Phylogenetic 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.]

中文翻译：

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多倍体复合物存在下系统发育网络的最大简约推断

系统发育网络为建模和分析网状进化历史提供了一个强大的框架。虽然已证明多倍体不仅在植物中而且在其他真核物种中普遍存在，但迄今为止在系统发育网络推断方面所做的大多数工作都假设二倍体杂交。尽管多倍体违反了这些方法背后的数学假设，但这些推理方法已成功应用于具有多倍体物种的数据集，并取得了不同程度的成功。最近开发了用于处理特定类型的多倍体的统计方法，因此可以更普遍地处理多倍体同时排除诸如不完整谱系分类等过程的简约方法。在本文中，我们介绍了一种新方法，用于根据包括多倍体物种的数据推断最简约的系统发育网络。以基因树拓扑为输入，该方法寻求一个系统发育网络，该网络在考虑多倍体的同时最大限度地减少深度聚结。我们展示了该方法在模拟数据和生物数据上的性能。推理方法以及以系统发育网络的形式评估进化假设的方法在 PhyloNet 软件包中实现并公开提供。[不完整的血统排序；最小化深度聚结；多标签树；多物种网络聚结；系统发育网络；多倍体。] 我们展示了该方法在模拟数据和生物数据上的性能。推理方法以及以系统发育网络的形式评估进化假设的方法在 PhyloNet 软件包中实现并公开提供。[不完整的血统排序；最小化深度聚结；多标签树；多物种网络聚结；系统发育网络；多倍体。] 我们展示了该方法在模拟数据和生物数据上的性能。推理方法以及以系统发育网络的形式评估进化假设的方法在 PhyloNet 软件包中实现并公开提供。[不完整的血统排序；最小化深度聚结；多标签树；多物种网络聚结；系统发育网络；多倍体。]