Maximum Parsimony Inference of Phylogenetic Networks in the Presence of Polyploid Complexes

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dc.citation.firstpage706en_US
dc.citation.issueNumber3en_US
dc.citation.journalTitleSystematic Biologyen_US
dc.citation.lastpage720en_US
dc.citation.volumeNumber71en_US
dc.contributor.authorYan, Zhien_US
dc.contributor.authorCao, Zhenen_US
dc.contributor.authorLiu, Yushuen_US
dc.contributor.authorOgilvie, Huw A.en_US
dc.contributor.authorNakhleh, Luayen_US
dc.date.accessioned2022-05-25T17:37:49Zen_US
dc.date.available2022-05-25T17:37:49Zen_US
dc.date.issued2022en_US
dc.description.abstractPhylogenetic networks provide a powerful framework for modeling and analyzing reticulate evolutionary histories. While polyploidy has been shown to be prevalent not only in plants but also in other groups of eukaryotic species, most work done thus far on phylogenetic network inference assumes diploid hybridization. These inference methods have been applied, with varying degrees of success, to data sets with polyploid species, even though polyploidy violates the mathematical assumptions underlying these methods. Statistical methods were developed recently for handling specific types of polyploids and so were parsimony methods that could handle polyploidy more generally yet while excluding processes such as incomplete lineage sorting. In this article, we introduce a new method for inferring most parsimonious phylogenetic networks on data that include polyploid species. Taking gene tree topologies as input, the method seeks a phylogenetic network that minimizes deep coalescences while accounting for polyploidy. We demonstrate the performance of the method on both simulated and biological data. The inference method as well as a method for evaluating evolutionary hypotheses in the form of phylogenetic networks are implemented and publicly available in the PhyloNet software package. [Incomplete lineage sorting; minimizing deep coalescences; multilabeled trees; multispecies network coalescent; phylogenetic networks; polyploidy.]en_US
dc.identifier.citationYan, Zhi, Cao, Zhen, Liu, Yushu, et al.. "Maximum Parsimony Inference of Phylogenetic Networks in the Presence of Polyploid Complexes." <i>Systematic Biology,</i> 71, no. 3 (2022) Oxford University Press: 706-720. https://doi.org/10.1093/sysbio/syab081.en_US
dc.identifier.digitalsyab081en_US
dc.identifier.doihttps://doi.org/10.1093/sysbio/syab081en_US
dc.identifier.urihttps://hdl.handle.net/1911/112428en_US
dc.language.isoengen_US
dc.publisherOxford University Pressen_US
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.en_US
dc.rights.urihttps://creativecommons.org/licenses/by-nc/4.0/en_US
dc.titleMaximum Parsimony Inference of Phylogenetic Networks in the Presence of Polyploid Complexesen_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpublisher versionen_US
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