Microsatellite genetic variation in small and isolated populations of Magnolia sieboldii ssp. japonica

Magnolia sieboldii ssp. japonica, distributed mainly in western Japan, is restricted to high elevation areas (1000-2000 m above sea level) and usually forms small isolated populations. Four microsatellite loci were assayed for 19 populations from six regions spanning the range of distribution, and the levels and distribution of genetic variation were estimated. All four loci were variable, with a total of 39 alleles, but the overall level of microsatellite genetic variation was low, especially compared with a related species, M. obovata. Genetic structure in M. sieboldii was characterised by low intrapopulational genetic variation (A = 3.74 and H(o) = 0.366 on average) and high genetic differentiation even among regional populations. Highly significant isolation-by-distance (IBD) models at the short distance were detected. Genetic drift and limited gene flow was considered to be important in determining the genetic structure within regions. Total genetic differentiation was remarkably high (F(ST) = 0.488 and R(ST) = 0.538), suggesting genetic barriers among regions. Neighbour-joining dendrograms relating the 19 populations, and further analysis on the IBD models, revealed that a stepwise mutation model was more suited than an infinite allele model to explain the genetic differentiation among regions. It is suggested that mutation at microsatellite loci might be influential in generating the genetic differentiation among regions. These results showed the potential of hypervariable microsatellite loci to evaluate the effects of genetic drift and population isolation within regions, and to detect genetic distinctiveness, in spite of the loss of overall genetic variation in M. sieboldii.     

Genetic variation of Avicennia marina (Forsk.) Vierh. (Avicenniaceae) in Vietnam revealed by microsatellite and AFLP markers

Genetic variation of Avicennia marina in the costal area of Vietnam was examined using microsatellite and AFLP markers. By using five microsatellite loci a total of 21 alleles were detected. The average number of alleles per locus per population ranged from 1.667 to 3.000. The observed heterozygosity varied from 0.180 to 0.263, with an average of 0.210 indicating relatively low level of genetic variation comparing to the previous studies on A. marina in the worldwide range. The expected heterozygosity was larger than the observed heterozygosity leading to positive inbreeding coefficients in all the six populations. Highly significant departures from Hardy-Weinberg Equilibrium were detected in four populations. AFLP analysis revealed a total of 386 loci, of which 232 (60.1%) were polymorphic. In congruent with microsatellite markers relatively low levels of genetic variation were detected at both gene and nucleotide levels (H = 0.086; pi = 0.0054). Reduced level of genetic variation was found in the central population, and in the southern populations. Both microsatellite and AFLP markers revealed large genetic differentiation (F(ST) = 0.262 and 0.338, respectively) indicating strong genetic structure among regional populations. Pairwise genetic distance by AFLP showed two populations in the north and the other two in the south are closely related each other.     

Comparison of genetic diversity at microsatellite loci and quantitative traits in hatchery populations of Japanese flounder Paralichthys olivaceus

Relationships of genetic diversity at microsatellite loci and quantitative traits were examined in hatchery-produced populations of Japanese flounder using a relatively straightforward experiment. Five hatchery populations produced by wild-caught and domesticated broodstocks were used to examine the effects of different levels (one to three generations) of domestication on the genetic characteristics of hatchery populations. Allelic richness at seven microsatellite loci in all hatchery populations was lower than that in a wild population. Genetic variation measured by allelic richness and heterozygosity tended to decrease with an increase in generations of domestication. In addition, the degree of genetic differentiation from a wild population increased with an increase in generations of domestication. Significant differences in three morphometric traits (dorsal and anal fin ray counts and vertebral counts) and three physiological traits (high temperature, salinity and formalin tolerance) were observed among the hatchery populations. The degree of phenotypic difference among populations was larger in morphometric traits than in physiological traits. The divergence pattern of some quantitative traits was similar to that observed at microsatellite loci, suggesting that domestication causes the decrease of genetic variation and the increase of genetic differentiation for some quantitative traits concomitantly with those for microsatellite loci. Significant positive correlation was observed between F _ST and the degree of phenotypic difference in the three morphometric traits and formalin tolerance, indicating that genetic variation at microsatellite loci predicts the degree of phenotypic divergence in some quantitative traits.     

Spatiotemporal genetic differentiation of Cuban natural populations of the pink shrimp <Emphasis Type="Italic">Farfantepenaeus notialis</Emphasis>

We analyzed the spatiotemporal genetic structure of Farfantepenaeus notialis populations using five microsatellites loci in order to understand the influence of natural events such as hurricanes on the genetic drift/migration balance as the main cause for the variation of allele frequencies over time. The results were compared with the previous ones obtained from allozymes and mtDNA. High and stable genetic diversity levels (He=0.879+/-0.0015) were found over eight years for the populations that inhabit the south Cuban platform, however significant changes of allele frequencies were detected over time. The F(ST) estimates, albeit low, revealed significant differences among populations inside the Ana Maria Gulf for 1995 but not for the 1999 and 2003 samples. The F(ST), AMOVA and the genetic distance analysis revealed the instability of the genetic structure over time in accordance with allozymes results. The correspondence of the microsatellite results with those obtained from allozymes confirm the effects of migration enhanced by natural events as the main cause of the temporal variation of allele frequencies. The genetic drift effect was discarded through the evaluation of Ne and the M ratio, while natural selection effects were rejected because of the lowest probability of microsatellite loci being under selective pressures. The microsatellite data are also consistent with the results obtained with mtDNA in detecting significant and persistent genetic differences between the Gulfs of Ana María and Batabanó for the years 1995 and 2003.     

黑头酸臭蚁微卫星标记的分离与开发(英文)

【目的】本研究旨在分离黑头酸臭蚁Tapinoma melanocephalum基因组微卫星标记,确定这些微卫星位点的多态性。【方法】使用454 GS-FLX焦磷酸测序技术开发来自中国华南陆地和岛屿的11个黑头酸臭蚁地理种群基因组微卫星位点。从随机设计的100对微卫星引物中筛选出10对引物,用于确定黑头酸臭蚁4个地理种群［东澳岛(DAD)、荷包岛(HBD)、梅州(MZ)和山咀(SJ)］10个微卫星位点的多态性,分析种群遗传多样性和种群分化。【结果】从11个黑头酸臭蚁地理种群基因组中成功开发和分离10对微卫星引物。在DAD, HBD, MZ和SJ 4个地理种群中,10个微卫星位点中7个有高多态性,这10个位点均显著偏离Hardy-Weinberg平衡;每个位点的等位基因数量(A)是3.50~9.00个,每个地理种群每个位点等位基因丰富度(A_R)在1.992~12.938之间。岛屿地理种群(DAD和HBD)的AR和预期杂合度(H_E)与大陆地理种群(MZ和SJ)的相比差异不显著。4个地理种群均显示高水平遗传分化(F_ST=0.15969);HBD和MZ种群与其他配对地理种群相比,遗传分化较高(F_ST=0.185),基因流较低,说明这两个种群基因流被限制。此外,遗传变异来自种群内个体之间。【结论】筛选新的微卫星位点能够为研究黑头酸臭蚁种群结构和繁殖结构提供有效工具,以深入了解其传播机制。     

Microsatellite and major histocompatibility complex variation in an endangered rattlesnake,the Eastern Massasauga (Sistrurus catenatus)

Genetic diversity is fundamental to maintaining the long‐term viability of populations, yet reduced genetic variation is often associated with small, isolated populations. To examine the relationship between demography and genetic variation, variation at hypervariable loci (e.g., microsatellite DNA loci) is often measured. However, these loci are selectively neutral (or near neutral) and may not accurately reflect genomewide variation. Variation at functional trait loci, such as the major histocompatibility complex (MHC), can provide a better assessment of adaptive genetic variation in fragmented populations. We compared patterns of microsatellite and MHC variation across three Eastern Massasauga (Sistrurus catenatus) populations representing a gradient of demographic histories to assess the relative roles of natural selection and genetic drift. Using 454 deep amplicon sequencing, we identified 24 putatively functional MHC IIB exon 2 alleles belonging to a minimum of six loci. Analysis of synonymous and nonsynonymous substitution rates provided evidence of historical positive selection at the nucleotide level, and Tajima's D provided support for balancing selection in each population. As predicted, estimates of microsatellite allelic richness, observed, heterozygosity, and expected heterozygosity varied among populations in a pattern qualitatively consistent with demographic history and abundance. While MHC allelic richness at the population and individual levels revealed similar trends, MHC nucleotide diversity was unexpectedly high in the smallest population. Overall, these results suggest that genetic variation in the Eastern Massasauga populations in Illinois has been shaped by multiple evolutionary mechanisms. Thus, conservation efforts should consider both neutral and functional genetic variation when managing captive and wild Eastern Massasauga populations.     

Assessment of population genetic structure in common wild rice Oryza rufipogon Griff. using microsatellite and allozyme markers

The genetic structure of five natural populations of common wild rice Oryza rufipogon Griff. from China, was investigated with 21 microsatellite loci and compared to estimates of genetic diversity and genetic differentiation detected by 22 allozyme loci. Microsatellite loci, as expected, have much higher levels of genetic diversity (mean values of A = 3.1, P = 73.3%, Ho = 0.358 and He = 0.345) than allozyme loci (mean values of A = 1.2, P = 12.7%, Ho = 0.020 and He = 0.030). Genetic differentiation detected by microsatellite loci ( FST = 0.468, mean I = 0.472) was higher than that for allozyme loci ( FST =0.388, mean I = 0.976). However, microsatellite markers showed less deviation from Hardy-Weinberg expectation (Wright's inbreeding coefficient FIS = -0.069) than do allozymes ( FIS = 0.337). These results suggest that microsatellite markers are powerful high-resolution tools for the accurate assessment of important parameters in population biology and conservation genetics of O. rufipogon, and offer advantages over allozyme markers.     

Contrasting patterns of mitochondrial and microsatellite population structure in fragmented populations of greater prairie-chickens

Greater prairie-chickens (Tympanuchus cupido pinnatus) were once found throughout the tallgrass prairie of midwestern North America but over the last century these prairies have been lost or fragmented by human land use. As a consequence, many current populations of prairie-chickens have become isolated and small. This fragmentation of populations is expected to lead to reductions in genetic variation as a result of random genetic drift and a decrease in gene flow. As expected, we found that genetic variation at both microsatellite DNA and mitochondrial DNA (mtDNA) markers was reduced in smaller populations, particularly in Wisconsin. There was relatively little range-wide geographical structure (FST) when we examined mtDNA haplotypes but there was a significant positive relationship between genetic (FST) and geographical distance (isolation by distance). In contrast, microsatellite DNA loci revealed significant geographical structure (FST) and a weak effect of isolation by distance throughout the range. These patterns were much stronger when populations with reduced levels of genetic variability (Wisconsin) were removed from the analyses. This suggests that the effects of genetic drift were stronger than gene flow at microsatellite loci, whereas these forces were in range-wide equilibrium at mtDNA markers. These differences between the two molecular markers may be explained by a larger effective population size (Ne) for mtDNA, which is expected in species such as prairie-chickens that have female-biased dispersal and high levels of polygyny. Our results suggest that historic populations of prairie-chickens were once interconnected by gene flow but current populations are now isolated. Thus, maintaining gene flow may be important for the long-term persistence of prairie-chicken populations.     

Genetic variation of Ardisia crenata in south China revealed by nuclear microsatellite

Ardisia crenata Sims,one of the most widely distributed Ardisia in the world,is an important ornamental and medicinal plant species.Using seven polymorphic nuclear microsatellite loci,we studied the genetic variation of 20 natural populations of A.crenata across its distribution center in south China.Significant deviation from the Hardy-Weinberg equilibrium in all populations and at all loci were detected,and the fixation index was high(FIS = 0.725),indicating that inbreeding may be dominant in the mixed mating system of this self-compatible species.The average genetic diversity within populations was relatively low(HS = 0.321).There was significant genetic differentiation among populations(FST = 0.583),which may have resulted from a high level of inbreeding and a low level of gene flow.Ardisia crenata in south China can be roughly divided into an eastern group and a western group,consistent with the floristic division of the Sino-Himalayan forest subkingdom and the Sino-Japanese forest subkingdom.There may be separated glacial refugia in each region.     

Macrogeographic population structure of the tsetse fly, Glossina pallidipes (Diptera: Glossinidae)

Tsetse flies are confined to sub-Saharan Africa where they occupy discontinuous habitats. In anticipation of area-wide control programmes, estimates of gene flow among tsetse populations are necessary. Genetic diversities were partitioned at eight microsatellite loci and five mitochondrial loci in 21 Glossina pallidipes Austin populations. At microsatellite loci, Nei's unbiased gene diversity averaged over loci was 0.659 and the total number of alleles was 214, only four of which were shared among all populations. The mean number of alleles per locus was 26.8. Random mating was observed within but not among populations (fixation index FST=0.18) and 81% of the genetic variance was within populations. Thirty-nine mitochondrial variants were detected. Mitochondrial diversities in populations varied from 0 to 0.85 and averaged 0.42, and FST=0.51. High levels of genetic differentiation were characteristic, extending even to subpopulations separated by tens and hundreds of kilometres, and indicating low rates of gene flow.     

Genetic diversity and differentiation between the two remaining populations of the critically endangered Mediterranean monk seal

The Mediterranean monk seal Monachus monachus , is a critically-endangered species of which only two populations, separated by c . 4000 km, remain: the eastern Mediterranean (150–300 individuals) and the Atlantic/western Sahara populations (100–130 individuals). We measured current levels of nuclear genetic variation at 24 microsatellite loci in 12 seals from the eastern Mediterranean and 98 seals from the western Sahara population and assessed differences between them. In both populations, genetic variation was found to be low, with mean allelic richness for the loci polymorphic in the species of 2.09 and 1.96, respectively. For most loci, the observed allele frequency distributions in both populations were discontinuous and the size ranges similar. The eastern Mediterranean population had 14 private alleles and the western Sahara had 18, but with a much larger sample size. Highly significant differences in allele frequencies between the two populations were found for 14 out of 17 loci. F _ST between the two populations was 0.578 and the estimated number of migrants per generation was 0.046, both clearly indicating substantial genetic differentiation. From a conservation perspective, these results suggest that each population may act as a source for introducing additional genetic variation into the other population.     

梨小食心虫微卫星标记的扩增稳定性及多态性分析

【目的】筛选适合我国梨小食心虫Grapholita molesta种群遗传学研究的微卫星位点,并依据所筛选的微卫星位点进行梨小食心虫地理种群的遗传多样性分析。【方法】利用欧洲梨小食心虫和苹果蠹蛾Cydia pomonella种群中已报道的11个微卫星位点, 分析各位点在我国12个种群257头梨小食心虫样本中的扩增稳定性,再进行其多态性分析,筛选适合的位点,然后进行种群遗传多态性分析。【结果】在分析的11个微卫星位点中, 位点Gm01, Gm03, Gm04和Cyd15无法稳定扩增; 位点Gm05扩增成功率较低, 位点Gm07遗传多态性较低; 而位点Gm02, Gm06, Gm08, Gm09和Gm10等扩增效果稳定且遗传多态性丰富。这5个稳定扩增的微卫星位点平均等位基因数量（N_A）为7.417~12.500, 平均观察杂合度（H_o）为0.366~0.655, 平均期望杂合度（H_e）为0.642~0.846, 多态信息含量（PIC）为0.800~0.935。【结论】本研究成功筛选出位点Gm02, Gm06, Gm08, Gm09和Gm10等5个微卫星位点。基于这5个微卫星位点标记的结果显示, 山东和陕西不同梨小食心虫地理种群均具有丰富的遗传多样性。 这5个位点可以适用于我国梨小食心虫种群的进一步遗传分析研究。     

Analysis of microsatellite DNA markers reveals no genetic differentiation between wild and hatchery populations of Pacific threadfin in Hawaii

Pacific threadfin, Polydactylus sexfilis, is popular fish in recreational fishing, as well as aquaculture in Hawaii. Its natural population has been continuously declining in the past several decades. Microsatellite DNA markers are useful DNA-based tool for monitoring Pacific threadfin populations. In this study, fifteen Microsatellite (MS) DNA markers were identified from a partial genomic Pacific threadfin DNA library enriched in CA repeats, and six highly-polymorphic microsatellite loci were employed to analyze genetic similarity and differences between the wild population and hatchery population in Oahu Island. A total of 37 alleles were detected at the six MS loci in the two populations. Statistical analysis of fixation index (F(ST)) and analysis of molecular variance (AMOVA) showed no genetic differentiation between the wild and hatchery populations (F(ST) = 0.001, CI(95%) = -0.01-0.021). Both high genetic diversity (H(o) = 0.664-0.674 and H(e) = 0.710-0.715) and Hardy-Weinberg equilibrium were observed in the wild and hatchery populations. Results of genetic bottleneck analysis indicated that the hatchery was founded with sufficient numbers of brooders as inbreeding coefficient is very low (F(IS) = 0.052-0.072) in both wild and hatchery populations. Further studies are needed for comprehensive determinations of genetic varieties of primary founder broodstocks and successive offspring of the hatchery and wild populations with increased number of Pacific threadfin sample collections.     

Population structure and conservation genetics of wild rice Oryza rufipogon (Poaceae): a region-wide perspective from microsatellite variation

Oryza rufipogon Griff. is the most agriculturally important but seriously endangered wild rice species. To better estimate how genetic structure can be used to obtained a conservation perspective of the species, genetic variability at six polymorphic microsatellite DNA loci was examined. High levels of genetic variability were detected at six loci in 1245 individuals of 47 natural populations covering most of the species' range in China (overall RS = 3.0740, HO = 0.2290, HS = 0.6700). Partitioning of genetic variability (FST = 0.246) showed that most microsatellite variation was distributed within populations. Significant departures from Hardy-Weinberg expectations and very strong linkage disequilibrium indicate a high degree of inbreeding in the species and severe subdivision within populations. A mean Nm value of 0.7662 suggested a limited gene flow among the assayed populations. Our study suggests that conservation and restoration genetics should focus in particular on the maintenance of historically significant processes such as high levels of outbreeding and gene flow and large effective population size in the species.     

Microsatellite loci isolated from the tropical tree Hymenaea courbaril L. (Fabaceae)

We developed 11 microsatellite markers for Hymenaea courbaril for the purpose of studying spatial genetic structure and gene flow. The microsatellite loci were screened in 44 trees from two populations. All loci were polymorphic, exhibiting between two and 16 alleles, and levels of expected heterozygosity from 0.174 to 0.909. Departures from Hardy-Weinberg equilibrium were detected for all loci in one population. The estimated null allele frequency is low or moderate. No locus combinations exhibited linkage disequilibrium.     

Balancing selection, random genetic drift, and genetic variation at the major histocompatibility complex in two wild populations of guppies (Poecilia reticulata)

Our understanding of the evolution of genes of the major histocompatibility complex (MHC) is rapidly increasing, but there are still enigmatic questions remaining, particularly regarding the maintenance of high levels of MHC polymorphisms in small, isolated populations. Here, we analyze the genetic variation at eight microsatellite loci and sequence variation at exon 2 of the MHC class IIB (DAB) genes in two wild populations of the Trinidadian guppy, Poecilia reticulata. We compare the genetic variation of a small (Ne, 100) and relatively isolated upland population to that of its much larger (Ne approximately 2400) downstream counterpart. As predicted, microsatellite diversity in the upland population is significantly lower and highly differentiated from the population further downstream. Surprisingly, however, these guppy populations are not differentiated by MHC genetic variation and show very similar levels of allelic richness. Computer simulations indicate that the observed level of genetic variation can be maintained with overdominant selection acting at three DAB loci. The selection coefficients differ dramatically between the upland (s > or = 0.2) and lowland (s < or = 0.01) populations. Parasitological analysis on wild-caught fish shows that parasite load is significantly higher on upland than on lowland fish, which suggests that large differences in selection intensity may indeed exist between populations. Based on the infection intensity, a substantial proportion of the upland fish would have suffered direct or indirect fitness consequences as a result of their high parasite loads. Selection by parasites plays a particularly important role in the evolution of guppies in the upland habitat, which has resulted in high levels of MHC diversity being maintained in this population despite considerable genetic drift.     

Maintenance of genetic differentiation across a transition zone in the sea: discordance between nuclear and cytoplasmic markers

To investigate the origin and maintenance of the genetic discontinuity between Atlantic and Mediterranean populations of the common sea bass (Dicentrarchus labrax) we analysed the genetic variation at a fragment of mitochondrial cytochrome b sequence for 18 population samples. The result were also compared with new or previously published microsatellite data. Seven mitochondrial haplotypes and an average nucleotidic divergence of 0.02 between Atlantic and Mediterranean populations that matches a Pleistocene allopatric isolation were found. The frequency variation at the cytochrome b locus was many times greater between Atlantic and Mediterranean populations (theta(C) = 0.67) than at microsatellite loci (theta(N)= 0.02). The examination of the different evolutionary forces at play suggests that a sex-biased hybrid breakdown is a likely explanation for part of the observed discrepancy between mitochondrial and nuclear loci. In addition, an analysis is made of the correlation between microsatellite loci points towards the possible existence of a hybrid zone in samples from the Alboran Sea.     

Range-wide genetic structure in a north-east Asian spruce (Picea jezoensis) determined using nuclear microsatellite markers

Aim We used microsatellite markers to determine the range‐wide genetic structure of Picea jezoensis and to test the hypothesis that the past population history of this widespread cold‐temperate spruce has resulted in a low level of genetic variation and in imprints of inbreeding and bottlenecks in isolated marginal populations. Location The natural range of the three infraspecific taxa of P. jezoensis throughout north‐east Asia, including isolated marginal populations. Methods We analysed a total of 990 individuals across 33 natural populations using four nuclear microsatellite loci. Population genetic structure was assessed by analysing genetic diversity indices for each population, examining clustering (model‐based and distance‐based) among populations, evaluating signals of recent bottlenecks, and testing for isolation by distance (IBD). Results The 33 populations were clustered into five groups. The isolated marginal groups of populations (in Kamchatka, Kii in Japan and South Korea) exhibited low levels of allelic richness and gene diversity and a complete or almost complete loss of rare alleles. A recent bottleneck was detected in the populations in Hokkaido across to mid‐Sakhalin. The IBD analysis revealed that genetic divergence between populations was higher for populations separated by straits. Main conclusions Picea jezoensis showed a higher level of genetic differentiation among populations (F_ST = 0.101) than that observed in the genus Picea in general. This might be attributable to the fact that historically the straits around Japan acted as barriers to the movement of seeds and pollen. The low levels of genetic diversity in the isolated marginal population groups may reflect genetic drift that has occurred after isolation. Evidence of a significant bottleneck between the Hokkaido and mid‐Sakhalin populations implies that the cold, dry climate in the late Pleistocene resulted in the decline and contraction of populations, and that there was a subsequent expansion followed by a founder effect when conditions improved. The high polymorphism observed in P. jezoensis nuclear microsatellites revealed cryptic genetic structure that organellar DNA markers failed to identify in a previous study.     

INTRASPECIFIC GENETIC DIVERSITY IN THE MARINE COCCOLITHOPHORE EMILIANIA HUXLEYI (PRYMNESIOPHYCEAE): THE USE OF MICROSATELLITE ANALYSIS IN MARINE PHYTOPLANKTON POPULATION STUDIES1

Using primer pairs for seven previously described microsatellite loci and three newly characterized microsatellite loci from the coccolithophore Emiliania huxleyi (Lohm.) Hay and Mohler, we assessed genetic variation within this species. Analysis of microsatellite length variants (alleles) was conducted for 85 E. huxleyi isolates representative of different ocean basins. These results revealed high intraspecific genetic variability within the E. huxleyi species concept. Pairwise comparison of a 1992 Coastal Fjord group (FJ92) (n=41) and a North East Atlantic (NEA) group (n=21), using F_ST as an indicator of genetic differentiation, revealed moderate genetic differentiation (F_ST=0.09894; P=0; significance level=0.05). Gene flow between the FJ92 and NEA groups was estimated to be low, which is in agreement with the moderate levels of genetic differentiation revealed by the microsatellite data. A genetic assignment method that uses genotype likelihoods to draw inference about the groups to which individuals belong was tested. Using FJ92 and NEA as reference groups, we observed that all the E. huxleyi groups tested against the two reference groups were unrelated to them. On a global biogeographical scale, E. huxleyi populations appear to be highly genetically diverse. Our findings raise the question of whether such a high degree of intraspecific genetic diversity in coccolithophores translates into variability in ecological function.     

Genetic variation of Ardisia crenata in south China revealed by nuclear microsatellite

Ardisia crenata Sims, one of the most widely distributed Ardisia in the world, is an important ornamental and medicinal plant species. Using 7 polymorphic nuclear microsatellite loci, we studied the genetic variation of 20 natural populations of A. crenata across its distribution centre, the south China. Significant deviation from Hardy-Weinberg equilibrium in all populations and at all loci were detected, and the fixation index was high (F_IS = 0.725), indicating that inbreeding may be dominant in the mixed mating system of this self-compatible species. The average genetic diversity within populations was relatively low (H_S = 0.321). There was significant genetic differentiation among populations (F_ST = 0.583), which may be resulted from high level of inbreeding and low level of gene flow. A. crenata in south China can be roughly divided into eastern group and western group, consistent with the floristic division of Sino-Himalayan forest subkingdom and Sino-Japanese forest subkingdom. It was suggested that there may be separated glacial refugia in each region.