Abstract:To further understand the molecular adaptation linked to fern radiation, evolutionary patterns of the rbcL sequences in the family Pteridaceae were examined using random-site and branch-site models along with the estimated time-scale of pteridaceous phylogeny. By comparing Models M1a/M2a and M7/M8 under random-site models, six amino acid sites (149I, 251M, 255V, 282F, 359S and 375F) were found to be positively selected. The site 282F plays an important role in maintaining Rubisco function. Under branch-site models, no adaptive site was identified in the epiphytic clade, whereas two sites(230A and 247C) were detected in the ceratopteridoid clade. In comparison with shade conditions, aquatic habitats may have imposed stronger selection on the pteridaceous RbcL subunits. Moreover, the phylogenetic tree reconstructed with uncorrelated lognormal distributed relaxed clock model shows that the pteridaceous fern radiations occurred during the Oligocene, suggesting possible roles played by the Paleocene-Eocene Thermal Maximum. These results provide new insights into how leptosporangiate ferns response to the terrestrial ecosystem changes caused by the rise of angiosperms.