We reconstructed a phylogenetic 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 samp
ling spanned 3114 genera represen
ting 323 fami
lies of Chinese vascular plants, covering more than 93% of all genera known from China. The comprehensive large phylogeny supports most relationships among and within fami
lies recognized by recent molecular phylogenetic studies for lycophytes, ferns (monilophytes), gymnosperms, and angiosperms. For angiosperms, most fami
lies in Angiosperm Phylogeny Group IV are supported as monophyletic, except for a paraphyletic Dipterocarpaceae and Santalaceae. The infrafami
lial relationships of several large fami
lies and monophyly of some large genera are well supported by our dense taxonomic samp
ling. 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 phylogeny of Chinese vascular plants pub
lically available for the creation of subtrees via SoTree (
http://www.darwintree.cn/flora/index.shtml), an automated phylogeny assembly tool for ecologists.