A robust phylogenomic framework supports a revised intrafamilial classification of Urticaceae

doi:10.1016/j.pld.2025.12.003

Plant Diversity ›› 2026, Vol. 48 ›› Issue (02): 289-306.DOI: 10.1016/j.pld.2025.12.003

• Articles • Previous Articles Next Articles

A robust phylogenomic framework supports a revised intrafamilial classification of Urticaceae

Xiao-Gang Fu^a,b, Jie Liu^a,c, Richard I. Milne^d, Alex K. Monro^e, Shui-Yin Liu^a, Qin Tian^f, Gregory W. Stull^g, Amos Kipkoech^a,b, Ting-Shuang Yi^a, De-Zhu Li^a,f, Zeng-Yuan Wu^a

a. Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
b. University of Chinese Academy of Sciences, Beijing 100049, China;
c. Key Laboratory for Plant and Biodiversity of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
d. Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JH, UK;
e. Identification & Naming Department, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK;
f. Center for Interdisciplinary Biodiversity Research & College of Forestry, Shandong Agricultural University, Tai’an 271018, China;
g. Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA

Received:2025-03-20 Revised:2025-12-03 Online:2026-05-19 Published:2026-03-25
Contact: Ting-Shuang Yi,E-mail:tingshuangyi@mail.kib.ac.cn;De-Zhu Li,E-mail:dzl@mail.kib.ac.cn;Zeng-Yuan Wu,E-mail:wuzengyuan@mail.kib.ac.cn
Supported by:
This research was funded by the National Natural Science Foundation of China (42171071), Yunnan Fundamental Research Projects (202401AT070190), the Top-notch Young Talents Project of Yunnan Provincial “Ten Thousand Talents Program” (YNWR-QNBJ-2020-293), CAS “Light of West China” Program, Key Research Program of Frontier Sciences, CAS (ZDBS-LY-7001), the Yunnan Revitalization Talent Support Program: Yunling Scholar Project (XDYC-YLXZ-2024-0021), the Science and Technology Basic Resources Investigation Program of China (No. 2019FY100900), and the National Natural Science Foundation of China, key international (regional) cooperative research project (No. 31720103903). Additionally, Jie Liu and Zeng-Yuan Wu were supported by the China Scholarship Council (202304910135 and 202304910138) for a one-year study at the University of Toronto, Canada. We extend our deepest gratitude to Profs. Wen-Tsai Wang (in memoriam) and Chia-Jui Chen of the Institute of Botany, Chinese Academy of Sciences, for their invaluable contributions and assistance in the often-challenging task of specimen identification. We are also grateful to Mr. Xue-Wen Liu and Mr. Tao Liu for their years of immense effort in field sampling. We thank the following herbaria and their dedicated curators and staff for permission to collect materials: Royal Botanic Gardens, Kew; Florida Museum of Natural History; Royal Botanic Garden Edinburgh; Kunming Institute of Botany, Chinese Academy of Sciences; Naturalis Biodiversity Center; The New York Botanical Garden; Institute of Botany, Chinese Academy of Sciences; and Universidade Federal de Pernambuco. We are deeply grateful to Nicholas J. Turland for his valuable comments regarding the new tribal name. Additionally, we are indebted to Prof. Gudrun Kadereit, Dr. Diego F. Morales-Briones, Dr. Luo Chen, Dr. Rahaingoson Fabien Robert, Ms. Ying Zhao, Ms. Li-Juan Deng, Ms. Yin-Lei Li, Mr. Wei Gu, and Mr. Zu-Chang Xu for their invaluable technical support and assistance. Molecular experiments were conducted at the Laboratory of Molecular Biology and data analysis was facilitated by the iFlora HPC Center (iFlora High-Performance Computing Center), Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences.

A robust phylogenomic framework supports a revised intrafamilial classification of Urticaceae

Xiao-Gang Fu^a,b, Jie Liu^a,c, Richard I. Milne^d, Alex K. Monro^e, Shui-Yin Liu^a, Qin Tian^f, Gregory W. Stull^g, Amos Kipkoech^a,b, Ting-Shuang Yi^a, De-Zhu Li^a,f, Zeng-Yuan Wu^a

a. Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
b. University of Chinese Academy of Sciences, Beijing 100049, China;
c. Key Laboratory for Plant and Biodiversity of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
d. Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JH, UK;
e. Identification & Naming Department, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK;
f. Center for Interdisciplinary Biodiversity Research & College of Forestry, Shandong Agricultural University, Tai’an 271018, China;
g. Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA

通讯作者: Ting-Shuang Yi,E-mail:tingshuangyi@mail.kib.ac.cn;De-Zhu Li,E-mail:dzl@mail.kib.ac.cn;Zeng-Yuan Wu,E-mail:wuzengyuan@mail.kib.ac.cn
基金资助:
This research was funded by the National Natural Science Foundation of China (42171071), Yunnan Fundamental Research Projects (202401AT070190), the Top-notch Young Talents Project of Yunnan Provincial “Ten Thousand Talents Program” (YNWR-QNBJ-2020-293), CAS “Light of West China” Program, Key Research Program of Frontier Sciences, CAS (ZDBS-LY-7001), the Yunnan Revitalization Talent Support Program: Yunling Scholar Project (XDYC-YLXZ-2024-0021), the Science and Technology Basic Resources Investigation Program of China (No. 2019FY100900), and the National Natural Science Foundation of China, key international (regional) cooperative research project (No. 31720103903). Additionally, Jie Liu and Zeng-Yuan Wu were supported by the China Scholarship Council (202304910135 and 202304910138) for a one-year study at the University of Toronto, Canada. We extend our deepest gratitude to Profs. Wen-Tsai Wang (in memoriam) and Chia-Jui Chen of the Institute of Botany, Chinese Academy of Sciences, for their invaluable contributions and assistance in the often-challenging task of specimen identification. We are also grateful to Mr. Xue-Wen Liu and Mr. Tao Liu for their years of immense effort in field sampling. We thank the following herbaria and their dedicated curators and staff for permission to collect materials: Royal Botanic Gardens, Kew; Florida Museum of Natural History; Royal Botanic Garden Edinburgh; Kunming Institute of Botany, Chinese Academy of Sciences; Naturalis Biodiversity Center; The New York Botanical Garden; Institute of Botany, Chinese Academy of Sciences; and Universidade Federal de Pernambuco. We are deeply grateful to Nicholas J. Turland for his valuable comments regarding the new tribal name. Additionally, we are indebted to Prof. Gudrun Kadereit, Dr. Diego F. Morales-Briones, Dr. Luo Chen, Dr. Rahaingoson Fabien Robert, Ms. Ying Zhao, Ms. Li-Juan Deng, Ms. Yin-Lei Li, Mr. Wei Gu, and Mr. Zu-Chang Xu for their invaluable technical support and assistance. Molecular experiments were conducted at the Laboratory of Molecular Biology and data analysis was facilitated by the iFlora HPC Center (iFlora High-Performance Computing Center), Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences.

Abstract

Abstract: Over the past decade, phylogenomics has significantly enhanced our understanding of relationships among numerous angiosperm lineages. However, comprehensive phylogenetic studies combining broad sampling of both genomic sequences and taxa within the nettle family (Urticaceae) are still lacking. Here, we reconstructed the phylogeny of Urticaceae (345 species across 89% of accepted genera) using concatenated and coalescent analyses from plastome and nuclear ribosomal DNA sequences. Different plastid datasets and tree inference methods yielded a consistent phylogenetic backbone, with 98% of nodes achieving > 90% bootstrap support — a significant improvement compared to 54% of nodes in the latest published phylogenetic study of Urticaceae. Plastid and nuclear phylogenetic relationships were largely congruent, with several exceptions that warrant further study. In the context of the updated phylogenetic relationships, we propose dividing the family into seven tribes that correspond to seven major clades or subclades, including a newly established tribe, Sarcochlamydeae stat. nov. Our phylogenetic analysis indicates that Debregeasia and Phenax are non-monophyletic. By combing morphological, molecular and distributional evidence, we describe a new genus Chiajuia gen. nov. Additionally, we propose synonymizing the following genera: Cypholophus (to Boehmeria), Haroldiella (to Pilea), Hemistylus, Neodistemon, Rousselia (all to Pouzolzia), Hesperocnide (to Urtica), and Pellionia (to Elatostema), while recognizing Elatostematoides, Gonostegia, Leptocnide, Margarocarpus, Scepocarpus, and Sceptrocnide as distinct genera. This robust phylogenomic framework and revised classification lays a foundation for future studies on the evolution and ecology of Urticaceae. The approach applied here may also serve as an important reference for other large plant families in angiosperms.

Key words: Chiajuia, Intrafamilial classification, Phylogenomics, Plastome, Sarcochlamydeae, Urticaceae

摘要： Over the past decade, phylogenomics has significantly enhanced our understanding of relationships among numerous angiosperm lineages. However, comprehensive phylogenetic studies combining broad sampling of both genomic sequences and taxa within the nettle family (Urticaceae) are still lacking. Here, we reconstructed the phylogeny of Urticaceae (345 species across 89% of accepted genera) using concatenated and coalescent analyses from plastome and nuclear ribosomal DNA sequences. Different plastid datasets and tree inference methods yielded a consistent phylogenetic backbone, with 98% of nodes achieving > 90% bootstrap support — a significant improvement compared to 54% of nodes in the latest published phylogenetic study of Urticaceae. Plastid and nuclear phylogenetic relationships were largely congruent, with several exceptions that warrant further study. In the context of the updated phylogenetic relationships, we propose dividing the family into seven tribes that correspond to seven major clades or subclades, including a newly established tribe, Sarcochlamydeae stat. nov. Our phylogenetic analysis indicates that Debregeasia and Phenax are non-monophyletic. By combing morphological, molecular and distributional evidence, we describe a new genus Chiajuia gen. nov. Additionally, we propose synonymizing the following genera: Cypholophus (to Boehmeria), Haroldiella (to Pilea), Hemistylus, Neodistemon, Rousselia (all to Pouzolzia), Hesperocnide (to Urtica), and Pellionia (to Elatostema), while recognizing Elatostematoides, Gonostegia, Leptocnide, Margarocarpus, Scepocarpus, and Sceptrocnide as distinct genera. This robust phylogenomic framework and revised classification lays a foundation for future studies on the evolution and ecology of Urticaceae. The approach applied here may also serve as an important reference for other large plant families in angiosperms.

关键词: Chiajuia, Intrafamilial classification, Phylogenomics, Plastome, Sarcochlamydeae, Urticaceae

Xiao-Gang Fu, Jie Liu, Richard I. Milne, Alex K. Monro, Shui-Yin Liu, Qin Tian, Gregory W. Stull, Amos Kipkoech, Ting-Shuang Yi, De-Zhu Li, Zeng-Yuan Wu. A robust phylogenomic framework supports a revised intrafamilial classification of Urticaceae[J]. Plant Diversity, 2026, 48(02): 289-306.

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A robust phylogenomic framework supports a revised intrafamilial classification of Urticaceae

A robust phylogenomic framework supports a revised intrafamilial classification of Urticaceae

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