A consensus phylogenomic approach highlights paleopolyploid and rapid radiation in the history of Ericales
A consensus phylogenomic approach highlights paleopolyploid and rapid radiation in the history of Ericales
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DOI：
10.1002/ajb2.1469
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发表时间：
2020-04-29
影响因子：
3
通讯作者：
Smith, Stephen A.
中科院分区：
文献类型：
--
作者：
Larson, Drew A.;Walker, Joseph F.;Smith, Stephen A.
前提大型基因组数据集提供了解决历史上顽固物种关系的希望。但是，不同的方法可能会产生矛盾的结果，尤其是当进化枝经历古老而快速的多样化时。在这里，我们分析了Ericales的古老辐射，并探讨了与物种推理，基因树信号相互冲突以及基因组重复的推断位置相关的不确定性来源。方法我们使用了基于树的同源性和正矫正的层次聚类方法检测，生成六个过滤的系统基因组，由97个转录组和基因组的数据组成。从多种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，串联和基于合并的方法，并在共识框架中进行了总结。我们的共识方法支持了一种支持的方法。拓扑主要与以前的研究一致，但表明数据无法解决几种古老的关系，因为缺乏信息性特征，对方法论的敏感性以及广泛的基因树冲突与古多倍体有关。我们在所有或大多数Ericalean家族的辐射之前找到了全基因组重复的证据，并证明树拓扑和异质进化率会影响基因组重复的推断放置。判断我们提供了有关Ericales史的几个假设，并确定地解决了基因组的重复。大多数节点，但证明一系列的古代差异对这些数据是无法反应的。古多倍体是否是观察到的系统发育冲突的主要来源，需要进一步研究。
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.