Polyploidy is a significant mechanism in eukaryotic evolution and is particularly prevalent in the plant kingdom. However, our knowledge about this phenomenon and its effects on evolution remains limited. A major obstacle to the study of polyploidy is the great difficulty in untangling the origins of allopolyploids. Due to the drastic genome changes and the erosion of allopolyploidy signals caused by the combined effects of hybridization and complex post-polyploid diploidization processes, resolving the origins of allopolyploids has long been a challenging task. Here we revisit this issue with the interesting case of subtribe Tussilagininae (Asteraceae: Senecioneae) and by developing HomeoSorter, a new pipeline for network inferences by phasing homeologs to parental subgenomes. The pipeline is based on the basic idea of a previous study but with major changes to address the scaling problem and implement some new functions. With simulated data, we demonstrate that HomeoSorter works efficiently on genome-scale data and has high accuracy in identifying polyploid patterns and assigning homeologs. Using HomeoSorter, the maximum pseudo-likelihood model of Phylonet, and genome-scale data, we further address the complex origin of Tussilagininae, a speciose group (ca. 45 genera and 710 species) characterized by having high base chromosome numbers (mainly x = 30, 40). In particular, the inferred patterns are strongly supported by the chromosomal evidence. Tussilagininae is revealed to comprise two large groups with successive allopolyploid origins: Tussilagininae s.s. (mainly x = 30) and the Gynoxyoid group (x = 40). Two allopolyploidy events first give rise to Tussilagininae s.s., with the first event occurring between the ancestor of subtribe Senecioninae (x = 10) and a lineage (highly probably with x = 10) related to the Brachyglottis alliance, and the resulting hybrid lineage crossing with the ancestor of Chersodoma (x = 10) and leading to Tussilagininae s.s. Then, after early diversification, the Central American group (mainly x = 30) of Tussilagininae s.s., is involved in a third allopolyploidy event with, again, the Chersodoma lineage and produces the Gynoxyoid group. Our study highlights the value of HomeoSorter and the homeolog-sorting approach in polyploid phylogenetics. With rich species diversity and clear evolutionary patterns, Tussilagininae s.s. and the Gynoxyoid group are also excellent models for future investigations of polyploidy.

中文翻译：

---

可靠的系统发育证据揭示了 Tussilagininae 亚族（菊科：千里光亚科）复杂但清晰的异源多倍体模式，并开发了一种新型同源分类管道


多倍体是真核进化中的重要机制，在植物界尤其普遍。然而，我们对这种现象及其对进化的影响的了解仍然有限。多倍体研究的一个主要障碍是很难解开异源多倍体的起源。由于杂交和复杂的后多倍体二倍化过程的综合作用造成基因组的剧烈变化和异源多倍体信号的侵蚀，解决异源多倍体的起源长期以来一直是一项具有挑战性的任务。在这里，我们以 Tussilagininae 亚族（菊科：千里光亚科）这个有趣的案例重新审视这个问题，并通过开发 HomeoSorter，这是一种通过将同源物与亲本亚基因组进行定相进行网络推理的新管道。该管道基于先前研究的基本思想，但进行了重大更改以解决扩展问题并实现一些新功能。通过模拟数据，我们证明 HomeoSorter 可以有效地处理基因组规模的数据，并且在识别多倍体模式和分配同源物方面具有很高的准确性。使用 HomeoSorter、Phylonet 的最大伪似然模型和基因组规模数据，我们进一步解决了 Tussilagininae 的复杂起源问题，这是一个物种类群（约 45 个属和 710 个物种），其特征是具有高基础染色体数（主要是 x = 30、40）。特别是，推断的模式得到了染色体证据的有力支持。 Tussilagininae 被发现包含两个具有连续异源多倍体起源的大类群：Tussilagininae ss（主要是 x = 30）和 Gynoxyoid 类群（x = 40）。两次异源多倍体事件首先产生了 Tussilagininae ss，第一个事件发生在千里光亚族的祖先 (x = 10) 和与 Brachyglottis 联盟相关的谱系（极有可能 x = 10）之间，以及由此产生的与 Chersodoma 祖先的杂交谱系杂交 (x = 10)然后，在早期多样化之后，Tussilagininae ss 的中美洲群体（主要是 x = 30）与 Chersodoma 谱系一起参与第三个异源多倍体事件，并产生了 Gynoxyoid 群体。我们的研究强调了同源排序器和同源排序方法在多倍体系统发育学中的价值。 Tussilagininae ss和Gynoxyoid组具有丰富的物种多样性和清晰的进化模式，也是未来多倍体研究的优秀模型。