2026-10-13T17:42:38Z https://www.scidb.cn/oai

10.57760/sciencedb.44967 2026-08-03T17:25:47Z

2026-08-03 When stable trees are not enough: conflict-aware infrageneric classification in Photinia (Maleae, Rosaceae) doi:10.57760/sciencedb.44967 en In phylogenomic studies of species-rich plant groups, stable summary trees do not automatically translate into defensible formal classifications when gene histories, plastid histories, morphology, species labels, and nomenclature are discordant. Evergreen Photinia sensu stricto (s.s.) provides a suitable case, because its generic boundary has been clarified, whereas its infrageneric classification remains complicated by historical names, species complexes, and cytonuclear conflict. We evaluated whether a conflict-aware infrageneric system can be implemented by integrating nuclear phylogenomics, complete plastome comparison, PhyParts and Quartet Sampling conflict analyses, species-complex audit, morphology, geography, and type-based nomenclatural assessment. The sampling included 51 ingroup accessions representing 23 species of Photinia s.s. and 26 outgroup taxa. Three nuclear orthology datasets, containing 502, 696, and 874 orthologs, were analysed using concatenation and coalescent approaches. Nuclear analyses repeatedly recovered five candidate lineages: an early-diverging P. davidiana–P. undulata lineage and four post-davidiana lineages. However, conflict analyses showed that several backbone nodes and species-complex regions were conflict-rich, especially the P. glabra–P. prunifolia complex, whereas most species-level instability was internal to candidate lineages. Morphological and geographical evidence did not provide single-character diagnoses, but supported practical diagnosis through repeated character combinations. We therefore recognize two subgenera and four sections in Photinia s.s.: subg. Davidianae, subg. Photinia, sect. Photinia, sect. Serratifoliae, sect. Integrifoliae, and sect. Loriformes. This classification separates lineage recovery from rank implementation and treats conflict as an explicit decision boundary rather than as either a reason for naming every clade or for abandoning formal classification more generally in conflict-rich and taxonomically difficult plant lineages. cytonuclear discordance; gene-history discordance; nomenclature; phylogenomics; Quartet Sampling; species complex Zheng Yawen Huang Jiaxin Huang Juelin Xu Chao Yang Tiantian Cheng Jin Wang Jinghong Huang Jian Liu Binbin EMBARGO https://creativecommons.org/licenses/by-sa/4.0/ dataset Science Data Bank