2026-10-13T19:26:47Z https://www.scidb.cn/oai

10.57760/sciencedb.40005 2026-06-16T16:09:09Z

2026-06-16 From phylogenomic backbone to infrageneric classification in Adenophora (Campanulaceae): dense plastid sampling supports an evidence-based infrageneric system doi:10.57760/sciencedb.40005 en A major challenge in contemporary systematics is not only to infer phylogenetic structure, but to translate conflict-rich evolutionary evidence into defensible classification. This problem is especially acute in Adenophora (Campanulaceae), where recent phylogenomic work has clarified the broader generic framework but has not yet yielded an operational infrageneric system. Here, we test whether dense plastid amplicon sampling can provide the intermediate evidential layer needed to connect phylogenomic structure with taxonomic implementation. We generated 136 new genome-skimming datasets and 19,504 newly sequenced plastid amplicon sequences, and analysed 61 plastid hypervariable regions for 691 accessions and 77 plastid coding sequences for 292 accessions. We also developed CotuAmplicon (https://github.com/PhyloAI/CotuAmplicon), a Linux-native, step-by-step workflow for tagged Illumina paired-end amplicon data that standardizes read processing, consensus generation, and species-by-clade membership mapping. Dense amplicon sampling substantially improved species-by-clade resolution across Adenophora and helped bridge the gap between phylogenomic backbone inference and infrageneric classification. Interpreted together with historical classifications, filtered morphology, species-complex evidence, and nomenclatural considerations, the recovered framework supports a broadened circumscription of Adenophora, including the former genus Hanabusaya, and an infrageneric system comprising three subgenera, seven sections within subg. Adenophora, and five well-supported subsections within sect. Adenophora. This framework includes two new subgenera at new rank, three new sections, and the retention or restoration of historically available infrageneric names where they can be linked to stable lineages and implemented nomenclaturally. More broadly, this study shows that amplicon sequencing is most useful not as a replacement for genome-scale phylogenomics, but as a dense membership-mapping layer that makes broad phylogenomic backbones classificatorily operational. It further supports an evidence-chain strategy for formal classification in conflict-rich lineages. amplicon sequencing; CotuAmplicon; species-level membership mapping; evidence-chain; conflict-aware taxonomy Zhaoqian Niu Wang Xiaoman Wang Ling Huang Jiaxin Zhou Shiliang Shi Shuo Cheng Jin Zhu Zhengge Zheng Yunfei Xu Chao Hong Deyuan Liu Binbin EMBARGO https://creativecommons.org/licenses/by-nc-sa/4.0/ dataset Science Data Bank