A phylogenomic analysis and revised infrageneric classification of Thesium (Santalaceae)

------------------------------------------------------------------------------------------ A phylogenomic analysis and revised infrageneric classification of Thesium (Santalaceae) ------------------------------------------------------------------------------------------ Natasha Lombard Foundational Biodiversity Science Division, National Herbarium, South African National Biodiversity Institute, Private Bag X101, Pretoria 0001, South Africa Department of Botany and Plant Biotechnology, University of Johannesburg, PO Box 524, Auckland Park 2006, South Africa [e-mail] Félix Forest Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom [e-mail] Olivier Maurin Meise Botanic Garden, Meise, 1860 Belgium Fédération Wallonie-Bruxelles, Service Général de l’Enseignement supérieur & de la Recherche scientifique, Bruxelles, 1080 Belgium Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom [e-mail] M. Marianne le Roux Foundational Biodiversity Science Division, National Herbarium, South African National Biodiversity Institute, Private Bag X101, Pretoria 0001, South Africa Department of Botany and Plant Biotechnology, University of Johannesburg, PO Box 524, Auckland Park 2006, South Africa [e-mail] Marge Poma, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom Abigail Carruthers Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom Ben-Erik van Wyk Department of Botany and Plant Biotechnology, University of Johannesburg, PO Box 524, Auckland Park 2006, South Africa [e-mail] ------------------------------------------------------------------------------------------ AUTHOR CONTRIBUTIONS BVW, FF, MLR and NL designed the study. BVW, FF, MLR, NL and OM sourced samples, AC and MAPA conducted lab work, and OM data analyses. FF, MLR, NL and OM interpreted the results. NL wrote most the manuscript, with input from BVW, FF, MLR and OM and all authors provided comments. ------------------------------------------------------------------------------------------ ABSTRACT A phylogenomic analysis and revised infrageneric classification of Thesium (Santalaceae) is presented based on targeted enrichment using the Angiosperms353 probe set. This first targeted sequencing study includes 138 samples representing 106 species (approximately 32% of the genus). Our results provide substantially improved resolution compared to previous studies that utilized only a few gene regions, with an almost fully supported backbone topology. Thesium (including Austroamericium, Chrysothesium, Kunkeliella, and Thesidium) is confirmed as monophyletic and sister to a clade containing Lacomucinaea and Osyridicarpos. We recognize six monophyletic subgenera with full or strong support: T. subg. Hagnothesium, T. subg. Thesium, T. subg. Spinosa (newly described), T. subg. Discothesium (with revised circumscription), T. subg. Frisea, and T. subg. Psilothesium. We found T. subg. Discothesium as previously delineated to be paraphyletic and described a new subgenus, T. subg. Spinosa, to ensure monophyly of all subgenera. We formally recognised 18 sections in Thesium, of which nine are newly described and two are raised from lower ranks. Our phylogenetic clades show a strong biogeographic signal and despite sporadic morphological synapomorphies, most subgenera and sections can be distinguished by of combination of their distribution and morphology. We provide the first genetic evidence of potential hybridization in Thesium paving the way for further exploration of this long-hypothesised compounding factor. This study provides a robust framework for future taxonomic, biogeographic, and evolutionary studies of this diverse and problematic genus. ------------------------------------------------------------------------------------------ KEYWORDS Angiosperms353, hemiparasites, hybridization, Thesiaceae, Santalales, systematics ------------------------------------------------------------------------------------------《百蕊草属（Thesium，檀香科Santalaceae）的系统基因组学分析及属下分类修订》 娜塔莎·隆巴德 南非国家生物多样性研究所国家标本馆基础生物多样性科学部，南非比勒陀利亚Private Bag X101，邮编0001 约翰内斯堡大学植物与植物生物技术系，南非奥克兰公园PO Box 524，邮编2006 邮箱：[e-mail] 费利克斯·福雷斯特 英国皇家植物园邱园，英国萨里郡里士满TW9 3AE 邮箱：[e-mail] 奥利维耶·莫兰 比利时梅斯梅斯植物园，比利时梅斯1860 瓦隆-布鲁塞尔联邦政府高等教育与科学研究总服务处，比利时布鲁塞尔1080 英国皇家植物园邱园，英国萨里郡里士满TW9 3AE 邮箱：[e-mail] M.玛丽安娜·勒鲁 南非国家生物多样性研究所国家标本馆基础生物多样性科学部，南非比勒陀利亚Private Bag X101，邮编0001 约翰内斯堡大学植物与植物生物技术系，南非奥克兰公园PO Box 524，邮编2006 邮箱：[e-mail] 玛吉·波马 英国皇家植物园邱园，英国萨里郡里士满TW9 3AE 阿比盖尔·卡鲁瑟斯 英国皇家植物园邱园，英国萨里郡里士满TW9 3AE 本-埃里克·范·维克 约翰内斯堡大学植物与植物生物技术系，南非奥克兰公园PO Box 524，邮编2006 邮箱：[e-mail] ### 作者贡献 BVW、FF、MLR与NL负责研究设计；BVW、FF、MLR、NL与OM负责样本采集；Abigail Carruthers与Marge Poma开展实验室工作，OM负责数据分析；FF、MLR、NL与OM负责结果解读；NL撰写论文主体部分，BVW、FF、MLR与OM提供修改建议，全体作者均对稿件进行审阅并提出修订意见。 ### 摘要 本研究利用被子植物353基因探针集（Angiosperms353）开展靶向富集测序，完成了百蕊草属（Thesium，檀香科Santalaceae）的系统基因组学分析与属下分类修订。这是针对该属的首个靶向测序研究，共纳入138份样本，对应106个物种（约占该属总物种数的32%）。相较于以往仅利用少数基因区域的研究，本研究的结果分辨率得到显著提升，拓扑结构主干几乎完全得到支持。百蕊草属（包含Austroamericium、Chrysothesium、Kunkeliella及Thesidium）被证实为单系类群，其姐妹演化支包含Lacomucinaea与Osyridicarpos两个属。我们确认6个单系亚属，均获得充分或强支持：哈格诺百蕊草亚属（T. subg. Hagnothesium）、百蕊草亚属（T. subg. Thesium）、新描述的棘刺百蕊草亚属（T. subg. Spinosa）、经修订范围界定的盘状百蕊草亚属（T. subg. Discothesium）、弗里西亚百蕊草亚属（T. subg. Frisea）以及裸萼百蕊草亚属（T. subg. Psilothesium）。本研究发现原界定范围的盘状百蕊草亚属为并系类群，因此新建立棘刺百蕊草亚属（T. subg. Spinosa）以确保所有亚属均为单系类群。我们正式认可百蕊草属内的18个组，其中9个为新建立的组，2个由更低分类等级提升而来。本研究的系统发育演化支呈现出显著的生物地理信号，尽管存在零星的形态共衍征，但大多数亚属和组可通过其分布区与形态特征的组合进行区分。我们首次提供了百蕊草属内存在潜在杂交现象的遗传学证据，为这一长期被推测的复合影响因子的进一步研究铺平了道路。本研究为这一多样且分类学棘手的属的后续分类学、生物地理学及演化生物学研究提供了坚实的框架。 ### 关键词 被子植物353基因探针集（Angiosperms353）、半寄生植物（hemiparasites）、杂交（hybridization）、百蕊草科（Thesiaceae）、檀香目（Santalales）、系统分类学（systematics）