Data from: A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny

The classification of the legume family proposed here addresses the long-known non-monophyly of the traditionally recognised subfamily Caesalpinioideae, by recognising six robustly supported monophyletic subfamilies. This new classification uses as its framework the most comprehensive phylogenetic analyses of legumes to date, based on plastid matK gene sequences, and including near-complete sampling of genera (698 of the currently recognised 765 genera) and ca. 20% (3696) of known species. The matK gene region has been the most widely sequenced across the legumes, and in most legume lineages, this gene region is sufficiently variable to yield well-supported clades. This analysis resolves the same major clades as in other phylogenies of whole plastid and nuclear gene sets (with much sparser taxon sampling). Our analysis improves upon previous studies that have used large phylogenies of the Leguminosae for addressing evolutionary questions, because it maximises generic sampling and provides a phylogenetic tree that is based on a fully curated set of sequences that are vouchered and taxonomically validated. The phylogenetic trees obtained and the underlying data are available to browse and download, facilitating subsequent analyses that require evolutionary trees. Here we propose a new community-endorsed classification of the family that reflects the phylogenetic structure that is consistently resolved and recognises six subfamilies in Leguminosae: a recircumscribed Caesalpinioideae DC., Cercidoideae Legume Phylogeny Working Group (stat. nov.), Detarioideae Burmeist., Dialioideae Legume Phylogeny Working Group (stat. nov.), Duparquetioideae Legume Phylogeny Working Group (stat. nov.), and Papilionoideae DC. The traditionally recognised subfamily Mimosoideae is a distinct clade nested within the recircum-scribed Caesalpinioideae and is referred to informally as the mimosoid clade pending a forthcoming formal tribal and/or clade-based classification of the new Caesalpinioideae. We provide a key for subfamily identification, descriptions with diagnostic charactertistics for the subfamilies, figures illustrating their floral and fruit diversity, and lists of genera by subfamily. This new classification of Leguminosae represents a consensus view of the international legume systematics community; it invokes both compromise and practicality of use.本研究提出的豆科（Leguminosae）分类系统，解决了长期以来学界公认的传统界定云实亚科（Caesalpinioideae）所存在的非单系性问题，新体系认可了6个支持率极高的单系亚科。该全新分类框架以迄今最全面的豆科系统发育分析（phylogenetic analyses）为基础，数据来源于质体matK基因序列（plastid matK gene sequences），涵盖了当前已确认的765个属中的近全部属（共698个），以及约20%的已知物种（总计3696个）。matK基因区域是豆科物种中测序最广泛的基因区域，且在多数豆科演化支（clade）中，该区域具有足够的变异度以生成支持度良好的演化支。本分析所解析得到的主要演化支，与其他基于完整质体和核基因集的系统发育研究结果一致，尽管后者的类群采样密度要低得多。相较于此前利用豆科大型系统发育研究解答演化问题的相关工作，本研究的分析更为完善：其最大化了属级类群的采样量，并基于一套经过全面整理、带有凭证标本且经分类学验证的序列集构建了系统发育树。所获得的系统发育树及基础数据均可浏览和下载，可为后续需要使用演化树的分析研究提供便利。在此，我们提出了一套获得国际豆科系统学界认可的全新分类系统，该体系反映了学界一致解析得到的系统发育结构，将豆科划分为6个亚科：重新界定的云实亚科（Caesalpinioideae DC.）、紫荆亚科（Cercidoideae Legume Phylogeny Working Group，stat. nov.）、决明亚科（Detarioideae Burmeist.）、盘壳栎亚科（Dialioideae Legume Phylogeny Working Group，stat. nov.）、杜帕尔克亚科（Duparquetioideae Legume Phylogeny Working Group，stat. nov.）以及蝶形花亚科（Papilionoideae DC.）。传统上界定的含羞草亚科（Mimosoideae）是嵌入重新界定后的云实亚科内的独立演化支，在新的云实亚科正式发布基于族和/或演化支的分类系统前，该类群暂被非正式称为含羞草演化支（mimosoid clade）。我们提供了亚科识别检索表、各亚科的诊断特征描述、展示其花与果实多样性的图解，以及按亚科归类的属列表。这套全新的豆科分类体系代表了国际豆科系统学界的共识观点，兼顾了学术妥协性与实际应用的便利性。