全 文 ：Received 17 Jun. 2003 Accepted 16 Aug. 2003
Supported by the Knowledge Innovation Program of the Chinese Academy of Sciences (KSCX2-1-106B).
* Author for correspondence. E-mail: .
http://www.chineseplantscience.com
Acta Botanica Sinica
植 物 学 报 2004, 46 (2): 171-179
Molecular Phylogeny of Section Parrya of Pinus (Pinaceae) Based on
Chloroplast matK Gene Sequence Data
ZHANG Zhi-Yong1,2, LI De-Zhu1*
(1. Laboratory of Plant Biodiversity and Biogeography, Kunming Institute of Botany,
The Chinese Academy of Sciences, Kunming 650204, China;
2. Agricultural College, Jiangxi Agricultural University, Nanchang 330045, China)
Abstract: The molecular phylogenetics of sect. Parrya Myre of Pinus L. was analyzed based on
chloroplast matK gene sequence data. The section was resolved as paraphyletic because members of the
sect. Strobus were nested within a clade composed by the Asian members of the section, including the
Vietnamese P. krempfii Lecomte, which was strongly supported with a bootstrap value of 92%. In this
topology, the three sampled species of sect. Strobus formed a strongly supported monophyletic group,
while their relationships of Asian species of sect. Parrya were not clear. P. krempfii was grouped with P.
gerardiana Wall. ex D. Don with low bootstrap support. The relationships among the Asian members of the
sect. Parrya, i.e. P. bungeana Zucc. ex Loud., P. gerardiana and the recently described endangered pine, P.
squamata X. W. Li, was not resolved, although the monophyly of the three pines was strongly supported in
the combined analysis of four cpDNA sequences. The topology of the neighbor joining tree revealed an
assemblage of the American members of the section, which also appeared in the majority rule tree with
weak bootstrap support. However, this assemblage was not resolved in the consensus tree of the
parsimonious analysis. The American subsect. Balfourianae Engelm. formed a weakly supported group
including P. aristata Engelm., while the relationships among and within the other two American subsections,
Cembroides Englem. and Rzedowskianae Carv., were not resolved, as the members of them formed a
polytomy in the consensus tree of the parsimonious analysis. The biogeographical implications of the
results are also discussed in this paper.
Key words: sect. Parrya ; Pinus ; molecular phylogeny; matK gene
Pinus L. (Pinaceae) is the largest genus of conifers and
a widespread genus of trees (sometimes shrubs) in the
Northern Hemisphere. Because of their diversity, in addi-
tion to their ecological importance as a major component of
many temperate forests and economical importance as a
source of timber, pines received much attention to their
taxonomy and phylogeny (Shaw, 1914; Pilger, 1926; Mirov,
1967; Little and Critchfield, 1969; van der Burgh, 1973;
Farjon, 1984; 1996; Schirone et al., 1991; Piovesan, 1993;
Price et al., 1998; Liston et al., 1999; Wang et al., 1999).
However, most studies were concentrated on subgen. Pinus,
or the hard pines (Li, 1997) and/or the sect. Strobus of the
subgen. Strobus with a few samples in sect. Parrya (Wang
et al., 1999). In contrast, sect. Parrya Mayr received less
attention. Bailey (1970) and Malusa (1992) studied two
American subsections of it, respectively. Zhang et al. (2003)
studied systematic position of the Chinese endemic spe-
cies P. squamata. As a very heterogeneous section, Parrya
comprises several subsections in different taxonomic treat-
ments of Pinus (Shaw, 1914; Pilger,1926; Little and
Critchfield, 1969; van der Burgh, 1973; Farjon, 1984; 1996;
Price et al., 1998). The common characters (maybe a
symplesiomorphy) among species of sect. Parrya are only
found in the wood anatomy: ray tracheids with smooth
walls and ray cells with small pits (Shaw, 1914; Mirov, 1967;
Farjon, 1984). In Shaw’s (1914) classification, species of
sect. Parrya were recognized to be included in the subsec-
tion of Paracembra, which comprised three groups, Group
Gerardianae, Group Balfourianae and Group Cembroides.
In comparison with Shaw’s system, Pilger’s classification
shows some changes in the arrangement of sect. Parrya
(named as sect. Paracembra in original literature). P.
krempfii, which is one of the most morphologically unique
species in Pinus, was added and placed close to P.
balfouriana and P. aristata. Little and Critchfield (1969)
arranged these pines in their classification of Pinus in a
way very similar to that of Shaw (1914), while they placed
P. krempfii in a independent subgenus, subgen.
Ducampopinus (A. Cheval) de Ferré rather than in the
subgen. Strobus. The classification of van der Burgh (1973)
Acta Botanica Sinica 植物学报 Vol.46 No.2 2004172
differed significantly in structure from that of Little and
Critchfield (1969). In his system, the sect. Parrya was di-
vided into three subsections: Balfourianae (including P.
krempfii), Gerardianae and Cembroides. This treatment
of sect. Parrya was followed by Farjon (1984) with some
amendments. Farjon (1984) pointed out that sect. Parrya
was very heterogeneous, which was divided into six
subsections, i.e. Krempfianae, Balfourianae, Aristatae,
Gerardianae, Nelsoniae and Cembroides. This classifica-
tion was later revised (Farjon, 1996), with a distinct change
which placed P. rzedowskii as a monotypic subsection in
sect. Parrya. Price et al. (1998) evaluated all data available
to them and proposed a comprehensive system of pines in
which sect. Parrya was treated to be comprised of subsec-
tions of Balfourianae, Krempfianae, Cembroides,
Rzedowskianae and Gerardianae. Little data was avail-
able for the newly discovered Chinese species P. squamata
X. W. Li at that time, which was tentatively placed in
subsect. Gerardianae with an annotation of probability of
change to be a new subsection.
Increasing studies especially evidence from molecular
systematics demonstrated that sect. Parrya was
paraphyletic (Strauss and Doerksen, 1990; Govindaraju et
al., 1992; Wang and Szmidt, 1993; Price et al., 1998; Liston
et al., 1999; Wang et al., 1999). However, the subsectional
relationships were not well resolved because of insuffi-
cient samples (Strauss and Doerksen, 1990; Govindaraju et
al., 1992; Wang and Szmidt, 1993; Wang et al., 1999) or for
the high levels of divergence of sequences (Liston et al.,
1999). The chloroplast matK gene sequence has been found
to be more variable than other coding cpDNA sequences
tested (Wolfe, 1991). Wang et al. (1999) used matK com-
bined with other three cpDNA sequences to reconstruct
phylogenetic relationships of Eurasian pines, but only five
species of two subsections in Parrya were sampled in their
analysis. In this study, we sampled most species of sect.
Parrya representing all subsections described by previ-
ous authors and some little known species such as P.
rzedowskii, P. nelsonii and P. squamata. Our main objec-
tives in this study were: (1) to provide additional informa-
tion for the assessment of relationships among subsec-
tions and species in sect. Parrya using matK gene sequence
data; and (2) to study the phylogenetic relationships of
several little known taxa in the light of molecular
phylogenetics based matK gene divergence.
1 Materials and Methods
1.1 Species sampled
Twenty-one species were included in this study
(Table 1), including three species of sect. Strobus, 15 spe-
cies of sect. Parrya representing all subsections and three
species of subgen. Pinus as outgroups. Because section
Strobus was a well monophyly in previous studies (Strauss
and Doerksen, 1990; Liston et al., 1999; Wang et al., 1999),
only three representatives were sampled in this study.
Vouchers are deposited in herbarium of Kunming Institute
of Botany, The Chinese Academy of Sciences except for
those whose DNA samples were provided by Dr. A. LISTON
of the Oregon State University, USA. The matK sequences
of 11 species were downloaded from GenBank, others were
sequenced during this study.
1.2 DNA isolation, PCR amplification and sequencing
Silica-gel-dried leaves or leaves from herbarium speci-
mens were used for genomic DNA isolation. Part of DNA
samples were from Dr. Aaron Liston. Genomic DNA was
isolated from needles using a modified CTAB procedure of
Doyle and Doyle (1987). The primers for matK were the
same as those used by Wang et al. (1999). The PCR reac-
tion volumes (20 mL) contained 1.5 U of AmpliTaq DNA
polymerase (Perkin-Elmer), Replitherm TM buffer, 1.5 mmol/L
MgCl2, 1 mmol/L dNTP, 0.15 mmol/L primer and 25-60 ng of
sample DNA. PCR reactions were performed in a GeneAmp
9600 (Perkin-Elmer, Applied Biosystems). PCR amplifica-
tion was carried out at 94 ℃ for initial denaturation, fol-
lowed by 30 cycles of denaturation at 94 ℃ for 45 s, primer
annealing at 58 ℃ for 50 s, an extension at 72 ℃ for 80 s,
and a termination at 72 ℃ for 5 min. PCR products were
purified by Watson’s purification kit prior to being
sequenced.
Double-stranded purified PCR products were sequenced
by using the Dideoxy Chain Termination method with an
ABI PRISMTM Bigdye Terminator Cycle Sequencing Ready
Reaction Kit and AmpliTaq DNA polymerase FS (Perkin-
Elmer, Norfolk, Connecticut). Reactions and programs were
chosen accord ing to recommendat ions o f the
manufacturers, with slight modification in some cases.
Samples were electrophoresed on an ABI 310 Genetic Ana-
lyzer (Applied Biosystems Inc.).
1.2.1 Phylogenetic analyses DNA sequences were
edited and aligned using SeqMan and Megalign
(DNASTAR), and adjusted manually where necessary. In
all phylogenetic analyses, characters were weighted
equally. Maximum parsimony (MP) analysis was performed
using PAUP 4.0b (Swofford 2001) treating gaps as the fifth
character. We used the heuristic search options with 1 000
random replications of stepwise data addition and TBR
branch-swapping. Tree fit measures from the MP analysis
were calculated using consistency (CI) and retention (RI)
ZHANG Zhi-Yong et al.: Molecular Phylogeny of Section Parrya of Pinus (Pinaceae) Based on Chloroplast matK Gene Sequence Data 173
indices. A genetic distance tree was also constructed by
using the neighbor joining (NJ) method (Swofford, 2001).
2 Results
2.1 Sequences analysis
The overall characteristics of pines’ matK gene were
discussed by Wang et al. (1999). The results showed that
the matK sequences analyzed in their study had a distinctly
higher evolutionary rate than rbcL sequence within subgen.
Pinus. In addition, the variation of matK in Pinus was even
higher than that in some noncoding regions of cpDNA.
However, the matK diverged at a rate very similar to rbcL
within their samples of subgen. Strobus. In our study the
average divergence for matK within sect. Parrya was 0.007
(Juke-Cantor distance), a little higher than the average di-
vergence within subgen. Strobus. No alignment gaps were
found among the taxa of sect. Parrya. The aligned se-
quences have 937 characters, among them 63 are variable
and 43 are parsimony-informative characters.
2.2 Phylogenetic analyses
A strict consensus tree of four most parsimonious trees
resulted from the unweighted parsimony analysis is shown
in Fig.1. The monophyly of subgen. Strobus was strongly
supported. However, within the sect. Parrya, only the
American subsect. Balfourianae, including P. aristata,
formed a weakly supported clade with a bootstrap value of
54%. The sampled species of sect. Strobus nested in a well
supported clade comprise Asian members of sect. Parrya
(92%, bootstrap value). Within this topology, P. krempfii
was unexpectedly grouped with P. gerardiana, but with
low bootstrap support (61%). The remaining species of sect.
Parrya all from North America, formed a polytomy with
little resolution.
The topology of the majority rule tree (Fig. 2) was slightly
different from the strict consensus tree. The monophyly of
subgen. Strobus, and a clade comprised Asian members of
sect. Parrya and sect. Strobus were resolved with strong
bootstrap support. All American species of sect. Parrya
formed a poorly resolved clade with low bootstrap support
(only 53%). Again, the three sampled species of sect.
Strobus was strongly supported as monophyletic but
nested within a clade comprised Asian members of Parrya.
The monophyly of subsect. Balfourianae was weakly sup-
ported with a bootstrap value of 54%. P. rzedowskii was
grouped with P. monophylla with low bootstrap support
(less than 50%). The relationships among members of
subsect. Cembroides were still unclear on the majority rule
tree. Again, because sect. Strobus was nested a clade
Table 1 List of species sampled, system of classification followed to Price et al. (1998)
Subgen. Sect. and subsect. Species
GenBank
Voucher information
accession No.
Strobus Lemmon Sect. Strobus
Subsect. Cembrae Lordon Pinus koraiensis Siebold et Zuccarini ABO19834*
Subsect. Strobi P. armandii Franchet ABO19841*
P. wallichiana Jackson ABO19838*
Sect. Parrya Mayr
Subsect. Balfourianae Engelmann P. aristata Engelmann ABO19842*
P. balfouriana Balfour ABO19843*
P. longaeva Bailey AY313930 DSG-03199
Subsect. Gerardianae Loudon P. bungeana Zuccarini ex Loudon ABO19845*
P. gerardiana Wallich ex D. Don ABO19844*
P. squamata X. W. Li AF473563 Zhang 001
Subsect. Cembroides Engelm. P. cembroides Zuccarini AY313928 Zhang 003
P. quadrifolia Parlatore AY313935 Zhang 004
P. maximartinezii Rzedoski AY313931 Zhang 005
P. remota (Little) Bailey AY313936 Zhang 002
P. monophylla Torrey et Frémont AY313932 DSG-02999
P. pinceana Gordon AY313934 DSG-07199
P. nelsonii Shaw AY313933 DSG-10798
Subsect. Krempfianae P. krempfii Lecomte ABO19831*
Little et Critchfield
Subsect. Rzedowskianae Carvajal P. rzedowskii Madrigal et Caballero AY313937 EAB-94
Pinus (outgroups) P. massoniana Lambert ABO19852*
P. tabulaeformis Carrière ABO19853*
P. yunnanensis Franchet ABO19847*
*, downloaded from GenBank.
Acta Botanica Sinica 植物学报 Vol.46 No.2 2004174
comprised Asian members of Parrya, the section became
paraphyletic.
The topology of the neighbor joining tree (Fig.3) was
somewhat similar to that of the majority rule tree but with
slightly better resolution. The monophyly of Asian mem-
bers of Parrya together with the three sampled species of
the subgen. Strobus formed a monophyletic clade with a
bootstrap support of 96%. However, the American mem-
bers of the section formed a clade with bootstrap support
below 50%. Within this topology, P. monophylla and P.
rzedowskii grouped together with low bootstrap support
(60%). Except for P. monophylla and P. cembroides, all
other members of subsect. Cembroides formed an assem-
blage with bootstrap support below 50%. The subsect.
Balfourianae was also weakly supported with a bootstrap
value of 51%.
3 Discussion
3.1 Systematic implications
As pointed out by earlier authors (Strauss and Doerksen,
1990; Wang and Szmidt,1993; Wang et al., 1999; Liston et
al., 1999), sect. Parrya was a paraphyletic group basal in
subgen. Strobus. Based on our majority rule tree and NJ
tree, American species of sect. Parrya formed a branch and
may be sister to the clade consisted of Asian members of
sect. Parrya and sect. Strobus. Although the former branch
was weakly supported, the later was strongly supported
with high bootstrap value. Similar topology was also sug-
gested by Wang et al. (1999) but without the samples of
subsect. Cembroides and subsect. Rzedowskianae. On
Fig.1. Strict consensus tree of four most parsimonious trees based on the matK sequences of 21 Pinus species. CI=0.929; RI=0.959;
Tree length is 70 steps. Bootstrap values > 50% are indicated above branches. The species of sect. Parrya are indicated in broadened lines.
ZHANG Zhi-Yong et al.: Molecular Phylogeny of Section Parrya of Pinus (Pinaceae) Based on Chloroplast matK Gene Sequence Data 175
Strauss and Doerksen’s (1990) trees, the representative of
Asian species of sect. Parrya, P. gerardiana, was also
clustered with members of sect. Strobus. All these studies
implied that Asian members of sect. Parrya and sect. Strobus
had close affinities, which may be one of early clades along
with the clade of American species of sect. Parrya after the
genus Pinus was evolved into two lineages of subgenera
Strobus and Pinus.
In the lineage of Asian members of sect. Parrya and
sect. Strobus, the relationships of Asian species of sect.
Parrya were still poorly resolved. P. krempfii, the morpho-
logically unusual species (with two peculiar, flat, some-
times hypostomatic leaves) endemic to south central Viet-
nam (Dallat Plateau), was grouped with P. gerardiana. This
is beyond our expectation, because P. krempfii is so mor-
phologically special that Chevalier (1944) elevated this spe-
cies to an independent monospecific genus in Pinaceae
and named it Ducampopinus krempfii. Some authors cre-
ated a separate subgenus, Ducampopinus, in the genus
Pinus to accommodate it (de Ferré, 1953; Gaussen, 1960;
Little and Critchfield, 1969). However, more and more stud-
ies showed that it has some linkages with subsect.
Gerardianae in respect of its cone morphology (Mirov,
1967), wood chemistry (Erdtman et al., 1966), cpDNA PCR-
RFLP variation (Wang et al., 2000) and cpDNA sequences
variation (Wang et al., 1999). Our results may reflect the
essence of their relationships. It is clear that P. krempfii is
a member of the subgen. Strobus but its relationships with
Fig.2. Majority rule tree of four most parsimonious trees of 70 steps based on matK sequences. Bootstrap values > 50% are indicated
above branches. The species of sect. Parrya are indicated in broadened lines.
Acta Botanica Sinica 植物学报 Vol.46 No.2 2004176
other members of the subgenus need to be further
investigated.
P. squamata X. W. Li is an extremely endangered spe-
cies of pine recently described from the northeastern cor-
ner of Yunnan Province, China (Li, 1992). Because of its
peculiarity, e.g. five needles per bundle and long-winged
seed, a new series, Squamatae X. W. Li et Hsueh (subgen.
Strobus sect. Parrya), was established to accommodate
this species. On the basis of an analysis of chemical con-
stituents of seed oils of P. bungeana and seven other re-
lated pines, Li and Zhu (1993) suggested that P. squamata
should be a member of the central American subsect.
Balfourianae of their new proposed subgen. Parrya. Our
previous study based on four cpDNA sequences and ITS
sequence data revealed that it was a member of the subsect.
Gerardianae (Zhang et al., 2003a). In the present study, P.
squamata was a stable member of the clade comprising
Asian members of the sect. Parrya and members of sect.
Strobus. But its relationships with P. bungeana and P.
gerardiana were not resolved in this study, which maybe
attribute to the low divergence rate of matK gene in Pinus.
As for the assemblage of American members of sect.
Parrya, only P. aristata, P. balfouriana and P. longaeva
formed a monophyletic group on different trees with low
bootstrap support, which corresponding to subsect.
Balfourianae. These pines thought to be a natural group
and closely related tertiary relics confined to high eleva-
tions in certain mountainous areas of southwestern states
in America. P. aristata was a member of subsect.
Balfourianae and the subsect. Aristatae (van der Burgh,
Fig.3. Neighbor joining tree of sect. Parrya based on the matK sequences of 21 Pinus species. The distances are marked above each
branch, bootstrap values above branches or denoted by arrows (in boldface).
ZHANG Zhi-Yong et al.: Molecular Phylogeny of Section Parrya of Pinus (Pinaceae) Based on Chloroplast matK Gene Sequence Data 177
1973) seemed to be unnecessary.
The relationships within subsect. Cembroides and P.
rzedowskii were not resolved on the NJ tree. However, P.
rzedowskii and P. monophylla clustered together, except
for P. cembroides, other members of subsect. Cembroides
formed an assemblage. The result implied that subsect.
Cembroides might not be a monophyletic group. Malusa
(1992) suggested that some members of subsect.
Cembroides were more closely related to taxa not in subsect.
Cembroides, and the “pinyon pines” (subsect. Cembroides
sens. lato.) were a paraphyletic group according to his cla-
distic analysis. The results based on the molecular system-
atic analysis of ITS (Liston et al., 1999) also showed that
subsect. Cembroides was not monophyletic.
P. rzedowskii, the poorly known pine, had been added
to sect. Parrya (Klaus, 1989) for its similar feature of wood
anatomy, but there was no evidence for this relationship
(Malusa, 1992). Taxonomically, Pinus rzedowskii is one of
the most interesting species in the genus. Its foliar mor-
phology and anatomy places it close to P. cembroides and
P. maximartinezii. Preliminary results from the analysis of
cpDNA of a limited number of Mexican pine species place it
and P. cembroides as unresolved clades away from P.
maximartinezii and other species in subgen. Strobus (Pérez
de la Rosa et al., 1995). The elongation of shoots prior to
leaf development is shared with P. maximartinezii. The
bark of P. rzedowskii is unlike any other in Strobus and at
least externally resembles that of species in subgen. Pinus.
The seed cones and seeds are also morphologically more
similar to some species in subgen. Pinus. The seeds are
likewise small, with well-developed, articulate wings three
to four times larger than the seeds. In this respect there is
no resemblance to either P. cembroides or P. maximartinezii,
nor to any other pinyon pine, in which the seeds are large
and the wings vestigial. The present analysis suggested
that P. rzedowskii might have a close relationship with P.
monophylla, in contrast with previous results, but its posi-
tion is not consistent on different trees and may collapse.
The phylogenetic relationships of this peculiar pine need
more studies.
P. nelsonii was described by Shaw (1914) based on E.
W. Nelson’s collection in June 1898 on a mountain above
Miquihuana, Tamaulipas, near the border with Nuevo León.
The very distinct connate leaves and the long pedunculate,
curious cones uniquely distinguished this pine from all oth-
ers that Shaw (1914) had known. Its connate leaves, held
together by persistent fascicle sheaths, are morphologi-
cally and anatomically distinct from any of the other “pin-
yon pines”. So van der Burgh (1973) elevated P. nelsonii to
a separate monotypic subsect. Nelsoniae, and Farjon (1996)
had also accepted the subsection but as a ditypic group
together with P. pinceana. However, other author still
placed P. nelsonii in subsect. Cembroides (Price et al.,
1998). Pérez de la Rosa et al. (1995) examined restriction site
variation in PCR-amplified fragments representing 12 Mexi-
can pine species and a single Picea species, revealing that
P. nelsonii had a isolated position. The results of ITS se-
quences analysis showed that P. nelsonii was basal to all
haploxylon pines. Our result preferred to support that P.
nelsonii was a real pinyon pines and should be included in
subsect. Cembroides. But because of the low bootstrap
support, the phylogenetic relationships of P. nelsonii merit
more investigation.
3.2 Biogeographical implications
In consideration of the paraphyly of sect. Parrya, we
should therefore be careful about any previous biogeo-
graphical studies on it. Strauss and Doerksen (1990) sug-
gested that the high diversity among species within sect.
Parrya was a reflection of the section’s ancientness. Many
of its current species and taxa may be relicts with long
evolutionary histories. Its biogeography was complex, sug-
gesting the possibility of more than one intercontinental
migration. Strauss and Doerksen (1990) also suggested that
the ancestral species in Parrya maybe originated from North
America, their progenitors appear to have given rise to a
currently Asian group of species, subsect. Gerardianae,
which then gave rise to the widespread sect. Strobus, which
occurs over substantial parts of both continents. In the
present analysis we are not sure if the species of sect.
Parrya in North America are more ancestral than Asian
members of the section. The members of American sect.
Parrya are sister group to Asian sect. Parrya and sect.
Strobus as shown in Fig.2 and Fig.3, which implied that the
progenitors of subgen. Strobus might give rise to two or
more clades of sect. Parrya very early and the ancestors of
subsect. Gerardianae may then give rise to species of sect.
Strobus subsequently. Some descendants of sect. Strobus
migrated into America through land bridges. Most mem-
bers of sect. Parrya disappeared from many middle-lati-
tude areas during early Tertiary and were replaced by the
diverse angiosperms of boreotropical flora, which were
adapted to the equable, tropical climate (Millar, 1993). A
few species of sect. Parrya shifted to some refuges during
the warm period of early Tertiary. Subsect. Cembroides
seems to have been limited to western North America and
Central American refuges, the small subsect. Balfourianae
appears to have been entirely concentrated in middle-lati-
tude Rocky Mountain refuge and a Tethys refuge area of
Acta Botanica Sinica 植物学报 Vol.46 No.2 2004178
pines in Southeast Asia also have fossil evidence and evi-
dence from extant pines such as P. krempfii, P. gerardiana,
P. bungeana and the recently-described P. squamata.
Nevertheless, the destinies of species in different refuges
are different. Within subsect. Cembroides, extensive radia-
tion and speciation were triggered by the active mountain-
building, cooling and drying of the climate afterward. For
Asia refuges, the climates were relatively stable and fit for
the development of angiosperms, so the species still re-
strict in refuges and have little chance to radiation and
speciation. For certain species such as P. squamata, the
living conditions are still threatened by broad-leave trees
(Zhang et al., 2003b). As revealed in the majority rule tree
(Fig.2) which was supported by earlier authors (Liston et
al., 1999; Wang et al., 1999) and our combined analysis of
five cpDNA sequences (Zhang, 2003), there were two ma-
jor evolutionary lineages in Pinus, i.e. subgen. Pinus and
subgen. Strobus. The Strobus lineage was separated into
two groups, the American members of sect. Parrya as one,
and a clade consisted of sect. Strobus and Asian members
of the sect. Parrya as the other. This distribution pattern
was similar to some angiosperm taxa (Wen, 1999) such as
bamboos (Clark et al., 1995).
Acknowledgements: We are very indebted to Dr. Aaron
Liston for his kindly providing DNA samples and to Dr.
Wang Xiao-Ru for her kindly providing data matrix. Hearty
thanks are due to Dr. Zsolt Debreczy for his presenting
many experimental materials. We thank Miss Tian Xin for
her reading an earlier version of the manuscript.
References:
Bailey D K. 1970. Phytogeography and taxonomy of Pinus sub-
sect. Balfourianae. Ann Mo Bot Gard，57:210-249.
Chevalier A. 1944. Notes sur les Coniféres de l’lndochine. Rev
Bot Appl Agric Tropicale, 24:7-34.
Clark L G, Zhang W, Wendel J F. 1995. A phylogeny of glass
family (Poaceae) based on ndhF sequence data. Syst Bot, 20:
436-460.
Doyle J J, Doyle J L. 1987. A rapid DNA isolation procedure for
small quantities of fresh leaf material. Phytochem Bull, 19:
11-15.
Erdtman H, Kimland B, Norin T. 1966. Wood constituents of
Ducampopinus krempfii (Lecomte) Chevalier (Pinus krempfii
Lecomte). Phytochemistry, 5:927-931.
Farjon A. 1984. Pines: drawings and Descriptions of the Genus
Pinus. Leiden: E. J. Brill & Dr W. Baxkhuys.
Farjon A. 1996. Biodiversity of Pinus (Pinaceae) in Mexico: spe-
ciation and palaeo-endemism. Bot J Linn Soc, 121:365-384.
de Ferré Y. 1953. Division de genre Pinus en quatres sous-genres.
Compt Rend Hebd Séances Acad Sci (Paris), 236:226-228.
Gaussen H. 1960. Les Gymnosperms Actuelles et Fossils. Fas-
cicle VI. Les Coniferales. Chap. XI. Généralités, Genre Pin-
us. Toulouse: Travaux du Laboratorie Forestier de Toulouse.
1-272.
Govindaraju D, Lewis P, Cullis C. 1992. Phylogenetic analysis
of pines using ribosomal DNA restriction fragment length
polymorphisms. Plant Syst Evol, 179:141-153.
Klaus W. 1989. Mediterranean pines and their history. Plant Syst
Evol, 162:133-163.
Li D Z. 1997. A reassessment of Pinus subgen. Pinus in China.
Edinb J Bot, 54:337-349.
Li X-P, Zhu Z-D. 1993. Studies on constituents of fatty acids
from seed oils of Pinus bungeana and its taxonomic position.
J Nanjing Forest Univ, 17:27-34. (in Chinese with English
abstract)
Li X-W. 1992. A new series and a new species of Pinus from
Yunnan. Acta Bot Yunnan, 14:259-260. (in Chinese with En-
glish abstract)
Liston A, Robinson W A, Pinero W D, Alvarez-buylla E R. 1999.
Phylogenetics of Pinus (Pinaceae) based on nuclear ribosomal
DNA internal transcribed spacer region sequences. Mol
Phylogenet Evol, 11:95-109.
Little E L Jr, Critchfield W B. 1969. Subdivisions of the Genus
Pinus. Washington DC: USDA Forest Service Miscellaneous
Publication. 1144.
Malusa J. 1992. Phylogeny and biogeography of the pinyon pines
(Pinus subsect. Cembroides). Syst Bot, 17:42-66.
Millar C I. 1993. Impact of the Eocene on the evolution of Pinus
L. Ann Mo Bot Gard, 80:471-498.
Mirov N T. 1967. The Genus Pinus. New York: Ronald Press
Company.
Pérez de la Rosa, Harris S A, Farjon A. 1995. Noncoding chloro-
plast DNA variation in Mexican pines. Theor Appl Genet, 91:
1101-1106.
Pilger R. 1926. Pinus. Engler A, Prantl K. Die Naturlichen
Pflanzenfamilien. Vol. ⅩⅢ. Leipzig: Wilhelm Engelmann.
331-342.
Piovesan G, Pelosi C, Schirone A, Schirone B. 1993. Taxonomic
evaluations of the genus Pinus (Pinaceae) based on electro-
phoretic data of salt soluble and in soluble seed storage
proteins. Plant Syst Evol, 186:57-68.
Price R A, Liston A, Strauss S H. 1998. Phylogeny and systemat-
ics of Pinus. Richardson D M. Ecology and Biogeography of
Pinus. Cambridge, UK: Cambridge University Press. 49-68.
Schirone B, Piovesan G, Bellarosa R, Pelosi C. 1991. A taxonomic
analysis of seed proteins in Pinus spp. (Pinaceae). Plant Syst
Evol, 178:48-53.
Shaw G R. 1914. The Genus Pinus. Massachusetts: The Murray
ZHANG Zhi-Yong et al.: Molecular Phylogeny of Section Parrya of Pinus (Pinaceae) Based on Chloroplast matK Gene Sequence Data 179
Printing Co.
Strauss S H, Doerksen A H. 1990. Restriction fragment analysis
of pine phylogeny. Evolution, 44:1081-1096.
Swofford D L. 2001. PAUP: Phylogenetic Analysis Using
Parsimony. Ver. 4.0b8. Massachusetts: Sinauer, Associates.
van der Burgh J. 1973. Hölzer der niederrheinischen
Braunkohlenformation. 2. Hölzer der Braunkohlengruben
“Maria Theresia” zu Herzogenrath, ‘Zukunft West’ zu
Eschweiler und “Victor” (Zülpich Mitte) zu Zülpich. Nebst
einer systematisch-anatomischen Bearbeitung der Gattung
Pinus L. Rev Palaeob Palynol, 15:73-275.
Wang X R, Szmidt A E. 1993. Chloroplast DNA-based phylog-
eny of Asian Pinus species (Pinaceae). Plant Syst Evol, 188:
197-211.
Wang X R, Szmidt A E, Hoang Nghia Nguyên. 2000. The phylo-
genetic position of the endemic flat-needle pine Pinus krempfii
(Pinaceae) from Vietnam, based on PCR-RFLP analysis of
chloroplast DNA. Plant Syst Evol, 220:21-36.
Wang X R, Tsumura Y, Yoshimaru H, Nagasaka K, Szmidt A E.
1999. Phylogenetic relationships of Eurasian pines (Pinus,
(Managing editor: WANG Wei)
Pinaceae) based on chloroplast rbcL, matK, rpL20-rpS18
Spacer, and trnV intron sequences. Am J Bot, 86:1742-1753.
Wen J. 1999. Evolution of eastern Asian and eastern north Ameri-
can disjunct distributions in flowering plants. Annu Rev Ecol
Syst, 30:421-455.
Wolfe K H. 1991. Protein-coding genes in chloroplast DNA: com-
pilation of nucleotide sequences, data base entries and rates of
molecular evolution. Vasil K. Cell Culture and Somatic Cell
Genetics of Plants. Vol. 7BI. San Diego: Academic Press. 467-
482.
Zhang Z-Y , Yang J-B, Li D-Z. 2003a. Phylogenetic relationships
of the extremely endangered species, Pinus squamata
(Pinaceae) inferred from four sequences of the chloroplast
genome and ITS of the nuclear genome. Acta Bot Sin, 45:530-
535.
Zhang Z-Y, Tao D-D, Li D. 2003b. An analysis of interspecific
associations of Pinus squamata with other dominant woody
species in community succession. Biodiv Sci,11:125-131.
(in Chinese with English abstract)