Royal Botanic Gardens, Kew, Richmond TW9 3DS, UK.
Department of Plant Biology and Ecology, University of Seville, 41012, Spain.
Ann Bot. 2023 Apr 28;131(4):635-654. doi: 10.1093/aob/mcad018.
Among the numerous pantropical species of the yam genus, Dioscorea, only a small group occurs in the Mediterranean basin, including two narrow Pyrenean endemics (Borderea clade) and two Mediterranean-wide species (D. communis and D. orientalis, Tamus clade). However, several currently unrecognized species and infraspecific taxa have been described in the Tamus clade due to significant morphological variation associated with D. communis. Our overarching aim was to investigate taxon delimitation in the Tamus clade using an integrative approach combining phylogenomic, spatial and morphological data.
We analysed 76 herbarium samples using Hyb-Seq genomic capture to sequence 260 low-copy nuclear genes and plastomes, together with morphometric and environmental modelling approaches.
Phylogenomic reconstructions confirmed that the two previously accepted species of the Tamus clade, D. communis and D. orientalis, are monophyletic and form sister clades. Three subclades showing distinctive geographic patterns were identified within D. communis. These subclades were also identifiable from morphometric and climatic data, and introgression patterns were inferred between subclades in the eastern part of the distribution of D. communis.
We propose a taxonomy that maintains D. orientalis, endemic to the eastern Mediterranean region, and splits D. communis sensu lato into three species: D. edulis, endemic to Macaronesia (Canary Islands and Madeira); D. cretica, endemic to the eastern Mediterranean region; and D. communis sensu stricto, widespread across western and central Europe. Introgression inferred between D. communis s.s. and D. cretica is likely to be explained by their relatively recent speciation at the end of the Miocene, disjunct isolation in eastern and western Mediterranean glacial refugia and a subsequent westward recolonization of D. communis s.s. Our study shows that the use of integrated genomic, spatial and morphological approaches allows a more robust definition of species boundaries and the identification of species that previous systematic studies failed to uncover.
在众多泛热带薯蓣属植物中，仅有一小部分存在于地中海盆地，包括两个狭窄的比利牛斯山特有种（Borderea 分支）和两个分布广泛的地中海种（D. communis 和 D. orientalis，Tamus 分支）。然而，由于与 D. communis 相关的显著形态变异，Tamus 分支中已经描述了几个目前尚未被识别的物种和种下分类单元。我们的总体目标是使用结合系统发育、空间和形态数据的综合方法来研究 Tamus 分支中的分类单元划定。
我们使用 Hyb-Seq 基因组捕获分析了 76 个标本，共测序了 260 个低拷贝核基因和质体基因组，同时还采用了形态计量学和环境建模方法。
系统发育重建证实，Tamus 分支中之前接受的两个种，D. communis 和 D. orientalis，是单系的，形成姐妹分支。在 D. communis 中鉴定出具有独特地理模式的三个亚分支。这些亚分支也可以从形态计量学和气候数据中识别出来，并推断出 D. communis 分布东部的亚分支之间存在基因渗入。
我们提出了一种分类法，维持了地中海东部特有种 D. orientalis，并将 D. communis s.l.分为三个种：D. edulis，特有于马卡罗尼西亚（加那利群岛和马德拉群岛）；D. cretica，特有于东地中海地区；以及 D. communis s.s.，广泛分布于西欧和中欧。推断出 D. communis s.s.和 D. cretica 之间的基因渗入可能是由于它们在中新世末期相对较近的分化、东地中海和西地中海冰川避难所的间断隔离以及随后 D. communis s.s.的向西再殖民化。我们的研究表明，使用综合基因组、空间和形态学方法可以更稳健地定义物种边界，并识别出以前系统学研究未能发现的物种。
