Phylogenomic insights into Adenophora and its allies (Campanulaceae): Revisiting generic delimitation and hybridization dynamics

doi:10.1016/j.pld.2025.05.010

Plant Diversity ›› 2025, Vol. 47 ›› Issue (04): 576-592.DOI: 10.1016/j.pld.2025.05.010

• Articles • Previous Articles Next Articles

Phylogenomic insights into Adenophora and its allies (Campanulaceae): Revisiting generic delimitation and hybridization dynamics

Xiao-Hua Lin (林晓华)^a,b,c, Si-Yu Xie (解思宇)^a,b,c, Dai-Kun Ma (马代锟)^a,b,d, Shuai Liao (廖帅)^e, Bin-Jie Ge (葛斌杰)^f, Shi-Liang Zhou (周世良)^a,b, Liang Zhao (赵亮)^c, Chao Xu (徐超)^a,b, De-Yuan Hong (洪德元)^a,b, Bin-Bin Liu (刘彬彬)^a,b

a. Key Laboratory of Systematic and Evolutionary Botany/State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China;
b. China National Botanical Garden, Beijing 100093, China;
c. College of Life Sciences & Herbarium of Northwest A&F University, Northwest A&F University, Yangling 712100, Shaanxi, China;
d. University of Chinese Academy of Sciences, Beijing 100049, China;
e. South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China;
f. Eastern China Conservation Center for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China

Received:2025-03-06 Revised:2025-05-01 Online:2025-08-13 Published:2025-08-13
Contact: Liang Zhao (赵亮),E-mail:biology_zhaoliang@126.com;Chao Xu (徐超),E-mail:xuchao@ibcas.ac.cn;De-Yuan Hong (洪德元),E-mail:hongdy@ibcas.ac.cn;Bin-Bin Liu (刘彬彬),E-mail:liubinbin@ibcas.ac.cn
Supported by:
This work was supported by the National Natural Science Foundation of China (grant numbers 32270216 and 32000163 to B.B.L.), the Youth Innovation Promotion Association CAS (2023086 to B.B.L.), and the Biological Resources Programme, Chinese Academy of Sciences (CAS-TAX-24-013 to B.B.L.).

Phylogenomic insights into Adenophora and its allies (Campanulaceae): Revisiting generic delimitation and hybridization dynamics

a. Key Laboratory of Systematic and Evolutionary Botany/State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China;
b. China National Botanical Garden, Beijing 100093, China;
c. College of Life Sciences & Herbarium of Northwest A&F University, Northwest A&F University, Yangling 712100, Shaanxi, China;
d. University of Chinese Academy of Sciences, Beijing 100049, China;
e. South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China;
f. Eastern China Conservation Center for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China

通讯作者: Liang Zhao (赵亮),E-mail:biology_zhaoliang@126.com;Chao Xu (徐超),E-mail:xuchao@ibcas.ac.cn;De-Yuan Hong (洪德元),E-mail:hongdy@ibcas.ac.cn;Bin-Bin Liu (刘彬彬),E-mail:liubinbin@ibcas.ac.cn
基金资助:
This work was supported by the National Natural Science Foundation of China (grant numbers 32270216 and 32000163 to B.B.L.), the Youth Innovation Promotion Association CAS (2023086 to B.B.L.), and the Biological Resources Programme, Chinese Academy of Sciences (CAS-TAX-24-013 to B.B.L.).

Abstract

Abstract: Hybridization and introgression have long obscured relationships within Adenophora and its relatives, complicating generic delimitation. Leveraging deep genome skimming (DGS) data, we generated a large dataset, including thousands of single-copy nuclear (SCN) genes and plastomes, to untangle this reticulate history. Specifically, 9.89 terabytes (TB) of DGS data from 165 samples—representing 48 species and 13 subspecies of Adenophora (out of ca. 72 species) plus 24 outgroup species—yielded 1506 SCN genes and 77 plastid coding sequences. Tree-like phylogenies inferred with both coalescent- and concatenation-based methods revealed pronounced gene tree heterogeneity. Subsequent analysis showed that incomplete lineage sorting contributed minimally to this discordance; instead, hybridization and introgression were the primary drivers of early diversification. Integrating phylogenomic, morphological, and geographic evidence, we propose a revised generic framework for this group. Adenophora is expanded to include Campanula delavayi and the Korean Peninsula endemic genus Hanabusaya. We also recommend reinstating Hyssaria as a distinct Central Asian genus and introducing two new genera, Boreoasia and Rosomala.

Key words: Campanula, Hanabusaya, Network, Polyphyly, Reticulation, Taxonomy

摘要： Hybridization and introgression have long obscured relationships within Adenophora and its relatives, complicating generic delimitation. Leveraging deep genome skimming (DGS) data, we generated a large dataset, including thousands of single-copy nuclear (SCN) genes and plastomes, to untangle this reticulate history. Specifically, 9.89 terabytes (TB) of DGS data from 165 samples—representing 48 species and 13 subspecies of Adenophora (out of ca. 72 species) plus 24 outgroup species—yielded 1506 SCN genes and 77 plastid coding sequences. Tree-like phylogenies inferred with both coalescent- and concatenation-based methods revealed pronounced gene tree heterogeneity. Subsequent analysis showed that incomplete lineage sorting contributed minimally to this discordance; instead, hybridization and introgression were the primary drivers of early diversification. Integrating phylogenomic, morphological, and geographic evidence, we propose a revised generic framework for this group. Adenophora is expanded to include Campanula delavayi and the Korean Peninsula endemic genus Hanabusaya. We also recommend reinstating Hyssaria as a distinct Central Asian genus and introducing two new genera, Boreoasia and Rosomala.

关键词: Campanula, Hanabusaya, Network, Polyphyly, Reticulation, Taxonomy

Xiao-Hua Lin (林晓华), Si-Yu Xie (解思宇), Dai-Kun Ma (马代锟), Shuai Liao (廖帅), Bin-Jie Ge (葛斌杰), Shi-Liang Zhou (周世良), Liang Zhao (赵亮), Chao Xu (徐超), De-Yuan Hong (洪德元), Bin-Bin Liu (刘彬彬). Phylogenomic insights into Adenophora and its allies (Campanulaceae): Revisiting generic delimitation and hybridization dynamics[J]. Plant Diversity, 2025, 47(04): 576-592.

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Phylogenomic insights into Adenophora and its allies (Campanulaceae): Revisiting generic delimitation and hybridization dynamics

Phylogenomic insights into Adenophora and its allies (Campanulaceae): Revisiting generic delimitation and hybridization dynamics

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