:00:00Z","timestamp":1631750400000}}],"reference-count":87,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2021,9,3]],"date-time":"2021-09-03T00:00:00Z","timestamp":1630627200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"publisher","award":["ANR-10-LABX-0001-01"],"award-info":[{"award-number":["ANR-10-LABX-0001-01"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"publisher","award":["ANR-16-IDEX-0006"],"award-info":[{"award-number":["ANR-16-IDEX-0006"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"publisher","award":["ANR-19-CE45-0012"],"award-info":[{"award-number":["ANR-19-CE45-0012"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]},{"name":"ATGC bioinformatic platform","award":["ANR-10-INBS-0009"],"award-info":[{"award-number":["ANR-10-INBS-0009"]}]},{"name":"ATGC bioinformatic platform","award":["ANR-11-INBS-0013"],"award-info":[{"award-number":["ANR-11-INBS-0013"]}]},{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"crossref","award":["ANR-10-LABX-04-01"],"award-info":[{"award-number":["ANR-10-LABX-04-01"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"crossref"}]},{"name":"High Performance Computing Platform MESO@LR"},{"name":"CIRAD - UMR AGAP HPC Data Center of the South Green Bioinformatics platform"},{"name":"CGIAR Research Program"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>For various species, high quality sequences and complete genomes are nowadays available for many individuals. This makes data analysis challenging, as methods need not only to be accurate, but also time efficient given the tremendous amount of data to process. In this article, we introduce an efficient method to infer the evolutionary history of individuals under the multispecies coalescent model in networks (MSNC). Phylogenetic networks are an extension of phylogenetic trees that can contain <jats:italic>reticulate<\/jats:italic> nodes, which allow to model complex biological events such as horizontal gene transfer, hybridization and introgression. We present a novel way to compute the likelihood of <jats:italic>biallelic<\/jats:italic> markers sampled along genomes whose evolution involved such events. This likelihood computation is at the heart of a Bayesian network inference method called S<jats:sc>napp<\/jats:sc>N<jats:sc>et<\/jats:sc>, as it extends the S<jats:sc>napp<\/jats:sc> method inferring evolutionary trees under the multispecies coalescent model, to networks. S<jats:sc>napp<\/jats:sc>N<jats:sc>et<\/jats:sc> is available as a package of the well-known <jats:sc>beast<\/jats:sc> 2 software.<\/jats:p>\n<jats:p>Recently, the <jats:monospace>MCMC_BiMarkers<\/jats:monospace> method, implemented in PhyloNet, also extended S<jats:sc>napp<\/jats:sc> to networks. Both methods take biallelic markers as input, rely on the same model of evolution and sample networks in a Bayesian framework, though using different methods for computing priors. However, S<jats:sc>napp<\/jats:sc>N<jats:sc>et<\/jats:sc> relies on algorithms that are exponentially more time-efficient on non-trivial networks. Using simulations, we compare performances of S<jats:sc>napp<\/jats:sc>N<jats:sc>et<\/jats:sc> and <jats:monospace>MCMC_BiMarkers<\/jats:monospace>. We show that both methods enjoy similar abilities to recover simple networks, but S<jats:sc>napp<\/jats:sc>N<jats:sc>et<\/jats:sc> is more accurate than <jats:monospace>MCMC_BiMarkers<\/jats:monospace> on more complex network scenarios. Also, on complex networks, S<jats:sc>napp<\/jats:sc>N<jats:sc>et<\/jats:sc> is found to be extremely faster than <jats:monospace>MCMC_BiMarkers<\/jats:monospace> in terms of time required for the likelihood computation. We finally illustrate S<jats:sc>napp<\/jats:sc>N<jats:sc>et<\/jats:sc> performances on a rice data set. S<jats:sc>napp<\/jats:sc>N<jats:sc>et<\/jats:sc> infers a scenario that is consistent with previous results and provides additional understanding of rice evolution.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1008380","type":"journal-article","created":{"date-parts":[[2021,9,3]],"date-time":"2021-09-03T17:43:08Z","timestamp":1630690988000},"page":"e1008380","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":23,"title":["On the inference of complex phylogenetic networks by Markov Chain Monte-Carlo"],"prefix":"10.1371","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6736-877X","authenticated-orcid":true,"given":"Charles-Elie","family":"Rabier","sequence":"first","affiliation":[]},{"given":"Vincent","family":"Berry","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5118-5223","authenticated-orcid":true,"given":"Marnus","family":"Stoltz","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4548-4606","authenticated-orcid":true,"given":"Jo\u00e3o D.","family":"Santos","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8842-3432","authenticated-orcid":true,"given":"Wensheng","family":"Wang","sequence":"additional","affiliation":[]},{"given":"Jean-Christophe","family":"Glaszmann","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8084-1464","authenticated-orcid":true,"given":"Fabio","family":"Pardi","sequence":"additional","affiliation":[]},{"given":"Celine","family":"Scornavacca","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2021,9,3]]},"reference":[{"issue":"6201","key":"pcbi.1008380.ref001","doi-asserted-by":"crossref","first-page":"1181","DOI":"10.1126\/science.1255274","article-title":"The coffee genome provides insight into the convergent evolution of caffeine biosynthesis","volume":"345","author":"F Denoeud","year":"2014","journal-title":"Science"},{"issue":"7656","key":"pcbi.1008380.ref002","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1038\/nature22380","article-title":"The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution","volume":"546","author":"H Badouin","year":"2017","journal-title":"Nature"},{"issue":"1","key":"pcbi.1008380.ref003","doi-asserted-by":"crossref","first-page":"2638","DOI":"10.1038\/s41467-018-05051-5","article-title":"A mosaic monoploid reference sequence for the highly complex genome of sugarcane","volume":"9","author":"O Garsmeur","year":"2018","journal-title":"Nature Communications"},{"issue":"18","key":"pcbi.1008380.ref004","doi-asserted-by":"crossref","first-page":"9102","DOI":"10.1093\/nar\/gks700","article-title":"Sequencing of the smallest Apicomplexan genome from the human pathogen Babesia microti","volume":"40","author":"E Cornillot","year":"2012","journal-title":"Nucleic Acids Research"},{"issue":"10","key":"pcbi.1008380.ref005","doi-asserted-by":"crossref","first-page":"4446","DOI":"10.1073\/pnas.1819778116","article-title":"White shark genome reveals ancient elasmobranch adaptations associated with wound healing and the maintenance of genome stability","volume":"116","author":"NJ Marra","year":"2019","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"6968","key":"pcbi.1008380.ref006","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1038\/nature02168","article-title":"The international HapMap project","volume":"426","author":"IH Consortium","year":"2003","journal-title":"Nature"},{"issue":"1","key":"pcbi.1008380.ref007","first-page":"2047","article-title":"The 3,000 rice genomes project","volume":"3","author":"3 RGP","year":"2014","journal-title":"GigaScience"},{"issue":"11","key":"pcbi.1008380.ref008","doi-asserted-by":"crossref","first-page":"745","DOI":"10.1038\/nrg3031","article-title":"Exome sequencing as a tool for Mendelian disease gene discovery","volume":"12","author":"MJ Bamshad","year":"2011","journal-title":"Nature Reviews Genetics"},{"key":"pcbi.1008380.ref009","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1016\/j.cpb.2016.12.003","article-title":"SNP-Seek II: A resource for allele mining and analysis of big genomic data in Oryza sativa","volume":"7","author":"L Mansueto","year":"2016","journal-title":"Current Plant Biology"},{"issue":"6019","key":"pcbi.1008380.ref010","doi-asserted-by":"crossref","first-page":"920","DOI":"10.1126\/science.1198878","article-title":"Classic selective sweeps were rare in recent human evolution","volume":"331","author":"RD Hernandez","year":"2011","journal-title":"Science"},{"issue":"29","key":"pcbi.1008380.ref011","doi-asserted-by":"crossref","first-page":"11983","DOI":"10.1073\/pnas.1019276108","article-title":"Demographic history and rare allele sharing among human populations","volume":"108","author":"S Gravel","year":"2011","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"11","key":"pcbi.1008380.ref012","doi-asserted-by":"crossref","first-page":"15164","DOI":"10.1038\/nplants.2015.164","article-title":"Three geographically separate domestications of Asian rice","volume":"1","author":"P Civ\u00e1\u0148","year":"2015","journal-title":"Nature Plants"},{"issue":"12","key":"pcbi.1008380.ref013","first-page":"3129","article-title":"Three new genome assemblies support a rapid radiation in Musa acuminata (wild banana)","volume":"10","author":"M Rouard","year":"2018","journal-title":"Genome Biology and Evolution"},{"key":"pcbi.1008380.ref014","volume-title":"Inferring phylogenies","author":"J Felenstein","year":"2004"},{"issue":"A","key":"pcbi.1008380.ref015","doi-asserted-by":"crossref","first-page":"27","DOI":"10.2307\/3213548","article-title":"On the genealogy of large populations","volume":"19","author":"JF Kingman","year":"1982","journal-title":"Journal of Applied Probability"},{"issue":"4","key":"pcbi.1008380.ref016","doi-asserted-by":"crossref","first-page":"1645","DOI":"10.1093\/genetics\/164.4.1645","article-title":"Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci","volume":"164","author":"B Rannala","year":"2003","journal-title":"Genetics"},{"key":"pcbi.1008380.ref017","volume-title":"Estimating species trees: practical and theoretical aspects","author":"LL Knowles","year":"2011"},{"issue":"2","key":"pcbi.1008380.ref018","doi-asserted-by":"crossref","first-page":"1095","DOI":"10.1534\/genetics.107.085753","article-title":"A two-stage pruning algorithm for likelihood computation for a population tree","volume":"180","author":"A RoyChoudhury","year":"2008","journal-title":"Genetics"},{"issue":"8","key":"pcbi.1008380.ref019","doi-asserted-by":"crossref","first-page":"1917","DOI":"10.1093\/molbev\/mss086","article-title":"Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis","volume":"29","author":"D Bryant","year":"2012","journal-title":"Molecular Biology and Evolution"},{"issue":"10","key":"pcbi.1008380.ref020","doi-asserted-by":"crossref","first-page":"2266","DOI":"10.1093\/molbev\/msm156","article-title":"Mapping human genetic ancestry","volume":"24","author":"I Ebersberger","year":"2007","journal-title":"Molecular Biology and Evolution"},{"issue":"6","key":"pcbi.1008380.ref021","doi-asserted-by":"crossref","first-page":"332","DOI":"10.1016\/j.tree.2009.01.009","article-title":"Gene tree discordance, phylogenetic inference and the multispecies coalescent","volume":"24","author":"JH Degnan","year":"2009","journal-title":"Trends in Ecology & Evolution"},{"issue":"3","key":"pcbi.1008380.ref022","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1093\/sysbio\/46.3.523","article-title":"Gene Trees in Species Trees","volume":"46","author":"WP Maddison","year":"1997","journal-title":"Systematic Biology"},{"issue":"7133","key":"pcbi.1008380.ref023","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1038\/nature05706","article-title":"Hybrid speciation","volume":"446","author":"J Mallet","year":"2007","journal-title":"Nature"},{"issue":"4","key":"pcbi.1008380.ref024","doi-asserted-by":"crossref","first-page":"721","DOI":"10.1128\/MMBR.00022-12","article-title":"Evolutionary role of interspecies hybridization and genetic exchanges in yeasts","volume":"76","author":"L Morales","year":"2012","journal-title":"Microbiology and Molecular Biology Reviews"},{"issue":"8","key":"pcbi.1008380.ref025","doi-asserted-by":"crossref","first-page":"2166","DOI":"10.1111\/evo.12099","article-title":"Phylogenomics reveals extensive reticulate evolution in Xiphophorus fishes","volume":"67","author":"R Cui","year":"2013","journal-title":"Evolution"},{"issue":"5","key":"pcbi.1008380.ref026","doi-asserted-by":"crossref","first-page":"eaav9188","DOI":"10.1126\/sciadv.aav9188","article-title":"Pervasive hybridizations in the history of wheat relatives","volume":"5","author":"S Glemin","year":"2019","journal-title":"Science Advances"},{"issue":"1","key":"pcbi.1008380.ref027","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1186\/s12862-018-1180-7","article-title":"Role of genetic introgression during the evolution of cultivated rice (Oryza sativa L.)","volume":"18","author":"P Civ\u00e1\u0148","year":"2018","journal-title":"BMC Evolutionary Biology"},{"issue":"1","key":"pcbi.1008380.ref028","doi-asserted-by":"crossref","first-page":"4721","DOI":"10.1038\/s41598-017-05100-x","article-title":"Genome-wide association study and genomic prediction in citrus: potential of genomics-assisted breeding for fruit quality traits","volume":"7","author":"MF Minamikawa","year":"2017","journal-title":"Scientific Reports"},{"issue":"1","key":"pcbi.1008380.ref029","doi-asserted-by":"crossref","first-page":"2518","DOI":"10.1038\/s41467-018-04963-6","article-title":"The origin and remolding of genomic islands of differentiation in the European sea bass","volume":"9","author":"M Duranton","year":"2018","journal-title":"Nature Communications"},{"issue":"1","key":"pcbi.1008380.ref030","doi-asserted-by":"crossref","first-page":"709","DOI":"10.1146\/annurev.micro.55.1.709","article-title":"Horizontal gene transfer in prokaryotes: quantification and classification","volume":"55","author":"EV Koonin","year":"2001","journal-title":"Annual Reviews in Microbiology"},{"issue":"1678","key":"pcbi.1008380.ref031","doi-asserted-by":"crossref","first-page":"20140335","DOI":"10.1098\/rstb.2014.0335","article-title":"Genome-scale phylogenetic analysis finds extensive gene transfer among fungi","volume":"370","author":"GJ Sz\u00f6ll\u0151si","year":"2015","journal-title":"Phil Trans R Soc B"},{"key":"pcbi.1008380.ref032","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9780511974076","volume-title":"Phylogenetic networks: concepts, algorithms and applications","author":"DH Huson","year":"2010"},{"key":"pcbi.1008380.ref033","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1007\/978-0-387-09760-2_7","volume-title":"Problem solving handbook in computational biology and bioinformatics","author":"L Nakhleh","year":"2010"},{"key":"pcbi.1008380.ref034","volume-title":"Introduction to Phylogenetic Networks","author":"DA Morrison","year":"2011"},{"issue":"4","key":"pcbi.1008380.ref035","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1007\/s00026-004-0228-0","article-title":"A framework for representing reticulate evolution","volume":"8","author":"M Baroni","year":"2005","journal-title":"Annals of Combinatorics"},{"issue":"2","key":"pcbi.1008380.ref036","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1016\/0040-5809(83)90013-8","article-title":"Properties of a neutral allele model with intragenic recombination","volume":"23","author":"RR Hudson","year":"1983","journal-title":"Theoretical Population Biology"},{"key":"pcbi.1008380.ref037","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1093\/gbe\/evq077","article-title":"A survey of combinatorial methods for phylogenetic networks","volume":"3","author":"DH Huson","year":"2011","journal-title":"Genome Biology and Evolution"},{"issue":"5","key":"pcbi.1008380.ref038","doi-asserted-by":"crossref","first-page":"786","DOI":"10.1093\/sysbio\/syy040","article-title":"Modeling hybridization under the network multispecies coalescent","volume":"67","author":"JH Degnan","year":"2018","journal-title":"Systematic Biology"},{"issue":"6217","key":"pcbi.1008380.ref039","doi-asserted-by":"crossref","first-page":"1258524","DOI":"10.1126\/science.1258524","article-title":"Extensive introgression in a malaria vector species complex revealed by phylogenomics","volume":"347","author":"MC Fontaine","year":"2015","journal-title":"Science"},{"issue":"6194","key":"pcbi.1008380.ref040","doi-asserted-by":"crossref","first-page":"1250092","DOI":"10.1126\/science.1250092","article-title":"Ancient hybridizations among the ancestral genomes of bread wheat","volume":"345","author":"T Marcussen","year":"2014","journal-title":"Science"},{"issue":"2","key":"pcbi.1008380.ref041","first-page":"283","article-title":"Displayed trees do not determine distinguishability under the network multispecies coalescent","volume":"66","author":"S Zhu","year":"2017","journal-title":"Systematic Biology"},{"key":"pcbi.1008380.ref042","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1093\/gbe\/evq077","article-title":"A Survey of Combinatorial Methods for Phylogenetic Networks","volume":"3","author":"DH Huson","year":"2010","journal-title":"Genome Biology and Evolution"},{"issue":"5","key":"pcbi.1008380.ref043","doi-asserted-by":"crossref","first-page":"478","DOI":"10.1093\/sysbio\/syp055","article-title":"Identifying hybridization events in the presence of coalescence via model selection","volume":"58","author":"LS Kubatko","year":"2009","journal-title":"Systematic Biology"},{"issue":"1","key":"pcbi.1008380.ref044","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1016\/j.tpb.2008.10.004","article-title":"Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: a model","volume":"75","author":"C Meng","year":"2009","journal-title":"Theoretical Population Biology"},{"issue":"2","key":"pcbi.1008380.ref045","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1093\/sysbio\/syq084","article-title":"Coalescent histories on phylogenetic networks and detection of hybridization despite incomplete lineage sorting","volume":"60","author":"Y Yu","year":"2011","journal-title":"Systematic Biology"},{"issue":"4","key":"pcbi.1008380.ref046","doi-asserted-by":"crossref","first-page":"e1002660","DOI":"10.1371\/journal.pgen.1002660","article-title":"The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection","volume":"8","author":"Y Yu","year":"2012","journal-title":"PLoS Genetics"},{"issue":"15","key":"pcbi.1008380.ref047","first-page":"S6","article-title":"Fast algorithms and heuristics for phylogenomics under ILS and hybridization","volume":"14","author":"BioMed Central","year":"2013","journal-title":"BMC bioinformatics"},{"issue":"46","key":"pcbi.1008380.ref048","doi-asserted-by":"crossref","first-page":"16448","DOI":"10.1073\/pnas.1407950111","article-title":"Maximum likelihood inference of reticulate evolutionary histories","volume":"111","author":"Y Yu","year":"2014","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"10","key":"pcbi.1008380.ref049","doi-asserted-by":"crossref","first-page":"S10","DOI":"10.1186\/1471-2164-16-S10-S10","article-title":"A maximum pseudo-likelihood approach for phylogenetic networks","volume":"16","author":"Y Yu","year":"2015","journal-title":"BMC Genomics"},{"issue":"3","key":"pcbi.1008380.ref050","doi-asserted-by":"crossref","first-page":"e1005896","DOI":"10.1371\/journal.pgen.1005896","article-title":"Inferring phylogenetic networks with maximum pseudolikelihood under incomplete lineage sorting","volume":"12","author":"C Sol\u00eds-Lemus","year":"2016","journal-title":"PLoS Genetics"},{"issue":"5","key":"pcbi.1008380.ref051","doi-asserted-by":"crossref","first-page":"e1006006","DOI":"10.1371\/journal.pgen.1006006","article-title":"Bayesian inference of reticulate phylogenies under the multispecies network coalescent","volume":"12","author":"D Wen","year":"2016","journal-title":"PLoS Genetics"},{"issue":"3","key":"pcbi.1008380.ref052","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1093\/sysbio\/syx085","article-title":"Coestimating reticulate phylogenies and gene trees from multilocus sequence data","volume":"67","author":"D Wen","year":"2018","journal-title":"Systematic Biology"},{"issue":"2","key":"pcbi.1008380.ref053","doi-asserted-by":"crossref","first-page":"504","DOI":"10.1093\/molbev\/msx307","article-title":"Bayesian inference of species networks from multilocus sequence data","volume":"35","author":"C Zhang","year":"2017","journal-title":"Molecular Biology and Evolution"},{"issue":"1","key":"pcbi.1008380.ref054","doi-asserted-by":"crossref","first-page":"e1005932","DOI":"10.1371\/journal.pcbi.1005932","article-title":"Bayesian inference of phylogenetic networks from bi-allelic genetic markers","volume":"14","author":"J Zhu","year":"2018","journal-title":"PLoS Computational Biology"},{"key":"pcbi.1008380.ref055","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1007\/978-3-030-10837-3_13","volume-title":"Bioinformatics and Phylogenetics","author":"RL Elworth","year":"2019"},{"issue":"18","key":"pcbi.1008380.ref056","doi-asserted-by":"crossref","first-page":"2277","DOI":"10.1093\/bioinformatics\/btt394","article-title":"Naive binning improves phylogenomic analyses","volume":"29","author":"MS Bayzid","year":"2013","journal-title":"Bioinformatics"},{"issue":"4","key":"pcbi.1008380.ref057","doi-asserted-by":"crossref","first-page":"e1003537","DOI":"10.1371\/journal.pcbi.1003537","article-title":"BEAST 2: a software platform for Bayesian evolutionary analysis","volume":"10","author":"R Bouckaert","year":"2014","journal-title":"PLoS Computational Biology"},{"issue":"4","key":"pcbi.1008380.ref058","doi-asserted-by":"crossref","first-page":"e1006650","DOI":"10.1371\/journal.pcbi.1006650","article-title":"BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis","volume":"15","author":"R Bouckaert","year":"2019","journal-title":"PLoS Computational Biology"},{"issue":"13","key":"pcbi.1008380.ref059","doi-asserted-by":"crossref","first-page":"i376","DOI":"10.1093\/bioinformatics\/bty295","article-title":"Inference of species phylogenies from bi-allelic markers using pseudo-likelihood","volume":"34","author":"J Zhu","year":"2018","journal-title":"Bioinformatics"},{"issue":"4","key":"pcbi.1008380.ref060","doi-asserted-by":"crossref","first-page":"e1004135","DOI":"10.1371\/journal.pcbi.1004135","article-title":"Reconstructible phylogenetic networks: do not distinguish the indistinguishable","volume":"11","author":"F Pardi","year":"2015","journal-title":"PLoS Computational Biology"},{"key":"pcbi.1008380.ref061","first-page":"746362","article-title":"Practical aspects of phylogenetic network analysis using PhyloNet","author":"Z Cao","year":"2019","journal-title":"bioRxiv"},{"issue":"29","key":"pcbi.1008380.ref062","first-page":"299","article-title":"The combination of linkage values and the calculation of distances between the loci of linked factors","volume":"8","author":"J Haldane","year":"1919","journal-title":"Journal of Genetics"},{"issue":"3-4","key":"pcbi.1008380.ref063","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1016\/0025-5564(78)90089-5","article-title":"Taxonomy with confidence","volume":"40","author":"JA Cavender","year":"1978","journal-title":"Mathematical Biosciences"},{"key":"pcbi.1008380.ref064","volume-title":"Introduction to Algorithms, Third Edition","author":"TH Cormen","year":"2009","edition":"3"},{"key":"pcbi.1008380.ref065","doi-asserted-by":"crossref","unstructured":"Gambette P, Berry V, Paul C. The structure of level-k phylogenetic networks. In: Annual Symposium on Combinatorial Pattern Matching. Springer; 2009. p. 289\u2013300.","DOI":"10.1007\/978-3-642-02441-2_26"},{"key":"pcbi.1008380.ref066","doi-asserted-by":"crossref","unstructured":"Berry V, Scornavacca C, Weller M. Scanning Phylogenetic Networks is NP-hard. International Conference on Current Trends in Theory and Practice of Informatics. Springer; 2020. p. 519\u2013530.","DOI":"10.1007\/978-3-030-38919-2_42"},{"issue":"1","key":"pcbi.1008380.ref067","doi-asserted-by":"crossref","first-page":"532","DOI":"10.1186\/1471-2105-9-532","article-title":"Extended Newick: it is time for a standard representation of phylogenetic networks","volume":"9","author":"G Cardona","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"pcbi.1008380.ref068","volume-title":"Monte Carlo strategies in scientific computing","author":"JS Liu","year":"2008"},{"issue":"5","key":"pcbi.1008380.ref069","doi-asserted-by":"crossref","first-page":"901","DOI":"10.1093\/sysbio\/syy032","article-title":"Posterior summarization in Bayesian phylogenetics using Tracer 1.7","volume":"67","author":"A Rambaut","year":"2018","journal-title":"Systematic Biology"},{"issue":"8","key":"pcbi.1008380.ref070","doi-asserted-by":"crossref","first-page":"2319","DOI":"10.1093\/gbe\/evw171","article-title":"Estimating the effective sample size of tree topologies from Bayesian phylogenetic analyses","volume":"8","author":"R Lanfear","year":"2016","journal-title":"Genome Biology and Evolution"},{"issue":"2","key":"pcbi.1008380.ref071","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1109\/TCBB.2009.2","article-title":"A metric on the space of reduced phylogenetic networks","volume":"7","author":"L Nakhleh","year":"2009","journal-title":"IEEE\/ACM Transactions on Computational Biology and Bioinformatics"},{"issue":"7421","key":"pcbi.1008380.ref072","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1038\/nature11532","article-title":"A map of rice genome variation reveals the origin of cultivated rice","volume":"490","author":"X Huang","year":"2012","journal-title":"Nature"},{"issue":"7703","key":"pcbi.1008380.ref073","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1038\/s41586-018-0063-9","article-title":"Genomic variation in 3,010 diverse accessions of Asian cultivated rice","volume":"557","author":"W Wang","year":"2018","journal-title":"Nature"},{"issue":"1","key":"pcbi.1008380.ref074","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1007\/BF00290078","article-title":"Isozymes and classification of Asian rice varieties","volume":"74","author":"JC Glaszmann","year":"1987","journal-title":"Theoretical and Applied genetics"},{"issue":"3","key":"pcbi.1008380.ref075","doi-asserted-by":"crossref","first-page":"832","DOI":"10.1093\/gbe\/evz039","article-title":"Origin of the aromatic group of cultivated rice (Oryza sativa L.) traced to the Indian subcontinent","volume":"11","author":"P Civ\u00e1\u0148","year":"2019","journal-title":"Genome Biology and Evolution"},{"issue":"5","key":"pcbi.1008380.ref076","doi-asserted-by":"crossref","first-page":"1358","DOI":"10.1093\/gbe\/evz084","article-title":"Fine scale genomic signals of admixture and alien introgression among Asian rice landraces","volume":"11","author":"JD Santos","year":"2019","journal-title":"Genome Biology and Evolution"},{"key":"pcbi.1008380.ref077","doi-asserted-by":"crossref","first-page":"1750","DOI":"10.3389\/fpls.2018.01750","article-title":"Misconceptions regarding the role of introgression in the origin of Oryza sativa subsp. indica","volume":"9","author":"P Civ\u00e1\u0148","year":"2018","journal-title":"Frontiers in Plant Science"},{"issue":"1","key":"pcbi.1008380.ref078","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1939-8433-5-20","article-title":"Specific patterns of genetic diversity among aromatic rice varieties in Myanmar","volume":"5","author":"KM Myint","year":"2012","journal-title":"Rice"},{"issue":"1","key":"pcbi.1008380.ref079","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1186\/s13059-020-1938-2","article-title":"Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice","volume":"21","author":"JY Choi","year":"2020","journal-title":"Genome Biology"},{"key":"pcbi.1008380.ref080","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1007\/978-1-4612-1694-0_15","volume-title":"Selected papers of hirotugu akaike","author":"H Akaike","year":"1998"},{"issue":"2","key":"pcbi.1008380.ref081","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1214\/aos\/1176344136","article-title":"Estimating the dimension of a model","volume":"6","author":"G Schwarz","year":"1978","journal-title":"The Annals of Statistics"},{"key":"pcbi.1008380.ref082","doi-asserted-by":"crossref","DOI":"10.7551\/mitpress\/9432.001.0001","volume-title":"ReCombinatorics: the algorithmics of ancestral recombination graphs and explicit phylogenetic networks","author":"D Gusfield","year":"2014"},{"issue":"1-2","key":"pcbi.1008380.ref083","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/0025-5564(81)90043-2","article-title":"Comparison of phylogenetic trees","volume":"53","author":"DF Robinson","year":"1981","journal-title":"Mathematical Biosciences"},{"issue":"2","key":"pcbi.1008380.ref084","first-page":"126","article-title":"Distributions of tree comparison metrics\u2014some new results","volume":"42","author":"MA Steel","year":"1993","journal-title":"Systematic Biology"},{"issue":"1","key":"pcbi.1008380.ref085","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1080\/10635150801886156","article-title":"Efficiency of Markov chain Monte Carlo tree proposals in Bayesian phylogenetics","volume":"57","author":"C Lakner","year":"2008","journal-title":"Systematic Biology"},{"key":"pcbi.1008380.ref086","doi-asserted-by":"crossref","first-page":"e9473","DOI":"10.7717\/peerj.9473","article-title":"Adaptive Metropolis-coupled MCMC for BEAST 2","volume":"8","author":"NF Mueller","year":"2020","journal-title":"PeerJ"},{"issue":"1-3","key":"pcbi.1008380.ref087","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1016\/j.tcs.2008.04.019","article-title":"Seeing the trees and their branches in the network is hard","volume":"401","author":"IA Kanj","year":"2008","journal-title":"Theoretical Computer Science"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1008380","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2021,9,16]],"date-time":"2021-09-16T00:00:00Z","timestamp":1631750400000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1008380","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,16]],"date-time":"2021-09-16T17:52:07Z","timestamp":1631814727000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1008380"}},"subtitle":[],"editor":[{"given":"Sergei L.","family":"Kosakovsky Pond","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2021,9,3]]},"references-count":87,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2021,9,3]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1008380","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.pcbi.1008380","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,9,3]]}}}