Analysis on the phylogenetic classification and molecular evolution of the matK gene in 40 fern species

The matK gene is the only group Ⅱ intron maturase encoded in the chloroplast genome. It is the potentiality left untested that applying the matK gene as the molecular marker reconstructs credible fern phylogenetic trees under estimated timescale. Using the relaxed molecular clock model, positive selection model, and co-evolutionary analysis, we attempted to unravel the evolutionary pattern of the matK gene. Results showed that matK had certain application value in the phylogenetic study of ferns, and the reliability of the phylogenetic tree was significantly enhanced when combined with rbcL and psaA. The study also indicated a few positively selected amino-acid sites in the MATK protein. Multiple pairs of amino-acid sites in the MATK protein evolved to form a co-evolutionary network. The modification of the MATK protein by site adaptation and the protein intra-network may be important factors that benefited the adaptive evolution of ferns under the change in photosynthetic environment after the rise of angiosperms.