PREMISE Large genomic data sets offer the promise of resolving historically recalcitrant species relationships. However, different methodologies can yield conflicting results, especially when clades have experienced ancient, rapid diversification. Here, we analyzed the ancient radiation of Ericales and explored sources of uncertainty related to species tree inference, conflicting gene tree signal, and the inferred placement of gene and genome duplications. METHODS We used a hierarchical clustering approach, with tree-based homology and orthology detection, to generate six filtered phylogenomic matrices consisting of data from 97 transcriptomes and genomes. Support for species relationships was inferred from multiple lines of evidence including shared gene duplications, gene tree conflict, gene-wise edge-based analyses, concatenation, and coalescent-based methods, and is summarized in a consensus framework. RESULTS Our consensus approach supported a topology largely concordant with previous studies, but suggests that the data are not capable of resolving several ancient relationships because of lack of informative characters, sensitivity to methodology, and extensive gene tree conflict correlated with paleopolyploidy. We found evidence of a whole-genome duplication before the radiation of all or most ericalean families, and demonstrate that tree topology and heterogeneous evolutionary rates affect the inferred placement of genome duplications. CONCLUSIONS We provide several hypotheses regarding the history of Ericales, and confidently resolve most nodes, but demonstrate that a series of ancient divergences are unresolvable with these data. Whether paleopolyploidy is a major source of the observed phylogenetic conflict warrants further investigation.

中文翻译：

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一致的系统基因组方法突出了 Ericales 历史上的古多倍体和快速辐射

前提 大型基因组数据集有望解决历史上顽固的物种关系。然而，不同的方法可能会产生相互矛盾的结果，尤其是当进化枝经历了古老而快速的多样化时。在这里，我们分析了埃里卡莱斯的古老辐射，并探索了与物种树推断、基因树信号冲突以及基因和基因组重复的推断位置相关的不确定性来源。方法我们使用层次聚类方法，通过基于树的同源性和直系同源性检测，生成六个过滤后的系统发育矩阵，其中包含来自 97 个转录组和基因组的数据。从多条证据中推断出对物种关系的支持，包括共享基因重复、基因树冲突、基于基因的边缘分析、串联、和基于聚结的方法，并在共识框架中进行了总结。结果我们的共识方法支持与先前研究基本一致的拓扑，但表明由于缺乏信息特征、对方法的敏感性以及与古多倍体相关的广泛基因树冲突，数据无法解决几个古老的关系。我们在所有或大多数 ericalean 家族辐射之前发现了全基因组重复的证据，并证明树拓扑结构和异质进化速率影响推断的基因组重复位置。结论我们提供了几个关于 Ericales 历史的假设，并自信地解决了大多数节点，但证明了这些数据无法解决一系列古老的分歧。