论文题目：Unraveling evolutionary pathways: allopolyploidization and introgression in polyploid Prunus (Rosaceae)
论文作者：Siyu Xie#, Xiaohua Lin#, Junru Wang#, Daikun Ma#, Na Su, Chao Xu, Yu Zhang, Hong Ma, Pan Li, Duoyuan Chen, Xin Zhong, Binjie Ge, Richard G.J. Hodel*, Liang Zhao* and Binbin Liu*
论文摘要：
Allopolyploidization, resulting from hybridization and subsequent Whole-genome duplication (WGD), is a fundamental mechanism driving evolutionary diversification across various lineages within the Tree of Life. The polyploid Prunus (Rosaceae), significant for its economic and agricultural value, provides an ideal model for investigating the evolutionary dynamics associated with allopolyploidy. In this study, we utilized Deep Genome Skimming (DGS) data to demonstrate a comprehensive analytical framework for elucidating the underlying allopolyploidy that includes a newly adapted tool (DGS-Tree2GD) tailored explicitly for accurately detecting WGD events. Additionally, we introduced two methods to evaluate the contribution of Incomplete Lineage Sorting (ILS) to lineage diversification. Phylogenomic discordance analyses revealed that allopolyploidization, rather than ILS, played a dominant role in the origin and dynamics of polyploid Prunus. Moreover, we inferred that the uplift of the Himalayas from the Middle to Late Miocene was a key driver in the rapid diversification of the Maddenia clade, an endemic group in East Asia. This geological event facilitated extensive hybridization and allopolyploidization, particularly the introgression between the Himalayas-Hengduan and Central-Eastern China clades. This case study demonstrates the robustness and efficacy of our analytical approach in precisely identifying WGD events and elucidating the evolutionary mechanisms underlying allopolyploidization in polyploid Prunus .
异源多倍体化源于杂交及随后的全基因组复制，是推动生命树中各谱系进化多样化的基本机制。具有重要经济和农业价值的李属（蔷薇科）多倍体，为研究异源多倍体化相关的进化动态提供了理想模型。本研究基于深度基因组浅层测序数据，整合形成了一套完整的、用于揭示异源多倍化形成机制的流程；其中包括一个新改进的工具（DGS-Tree2GD），该工具专门用于准确检测全基因组复制事件。此外还引入了两种方法用以评估不完全谱系分选对谱系多样化的贡献。系统发育基因组学及冲突分析表明，广义李属多倍体类群的起源和演化主要受异源多倍化事件驱动，而非不完全谱系分选。中晚中新世喜马拉雅造山运动是东亚特有类群臭樱分支快速演化的关键因素，这一地质事件促进了类群间杂交与异源多倍化事件发生，推动了喜马拉雅-横断山脉支系与中国中部-东南部地区支系间广泛的基因渗入。本案例研究证明，我们的分析方法在识别全基因组复制事件以及阐明李属多倍体异源多倍体化背后的进化机制方面具有稳健性和有效性。
论文链接：https://doi.org/10.1111/tpj.70320