Reconstruct The Phylogeny Of Pteridophytes Based On Different Molecular Characters Of Chloroplast Genes

Pteridophytes are the most primitive group of vascular plants and have special status in the plant kingdom.At present,the taxonomic framework of pteridophytes is clear,but the taxonomic relationship in their basal taxa and higher order groups are still controversial.With the development of sequencing technology,the chloroplast genome has been widely used in study of phylogenetic relationships of plants.Phylogenetic tree constructed by multi-gene tandem is more advantageous than single gene.In this study,the chloroplast complete genome data of 62 species of plants(including 60 Pteridophytes and 2 lycophytes)in the NCBI database were chose,and then 51 chloroplast common coded genes were selected.The chloroplast common genes are connected and base substitutions,indels,second and third base of codon of common genes were extracted.Based on this five different data sets above,MEGA7,PAUP4.0 and MrBayes3.2 softwares are used to construct Maximum Likelihood,Neighbor-Joining,Maximum Parsimony,and Bayesian phylogenetic tree respectively.Phylogenetic relationship of pteridophytes is reconstructed,the characteristics of different methods to construct phylogenetic trees is analyzed and compared,and the effects of different molecular characters on the construction of phylogenetic trees are explored.The main results are as follows:(1)The phylogenetic tree constructed by the four methods shows that most of their topological structures are similar,but the classification relationships of some groups are different.On the topological structure,the Maximum Parsimony trees are more similar to the Bayesian trees,while the Maximum Likelihood trees are more similar to the Neighbor-Joining trees;on basal pteridophytes,the relative positions between Equisetaceae,Ophioglossidae,and Marattiaceae are inconsistent;the Maximum Parsimony trees are similar to the classification relation with the Bayesian trees,which are consistent with the currently recognized pteridophytes molecular classification system;on the higher order group of pteridophytes,the relationship between the Aspleniaceae and other members of the Aspleniineae are unstable;the Bayesian trees obtained from different data sets shows that the Aspleniineae is a monophyletic group,but most of the other three methods trees shows that it is a paraphyletic group;according to the results obtained from different data sets,the Bayesian trees have better branch relationship and rate of support than others methods,and the tree is hardly influenced by the data sets.Moreover,the Bayesian method has better resolution in the case of fast evolution rate,which has lower sensitivity to Long Branch Attraction,and can effectively reduce the influence of Long Branch Attraction.(2)The phylogenetic trees constructed from different data sets show that the phylogenetic tree constructed from gene tandem data set are the best;the phylogenetic trees constructed from the base substitution data set are the most similar to the phylogenetic trees constructed by gene tandem data set;the Maximum Likelihood tree constructed from the base substitution data set are better than the gene tandem data set;the Maximum Likelihood tree and Neighbor-Joining tree constructed by indels molecular characters appear more branches with low rate of support.The Bayesian tree is more effective for inserting / deletion data and obtains the best results.The second base of codon has a poor resolution to the higher order groups of pteridophytes,so it is difficult to get a good topological relationship of phylogenetic tree;the phylogenetic tree constructed by the third base of codon has a certain resolution,but the resolution of some branches is still not clear.It is obviously shows in the relative positions of the Depana,Woodsiaceae,Blechnaceae,and Onocleaceae.