Data_Sheet_1_Evolution in the Model Genus Antirrhinum Based on Phylogenomics of Topotypic Material.docx

Researchers in phylogenetic systematics typically choose a few individual representatives of every species for sequencing based on convenience (neighboring populations, herbarium specimens, samples provided by experts, garden plants). However, few studies are based on original material, type material or topotypic material (living specimens from the locality where the type material was collected). The use of type or topotypic material in phylogenetic studies is paramount particularly when taxonomy is complex, such as that of Antirrhinum (Plantaginaceae). In this paper, we used topotypic materials of Antirrhinum at the species level (34 species proposed by previous authors), 87 specimens representing the species distributions and >50,000 informative nucleotide characters (from ∼4,000 loci) generated by the genotyping-by-sequencing (GBS) technique: (i) to test two explicit taxonomic hypotheses widely followed by local taxonomic treatments; (ii) to robustly estimate phylogenetic relationships; (iii) to investigate the evolution of key morphological characters and biogeographic centers of differentiation. Two GBS phylogenies based on two datasets (87 localities and 34 topotypic specimens) revealed that: (1) Sutton’s (1988) taxonomic account is the most congruent with phylogenetic results, whereas division of Antirrhinum into three major clades disagrees with Rothmaler’s (1956) infrageneric classification; (2) monophyly of populations currently included in the same species is primarily supported; (3) the historically recognized Antirrhinum majus group is not monophyletic; (4) sister-group relationships are robust for eight species pairs; (5) the evolutionary radiation of 26 species since the Pliocene is underpinned given a high rate of diversification (0.54 spp. Myr–1); (6) a geographic pattern of speciation is reconstructed, with northern Iberia as the center of early diversification followed by more recent speciation in southeastern Iberia; and (7) multiple acquisitions of key taxonomic characters in the course of Antirrhinum diversification are strongly supported, with no evidence of hybridization between major clades. Our results also suggest incipient speciation in some geographic areas and point to future avenues of research in evolution and systematics of Antirrhinum.

在系统发育系统学领域，研究者们通常基于便利性原则（如邻近种群、标本馆标本、专家提供的样本、园艺植物）选取每个物种的少数个体进行测序。然而，基于原始材料、模式材料或典型材料的少数学术研究却基于上述原则。在系统分类复杂的情况下，如龙牙草属（Plantaginaceae）的分类，使用模式或典型材料在系统发育研究中尤为重要。在本研究中，我们采用了龙牙草属的典型材料（根据前人提出的34个物种），选取了代表物种分布的87个标本，以及通过基因分型测序（GBS）技术生成的超过50,000个具有信息量的核苷酸位点（来自约4,000个位点），旨在：（一）检验两种被地方分类处理广泛采用的明确分类假设；（二）稳健地估计系统发育关系；（三）研究关键形态学特征和分化生物地理中心的进化；（四）基于两个数据集（87个地点和34个典型标本）构建了两种GBS系统发育树，揭示了以下结果：（1）Sutton（1988年）的分类描述与系统发育结果最为一致，而将龙牙草属划分为三个主要类群与Rothmaler（1956年）的亚属分类相悖；（2）目前被归入同一物种的种群的单系性主要得到支持；（3）历史上认可的龙牙草属大组并非单系；（4）八个物种对的姐妹群关系稳健；（5）自上新世以来，26个物种的辐射进化在高度多样性的背景下得到证实（0.54物种/百万年）；（6）重建了物种形成的地理模式，早期多样性中心位于伊比利亚北部，随后在伊比利亚东南部出现更近期的物种形成；（7）在龙牙草属的多样性过程中，关键分类特征的多次获得得到强有力的支持，且无主要类群间杂交的证据；（8）我们的结果还表明，某些地理区域出现了初始物种形成，并为龙牙草属的进化和系统学研究指出了未来的研究方向。