Reported in the present paper is a robust chloroplast matK gene phylogeny of Taxaceae,
Cephalotaxaceae and Podocarpaceae represented by 10 species of seven genera, with three species of
the Pinaceae as outgroups. The matk length of the 13 species ranges from 1488 bp to 1548 bp,
which results from indels, in particular, 1-bp(base pair) insertion near the 3’ end of the gene in
some groups. A 27 bp deletion was found at the nucleotide position 213 from the 5’ end of the matk
gene of Pseudotaxus chienii. The aligned sequences used in PAUP and MEGA analyses were 1568
bp and 1494 bp respectively. In the matK gene, the rates of variation at the first, second and third
codon positions are similar although the mean frequency of synonymous substitution is approximately
twice as high as that of nonsynonymous substitution. Branch-and-Bound search found only one most
parsimonious tree (tree length = 895, CI = 0.850, RI = 0. 876), in which all clades were strongly
supported by bootstrap test. According to the tree, Taxaceae and Cephalotaxaceae are monophyletic
groups, and the sister group relationship between the two families was confirmed. Taxus is closely
related to Pseudotaxus while Torreya is the sister group of Amentotaxus. In addition, the close rela-
tionship between Nageia and Podocarpus was resolved. The present study supports the generic sta-
tus of Pseudotaxus and Amentotaxus in point of cladistic analysis and genetic distance, but contra-
dicts the establishment of the family Nageiaceae.
