Phylogeny and evolutionary history of subfamily Microsoroideae (Polypodiaceae): new insights from plastome and nuclear gene data

Subfamily Microsoroideae represent the third largest subfamily within Polypodiaceae. However, due to insufficient sampling, limited informative sites and considerable morphological diversification, the generic-level classification within Microsoroideae has been contentious. Furthermore, the origin and diversification history of this subfamily remain unclear. With the most extensive sampling to date, we provide a comprehensive and systematic elucidation of the evolutionary history of Microsoroideae. Our key findings include the following: (1) Microsoroideae can be divided into 5 superclades and 17 fully supported clades based on the plastome dataset, while nuclear gene dataset supports the division of Microsoroideae into 6 superclades and 19 monophyletic clades; (2) significant cytonuclear discordance and gene tree conflicts exist within Microsoroideae and can be explained by incomplete lineage sorting-particularly regarding the conflicting phylogenetic positions of Bosmania, and introgressive hybridization; (3) molecular dating consistently indicates that Microsoroideae originated in the early Eocene and began to diversify around the middle Eocene; (4) ancestral area reconstruction supports the Asian continent as both the origin and diversification centres of Microsoroideae; (5) paleoenvironmental changes, geological events and a series of dispersal and vicariance events are the primary drivers of the current distribution of Microsoroideae; (6) diversification rate analyses reveal that abrupt changes in the diversification rate of the maternal lineages of Microsoroideae are associated with the Middle Eocene Climatic Optimum; (7) nuclear gene data show that the diversification rate of the Lecanopteris clade is significantly higher than other clades, which is linked to its unique ant-associated traits; and (8) the diversification rates of Microsoroideae inferred from nuclear gene data exhibit different trends compared with those inferred from plastome data. This discrepancy may arise from frequent hybridization and polyploidization, which buffer environmental pressures. The findings not only have significant implications for the classification of Microsoroideae but also provide insights for the adaptive evolution of ferns.