WANG, XIAO-QUAN, DAVID C. TANK*, AND TAO SANG. Laboratory of Sytematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China, , Department of Botany and Plant Pathology, Michigan State University, East Lansing, MI 48824. - Phylogeny and divergence times in Pinaceae: evidence from three genomes.
In Pinaceae, the chloroplast, mitochondrial, and nuclear genomes are
paternally, maternally, and biparentally inherited, respectively.
Examining congruence and incongruence of gene phylogenies among the
three genomes should provide insights into phylogenetic relationships
within the family. Here we studied intergeneric relationships of
Pinaceae using sequences of the chloroplast matK gene, the
mitochondrial gene encoding subunit 5 of NADH dehydrogenase
(nad5), and the low-copy nuclear gene encoding 4-coumarate :
coenzyme A ligase (4CL). The 4CL gene may exist as a single copy in
some species of Pinaceae, but constitutes a small gene family with two
or three members in others. Duplication and deletion of the 4CL gene
occurred at a tempo such that paralogous loci are maintained within
but not between genera. Exons of the 4CL gene have diverged
approximately twice as fast as the matK gene and five times
more rapidly than the nad5 gene. The partition-homogeneity
test indicates that the three data sets are homogeneous. A combined
analysis of the three gene sequences generated a well resolved and
strongly supported phylogeny. The combined phylogeny, which is
topologically congruent with the three individual gene trees based on
the Templeton test, is likely to represent the organismal phylogeny of
Pinaceae. This phylogeny agrees, to a certain extent, with previous
phylogenetic hypotheses based on morphological, anatomical, and
immunological data. Disagreement between the previous hypotheses and
the three-genome phylogeny suggests that morphology of both vegetative
and reproductive organs has undergone convergent evolution within the
pine family. The strongly supported monophyly of Nothotsuga
longibracteata, Tsuga mertensiana, and Tsuga
canadensis on all three gene phylogenies provides evidence against
previous hypotheses of intergeneric hybrid origins of Nothotsuga
longibracteata and Tsuga mertensiana. Divergence times of
the genera were estimated based on sequence divergence of the
matK gene, and they correspond well with the fossil record.
Key words: chloroplast matK, gene duplication and deletion, mitochondrial nad5, molecular clock, nuclear gene 4CL, Pinaceae