Haloxylon ammodendron (CA Mey.) Bunge, the dominant tree species in many xerophytic deserts of Asia, plays an important role in the maintenance of the structure and function of these ecosystems. Despite its ecological and economic importance, nearly nothing is known about its genetic attributes. In this study, RAPD and ISSR markers were used to investigate the genetic diversity and structure of four natural populations of H. ammodendron. Five RAPD primers amplified 61 bands with 51 (83.6%) polymorphic and eight ISSR primers amplified 195 bands with 175 (89.7%) polymorphic. The genetic diversity, estimated by Shannon’s index, was 0.333 (by RAPDs) and 0.367 (by ISSRs). Both RAPD and ISSR analyses revealed a high level of genetic diversity in natural populations of H. ammodendron. Furthermore, analysis of molecular variance (AMOVA) was used to apportion the variation within and between populations. The proportion of variation attributable to within-population differences was very high (138.2% by RAPDs; 89.4% by ISSRs). No genetic differentiation was detected among populations using RAPDs (P = 0.999), while only a small amount of variation (10.6%) was detected among populations using ISSRs. We suggest that the present genetic structure is due to high levels of gene flow.
全 文 :Received 10 Nov. 2003 Accepted 14 Jan. 2004
Supported by the Knowledge Innovation Project of The Chinese Academy of Sciences (KZCX1-10-05).
* Author for correspondence. Tel: +86 (0)10 62591431 ext. 6223; E-mail:
① China National Report on the Implementation of United Nations Convention to Combat Desertification and National Action Programme
to Combat Desertification. 2000. Prepared by secretariat of China National Committee for the Implementation of the United Nations
Convention to Combat Desertification (CCICCD). http://www.unccd.int/cop/reports/asia/national/2000/china-eng.pdf.
http://www.chineseplantscience.com
Acta Botanica Sinica
植 物 学 报 2004, 46 (6): 675-681
Population Genetic Structure of a Dominant Desert Tree, Haloxylon
ammodendron (Chenopodiaceae), in the Southeast Gurbantunggut
Desert Detected by RAPD and ISSR Markers
SHENG Yan1, ZHENG Wei-Hong2, PEI Ke-Quan1, MA Ke-Ping1*
(1. Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China;
2. College of Life Sciences and Technology, Qiqihaer University, Qiqihaer 161006, China)
Abstract: Haloxylon ammodendron (CA Mey.) Bunge, the dominant tree species in many xerophytic
deserts of Asia, plays an important role in the maintenance of the structure and function of these
ecosystems. Despite its ecological and economic importance, nearly nothing is known about its genetic
attributes. In this study, RAPD and ISSR markers were used to investigate the genetic diversity and
structure of four natural populations of H. ammodendron. Five RAPD primers amplified 61 bands with 51
(83.6%) polymorphic and eight ISSR primers amplified 195 bands with 175 (89.7%) polymorphic. The genetic
diversity, estimated by Shannon’s index, was 0.333 (by RAPDs) and 0.367 (by ISSRs). Both RAPD and ISSR
analyses revealed a high level of genetic diversity in natural populations of H. ammodendron. Furthermore,
analysis of molecular variance (AMOVA) was used to apportion the variation within and between populations.
The proportion of variation attributable to within-population differences was very high (138.2% by RAPDs;
89.4% by ISSRs). No genetic differentiation was detected among populations using RAPDs (P = 0.999), while
only a small amount of variation (10.6%) was detected among populations using ISSRs. We suggest that the
present genetic structure is due to high levels of gene flow.
Key words: Haloxylon ammodendron; RAPD; ISSR; genetic structure; gene flow
The survival of plant populations, their evolutionary
potential, and their ability to adapt to changing environmen-
tal conditions are determined by their genetic variability
(Lacerda et al., 2001). The amount and partitioning of genetic
variation among and within populations result from the dy-
namic processes of gene flow, selection, inbreeding, ge-
netic drift, and mutation (Hartl and Clark, 1994). Thus,
knowledge of the current genetic structure of a population
not only allows inference about past processes, but also
can predict evolutionary responses (Fisher et al., 2000).
Population genetic studies also provide fundamental in-
formation for the conservation and/or sustainable use of
a species.
Haloxylon ammodendron (Chenopodiaceae) is a xero-
phytic desert tree species that is both highly drought-re-
sistant and salt-tolerant. H. ammodendron occurs natu-
rally in a variety of habitats in Asian and African deserts,
including gravel desert, clay desert, fixed and semi-fixed
sandy land, and saline land (Chen et al., 1983; Tobe et al.,
2000). The Gurbantunggut desert has the most extensive
natural H. ammodendron forest in China and is the only
desert in China dominated by semi-mobile sand dunes①.
These trees are highly valued and called “coal in the desert”
because its woody stems and branches are an important
fuel source for local people. The tender branches also pro-
vide good camel fodder in winter and spring, and, Cistanche
deserticola, a root parasite of H. ammodendron, is a valu-
able medicinal plant (Peng and Xu, 1996). In recent decades,
land reclamation, cultivation, over-grazing, over-cutting and
harvesting of C. deserticola have resulted in the destruc-
tion of H. ammodendron forests and the development of
mobile sand dunes.
Despite the ecological and economic importance of H.
ammodendron, little is known about its genetic aspects. In
this paper, we report the results of a study on the genetic
diversity and structure of four populations of H.
ammodendron using both RAPDs and ISSRs. Our prin-
ciple objectives were to assess the level of genetic diver-
sity and investigate the genetic variation within and be-
tween natural populations of H. ammodendron.
Acta Botanica Sinica 植物学报 Vol.46 No.6 2004676
1 Materials and Methods
1.1 Study site and sampling
Our study was conducted at four sites in the Southeast
Gurbantunggut desert (Fig.1; Table 1). Preliminary investi-
gations revealed that the four sites represent three differ-
ent Haloxylon ammodendron community types. Commu-
nities A and C are monospecific stands of H. ammodendron,
the only arborescent species in both the overstory and
understory. The herbaceous layer is dominated by
Ceratocarpus arenarium, Atriplex dimorphostegia and
Suaeda microphylla, etc. These communities comprise
rather stable habitats with well-established H .
ammodendron populations and occur on windward slopes
and on the interval of fixed sand dunes. Community B oc-
curs on gray-brown desert soil that has significantly higher
soil water content and total salinity. These communities
are co-dominated by H. ammodendron and Reaumuria
soongorica. The habitat is highly disturbed by local resi-
dents who dig Cistanche deserticola that parasitizes the
roots of H. ammodendron and by goat herders who collect
H. ammodendron for firewood and sheep feed in winter.
Community D is located on semi-fixed sand hills and is co-
dominated by H. ammodendron and Tamarix ramosissima.
The density of living and dead shrubs, their stem diameters,
and the canopy height of living shrubs of H. ammodendron
population are significantly lower than in the other sites
suggesting these shrubs are younger than those in the
other three community types.
Young annual cylindrical shoots were used as plant
material, because the leaves of H. ammodendron are re-
duced to scales (Pyankov et al., 1999). In each of the four
populations, shoot tissues were taken from 39-40 mature
individuals (Table 1), the plant tissue was air-dried at room
temperature (Thomson and Henry, 1993) and transported
back to Institute of Botany, The Chinese Academy of
Sciences, Beijing.
1.2 DNA analysis
1.2.1 Genomic DNA extraction Genomic DNA was
extracted from ca. 1 g of dried branches using a modified
method of Doyle and Doyle (1987). The tissue was ground
to fine powder in liquid nitrogen and incubated at 65 ℃ for
60 min in 2 mL of 2×CTAB isolation buffer (100 mmol/L
Tris-HCl, pH 8.0, 1.4 mol/L NaCl, 20 mmol/L EDTA, 2%
hexadecyltrimethyl-ammonium bromide (CTAB), 0.2% b-
mercaptoethanol. The sample was mixed with an equal vol-
ume of Tris-Phenol, centrifuged at 10 000g for 10 min and
then the supernatant collected in a clean tube. An equal
volume of chloroform-isoamyl alcohol (CI, 24:1) was added
to extract DNA. After being mixed by inversion for 10 min,
the mixture was centrifuged at 10 000g for 10 min. The su-
pernatant was then mixed with 0.5 mL ice-cold isopropanol
and 0.1 mL 2 mol/L KAc to precipitate the DNA. The DNA
was recovered as a pellet by centrifugation at 10 000g for 5
min, washed twice with 0.6 mL of 70% ethanol, air-dried at
room temperature and resuspended in 0.2 mL of 0.1×TE
buffer (10 mmol/L Tris-HCl, 1 mmol/L EDTA). All DNA
samples were purified using Wizard DNA Clean-Up System
(Promega, Madison, Wisconsin, USA). After visual quanti-
fication and comparison with standard DNA concentrations,
DNA samples of 50 ng/mL were prepared.
1.2.2 RAPD amplification Fifteen primers from
Shenggong Inc. were initially screened against four plants,
Table 1 Locations of Haloxylon ammodendron populations used for RAPD and ISSR analysis
Population Location
Latitude Longitude Altitude Aspect Slope Sample
(°N) (°E) (m) (°) (°) size
A Beishawo, Fukang City, Xinjiang 44.24 87.52 443 25 ES 21 40
B Xingonglu, Fukang City, Xinjiang 44.13 87.50 468 - 0 39
C Beishawo, Fukang City, Xinjiang 44.25 87.55 438 - 0 39
D Wucaiwuan, Jimusaer County, Xinjiang 44.23 88.47 525 15 NE 39 40
Fig.1. Map showing the four sites of Haloxylon ammodendron
populations used in this study for analysis of genetic diversity.
See Table 1 for reference to the specific population locations.
SHENG Yan et al.: Population Genetic Structure of a Dominant Desert Tree, Haloxylon ammodendron (Chenopodiaceae), in the
Southeast Gurbantunggut Desert Detected by RAPD and ISSR Markers 677
one from each population. In order to avoid biasing esti-
mates of polymorphism, the selection of primers for band
scoring was dependent only on the clearness and repeat-
ability of RAPD fragments and not on the level of
polymorphism. Reactions were carried out in a volume of
25 mL consisting of 2.5 mmol/L MgCl2, 0.2 mmol/L dNTPs,
0.4 mmol/L of primer, 1 unit of Taq DNA polymerase
(Promega, Madison, USA), 1×Taq DNA polymerase buffer
and 30 ng of template DNA. PCR amplifications were per-
formed in a PTC-200 thermocycler (MJ Research, Inc.,
Watertown, Massachusetts, USA) under the following
conditions: 94 ℃ for 3 min; 40 cycles of 94 ℃ for 30 s, 36 ℃
for 1 min, 72 ℃ for 2 min; 72 ℃ for 10 min. PCR products
were then stored at 4 ℃. The amplification products were
analyzed by electrophoresis on 1.8% agarose gels in 1×
TBE (Tris-EDTA-borate) buffer, and stained with ethidium
bromide. After running for approximately 6 h at 50 V, the
gel was photographed by an Alpha Ease FC Imaging
System (Alpha Innotech Corporation). Scoring of the
bands was performed by visual analysis of the gel
photographs. Molecular size of the fragments was esti-
mated using a 200-bp DNA ladder (Life Technologies,
Gibco).
1.2.3 ISSR amplification Twenty-one primers from
Shenggong Inc. (Shanghai, China) were initially screened
against four plants, one from each population. The design
of primers was based on SSR motifs reported for flowering
plants (Wolfe et al., 1998a; 1998b; Wolfe and Liston, 1998)
and recommended at the website (http://www.biosci.ohio-
state.edu/~awolfe/ISSR/ISSR.html). Reactions were carried
out in a volume of 25 mL consisting of 1.5 mmol/L MgCl2,
0.2 mmol/L dNTPs, 1.25 mmol/L of primer, 1.25 units of Taq
DNA polymerase (Promega, Madison, USA), 1×Taq DNA
polymerase buffer and 20 ng of template DNA. PCR ampli-
fications were performed in a PTC-200 thermocycler (MJ
Research, Inc., Watertown, Massachusetts, USA) under
the following conditions: 94 ℃ for 1.5 min; 35 cycles of 94
℃ for 40 s, 49 ℃ for 45 s, 72 ℃ for 1.5 min; linked to 94 ℃
for 45 s, 44 ℃ for 45 s, 72 ℃ for 5 min. PCR products were
then stored at 4 ℃. Bands were separated by electrophore-
sis on 2.0% agarose gel with ethidium bromide, and visual-
ized in the same way as in the RAPD analysis.
1.2.4 Data analysis Amplified fragments were scored for
presence (1) or absence (0) of homologous bands and two
matrices of different RAPD and ISSR phenotypes were
assembled. These two matrices were used in the subse-
quent statistical analyses. Only data from intensely stained,
unambiguous, clear bands were used for statistical analysis.
A RAPD marker or an ISSR marker was determined to be
polymorphic when it was found in less than 95% of the
individuals sampled (i.e. absent in eight or more individuals).
Genetic diversity was estimated using the percentage of
polymorphic loci and Shannon’s index, which was calcu-
lated by the following formula:
HO =-Σpi×lnpi
where k is the total number of kinds of RAPD or ISSR
fragments, and pi is the frequency of a given band. A
pairwise Nei-Li distance matrix was generated using DCFA
1.1 program written by Zhang and Ge (2002) and was used
as the input for an analysis of molecular variance (AMOVA,
Excoffier et al., 1992). Using AMOVA, we calculated vari-
ance components and their significance levels for variation
among and within the four populations. Pairwise genetic
distances (FST) among the four populations were also ob-
tained from AMOVA and were used to construct a UPGMA
tree (routine UPGMA of NTSYS-pc package; Rohlf, 1998).
The AMOVA analysis was performed using the
WINAMOVA 1.5 program (ftp: 129.194.113.1).
2 Results
2.1 RAPD polymorphism
Of the 15 RAPD primers screened, 5 produced clear and
repeatable fragments and were selected for further analysis
(Table 2). A summary of the genetic data for each of the four
populations of H. ammodendron is given in Table 3. A total
of 61 bands ranging from 220 to 2 020 bp were scored,
corresponding to an average of 15.3 bands per primer; of
these 83.6% (51 in total) were polymorphic among 158 plants.
The percentage of polymorphic loci and the Shannon’s
index for each population are shown in Table 3, in which
population A exhibited the highest level of variability (P%
= 65.6; H0 = 0.328), while population C gave the lowest (P%
= 49.2; H0 = 0.264).
2.2 ISSR polymorphism
Eight ISSR primers that produced clear and repeatable
fragments were selected for further analysis (Table 2). These
primers consistently amplified a total of 195 scorable mark-
ers that ranged from 165 to 2 300 bp in size. Each primer
generated 19 to 29 bands with a mean of 24.4 of which 175
(89.7%) were polymorphic across the 158 plants. The per-
centage of polymorphic bands within populations ranged
from 69.7% to 82.6% with a mean percentage of 74% (Table
3). The mean genetic diversity within populations estimated
by Shannon’s index was 0.328, ranging from 0.314 to 0.355
(Table 3). The highest value of Shannon’s index was found
in population D, similar to the highest number of polymor-
phic markers.
k
i=1
Acta Botanica Sinica 植物学报 Vol.46 No.6 2004678
2.3 The genetic structure detected by RAPDs and ISSRs
The AMOVA analysis from the distance matrices for the
158 individuals permitted a partitioning of the overall varia-
tion into two levels (Table 4). The proportion of variation
attributable to within-population differences was very high
(138.2% by RAPDs; 89.4% by ISSRs). No genetic differen-
tiation was detected among populations using RAPDs (P
= 0.999), while only a small amount of variation (10.6%) was
detected among populations with ISSRs.
The genetic relationship of the four populations was
illustrated using the UPGMA dendrograms based on the
pairwise ΦST values (Fig.2a, b). Values of ΦST based on
RAPDs ranged from -2.195 5 (A-B) to 0.018 9 (A-D), indi-
cating that the populations A and B were the most similar
and populations A and D were the most different. Values of
ΦST based on ISSRs ranged from 0.073 5 (C-D) to 0.135 4
(A-D), indicating that the populations C and D were the
most similar and populations A and D were the most
different.
3 Discussion
3.1 Genetic diversity
In four populations of H. ammodendron, we found that
83.6% (using RAPD markers) and 89.7% (using ISSR
markers) of the bands were polymorphic and Shannon’ in-
dex of genetic diversity was estimated to be 0.333 (by
RAPDs) and 0.367 (by ISSRs). These values can be com-
pared with other woody plant species with similar life
Table 2 Primers for RAPD and ISSR analyses
Primer Primer sequence (5-3)*
RAPD-S381 GGCATGACCT
RAPD-S383 CCAGCAGCTT
RAPD-S385 ACGCAGGCAC
RAPD-S388 AGCAGGTGGA
RAPD-S1183 GAGGTGTCTG
ISSR-4 ACACACACACACACACYT
ISSR-6 CACACACACACARY
ISSR-7 CACACACACACARG
ISSR-9 CTCCTCCTCCTCRC
ISSR-11 BDBACAACAACAACAACA
ISSR-12 BBBGAAAGAAAGAAAGAA
ISSR-13 ACACACACACACACACYG
ISSR-14 CACCACCACCACRC
*, B=C/G/T; D=A/G/T; R=A/T; Y=G/C.
Table 3 Estimates of genetic diversity at RAPD and ISSR loci
of Haloxylon ammodendron populations
Population
RAPDs ISSRs
P (%) H0 P (%) H0
A 4 0(6 5 . 6) 0.328 1 3 6(6 9 . 7) 0.325
B 3 4(5 5 . 7) 0.311 1 3 8(7 0 . 8) 0.316
C 3 0(4 9 . 2) 0.264 1 4 2(7 2 . 8) 0.314
D 3 6(5 9 . 0) 0.285 1 6 1(8 2 . 6) 0.355
Total 5 1(8 3 . 6) 0.333 1 7 5(8 9 . 7) 0.367
H0, mean genetic diversity estimated by Shannon’s index; P (%),
number (and percentage) of polymorphic markers.
Table 4 Analysis of molecular variance (AMOVA) for 158 individuals in the four populations of Haloxylon ammodendron
Source of variance df SSD MSD Variance component Total (%) P-value
RAPDs Among populations 3 -3.750 -1.250 -0.076 -38.2 0.999
Within populations 154 20.979 0.276 0.276 138.2 < 0.001
ISSRs Among populations 3 2.425 0.808 0.017 10.6 < 0.001
Within populations 154 21.980 0.143 0.143 89.4 < 0.001
Fig.2. Dendrograms of the four Haloxylon ammodendron populations obtained by UPGMA cluster analysis of the matrix of pairwise
ΦST values based on RAPDs (a) and ISSRs (b).
SHENG Yan et al.: Population Genetic Structure of a Dominant Desert Tree, Haloxylon ammodendron (Chenopodiaceae), in the
Southeast Gurbantunggut Desert Detected by RAPD and ISSR Markers 679
histories. Ge and Sun (1999) revealed a surprisingly low
genetic variation by both allozymes (P = 4.76%) and ISSRs
(P = 16.18%) in a widespread, long-lived, woody, perennial
species. Lacerda et al. (2001) using RAPD markers, found
values of Shannon’s index between 0.301 and 0.367 for a
woody perennial plant with considerable levels of genetic
diversity. In comparison, H. ammodendron presented a
comparable level of genetic diversity. The few other stud-
ies of population genetic diversity of long-lived desert pe-
rennials also revealed high levels of genetic polymorphism
(Schuster et al., 1994; Martínez-Palacios et al., 1999;
Shrestha et al., 2002).
The high intrapopulation genetic variability may be a
consequence of adaptation to a highly heterogeneous and
stressful environment. Theoretically, spatiotemporal varia-
tions of diversifying selection can maintain genetic poly-
morphism (Hedrick et al., 1976; Nevo and Beiles, 1988).
Many studies have shown strong relationships between
levels of genetic polymorphism and degree of environmen-
tal heterogeneity and stress (Hedrick, 1986; Nevo, 2001).
However, in this study, it was not clear as to what propor-
tion of polymorphic loci were maintained by environmental
heterogeneity. The arid environment of H. ammodendron
is characterized by highly diverse soils, variable water
distribution, and varying slope and aspect that create a
mosaic of microhabitats and vegetation patterns across the
landscape (Song and Jia, 2000; Huang, 2002). Precipitation,
the most important requirement for plant growth in arid
environments is low, while annual fluctuations are high
(Geng, 1986). Accordingly, we hypothesize that such a het-
erogeneous and stressful environment may lead to the
maintenance of high levels of intrapopulation genetic
variation. An alternative hypothesis is that the genetic
variation observed in the species is neutral. Further
experiments, such as examining levels of polymorphism
among populations in environments that differ in their
degree of stress or heterogeneity, are needed to support
our hypothesis.
3.2 Population genetic structure
Both RAPD and ISSR markers revealed that H.
ammodendron populations held more genetic variation
within populations than among populations. No genetic
differentiation was detected among populations using
RAPD, and little differentiation using ISSRs. According to
Hamrick and Godt (1989), reproductive biology is the most
important factor in determining the genetic structure of
plant populations. They have shown that outcrossing plant
species tend to exhibit between 10% and 20% genetic varia-
tion among populations while selfing species exhibit, on
average, 50% variation between populations. Studies on
the biology of flowering and pollination in H. ammodendron
indicate it is an outcrosser (Tursunov et al., 1989). Although
several different types of pollination are possible, such as
xenogamy, geitonogamy and autogamy, the presence of
three groups of androgenous flowers with anthers and
stigma that differ in time of maturation promotes cross-
pollination by anemophily in this species (Tursunov et
al., 1989). However, Hamrick and Godt (1996) pointed
out that life history traits alone only explain a relatively
low amount of the variation in genetic structure. The
high intrapopulation variability and genetic homogene-
ity across populations could have arisen by high levels of
gene flow.
H. ammodendron exchanges its genes mainly through
seeds and pollen (Song and Jia, 2000). In the young forest,
vegetative propagation by dormant buds on the trunk or
branches has been reported when the plant is damaged
(Huang, 2002), but in mature natural populations like we
studied, vegetative propagation is infrequent. Seeds are
small (2.5 mm in diameter, mass weight of 1 000 grains: (2.99
± 0.04) g) (Huang, 2002), bearing winglike membranes. Seed
longevity of H. ammodendron is very short under natural
conditions, and very few seeds can survive in the soil for
more than 10 months (Huang, 2002). During dispersal, a
rare seed may fall more than five miles away from the cano-
pies of their maternal trees (Mamedov and Osipov, 1985;
Sheng et al., unpublished data); however, dispersal and
germination investigations of H. ammodendron suggest
that long-distance seed dispersal is rare. Absence of adap-
tation for long-distance dispersal in desert plants has long
been recognized. Ellner and Shmida (1981) argued that
atelechory (the absence of dispersal-enhancing characters)
in desert species is an adaptive response to the extremely
low benefit of long-range dispersal mechanisms in deserts.
Pollen is small, 19.1 mm in diameter (Pan, 1993), round or
nearly round, and dispersed by wind (Wu et al., 1992). Due
to the high frequency of strong winds and the low vegeta-
tion cover across the desert landscape, the long-distance
dispersal of pollen by wind is highly alike. After pollination
and fertilization in May, the ovaries do not begin to de-
velop until September (Song and Jia, 2000), and this special
adaptation of summer dormancy ensures effective pollen
flow. Therefore, ample gene flow among populations might
be attributed primarily to pollen movement. Further studies
on pollination biology and parentage analysis using co-
dominant markers, such as microsatellites, are needed to
better understand mechanisms that maintain genetic varia-
tion in these populations.
Acta Botanica Sinica 植物学报 Vol.46 No.6 2004680
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