We reconstructed a phylo
genetic tree of Chinese vascular plants (Tracheophyta) using sequences of the chloroplast
genes
atpB,
matK,
ndhF, and
rbcL and mitochondrial
matR. We produced a matrix comprising 6098 species and including 13 695 DNA sequences, of which 1803 were newly
generated. Our taxonomic sampling spanned 3114
genera representing 323 families of Chinese vascular plants, covering more than 93% of all
genera known from China. The comprehensive large phylo
geny supports most relationships among and within families recognized by recent molecular phylo
genetic studies for lycophytes, ferns (monilophytes), gymnosperms, and angiosperms. For angiosperms, most families in Angiosperm Phylo
geny Group IV are supported as monophyletic, except for a paraphyletic Dipterocarpaceae and Santalaceae. The infrafamilial relationships of several large families and monophyly of some large
genera are well supported by our dense taxonomic sampling. Our results showed that two species of
Eberhardtia are sister to a clade formed by all other taxa of Sapotaceae, except
Sarcosperma. We have made our phylo
geny of Chinese vascular plants publically available for the creation of subtrees via SoTree (
http://www.darwintree.cn/flora/index.shtml), an automated phylo
geny assembly tool for ecologists.