We give an overview of recently developed methods to reconstruct phylog-enies of taxa that include allopolyploids that have originated in relatively recent times—in other words, taxa for which at least some of the parental lineages of lower ploidy levels are not extinct and for which ploidy information is clearly shown by variation in chromosome counts. We review how these methods have been applied to empirical data, discuss challenges, and outline prospects for future research. In the absence of recombination between parental subgenomes, the allopolyploid phylogenetic histories can in principle be treated as genome tree inference. However, without whole genome or whole chromosome data, sequences must be assigned from genes sampled to parental subgenomes. The new version of the AlloppNET method, which now can handle any number of species at the diploid and tetraploid level and any number of hybridizations, is a promising attempt that can also treat gene tree discordance due to the coalescent process. The ...

中文翻译：

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异源多倍体的系统发育

我们概述了最近开发的重建类群系统发育的方法，其中包括起源于相对较新时期的异源多倍体——换句话说，至少一些低倍性水平的亲本谱系没有灭绝的类群染色体计数的变化清楚地显示了倍性信息。我们回顾了这些方法如何应用于经验数据，讨论挑战并概述未来研究的前景。在父母亚基因组之间没有重组的情况下，异源多倍体系统发育历史原则上可以被视为基因组树推断。然而，在没有全基因组或全染色体数据的情况下，序列必须从采样的基因分配到亲本亚基因组。新版本的 AlloppNET 方法，现在可以在二倍体和四倍体水平处理任意数量的物种以及任意数量的杂交，这是一个很有希望的尝试，它也可以处理由于聚结过程引起的基因树不一致。这 ...