Phylogenomic Evidence Of Bryophytes\u27 Monophyly Using Complete And Incomplete Data Sets From Chloroplast Proteomes

It is well recognized that bryophytes form the basal clade of land plants. However, the paraphyletic or monophyletic origin of bryophytes remains controversial. To get new insight into bryophytes\u27 relationship we analyzed four data sets, 1 complete (common orthologous protein sequences; COPs) and 3 incomplete (COPs + 1, COPs + 1 + 3 and COPs + 1 + 3 + 2 data sets with 0.16%, 3.2% and 3.77% missing data, respectively) from chloroplast proteomes, representing 1 charophycean alga (outgroup), 5 bryophytes, 4 pteridophytes and 6 gymnosperms. Maximum likelihood analyses under cpREV model of all four data sets showed monophyly of bryophytes with 100% bootstrap support. Further, sister relationship of mosses and liverworts has been inferred with strong bootstrap support in all data sets. Although all incomplete data sets have gradually increasing missing data, the trees obtained from them have higher levels of bootstrap support for most of the nodes in comparison to the tree from complete data set. This study also demonstrated the importance of using longer sequences even with missing data for phylogeny reconstruction. © 2011 Society for Plant Biochemistry and Biotechnology