Phylogenomics provides comprehensive insights into the phylogenetic and evolutionary uncertainty in Allium subgenus Alpinoprasum (Amaryllidaceae).
TL;DR
The findings illustrate how the interplay of ILS, polyploidy, and localized hybridization has shaped plant diversity in the Hengduan Mountains and adjacent regions, offering an integrative perspective on the maintenance of phylogenetic signals in rapid alpine radiations.
Abstract
Phylogenomics, with its abundant informative sites, provides a powerful approach to resolving complex phylogenetic relationships and rapid radiation. Studies on Allium subgenus Alpinoprasum (Amaryllidaceae) have long been hindered by unresolved relationships and complex radiation. In this study, transcriptomic and low-coverage genome skimming data were integrated to investigate the relationships and evolution of this group. We compiled 35 morphological, phenological, and ecologicalcharactersand extracted 1,811 low-copy nuclear genes (LCGs) along with 112 plastid genes for phylogenetic reconstruction. Phylogenetic discordance and radiation were investigated using multiple methods, such as coalescent simulations, MSCquartets, and D-statistics. Our results suggest that the phylogenetic conflict is highly consistent with extensive incomplete lineage sorting (ILS), which can be plausibly interpreted through a scenario of rapid budding speciation, particularly within the A. sikkimense complex. Within this subgenus, budding speciation emerges as a highly reasonable working hypothesis to explain how numerous narrowly endemic species rapidly diversified around a widespread progenitor. During this radiation, polyploidization may have played a significant stabilizing role by potentially facilitating lineage sorting and establishing reproductive barriers, thereby modulating the effects of ILS. Furthermore, hybridization and introgression may have exhibited localized dual effects: directional introgression appeared to enhance local topological stability in specific lineages, while simultaneously contributing to increased phylogenetic complexity at terminal nodes. Overall, our findings illustrate how the interplay of ILS, polyploidy, and localized hybridization has shaped plant diversity in the Hengduan Mountains (HDMs) and adjacent regions, offering an integrative perspective on the maintenance of phylogenetic signals in rapid alpine radiations.