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）并非单系群的学术难题，新系统共认可6个得到强力支持的单系亚科（monophyletic subfamilies）。

这套全新的分类系统以迄今最全面的豆科系统发育分析（phylogenetic analyses）框架为基础，其数据源于质体matK基因（matK gene）序列，涵盖当前已确认的765个豆科属中的近全部类群（698个属），以及约20%的已知物种（共3696种）。

matK基因区段是豆科类群中测序最为广泛的基因区域，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。本分析解析得到的主要演化支，与其他基于全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更为稀疏。相较于此前利用豆科大尺度系统发育树（phylogenetic tree）解答演化问题的相关研究，本研究的分析更为精进：其一，最大化了属级类群的采样量；其二，基于一套经全面整理、带有凭证标本且经过分类学验证的序列集构建了系统发育树。

本研究获得的系统发育树及基础数据可开放浏览与下载，可为后续依赖系统发育树的分析工作提供便利。

在此，我们提出一套经国际豆科系统学共同体联名认可的全新豆科分类系统，该系统契合学界一致解析得到的系统发育结构，共认可6个亚科：重新界定的云实亚科（Caesalpinioideae DC.）、紫荆亚科（Cercidoideae 豆科系统发育工作组(Legume Phylogeny Working Group)，新等级(stat. nov.)）、甘豆亚科（Detarioideae Burmeist.）、摘亚木亚科（Dialioideae 豆科系统发育工作组(Legume Phylogeny Working Group)，新等级(stat. nov.)）、Duparquetia亚科（Duparquetioideae 豆科系统发育工作组(Legume Phylogeny Working Group)，新等级(stat. nov.)）以及蝶形花亚科（Papilionoideae DC.）。

传统界定的含羞草亚科（Mimosoideae）是嵌套于重新界定后的云实亚科内的独立演化支，待正式发表针对新云实亚科的族级或基于演化支的分类系统前，该类群被非正式称为含羞草演化支。

本研究提供了亚科鉴定检索表、各亚科的诊断特征描述、展示其花与果实多样性的插图，以及按亚科归类的属名录。

这套全新的豆科分类系统代表了国际豆科系统学共同体的共识，兼顾了学术妥协性与实际应用的便利性。