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 postpolyploid 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 2 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：

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强有力的系统发育证据揭示了 Tussilagininae 亚部落 （Asteraceae： Senecioneae） 复杂但清晰的同种异体多倍体模式，并开发了一种新的同源分选管道


多倍体是真核生物进化中的一个重要机制，在植物界尤为普遍。然而，我们对这种现象及其对进化的影响的了解仍然有限。研究多倍体的一个主要障碍是解开同种异体多倍体起源的巨大困难。由于杂交和复杂的后多倍体二倍体化过程的综合作用导致基因组的剧烈变化和同种异体多倍体信号的侵蚀，解决同种异体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，我们通过亚部落 Tussilagininae（菊科：Senecioneae）的有趣案例重新审视这个问题，并通过开发 HomeoSorter，一种通过将同源同源分阶段到亲本亚基因组来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，我们证明了 HomeoSorter 在基因组规模的数据上高效工作，并且在识别多倍体模式和分配同源体方面具有很高的准确性。使用 Phylonet 的最大伪似然模型 HomeoSorter 和基因组规模数据，我们进一步解决了 Tussilagininae 的复杂起源，Tussilagininae 是一个特异类群（约 45 个属和 710 个物种），其特征是具有高碱基染色体数（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 由 2 大类群组成，具有连续的同种异体多倍体起源：Tussilagininae s.s.（主要是 x = 30）和 Gynoxyoid 组 （x = 40）。两个同种异体多倍体事件首先产生 Tussilagininae s.s.，第一个事件发生在 Senecioninae 亚部落的祖先 （x = 10） 和与 Brachyglottis 联盟相关的谱系（很可能是 x = 10）之间，以及由此产生的杂交谱系与切尔索多马的祖先 （x = 10） 杂交并导致 Tussilagininae s.s。然后，经过早期多样化，Tussilagininae s.s. 的中美洲组（主要是 x = 30）再次参与切尔索多马谱系的第三种同种异体多倍体事件，并产生 Gynoxyoid 组。我们的研究强调了 HomeoSorter 和同源分选方法在多倍体系统发育学中的价值。Tussilagininae s.s. 和 Gynoxyoid 组具有丰富的物种多样性和清晰的进化模式，也是未来研究多倍体的优秀模型。