Phylogenomic conflict in Moraceae: Evidence for pervasive introgression and incomplete lineage sorting

doi:10.1016/j.pld.2026.04.003

Plant Diversity ›› 2026, Vol. 48 ›› Issue (04): 688-703.DOI: 10.1016/j.pld.2026.04.003

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Phylogenomic conflict in Moraceae: Evidence for pervasive introgression and incomplete lineage sorting

Chen-Xuan Yang^a,b,c, Shui-Yin Liu^d, Qin Tian^a,b,c, Wei Gu^a,b,c, Qing Lu^a,b,c, Robert P. Guralnick^e, Gregory W. Stull^f, Heather R. Kates^e, Ryan A. Folk^g, Douglas E. Soltis^e,h, Pamela S. Soltis^e, Elliot M. Gardnerⁱ, Ting-Shuang Yi^a,b,c

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. Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650201, China;
c. Key Laboratory of Plant Diversity and Specialty Crops, Chinese Academy of Sciences, Beijing 100093, China;
d. Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China;
e. Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA;
f. Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington DC 20013, USA;
g. Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA;
h. Department of Biology, University of Florida, Gainesville, FL 32611, USA;
i. Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA

Received:2026-02-01 Revised:2026-04-07 Accepted:2026-04-14 Online:2026-04-21 Published:2026-07-25
Contact: Ting-Shuang Yi,E-mail:tingshuangyi@mail.kib.ac.cn
Supported by:
This research was supported by the Yunnan Revitalization Talent Support Program: Yunling Scholar Project (XDYC-YLXZ-2024-0021), the Basic Research Project of Yunnan Province (No. 202401BC070001), the National Natural Science Foundation of China, key international (regional) cooperative research project (No. 31720103903), the Yunling International High-end Experts Program of Yunnan Province, China (No. YNQR-GDWG-2017-002 and No. YNQR-GDWG-2018-012). We are grateful to the following institutes for providing specimens or silica-dried materials: Herbarium of Kunming Institute of Botany, Chinese Academy of Sciences (KUN); the Germplasm Bank of Wild Species and Molecular Biology Experiment Center, Kunming Institute of Botany, Chinese Academy of Sciences; the herbarium of the California Academy of Sciences; the Missouri Botanical Garden; the New York Botanical Garden; the Ohio State University Herbarium; and the University of Texas Herbarium. We are also grateful to Jia-Jin Wu for help with sampling; to Hua-Feng Wang, Diego F. Morales-Briones, Nelson Zamora Villalobos, Rong Zhang, Hui Liu, Si-Yun Chen, Xiao-Gang Fu, Ying-Ying Yang, and Henrique Borges Zamengo for their generous technical support and valuable assistance; to Shuai Liao for assistance in identifying specimens; and to the iFlora High Performance Computing Center of the Germplasm Bank of Wild Species(iFlora HPC Center of GBOWS, KIB, CAS) for computing. We appreciate the photos provided by Qin Tian of the Honghe Tropical Agriculture Institute of Yunnan, China.

Phylogenomic conflict in Moraceae: Evidence for pervasive introgression and incomplete lineage sorting

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. Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650201, China;
c. Key Laboratory of Plant Diversity and Specialty Crops, Chinese Academy of Sciences, Beijing 100093, China;
d. Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China;
e. Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA;
f. Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington DC 20013, USA;
g. Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA;
h. Department of Biology, University of Florida, Gainesville, FL 32611, USA;
i. Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA

通讯作者: Ting-Shuang Yi,E-mail:tingshuangyi@mail.kib.ac.cn
基金资助:
This research was supported by the Yunnan Revitalization Talent Support Program: Yunling Scholar Project (XDYC-YLXZ-2024-0021), the Basic Research Project of Yunnan Province (No. 202401BC070001), the National Natural Science Foundation of China, key international (regional) cooperative research project (No. 31720103903), the Yunling International High-end Experts Program of Yunnan Province, China (No. YNQR-GDWG-2017-002 and No. YNQR-GDWG-2018-012). We are grateful to the following institutes for providing specimens or silica-dried materials: Herbarium of Kunming Institute of Botany, Chinese Academy of Sciences (KUN); the Germplasm Bank of Wild Species and Molecular Biology Experiment Center, Kunming Institute of Botany, Chinese Academy of Sciences; the herbarium of the California Academy of Sciences; the Missouri Botanical Garden; the New York Botanical Garden; the Ohio State University Herbarium; and the University of Texas Herbarium. We are also grateful to Jia-Jin Wu for help with sampling; to Hua-Feng Wang, Diego F. Morales-Briones, Nelson Zamora Villalobos, Rong Zhang, Hui Liu, Si-Yun Chen, Xiao-Gang Fu, Ying-Ying Yang, and Henrique Borges Zamengo for their generous technical support and valuable assistance; to Shuai Liao for assistance in identifying specimens; and to the iFlora High Performance Computing Center of the Germplasm Bank of Wild Species(iFlora HPC Center of GBOWS, KIB, CAS) for computing. We appreciate the photos provided by Qin Tian of the Honghe Tropical Agriculture Institute of Yunnan, China.

Abstract

Abstract: Although the phylogenetic backbone of Moraceae, an ecologically important angiosperm family in tropical rainforests, has been significantly improved, phylogenetic discordance among nuclear genes and between nuclear and plastid genomes remains common at various phylogenetic depths. However, the patterns and causes of this discordance across the entire family have not been systematically investigated. Here, we reconstructed a comprehensive phylogeny of 319 species of Moraceae using sequences from nuclear and plastid gene datasets to investigate family-wide phylogenetic conflict, identify the evolutionary drivers of conflict, and inform taxonomic revision. Phylogenetic analyses showed general congruence at the section level and above in nuclear datasets, but notable conflicts occurred at several nodes (e.g., Chlorophoreae, Bagassa, and Sloetiopsis). Discordance between nuclear and plastid trees was widespread, especially within the tribes Antiarideae, Artocarpeae, Dorstenieae, and Ficeae. Coalescent simulations and phylogenetic network analyses suggest that the observed discordance arises from a combination of incomplete lineage sorting and ancient hybridization. Based on integrated phylogenetic and morphological evidence, we propose several taxonomic revisions for the family. Overall, this work elucidates the evolutionary history of Moraceae, emphasizing the role of hybridization in its diversification, and provides a robust phylogenetic framework for future research on its classification, biogeography, and diversification.

Key words: Incomplete lineage sorting, Introgression, Moraceae, Phylogenomics, Phylogenetic discordance, Taxonomic revision

摘要： Although the phylogenetic backbone of Moraceae, an ecologically important angiosperm family in tropical rainforests, has been significantly improved, phylogenetic discordance among nuclear genes and between nuclear and plastid genomes remains common at various phylogenetic depths. However, the patterns and causes of this discordance across the entire family have not been systematically investigated. Here, we reconstructed a comprehensive phylogeny of 319 species of Moraceae using sequences from nuclear and plastid gene datasets to investigate family-wide phylogenetic conflict, identify the evolutionary drivers of conflict, and inform taxonomic revision. Phylogenetic analyses showed general congruence at the section level and above in nuclear datasets, but notable conflicts occurred at several nodes (e.g., Chlorophoreae, Bagassa, and Sloetiopsis). Discordance between nuclear and plastid trees was widespread, especially within the tribes Antiarideae, Artocarpeae, Dorstenieae, and Ficeae. Coalescent simulations and phylogenetic network analyses suggest that the observed discordance arises from a combination of incomplete lineage sorting and ancient hybridization. Based on integrated phylogenetic and morphological evidence, we propose several taxonomic revisions for the family. Overall, this work elucidates the evolutionary history of Moraceae, emphasizing the role of hybridization in its diversification, and provides a robust phylogenetic framework for future research on its classification, biogeography, and diversification.

关键词: Incomplete lineage sorting, Introgression, Moraceae, Phylogenomics, Phylogenetic discordance, Taxonomic revision

Chen-Xuan Yang, Shui-Yin Liu, Qin Tian, Wei Gu, Qing Lu, Robert P. Guralnick, Gregory W. Stull, Heather R. Kates, Ryan A. Folk, Douglas E. Soltis, Pamela S. Soltis, Elliot M. Gardner, Ting-Shuang Yi. Phylogenomic conflict in Moraceae: Evidence for pervasive introgression and incomplete lineage sorting[J]. Plant Diversity, 2026, 48(04): 688-703.

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Phylogenomic conflict in Moraceae: Evidence for pervasive introgression and incomplete lineage sorting

Phylogenomic conflict in Moraceae: Evidence for pervasive introgression and incomplete lineage sorting

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