Abstract: RPS4 (ribosomal protein small subunit 4) is one of the primary rRNA-binding proteins that initiate assembly of the 30S subunit in prokaryotes and plant chloroplast. In ferns, RPS4 is encoded by chloroplast gene rps4. Recently polypod ferns have been demonstrated to undergo diversification in the Cretaceous after the rise of angiosperms. To further test this proposal, an adaptive evolutionary analysis was performed on the rps4 gene sequences of 23 types of ferns, under the branch model, site model and branch-site model developed by Yang et al. The results from branch model indicated that 4 lineages were under the positive selection with ω>1. No positive selected sites were detected under the branch-site model, however, 85 negative selected sites were identified under the site model. There were only 2 lineages from Polypodiaceous ferns which are under positive selection. And this finding was constant with the proposal we had mentioned before. Moreover, the fact that rps4 was under highly negative selection indicated that the function and structure of rps4 had been almost stabilized.

Key words: Monilophytes, RPS4, rps4 gene, adaptive selection