Resolving the tribal affiliation of the East Asia clade: phylogenomic evidence for its inclusion into Komarovieae (Apiaceae: Apioideae)

Abstract Background and Aims The East Asia (or Physospermopsis) clade persists as one of the most taxonomically recalcitrant lineages in Apiaceae subfamily Apioideae. Despite previous delimitation efforts, myriad phylogenetic issues remain unsettled spanning from chaotic interrelationships amongst constituent genera to affiliations with tribe Komarovieae. Methods In this study, we sampled 75 accessions from the East Asia clade, Komarovieae and nine other tribes/clades of Apioideae, and leveraged integrated nuclear (262 genes) and plastid genomic data (81 loci) from genome skimming to further our understanding of this challenging group. Both coalescent-based and concatenation-based approaches were employed. Key Results Phylogenetic trees inferred from nuclear genes and chloroplast data yielded largely congruent topologies, with affiliations among previously recognized tribes and other major clades being well-resolved. However, monophyly of the East Asia clade is robustly rejected; instead, analyses provide strong evidence that the East Asia clade is paraphyletic, with a monophyletic Komarovieae arising from within. Most genera within the East Asia clade are not resolved as monophyletic, with their members widely intermingled. By integrating these phylogenomic results with previously available morphological and phylogenetic evidence, we reinstate the genus Dactylaea to accommodate Sinocarum schizopetalum and discuss implications for taxonomic changes to problematic species previously recognized in Acronema, Hymenidium, Pimpinella, and Tongoloa. Accordingly, we merge the East Asia clade into an expanded Komarovieae, which now comprises representatives of 21 genera. Conclusion These results provide a robust phylogenetic framework for this systematically challenging group, while also highlighting the need for comprehensive taxonomic revision of the many non-monophyletic genera within the East Asia clade.