Phylogenomics is increasingly used to infer deep-branching relationships while revealing the complexity of evolutionary processes such as incomplete lineage sorting, hybridization/introgression and polyploidization. We investigate the deep-branching relationships among subfamilies of the Leguminosae (or Fabaceae), the third largest angiosperm family. Despite their ecological and economic importance, a robust phylogenetic framework for legumes based on genome-scale sequence data is lacking. We generated alignments of 72 chloroplast genes and 7621 homologous nuclear-encoded proteins, for 157 and 76 taxa, respectively. We analysed these with maximum likelihood, Bayesian inference, and a multispecies coalescent summary method, and evaluated support for alternative topologies across gene trees. We resolve the deepest divergences in the legume phylogeny despite lack of phylogenetic signal across all chloroplast genes and the majority of nuclear genes. Strongly supported conflict in the remainder of nuclear genes is suggestive of incomplete lineage sorting. All six subfamilies originated nearly simultaneously, suggesting that the prevailing view of some subfamilies as 'basal' or 'early-diverging' with respect to others should be abandoned, which has important implications for understanding the evolution of legume diversity and traits. Our study highlights the limits of phylogenetic resolution in relation to rapid successive speciation.

中文翻译：

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大规模的基因组序列数据解决了豆科植物系统发育中最深的差异，并支持所有六个亚科的近乎同时的进化起源。

系统经济学越来越多地用于推断深层分支关系，同时揭示进化过程的复杂性，例如不完全的谱系分类，杂交/渗入和多倍体化。我们调查豆科（或豆科），第三大被子植物科的亚科之间的深支关系。尽管它们具有生态和经济重要性，但缺乏基于基因组规模序列数据的健壮的豆科植物系统发育框架。我们分别产生了157个和76个分类单元的72个叶绿体基因和7621个同源核编码蛋白的比对。我们以最大似然，贝叶斯推断和多物种合并摘要方法对这些方法进行了分析，并评估了对跨基因树的替代拓扑的支持。尽管所有叶绿体基因和大多数核基因中都缺乏系统发育信号，但我们仍解决了豆科植物系统发育中最深的分歧。其余核基因中强烈支持的冲突提示谱系分选不完整。这六个亚科几乎是同时起源的，这表明某些亚科相对于其他亚科的“基础”或“早期分化”的普遍观点应被放弃，这对于理解豆类多样性和性状的演变具有重要意义。我们的研究突出了与快速连续物种形成相关的系统发育分辨率的局限性。其余核基因中强烈支持的冲突提示谱系分选不完整。这六个亚科几乎是同时起源的，这表明某些亚科相对于其他亚科的“基础”或“早期分化”的普遍观点应被放弃，这对于理解豆类多样性和性状的演变具有重要意义。我们的研究突出了与快速连续物种形成相关的系统发育分辨率的局限性。其余核基因中强烈支持的冲突提示谱系分选不完整。这六个亚科几乎是同时起源的，这表明某些亚科相对于其他亚科的“基础”或“早期分化”的普遍观点应被放弃，这对于理解豆类多样性和性状的演变具有重要意义。我们的研究突出了与快速连续物种形成相关的系统发育分辨率的局限性。