Impact of incomplete lineage sorting and natural selection on the phylogenetic and taxonomic uncertainties of Aspidistra in Taiwan

Background: The inconsistency between morphological and genetic evidence has consistently presented a challenge in taxonomy. The genus Aspidistra (Asparagaceae) comprises perennial herbs found primarily in eastern and southeastern Asia. This group has received limited systematic study despite the continuous publications of new species in recent years. Most species of Aspidistra have narrow distributions, and a large number of them are endemic. This study examined five Aspidistra species in Taiwan, which are part of a total of around 200 Aspidistra species found throughout Asia. In this study, we sampled all Aspidistra taxa in Taiwan to explore their phylogenetic relationships. We utilized transcriptome data for phylogenetic reconstruction and employed gene genealogy interrogation (GGI) to identify conflicts between gene trees and the species tree. Additionally, we tested nine evolutionary scenarios for these taxa by incorporating population-level genetic data. We obtained a well-supported species tree but also detected a high proportion of incomplete lineage sorting (ILS) phenomena. Results: The results revealed that the two varieties of A. daibuensis failed to form monophyly despite morphological similarities. However, about 20.8% of the genes did not reject the topology that grouped them together. Among these genes, we identified positive signals in photosynthesis-related genes, suggesting their similarities arose from convergent evolution. Furthermore, we used a phylogenetic signal test to identify the evolutionary meaningful traits and found that the stigma width can reflect the phylogenetic relationships among these species. Conclusions: Our study provides new insights into the evolutionary dynamics and taxonomy of Aspidistra in Taiwan, revealing key genetic and morphological patterns shaping species divergence. Phylogenetic analysis revealed substantial ILS, with numerous genes supporting alternative tree topologies. Despite morphological similarities, A. daibuensis var. daibuensis and var. longkiauensis exhibit non-monophyletic relationships, challenging their previous classification. Genes associated with chloroplastic function and photomorphogenic adaptation suggest convergent evolution. Moreover, stigma shape emerges as a robust diagnostic trait for species delimitation. These findings underscore the complex interplay of genetics, morphology, and adaptation, emphasizing the need for further integrative research.