Ringelberg Jens J, Koenen Erik J M, Iganci João R, de Queiroz Luciano P, Murphy Daniel J, Gaudeul Myriam, Bruneau Anne, Luckow Melissa, Lewis Gwilym P, Hughes Colin E
Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008, Zurich, Switzerland University of Zurich Zurich Switzerland.
Present address: Evolutionary Biology & Ecology, Université Libre de Bruxelles, Faculté des Sciences, Campus du Solbosch - CP 160/12, Avenue F.D. Roosevelt, 50, 1050 Bruxelles, Belgium Université Libre de Bruxelles Bruxelles Belgium.
PhytoKeys. 2022 Aug 22;205:3-58. doi: 10.3897/phytokeys.205.85866. eCollection 2022.
Subfamily Caesalpinioideae with ca. 4,600 species in 152 genera is the second-largest subfamily of legumes (Leguminosae) and forms an ecologically and economically important group of trees, shrubs and lianas with a pantropical distribution. Despite major advances in the last few decades towards aligning genera with clades across Caesalpinioideae, generic delimitation remains in a state of considerable flux, especially across the mimosoid clade. We test the monophyly of genera across Caesalpinioideae via phylogenomic analysis of 997 nuclear genes sequenced via targeted enrichment (Hybseq) for 420 species and 147 of the 152 genera currently recognised in the subfamily. We show that 22 genera are non-monophyletic or nested in other genera and that non-monophyly is concentrated in the mimosoid clade where ca. 25% of the 90 genera are found to be non-monophyletic. We suggest two main reasons for this pervasive generic non-monophyly: (i) extensive morphological homoplasy that we document here for a handful of important traits and, particularly, the repeated evolution of distinctive fruit types that were historically emphasised in delimiting genera and (ii) this is an artefact of the lack of pantropical taxonomic syntheses and sampling in previous phylogenies and the consequent failure to identify clades that span the Old World and New World or conversely amphi-Atlantic genera that are non-monophyletic, both of which are critical for delimiting genera across this large pantropical clade. Finally, we discuss taxon delimitation in the phylogenomic era and especially how assessing patterns of gene tree conflict can provide additional insights into generic delimitation. This new phylogenomic framework provides the foundations for a series of papers reclassifying genera that are presented here in (ALS) 14 Part 1, for establishing a new higher-level phylogenetic tribal and clade-based classification of Caesalpinioideae that is the focus of ALS14 Part 2 and for downstream analyses of evolutionary diversification and biogeography of this important group of legumes which are presented elsewhere.
云实亚科约有4600种，分属于152个属，是豆科（Leguminosae）的第二大亚科，形成了一个在生态和经济方面都很重要的树木、灌木和藤本植物类群，分布于泛热带地区。尽管在过去几十年里，在使云实亚科各属与分支相对应方面取得了重大进展，但属的界定仍处于相当不稳定的状态，尤其是在含羞草类分支中。我们通过对420个物种和该亚科目前认可的152个属中的147个属进行靶向富集测序（Hybseq），对997个核基因进行系统发育基因组分析，来检验云实亚科各属的单系性。我们发现有22个属不是单系的，或者嵌套在其他属中，并且非单系性集中在含羞草类分支中，在该分支中，90个属中约25%被发现不是单系的。我们提出了这种普遍存在的属非单系性的两个主要原因：（i）广泛的形态趋同，我们在此记录了一些重要性状的趋同情况，特别是在界定属时历史上强调的独特果实类型的反复演化；（ii）这是由于缺乏泛热带分类学综合研究以及先前系统发育研究中的采样不足，导致未能识别跨越旧世界和新世界的分支，或者相反，未能识别非单系的跨大西洋属，而这两者对于界定这个大型泛热带分支中的属至关重要。最后，我们讨论了系统发育基因组时代的分类单元界定，特别是评估基因树冲突模式如何能为属的界定提供更多见解。这个新的系统发育基因组框架为一系列重新分类属的论文奠定了基础，这些论文将在（ALS）14第1部分中呈现，为建立一个基于系统发育部落和分支的云实亚科新的高级分类体系奠定基础，这是ALS14第2部分的重点，也为在其他地方呈现的对这一重要豆科植物类群的进化多样化和生物地理学的下游分析奠定基础。
