Population structure and genetic diversity of Stipa grandis P. Smirn,a dominant species in the typical steppe of northern China

Random amplified polymorphic DNA (RAPD) markers were used to characterize genetic heterogeneity within and among five populations of Stipa grandis in the Xilingol Plateau. Estimates of the percentage of polymorphic bands, Shannon's diversity information index and Nei's gene diversity index were comparatively high in the five populations, and the Population GSM was found to have the highest genetic diversity among all populations. An analysis of molecular variance indicated that the majority of variation existed within populations (74.12%), and that there was significant differentiation among populations (Φ_ST = 25.88%, P < 0.001). Genetic distance (Φ_ST) ranged from 0.198 to 0.310 and the differentiation between pair-wise populations was significant when individual pairs of populations were compared. Based on the Φ_ST values, gene flow (Nm) was estimated and was found to vary from 0.556 to 1.013 between pair-wise populations and 0.7412 among populations. The results of UPGMA cluster analysis and nonmetric multi-dimensional scaling analysis indicated that most variation occurred within populations and that genetic differentiation had happened between populations. These findings are important for a better understanding of the adaptive strategy of S. grandis in northern China and will be useful for conservation managers to work out an effective strategy to protect this important species.     

Assessing genetic diversity of populations of topmouth culter (Culter alburnus) in China using AFLP markers

Genetic diversity of five wild populations and a cultured population of topmouth culter (Culter alburnus) was investigated using amplified fragment length polymorphism (AFLP). A total of 373 reproducible bands amplified with seven AFLP primer combinations were obtained from 163 fish. The percentage of polymorphic loci ranged widely from 37.0% to 69.2% within distinct populations. The cultured population appeared to have a lower level of polymorphism (37.0%), gene diversity (0.121 ± 0.188) and Shannon's Information index (0.183 ± 0.263) than the wild populations. Analysis of molecular variance (AMOVA) revealed that average F_ST value overall loci was 0.2671, and the percentage of variation within population (73.29%) was larger than among populations (26.71%) (P < 0.01). The six populations were clustered into two major clades with UPGMA. The results from analysis of population pairwise gene flow indicated moderate gene flow among populations. Our study indicated that the genetic diversity of the cultured population was reduced compared with the wild populations. Geographic isolation, habitat, and artificial selection all may have played important roles in population differentiation. The information may be beneficial to future broodstock selection and defining conservation management for the different populations of topmouth culter.     

Microsatellite analysis reveals the genetic structure and gene flow of the aquatic quillwort Isoetes sinensis, a critically endangered species in China

Isoetes sinensis is a critically endangered aquatic quillwort, occurring in two fragmented sites of China (Xiuning county of Anhui; Jiande county of Zhejiang). During a five-year period (2004-2009), the areas and sizes of the two populations diminished dramatically due to intensive human activities. Genetic structure of the species was investigated using simple sequence repeat makers (SSRs). For seven nuclear microsatellites, high levels of genetic diversity were found within populations (H_E = 0.324-0.447). Strong genetic differentiation was detected between populations (G_ST = 0.376), while weak genetic differentiation was found within populations (G_ST = 0.026-0.080). Notably, in contrast to the source-sink model suggested by previous study (Chen et al., 2009), the migration pattern of I. sinensis along the Xin’an River is best explained by the linear symmetrical non-adjacent flow model (LSNF), which indicates that intensive human activities of recent years have greatly affected the gene exchange pattern among I. sinensis subpopulations.     

Genetic diversity and biogeography of the traditional Chinese medicine, Gardenia jasminoides, based on AFLP markers

Gardenia jasminoides Ellis is used in traditional Chinese medicine (TCM) in China. Levels of genetic variation and patterns of population structure within and among eight wild or cultivated populations of G. jasminoides Ellis in China were investigated using amplified fragment length polymorphism (AFLP) markers. Of the 11 primers screened, four produced highly reproducible AFLP bands. Using these primers, 244 discernible DNA fragments were generated with 165 bands (67.6%), were polymorphic, indicating considerable genetic variation at the species level. In contrast, there were relatively low levels of polymorphism at the population level with the percentage of polymorphic bands (PPB) ranging from 36.89% to 59.43%. Genetic diversity within populations ranged from 0.2086 to 0.3108, averaging 0.2392 at the species level. A high level of genetic differentiation among populations was detected based on Nei's genetic diversity analysis (76.59%), Shannon's index analysis (64.8%) and AMOVA analysis (72.75%). No significant statistical differences (analysis of molecular variance [AMOVA], p = 0.0639) in AFLP variation were found between regions. However, the variance among populations and within populations differed significantly (p < 0.001). An indirect estimate of historical levels of gene flow (N_m = 1.7448) was consistent with the high mean genetic identity (mean I = 0.9263) found among populations. There is an association between geographic and genetic distances between populations. Presently gene change exists between populations.     

Inter-simple sequence repeat (ISSR) analysis of genetic variation of Chondrus crispus populations from North Atlantic

ISSR analysis was used to investigate genetic variations of 184 haploid and diploid samples from nine North Atlantic Chondrus crispus Stackhouse populations and one outgroup Yellow Sea Chondrus ocellatus Holmes population. Twenty-two of 50 primers were selected and 163 loci were scored for genetic diversity analysis. Genetic diversity varied among populations, percentage of polymorphic bands (PPB) ranged from 27.0 to 55.8%, H (Nei's genetic diversity) ranged from 0.11 to 0.20 and I (Shannon's information index) ranged from 0.16 to 0.30. Estimators PPB, H and I had similar values in intra-population genetic diversity, regardless of calculation methods. Analysis of molecular variance (AMOVA) apportioned inter-population and intra-population variations for C. crispus, showing more genetic variance (56.5%) occurred in intra-population, and 43.5% variation among nine populations. The Mantel test suggested that genetic differentiation between nine C. crispus populations was closely related with geographic distances (R = 0.78, P = 0.002). Results suggest that, on larger distance scale (ca. >1000 km), ISSR analysis is useful for determining genetic differentiations of C. crispus populations including morphologically inseparable haploid and diploid individuals.     

Mating system and population genetic structure of Bruguiera gymnorrhiza (Rhizophoraceae), a viviparous mangrove species in China

In order to explain the diversity patterns and develop the conservation strategies, the population genetic structures and the mating systems of Bruguiera gymnorrhiza from the coastlines of south China were investigated in this study. The mating system parameters were analyzed using progeny arrays for allozyme markers. The multilocus outcrossing rates (tm) ranged from 0.845 (Fugong) to 0.267 (Dongzhai harbor). High allozyme variations within the five collected populations were determined and compared with the published data of other plant species with the mixed mating systems. At species level, the percentage of polymorphic loci (P) was 80%, the average number of alleles per locus (A) was 2.440, and the heterozygosity (He) was 0.293. The total gene diversity within each population (H_S = 0.2782) and the coefficient of genetic differentiation (G_ST = 0.0579) among the populations were estimated. On the basis of this population genetic structure, it is suggested that the gene flow (Nm = 3.85) is quite high, which is possibly related to its water-dispersed hypocotyls. It is also suggested that the mating system of this species is of mixed mating.     

Genetic differentiation in endangered Gynostemma pentaphyllum (Thunb.) Makino based on ISSR polymorphism and its implications for conservation

Studies were performed to investigate the genetic variation of 14 natural populations of Gynostemma pentaphyllum (Thunb.) Makino, an outcrossing clonal plant species in China, using inter-simple sequence repeat (ISSR) markers. Fourteen selected primers were used to amplify DNA samples from 140 individuals, and totally 194 loci were detected. The percentage of polymorphic bands (PPBs) showed that the genetic diversity was pretty high at the species level (PPB = 96.39%) but quite low at the population level (PPB = 1.03–25.26%). Shannon's information index (I) and Nei's gene diversity (h) displayed a similar trend to PPB. According to the hierarchical analysis of molecular variance (AMOVA) and Nei's analysis of gene diversity, the percentages of genetic variation among populations were 88.66 and 88.94%, respectively, indicating a high level of inter-population genetic differentiation. The low levels of genetic diversity within populations and high genetic differentiation among populations were assumed to result from the limited gene flow, the clonal nature and genetic drift. Based on the genetic data, effective conservation strategies were proposed for conserving this traditional Chinese medicinal herb. Concerning the management of G. pentaphyllum, we suggested that in situ conservation be an important and practical measure for maintaining the genetic diversity and that a possibly maximum number of populations be conserved. Populations EMS and HLT, in which particularly low levels of genetic variation were characterized, should be given the priority for ex situ conservation.     

Population genetic structure and historical demography of grey mullet, Mugil cephalus, along the coast of China,inferred by analysis of the mitochondrial control region

Population genetic structure and historical demography of grey mullet, Mugil cephalus, along the coast of China were examined with a 389-bp segment of mtDNA control region. In total, 117 samples were collected from seven locations and 77 haplotypes were obtained. No haplotype was concurrently presented in all the samples, and samples in Southern and Northern regions had distinctly different haplotypes. Sorting of the data cladistically into phylogenetic trees indicated that these haplotypes can be divided into two main clades. Analysis of molecular variance (AMOVA) indicated significant genetic differentiation among subpopulations in different regions (φ_CT = 0.9505, p < 0.01). The average pairwise differences and φ_ST values (0.8943–0.9464) between regional populations were significant. The net Tumura and Nei genetic distance (0.5577 ± 0.1421) between the two groups was large. The deep and unique divergence between the two groups suggested that each group is likely to represent a distinct species. In contrast to the great genetic divergence on a broad scale, small but significant population subdivisions at a less spatial scale were also detected both in Southern and Northern regions, which support the conclusion that M. cephalus has limited dispersal potential. High haplotype diversity (h = 0.8716 ± 0.1462) and low nucleotide diversity (π = 0.0046 ± 0.0030) were found among the three Northern samples. Among the four Southern samples, however, extraordinarily high levels of both haplotype diversity (h = 0.9886 ± 0.0057) and nucleotide diversity (π = 0.0425 ± 0.0212) were detected. The different polymorphisms suggest an apparent distinguishing demographic history between regionally Southern and Northern populations, though mismatch distribution analyses and neutrality tests implied a late Pleistocene population expansion of both Northern and Southern populations.     

Genetic diversity of the endangered species Kirengeshoma palmata (Saxifragaceae) in China

In order to investigate the levels of genetic diversity of the endangered species Kirengeshoma palmata (Saxifragaceae), four extant populations were sampled and analyzed using inter-simple sequence repeats (ISSR) markers. We expected a low genetic diversity level, but our results revealed a high level of intraspecific genetic diversity, probably resulting from this species being in a refuge during the last glaciation (at population level: P = 63.25%, A_e = 1.47, H_E = 0.26 and H_O = 0.37; at species level: P = 79.00%, A = 1.5538, H_T = 0.2586 and H_sp = 0.3104). A low level of genetic differentiation among populations was detected based on Nei's genetic diversity analysis (16.69%) and AMOVA (19.36%). Populations shared high levels of genetic identity. Insect pollination and seed dispersal by wind may have facilitated extensive gene flow and are likely responsible for this present structure of genetic variation.     

Host-associated genetic differentiation in rice grasshopper, Oxya japonica, on wild vs. cultivated rice

Rice grasshopper, Oxya japonica, is one of the most important pests in south China, mainly inhabiting fields of wild rice (Oryza rufipogon) and cultivated rice (Oryza sativa). In this study, we used AFLP marker to investigate the genetic diversity and population structure of rice grasshoppers collected from south China, with emphasis on testing the hypothesis that there was significant genetic differentiation among grasshopper populations associated with different hosts (i.e. wild vs. cultivated rice). Seven populations consisting of 104 individuals were sampled from Hainan Island and the mainland of south China. Eight primer combinations produced 564 reliable bands, of which 563 were polymorphic. O. japonica showed considerable genetic variation at population level, with gene diversity (H_E) ranging from 0.1103 to 0.2035. Genetic diversity were studied on seven populations, and generally three populations from wild rice had higher levels of genetic diversity (H_E = 0.1635) than the other four populations feeding on cultivated rice (H_E = 0.1327). We observed high population differentiation, with F_st ranging from 0.4172 to 0.7652 among the seven populations. However, Mantel test detected no significant correlation between genetic distance and geographical distance (r = 0.3541; p = 0.0689). By contrast, we found significant genetic differentiation between groups collected from different hosts. These data suggested that the anthropogenic activity in cultivated rice fields (i.e. pesticides, fertilization and cultivation) could have played an important role in shaping the genetic structure of O. japonica.     

Genetic diversity within and among populations of the endangered species Taxus fuana (Taxaceae) from Pakistan and implications for its conservation

The West Himalayan yew, Taxus fuana Nan Li & R.R. Mill (Taxaceae), is an endangered species endemic to the Western Himalayas. An investigation of the genetic diversity of wild populations of T. fuana in Pakistan was undertaken. The genetic diversity and genetic structure was quantified using random amplified polymorphic DNA (RAPD) variation in 219 individuals of the 10 populations. Of the 32 universal primers screened 16 produced highly reproducible, clear RAPD bands. Using these primers, 193 discernible DNA fragments were generated, of which 164 (84.97%) were polymorphic. The statistical results indicated that there was a relatively low genetic diversity within populations (with percentages of polymorphic bands, PPB, ranging from 29.53 to 50.26%, with an average of 38.34% and a Nei's genetic diversity index (H_E) of 0.1165), and a high genetic differentiation among populations (G_ST = 0.5842, Φ_ST = 0.5685) within these populations. The gene flow (N_m) was low with only 0.3558.     

Conservation genetics of endangered medicinal plant Commiphora wightii in Indian Thar Desert

To ascertain the conservation priorities and strategies for Commiphora wightii, an endangered medicinal plant of Indian Thar Desert, genetic diversity was estimated within and among different populations. The total of 155 amplification products were scored using ten each of RAPD and ISSR primers, exhibiting an overall 86.72% polymorphism across 45 individuals representing eight populations. The cumulative data of two markers were used to compute pair-wise distances. The Neighbor-Joining tree revealed high genetic differentiation among populations except Kiradu population. Nei's gene diversity (h) ranged between 0.082 and 0.193 with total diversity at species level is 0.294. Shannon's information index (I) ranged between 0.118 and 0.275 with an overall diversity of 0.439. Analysis of molecular variance showed more diversity among population level (56.65%) than at within population level (43.35%). The low gene flow value (Nm = 0.349) and high coefficient of genetic differentiation (G_ST = 0.589) and high fixation index (F_ST = 0.566) demonstrated elevated genetic differentiation among the population and can be predicted that these populations are not in Hardy–Weinberg proportions. Principal Co-ordinate Analysis confirms that Akal population has become phylogenetically more distinct and less diverse than the rest of the samples. Mantel's test revealed no correlation between genetic and geographical distances of populations (R² = 0.122). Overall highest diversity was observed in the population of Machiya Safari Park and Kiradu, while lowest in Akal population, later may constitute an evolutionary significant unit, having merit for special management.     

Genetic diversity of wild populations of Rheum tanguticum endemic to China as revealed by ISSR analysis

Rheum tanguticum is an important but endangered traditional Chinese medicine endemic to China. The wild resources have been declining. Establishing the genetic diversity of the species would assist in its conservation and breeding program. Inter-simple sequence repeats (ISSR) markers were used to assess the genetic diversity and population genetic structure in 13 wild populations of R. tanguticum from Qinghai Province. Thirteen selected primers produced 329 discernible bands, with 326 (92.94%) being polymorphic, indicating high genetic diversity at the species level. The Nei's gene diversity (He) was estimated to be 0.1724 within populations (range 0.1026–0.2104), and 0.2689 at the species level. Analysis of molecular variance (AMOVA) showed that the genetic variation was found mainly within populations (71.02%), but variance among populations was only 28.98%. In addition, Nei's differentiation coefficients (G_st) was found to be high (0.3585), confirming the relatively high level of genetic differentiation among populations. Mantel test revealed a significant correlation between genetic and geographic distances (r = 0.573, P = 0.002), and the unweighted pair-group method using arithmetic average (UPGMA) clustering and Principal coordinates analysis (PCoA) demonstrated similar results. Meanwhile, the genetic diversity of R. tanguticum positively correlated with altitude and annual mean precipitation, but negatively correlated with latitude and annual mean temperature. This result might be an explanation that the natural distribution of R. tanguticum is limited to alpine cold areas. We propose conservation strategy and breeding program for this plant.     

PCR-RFLP analysis of mitochondrial DNA cytochrome b gene among Haruan (Channa striatus) in Malaysia

Haruan (Channa striatus) is in great demand in the Malaysian domestic fish market. In the present study, mtDNA cyt b was used to investigate genetic variation of C. striatus among populations in Peninsular Malaysia. The overall population of C. striatus demonstrated a high level of haplotype diversity (h) and a low-to-moderate level of nucleotide diversity (π). Analysis of molecular variance (AMOVA) results showed a significantly different genetic differentiation among 6 populations (F_ST = 0.37566, P = 0.01). Gene flow (Nm) was high and ranged from 0.32469 to infinity (∞). No significant relationship between genetic distance and geographic distance was detected. A UPGMA tree based on the distance matrix of net interpopulation nucleotide divergence (d_A) and haplotype network of mtDNA cyt b revealed that C. striatus is divided into 2 major clades. The neutrality and mismatch distribution tests for all populations suggested that C. striatus in the study areas had undergone population expansion. The estimated time of population expansion in the mtDNA cyt b of C. striatus populations occurred 0.72-6.19 million years ago. Genetic diversity of mtDNA cyt b and population structure among Haruan populations in Peninsular Malaysia will be useful in fisheries management for standardization for Good Agriculture Practices (GAP) in fish-farming technology, as well as providing the basis for Good Manufacturing Practices (GMP).     

Population genetic differentiation of Schisandra chinensis and Schisandra sphenanthera as revealed by ISSR analysis

Schisandra chinensis (Turcz.) Baill. and Schisandra sphenanthera Rehd. et Wils. are well-known Chinese medicinal plants. The population genetic variation of the two species was studied using inter simple sequence repeat (ISSR) molecular markers. High levels of genetic diversity are revealed in both S. chinensis (P = 88.36%, h = 0.2894, I = 0.4396) and S. sphenanthera (P = 84.09%, H = 0.2782, I = 0.4280). However, the population genetic differentiation is significantly different between the two species. The S. sphenanthera harbors as high as 27% of the genetic variation among populations but 73% within populations, whereas in S. chinensis 17% of the genetic variation occurs among populations and 83% within populations. Both significant (P < 0.05) heterozygosity excess and shifted mode of allele frequency distribution are detected in four out of six populations of S. chinensis and one out of five populations of S. sphenanthera, suggesting the occurrence of recent population bottlenecks in the two species. The different patterns of genetic variation in S. chinensis and S. sphenanthera are discussed in relation to their differences in pollination mechanism, geographic distribution and historical events, and the level of gene flow and genetic drift.     

Assessment of genetic differentiation in the large yellow croaker, Pseudosciaena crocea Richardson,and its first hybrid filial generations with AFLP markers

The genetic diversity (the digital characteristics) of four populations (120 individuals) of breeding large yellow croakers, Pseudosciaena crocea Richardson, was analyzed with amplified fragment length polymorphism (AFLP) markers. Ten primer combinations amplified 248 bands, of which 39.52% were polymorphic. Shannon's information index of the Daiqv (DQ) population was higher than that of the Minyu (MY) population, at 0.2167 and 0.2074, respectively. Additionally, the Shannon's information index value for the minus-hybrid (DQ population♂ × MY population♀) first hybrid generation was higher than the value for the plus-hybrid (MY population♂ × DQ population♀) first hybrid generation at 0.1687 and 0.1613, respectively. The F_ST of the parental generation was lower than that of the filial generation at 0.0329 and 0.0891, respectively. Gene flow was very high according to F_st values in both parental and filial generations. The UPGMA clustering analysis based on genetic similarity organized the four populations into three groups. The minus-hybrid stock was the most distinct as compared to the other populations.     

Low genetic variation detected within the widespread mangrove species Nypa fruticans (Palmae) from Southeast Asia

Genetic diversity within and among six natural populations of Nypa fruticans from China, Vietnam, and Thailand was assessed using SSR and ISSR analysis. Our results showed an extremely low level of genetic diversity of N. fruticans (at the species level, P = 11.76% and 2.88%, He = 0.0279 and 0.0113, I = 0.0470 and 0.0167 by SSRs and ISSRs, respectively) across a total of 183 individuals. No genetic variation was detected within any population except for the Thailand population by SSRs (P = 11.76%, He = 0.0417; I = 0.0622). The bottlenecks during glacial epochs, founder effects, and propagation pattern may be responsible for the extremely low level of genetic diversity of N. fruticans.     

Chloroplast DNA variation and phylogeographic patterns in the Chinese endemic marsh herb Sagittaria potamogetifolia

We examined chloroplast DNA (cpDNA) atpB–rbcL intergenic spacer sequences variation within Sagittaria potamogetifolia, an endangered and endemic marsh herb in China. Sequence data were obtained from 54 individuals in six extant populations of the species. Sequences appeared to evolve neutral (Tajima's criterion D = −1.59826, 0.1 > P > 0.05 and Fu and Li's tests D* = −1.44484, P > 0.1; F* = −1.83446, P > 0.1). Eleven haplotypes were identified in S. potamogetifolia. A relatively high level of haplotype diversity (h = 0.0.699) and low level of nucleotide diversity (pi = 0.0035 ± 0.0020) were detected in S. potamogetifolia. Pairwise comparisons of F_st and Nm deduced from cpDNA variation suggested no significant genetic differentiation between populations of S. potamogetifolia excepted for the WY-1 population. Low genetic differentiation among populations and also among regions was consistently indicated by both hierarchical analyses of molecular variance (AMOVA) and the structure of a neighbor-joining tree. Lack of population differentiation between populations or between regions in cpDNA sequences may be due to effects of lower substitution rates or lineage sorting. In the minimum spanning network, all tip haplotypes except for the haplotype J were unique to a particular population, while the interior nodes except for the haplotype E were widespread (haplotype A). From nested clade analysis (NCA), the evolutionary events such as restricted gene flow with isolation by distance and allopatric fragmentation were inferred to responsible for the current distribution of S. potamogetifolia populations, as well as their genetic diversity.     

Ecological genetics of Reaumuria soongorica (Pall.) Maxim. population in the oasis–desert ecotone in Fukang,Xinjiang, and its implications for molecular evolution

Using inter-simple sequence repeat (ISSR) markers, studies were performed to characterize the population genetic diversity and structure of Reaumuria soongorica (Pall.) Maxim. in the oasis–desert ecotone in Fukang, Xinjiang. Eleven primers were screened to amplify DNA sequences from 132 individuals, which corresponded to seven subpopulations. Totally, 176 loci, all of them polymorphic, were detected, and the percentage of polymorphic bands (PPB) was 100%, indicating a relatively high genetic diversity within the R. soongorica population. According to the hierarchical analysis of molecular variances (AMOVA), the analysis of Shannon's diversity and Nei's analysis of gene diversity, the percentages of genetic variation among subpopulations were 15.87%, 16.28% and 14.58%, respectively, which meant that 83.72–85.42% of total genetic variation occurred within subpopulations. Besides, POPGENE analysis also revealed a relatively high gene flow (N_m = 2.9290) among subpopulations. Correlation analysis showed that there existed no significant correlation between the ISSR-based genetic diversity of the seven R. soongorica subpopulations and their ecological factors (mainly in soil) (P > 0.05). However, on the other hand, Mantel test revealed a significant correlation between inter-subpopulation genetic distances and geographic distances (r = 0.637, P < 0.01), indicating that geographic distance was among the important factors affecting the population genetic structure of R. soongorica. Meanwhile, a comparative analysis was performed between the present ISSR-based and the previously published RAPD-based results, and revealed obvious discrepancies, implying the different evolutionary patterns of the genomic regions sampled by ISSR and RAPD markers.     

Analysis of the genetic structure of Rhodiola rosea (Crassulaceae) using inter-simple sequence repeat (ISSR) polymorphisms

The genetic diversity and differentiation of eleven R. rosea populations from different parts of its wide area of occurrence were studied by ISSR markers. Using eight primers, 252 DNA fragments were generated, and 243 of those DNA fragments were found to be polymorphic, indicating a high genetic variability at the species level (P = 96.4%, h = 0.176, SI = 0.291). Relatively low levels of diversity were determined at the population level (P 30.6-59.1%, h 0.088-0.165, SI 0.137-0.257). AMOVA analysis revealed that the majority of the genetic variation was within populations (65.42%), and the variance among populations was 34.58%. Cluster analysis revealed two groups of R. rosea populations; these groups likely represent distinct evolutionary lines in the species, which are different in genetic structure, evolutionary history and chorological migration routes.