背景回顾：Fabaceae are the third largest angiosperm family, with 765 genera and ～19 500 species. They are important both economically and ecologically, and global Fabaceae crops are intensively studied in part for their nitrogen-fixing ability. 

提出问题：However, resolution of the intrasubfamilial Fabaceae phylogeny and divergence times has remained elusive, precluding a reconstruction of the evolutionary history of symbiotic nitrogen fixation in Fabaceae.

主要研究：Here, we report a highly resolved phylogeny using >1500 nuclear genes from newly sequenced transcriptomes and genomes of 391 species, along with other datasets, for a total of 463 legumes spanning all 6 subfamilies and 333 of 765 genera.

结果1-单系起源：The subfamilies are maximally supported as monophyletic. The clade comprising subfamilies Cercidoideae and Detarioideae is sister to the remaining legumes, and Duparquetioideae and Dialioideae are successive sisters to the clade of Papilionoideae and Caesalpinioideae.

结果2-分子钟估计：Molecular clock estimation revealed an early radiation of subfamilies near the K/Pg boundary, marked by mass extinction, and subsequent divergence of most tribe-level clades within ～15 million years.

结果3-全基因组加倍：Phylogenomic analyses of thousands of gene families support 28 proposed putative whole-genome duplication/whole-genome triplication events across Fabaceae, including those at the ancestors of Fabaceae and five of the subfamilies, and further analyses supported the Fabaceae ancestral polyploidy.

结果4-根瘤菌固氮共生演化：The evolution of rhizobial nitrogen-fixing nodulation in Fabaceae was probed by ancestral character reconstruction and phylogenetic analyses of related gene families and the results support the hypotheses of one or two switch(es) to rhizobial nodulation followed by multiple losses.

结论：Collectively, these results provide a foundation for further morphological and functional evolutionary analyses across Fabaceae.

豆科是第三大被子植物科，包含765个属，约19500个种。豆科植物具有非常重要的经济和生态价值，并且全球对于豆科作物的固氮能力进行了细致而深入的研究。但是，豆科亚科内部的系统发育关系以及分化时间仍然不清晰，从而对重建豆科共生固氮演化史造成了一个严峻的挑战。本文中，作者基于来自391个物种的新测序转录组和基因组数据，利用超过1500个核基因，与其他类型数据一起，对横跨6个亚科、333个属的463个豆科物种进行了高分辨率的系统发育树构建。结果显示，这些亚科极有可能是单系起源的。包含紫荆亚科（Cercidoideae）和甘豆亚科（Detarioideae）的支系是其余豆科植物的姊妹枝，而三姜豆亚科（Duparquetioideae）和酸榄豆亚科（Dialioideae）依次是（蝶形花亚科Papilionoideae + 狭义云实亚科Caesalpinioideae）支系的姊妹枝。分子钟估计显示豆科在白垩纪/古近纪（K/Pg）界线附近出现亚科的早期辐射，并出现大规模的灭绝，随后在大约15万年内大多数族级分支出现分化。对于数千个基因家族的系统发育基因组学分析显示，在豆科植物中发生过28个假定的全基因组复制（WGD）/全基因组三倍化（WGT）事件，包括在豆科祖先及5个亚科的祖先中，并且进一步的分析支持了豆科的祖先种是多倍体。通过家谱重建和相关基因家族的系统发育分析，作者探讨了豆科根瘤菌固氮结瘤的演化过程，揭示了一次或两次向根瘤菌结瘤共生体的转换，而后又发生了多次丢失。综上，本文的研究结果为进一步研究豆科植物的形态和功能演化提供了基础。