Micro-geographic landscape features demarcate seedling genetic structure in the stream lily,Helmholtzia glaberrima

In this study, 169 stream lily (Helmholtzia glaberrima) seedlings from six micro-drainages were genotyped with AFLP markers to quantify the impact that topographic landscape features and altitude may have in shaping patterns of genetic diversity within individual populations. A global analysis of genetic diversity detected significant genetic differentiation among micro-drainages (F_ST = 0.22, P < 0.01). The observed genetic structure of sampled sites conformed to a hierarchical model of gene flow. Assignment tests also supported a hierarchical model of gene flow as only one dispersal event among the sampled micro-drainages was detected. This suggests that opportunities for seed dispersal in H. glaberrima are highly constrained by patterns of hydrographic networks even at a local scale. In contrast, altitude had little impact on partitioning of genetic diversity as no increase in genetic diversity was evident among individuals in the upper (0.18 ± 0.02), and lower (0.17 ± 0.02) areas of micro-drainages. Overall these results suggest that the influence of freshwater landscape features can vary widely the effect on the patterns of genetic diversity of seedlings in stream lily populations.     

Genetic diversity of the endangered Chinese endemic plant Monimopetalum chinense revealed by amplified fragment length polymorphism (AFLP)

Monimopetalum chinense Rehd. is an endangered woody vine endemic to eastern China. Using amplified fragment length polymorphism (AFLP) markers, we examined levels of genetic variation within and among eleven populations located across the species’ distribution. Although modest levels of heterozygosity were detected, other measures of genetic diversity registered relatively high levels of variability, both at the species level (P = 91.0%, H_E = 0.232, I_S = 0.365) and at the population level (P = 53.0%, H_E = 0.155, I_S = 0.239). Populations also exhibited high levels of genetic differentiation (Nei’s genetic diversity analysis, G_ST = 0.330), corresponding to isolation-by-distance and hierarchical population structure. These results indicate that, despite low levels of gene flow, populations of M. chinense still harbor substantial amounts of genetic diversity. Management plans for the species should include measures that ensure genetic diversity remains high within and among extant populations.     

Genetic diversity and population structure of the red stingray,Dasyatis akajei inferred by AFLP marker

To examine population genetic diversity and variation of the red stingray Dasyatis akajei, samples from 1 freshwater region and 6 coastal localities within its distribution range were analyzed by using amplified fragment length polymorphism (AFLP) technology. A total of 207 loci were identified by 4 primer combinations from 87 individuals, 174 of which were polymorphic (84.1%). A high level of Nei's gene diversity was observed with the overall value of 0.230 ± 0.179. No significant genealogical clusters associated with sampling sites were revealed on the UPGMA tree. Both analysis of molecular variance (AMOVA, Φ_ST = 0.085, P = 0.00) and pairwise F_ST indicated significant genetic differentiation among four marine samples. However, no particular genetic differentiation was detected between marine and the limited sampling freshwater populations (AMOVA, Φ_CT = 0.056, P > 0.05). Except for the TZ vs. WZ (5.193), the gene flow estimates (N_m) demonstrated the effective immigrants were 1.918-2.976, suggesting low level dispersal between pairwise marine populations. Species-specific habits (demersal and sluggish habits) are probably responsible for the population structuring.     

Genetic diversity and gentiopicroside content of four Gentiana species in China revealed by ISSR and HPLC methods

G. macrophylla pall, G. dahurica Fisch, G. straminea Maxim, and G. crassicaulis Duthie ex Burk are the major cultivated Gentiana species in Gansu Province, China. The present study has collected 107 wild samples from 19 natural populations and focused on the analysis of their medicinal ingredients, genetic diversity, and relationship, concerning four species’s worrying situation and solutions. High performance liquid chromatography (HPLC) results show that their gentiopicroside contents are 9.75 ± 2.0%, 9.29 ± 2.6%, 8.18 ± 3.2%, and 7.96 ± 3.2% respectively and higher than the criterion standard for Radix Gentianae in Chinese Pharmacopoeia. Low genetic polymorphism was found among these four species with H_E (expected heterozygosity) = 0.147, G_ST (interspecies coefficient of gene differentiation) = 0.3207, and N_m (gene flow) = 1.0593. The unweighted pair group method with arithmetic mean (UPGMA) analysis was performed with POPGENE 1.31 software and Nei’s method but did not clearly differentiate these four species. Their medicinal ingredients did not correlate with the genetic variants (r = ?0.179, P = 0.586). The results indicate that there is no significant difference among four species in regard to the traits of medicinal qualities. All four Gentiana species can be widely cultivated to not only meet the demand of domestic and international market for Chinese traditional medicine, but also help the local conservation of the wild Gentiana resources in China.     

Genetic diversity of Stemona parviflora: A threatened myrmecochorous medicinal plant in China

The plant species Stemona parviflora, which is endemically distributed in Hainan and Guangdong Provinces of China, is an important constituent of Chinese traditional medicine “Baibu”. Based on AFLP analysis, at the species level, the percentage of polymorphic bands (PPB), gene diversity H, and Shannon's information index I of S. parviflora are 100%, 0.2826, and 0.4458, respectively. The genetic differentiation among populations is low (G_st = 0.0799), while the gene flow among these populations is high (N_m = 5.754). Actually, no distinguishable genetic structure is inferred according to the AFLP analysis in this study. There was no significant positive correlation between genetic distance and geographic distance either. Based on its medicinal use, seed dispersal pattern (myrmecochory), mating system, fragmentation of the natural habitat by rubber and eucalyptus planting, and the historical formation and transition of Hainan island and Guangdong provinces, we discuss the current threatened condition of the traditional medicinal plant S. parviflora. In/ex situ conservation tactics are recommended to save this important species.     

A comparison of genetic structuring of Yellowcheek Darters (Etheostoma moorei) using AFLPs and allozymes

The goals of this study were to characterize the genetic structure of 6 populations of Etheostoma moorei (Yellowcheek Darter), endemic to the Little Red River watershed of central Arkansas, to estimate the levels of gene flow within isolated streams, and to compare AFLP genetic diversity and distance data to our previously published allozyme data. The Yellowcheek Darter is a candidate species for listing under the Endangered Species Act. This darter is found in previously connected headwater streams presently isolated and partially inundated downstream by Greers Ferry Reservoir. AFLP data for the Yellowcheek Darter was concordant with previous work utilizing allozymes (r_s = 0.682; p < 0.01), yet genetic differences among populations were greater in magnitude. Genetic diversity (polymorphism = 92.7; heterozygosity = 0.496) is higher for the Yellowcheek Darter than would be expected for a species in decline, and greater for AFLP versus allozyme data. Genetic structuring among streams was also more evident using AFLP data. Gene flow levels are indicative of a metapopulation structure within streams (F_ST = 0.003 − 0.010), with genetic structuring indicating distinct populations among streams.     

Genetic variation and clonal diversity in populations of Nelumbo nucifera (Nelumbonaceae) in central China detected by ISSR markers

To obtain accurate estimates of population structure for purposes of conservation planning for wild lotus (Nelumbo nucifera Gaertn.) in central China, genetic diversity among and within six populations, and clonal diversity within another two populations of the species were analyzed. The genetic diversity was high (percentage of polymorphic bands, PPB = 90.0%; Shannon's information index, I = 0.383 ± 0.234) at the species level, but low within individual study populations (PPB = 35.8%; Shannon's information index I = 0.165 ± 0.241). The mean coefficient of gene differentiation (G_st) was 0.570, indicating that 43.0% of the genetic diversity resided within the population. Analysis of molecular variance (AMOVA) indicated that 50.47% of the genetic diversity among the study populations was attributed to geographical location while 12.3% was attributed to differences in their habitats. An overall value of mean estimated number of gene flow (N_m = 0.377) indicated that there was limited gene flow among the sampled populations. The level of clonal diversity found within the populations was considerably high (Simpson's diversity index, D = 0.985) indicating that clonal diversity contributes to a major extent to the overall genetic variation in the genetic structure of N. nucifera. On the basis of the high G_st and D values detected in this study we recommend that any future conservation plans for this species should be specifically designed to include those representative populations with the highest genetic variation for both in situ conservation and germplasm collection expeditions.     

Assessing the genetic diversity and population structure of Culter alburnus in China based on mitochondrial 16S rRNA and COI gene sequences

The genetic diversity and population genetic structure of Culter alburnus were investigated using mitochondrial cytochrome c oxidase subunit I (COI) and ribosomal 16S subunit (16S rRNA) gene sequences. A total of 89 individuals from four localities were included in the analysis. Overall, 12 polymorphic sites were observed and 10 haplotypes were defined. The C. alburnus populations were characterized by high haplotype diversity (0.587 ± 0.047) and low nucleotide diversity (0.00197 ± 0.00073). Pairwise fixation index (F_ST) analysis indicated significant genetic differentiation among different populations. The hierarchical analysis of molecular variance (AMOVA) analysis also showed significant genetic divergence (φ_ST = 0.3792, P < 0.01) among these populations. The present results suggest that subdivisions exist among four C. alburnus populations, and should be considered as different management unit for effective conservation and management purposes. This study provides new information for genetic assessment and will be crucial for establishing fisheries management and strategies for this species.     

Genetic diversity and structure of natural Pinus tabulaeformis populations in North China using amplified fragment length polymorphism (AFLP)

Chinese pine (Pinus tabulaeformis carr.), endemic to China, is a conifer species with extensive and fragmented distribution in North China. In this study, the genetic diversity and structure of 20 natural populations of this species were investigated using amplified fragment length polymorphism (AFLP) markers. A total of 445 fragments were revealed with 8 pairs of primers, 379 (85.17%) of which were polymorphic. A moderate level of genetic diversity was detected at the species level (Shannon's information index I = 0.356, Nei's gene diversity H_E = 0.271) and at the population level (I = 0.219, H_E = 0.206). Most of genetic variation was within populations while a considerable level of genetic differentiation was detected (G_ST = 0.352, Ф_ST = 0.304). The high differentiation could be attributed to the complex and fragmented habitats, and a limited gene flow among populations (N_m = 0.572). The Mantel test indicated that there was significant correlation (r = 0.455, P < 0.001) between Nei's genetic distance and geographical distance among all the populations. The results suggested that proper countermeasures should be taken to prevent the habitat further deterioration and maintain the genetic diversity of this species.     

Conservation genetics of Heritiera littoralis (Sterculiaceae), a threatened mangrove in China,based on AFLP and ISSR markers

AFLP and ISSR markers were used to determine the genetic variations in eight mangrove and non-mangrove populations of Heritiera littoralis (Sterculiaceae), a threatened species in China. Our results showed a moderate to high level of genetic variation in this species (P = 63.69%, H_T = 0.20 for AFLP; P = 76.07%, H_T = 0.22 for ISSR), and a relatively high level of genetic differentiation among populations (G_ST = 0.24 for AFLP and 0.27 for ISSR). Life history traits, long-distance dispersal of floating seeds, and local environments may play important roles in shaping the genetic diversity and genetic structure of this species. Investigation of the plant’s reproductive capacity showed that the natural seed production of H. littoralis was low, as was the germination rate and the transformation rate from juvenile to adult. H. littoralis is seriously threatened and is in urgent need of conservation in China.     

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.     

Genetic diversity of Lilium tsingtauense in China and Korea revealed by ISSR markers and morphological characters

To study the genetic diversity and population structure of Lilium tsingtauense Gilg (Qingdao Lily), we collected 648 samples from 12 sites in China and Korea, and analyzed their Inter-Simple Sequence Repeat (ISSR) molecular markers and morphological characters. ISSR data revealed a relatively high genetic diversity at the species level, with 72.31% polymorphic loci, effective numbers of alleles of 1.437, average expected heterozygosity of 0.231 and Shannon’s information index of 0.369. Considerable genetic differentiation among the natural populations (G_ST = 0.144) and the gene flow (N_m = 1.487) were detected. AMOVA analysis and UPGMA-dendrogram suggested a hierarchical regional structure among populations, and spatial autocorrelation analysis showed a micro-scaled spatial structure. Furthermore, there was a high correlation between morphological characters and genetic parameters obtained from ISSR parameters. There was only a low genetic differentiation among the different morphological types of L. tsingtauence in China. Based on these findings, we recommend in situ and ex situ conservation strategies for the preservation of L. tsingtauense.     

Genetic characterization of <Emphasis Type="Italic">Brycon hilarii</Emphasis> (Characiformes) populations within the Pantanal: Aspects of their conservation within a globally important neotropical wetland

Brycon hilarii, a characid species endemic to the Upper Paraguay hydrographic basin, is important to regional artisanal and sports fisheries. To develop effective strategies for conservation of this species in the face of potential environmental changes in the Pantanal region, we characterized genetic structuring within and among six B. hilarii collections based on variation at five microsatellite DNA markers. Within-population genetic variability was high, with 75 different alleles; mean average allelic richness per locus per sample location ranged from 6.06 to 7.99. Nei’s gene diversity (hs) varied among drainages from 0.66 (±0.2) to 0.69 (±0.2), with an average across the four genetically identified populations of 0.68 (±0.02). Analyses of Jost’s D _EST and F _ST-like indices, AMOVA, and Structure-based clustering analyses indicated that B. hilarii populations exhibit a low level of genetic structure, with some indications that the Taquari River population is somewhat distinct from others. Results of K-means analysis suggested little or no structuring, with weakly differentiated populations above and below the confluence of the Paraguay and Taquari rivers. Because B. hilarii populations in the Pantanal are linked by high levels of gene flow, habitat alterations that would interfere with gene flow may jeopardize the long-term persistance of the species.     

Genetic diversity of castor bean (Ricinus communis L.) in Northeast China revealed by ISSR markers

Inter-Simple Sequence Repeat (ISSR) markers were employed to analyze the genetic diversity of Ricinus communis L. in northeastern China plants. We selected ten primers that produced clear, reproducible and multiple bands for these experiments and 179 bands were obtained across 39 genotypes. Polymorphic band ratios ranged from 100% to a minimum of 78.9% with an average of 96.4% while band numbers were comprised between 13 (UBC823) and 23 (UBC856). The results obtained from UPGMA clustering dendrogram and PCoA lead to 39 distinct castor bean accessions belonging to four major groups. We found that all groups shared a common node with 66% similarity while Jaccard's similarity coefficient ranged from 0.58 to 0.92. Compatible inference was also observed from the high values of heterozygosity (Ht = 0.3378 ± 0.0218), Nei's genetic diversity (H = 0.1765 ± 0.2090), and Shannon's information index (I = 0.4942 ± 0.1872). In addition, our data reveal a Nei's genetic differentiation index (G_ST) of 0.3452 and estimated the gene flow (Nm) at 0.9482. These findings clearly suggest a genetic diversity in castor bean germplasms from various geographic origins and contribute to our understanding of breeding and conservation of castor beans.     

Genetic structure in the paleoendemic and endangered Petagnaea gussonei (Spreng.) Rauschert (Saniculoideae, Apiaceae) and implications for its conservation

Our investigation aims to understand the genetic structure and evolutionary history of Petagnaea gussonei, an ancient and endangered species belonging to the Saniculoideae subfamily (Apiaceae). It is paleoendemic to Sicily, with a small number of populations in the Nebrodi Mountains. A total of seven chloroplast microsatellite repeat loci and 12 AFLP primer combinations were used to screen 115 individuals corresponding to 17 populations. The ratio of seed to pollen flow was also calculated using the modified Ennos equation. A relatively high level of genetic diversity was detected with AFLPs (e.g., 0.045 < H < 0.278), and a moderate variation was also found using cpSSRs (0 < Hk < 0.667). Two different haplotypes (B and W) were identified, with five populations being monomorphic for haplotype B. There was no genetic differentiation on the basis of haplotypic frequency (G _ST) and similarity (R _ST), and no phylogeographic structure was detected among the populations. AFLP values also confirmed that the populations are not very genetically differentiated. The principal component analysis based on pairwise genetic differences showed three groupings without a geographical correlation. The AMOVA analysis indicates that the amount of variation is higher within populations (82 %) than among populations (18 %). Results of the pollen flow/seed flow ratio indicated positive values for each population, indicating that gene flow by seed is not more efficient than by pollen. Instead, the total pollen/seed flow for all population presents a negative value, suggesting that pollen dispersal does not appear to be more effective over the long range for gene flow than seed dispersal. This differentiation level supports the hypothesis that the fragmentation and isolation of the residual populations is in progress. This phenomenon is due not only to post-ice age climate changes, but also to direct and indirect anthropic actions.     

Genetic diversity of natural populations of Larix principis-rupprechtii in Shanxi Province,China

Prince Rupprecht's Larch (Larix principis-rupprechtii Mayr.) is one of dominant components of middle and high elevation forests in North China. Shanxi Province is well known as “the Hometown of Prince Rupprecht's Larch” in China. In this study, six natural populations of this species across Shanxi were selected to investigate the genetic variation of the species using amplified fragment length polymorphism (AFLP) markers. Results showed that in comparison with some other species of Larix, higher genetic diversity was revealed at the species level for L. principis-rupprechtii (percentage of polymorphic loci PPL = 71.9%, Nei's gene diversity H_E = 0.225, Shannon information index I = 0.341). Most of genetic variation existed within populations (80.5%), while the genetic differentiation among populations was significant (p < 0.001) and higher (G_st = 0.194) than most other species of Larix. The differentiation can be attributed to the limited gene flow (N_m = 1.035) among populations, which could be due to the spatial isolation and habitat fragmentation. The six populations can be divided into three groups based on the Nei's genetic distances between populations (from 0.033 to 0.076). There was no significant correlation (r = 0.268, p > 0.05) between genetic distance and geographic distance among populations. The measures for in-situ or ex-situ conservation should be taken to preserve the genetic diversity of this species.     

Assessment of genetic diversity and relationships among maize (<Emphasis Type="Italic">Zea mays</Emphasis> L.) Italian landraces by morphological traits and AFLP profiling

In the present study we have analyzed the genetic diversity pattern in a sample of 54 Italian maize landraces, using morphological traits and molecular markers. Although the 54 landraces surveyed in this study were restricted to Lombardy, the core region of maize production in Italy, our data revealed a large genetic heterogeneity for both morphological and molecular traits in the accessions analyzed. Additionally, our data confirm that the AFLP markers produced a high frequency of polymorphic bands and were able to unequivocally fingerprint each of the landraces considered. Cluster analysis based on AFLP markers displayed a clearer separation of the accessions in comparison to morphological data. Different populations were divided into four major clusters reflecting the geographical origin and seasonal employment of the landraces analyzed. Molecular analysis of variance showed significant (P < 0.01) differences among groups, among populations within groups, and among individuals within populations. Approximately 74% of the total variance could be attributed to differences within populations. Conversely, a lower level of differentiation was detected among groups (~4%). Regarding population structures, the genetic distance between populations (F _ST = 0.25 ± 0.3) and the degree of inbreeding within groups (F _SC = 0.22 ± 0.2), did not diverge significantly, while both significantly differed from the degree of relatedness between markers within groups (F _CT = 0.04 ± 0.03). Results are discussed in relation to a suitable conservation method.     

Lack of genetic structure in endangered large yellow croaker Larimichthys crocea from China inferred from mitochondrial control region sequence data

The large yellow croaker Larimichthys crocea is an important commercial marine fish species in China. However, information about the population structure of this species is limited. In the present study, mitochondrial DNA (mtDNA) control region was sequenced from four populations of the yellow croaker in the southern Yellow Sea, East China Sea and South China Sea to investigate the genetic structure of this species. A total of 54 haplotypes were detected among 62 individuals of large yellow croaker. High levels of population genetic diversity were observed. Among the four populations, the haplotype diversity was between 0.9895 ± 0.0193 (Xiamen) and 1.0000 ± 0.0524 (Lvsi, Zhoushan). The nucleotide diversity ranged from 0.0208 ± 0.0108 (Xuwen) to 0.0246 ± 0.0138 (Lvsi). The results of AMOVA detected no significant differences among populations. The conventional F_ST statistics were negative and insignificant values. These indicated lack of population genetic structure throughout the Yellow Sea, East China Sea and South China Sea, and random mixing of individuals among the samples. Biological characters of large yellow croaker and lack of physical barrier in the studied area could be the reasons for lack of genetic structure in this species.     

Complex genetic structures of Sardinella zunasi in the Northwest Pacific detected by AFLP markers

Seventy-one Sardinella zunasi individuals collected from 5 locations in the Northwest Pacific were used in an AFLP analysis to examine the population genetic structure of S. zunasi. Using 4 selective primer combinations, 414 putative loci were detected, including 340 polymorphic loci (82.13%). Both AMOVA and pairwise F_ST analysis detected significant population genetic structure between Chinese and Japanese populations, supporting separate stocks in this species. The UPGMA trees also detected significant spatial structure within S. zunasi. Pleistocene glaciations are hypothesized to be responsible for the genetic differentiation. The significant genetic differentiation found among S. zunasi populations might also be due to geographic isolation, because a pattern of isolation-by-distance was observed. The weaker but significant structures between the Japanese Aichi and Kagawa populations might be impacted by the semi-enclosed coastal topography there. No significant genetic structure was detected among the Chinese populations, perhaps because of S. zunasi’s migratory behavior and ocean current patterns.