The phylogeny and systematics of the genus have been studied with a variety of diverse data types, including an increasing amount of molecular data. However, strong phylogenetic discordance and high levels of uncertainty have prevented the identification of a consistent phylogeny. The difficulty in establishing phylogenetic consensus and evidence for genealogical discordance make a compelling test case to assess the relative contribution of incomplete lineage sorting (ILS), gene flow and gene tree estimation error on phylogenetic reconstruction. In this study, we obtained 75 transcriptomes of 38 species across 10 subgenera. Whole plastid genome, single copy genes and consensus CDS were generated to estimate phylogenetic trees both using coalescence and concatenation methods. Multiple approaches including coalescence simulation, quartet sampling, reticulate network inference, sequence simulation, theta of ILS and reticulation index were carried out across the CDS gene trees to investigate the degrees of ILS, gene flow and gene tree estimation error. Afterward, a regression analysis was used to test the relative contributions of each of these forms of uncertainty to the final phylogeny. Despite extensive topological discordance among gene trees, we found a fully supported species tree that agrees with the most of well-accepted relationships and establishes monophyly of the genus . We presented clear evidence for substantial ILS across the phylogeny of Further, we identified two ancient hybridization events for the formation of the second evolutionary line and subg. as well as several introgression events between recently diverged species. Our regression analysis revealed that gene tree inference error and gene flow were the two most dominant factors explaining for the overall gene tree variation, with the difficulty in disentangling the effects of ILS and gene tree estimation error due to a positive correlation between them. Based on our efforts to mitigate the methodological errors in reconstructing trees, we believed ILS and gene flow are two principal reasons for the oft-reported phylogenetic heterogeneity of . This study presents a strongly-supported and well-resolved phylogenetic backbone for the sampled species, and exemplifies how to untangle heterogeneity in phylogenetic signal and reconstruct the true evolutionary history of the target taxa.

中文翻译：

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葱属（Amayllidaceae）内不完整的谱系排序和基因流

人们已经使用各种不同的数据类型（包括越来越多的分子数据）对该属的系统发育和系统学进行了研究。然而，强烈的系统发育不一致和高度的不确定性阻碍了一致的系统发育的鉴定。建立系统发育共识的困难和谱系不一致的证据成为一个令人信服的测试案例，用于评估不完全谱系排序（ILS）、基因流和基因树估计误差对系统发育重建的相对贡献。在这项研究中，我们获得了 10 个亚属 38 个物种的 75 个转录组。生成整个质体基因组、单拷贝基因和共有 CDS，以使用合并和串联方法估计系统发育树。在 CDS 基因树上采用了合并模拟、四重采样、网状网络推理、序列模拟、ILS θ 和网状指数等多种方法来研究 ILS 程度、基因流和基因树估计误差。随后，使用回归分析来测试每种形式的不确定性对最终系统发育的相对贡献。尽管基因树之间存在广泛的拓扑不一致，但我们发现了一个完全支持的物种树，它符合大多数公认的关系，并建立了属的单系性。我们为整个系统发育史中的大量ILS提供了明确的证据，此外，我们还确定了两个古老的杂交事件，用于形成第二个进化系和亚类。以及最近分化的物种之间的一些基因渗入事件。我们的回归分析表明，基因树推断误差和基因流是解释整体基因树变异的两个最主要因素，由于它们之间呈正相关，因此很难区分 ILS 和基因树估计误差的影响。基于我们为减轻重建树木的方法学错误所做的努力，我们认为ILS和基因流是经常报道的系统发育异质性的两个主要原因。这项研究为样本物种提供了强有力的支持和良好解析的系统发育主干，并举例说明了如何理清系统发育信号中的异质性并重建目标类群的真实进化历史。