Reticulate evolution is a common and important driving force in angiosperm evolution. In this study, we analyzed the phylogenetic signals of genomic regions with different inheritance patterns to understand the evolutionary process of organisms using species-rich Himalaya–Hengduan taxa of bamboos (Fargesia Franchet and Yushania Keng). We constructed phylogenetic trees using different sampling strategies and reconstruction methods based on genome skimming and double digest restriction-site-associated DNA sequencing data. We assessed the congruence of topologies generated from different datasets and employed several approaches to reveal the causes of phylogenetic incongruence, including the detection of hybridization and introgression using PhyloNetworks and the D-statistic test (ABBA-BABA test). We found that, in the plastome-based phylogeny, Fargesia bamboos can be clustered into three groups and Yushania was nested within one of them, which contradicts the nuclear–double digest restriction-site-associated DNA sequencing-based phylogeny. Moreover, the genetic variation of chloroplast DNA is significantly correlated with geographical distribution. The strong signal of incomplete lineage sorting, hybridization, introgression, and cytoplasmic gene flow found among genera and species suggests that reticulate evolution is the main cause for the phylogenetic incongruence between nuclear and chloroplast datasets. Our results add evidence that genomes with different inheritance patterns can reveal distinct evolutionary histories of species and suggest that reticulate evolution is prevalent in rapidly diversifying groups.

中文翻译：

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Fargesia 和 Yushania 的系统基因组学揭示了网状进化的历史

网状进化是被子植物进化过程中常见且重要的驱动力。在这项研究中，我们分析了具有不同遗传模式的基因组区域的系统发育信号，以了解利用物种丰富的喜马拉雅-横断竹类群（Fargesia Franchet 和Yushania Keng）的生物进化过程。我们基于基因组撇取和双酶切限制位点相关的 DNA 测序数据，使用不同的采样策略和重建方法构建了系统发育树。我们评估了从不同数据集生成的拓扑的一致性，并采用了几种方法来揭示系统发育不一致的原因，包括使用 PhyloNetworks 和D- 统计检验（ABBA-BABA 检验）。我们发现，在基于塑性体的系统发育中，Fargesia竹可以分为三个组和玉山竹嵌套在其中之一中，这与基于核双消化限制位点相关 DNA 测序的系统发育相矛盾。此外，叶绿体DNA的遗传变异与地理分布显着相关。在属和种之间发现的不完整谱系分类、杂交、基因渗入和细胞质基因流动的强烈信号表明，网状进化是核和叶绿体数据集之间系统发育不一致的主要原因。我们的结果增加了证据表明具有不同遗传模式的基因组可以揭示物种的不同进化历史，并表明网状进化在快速多样化的群体中普遍存在。