Genetic diversity of common carp from two largest Chinese lakes and the Yangtze River revealed by microsatellite markers

Six polymorphic microsatellites (eight loci) were used to study the genetic diversity and population structure of common carp from Dongting Lake (DTC), Poyang Lake (PYC), and the Yangtze River (YZC) in China. The gene diversity was high among populations with values close to 1. The number of alleles per locus ranged from 2 to 11, and the average number of alleles among 3 populations ranged from 6.5 to 7.9. The mean observed (H _O) and expected (H _E) heterozygosity ranged from 0.4888 to 0.5162 and from 0.7679 to 0.7708, respectively. Significant deviations from Hardy–Weinberg Equilibrium expectation were found at majority of the loci and in all three populations in which heterozygote deficits were apparent. The analysis of molecular variance (AMOVA) indicated that the percent of variance among populations and within populations were 3.03 and 96.97, respectively. The Fst values between populations indicated that there were significant genetic differentiations for the common carp populations from the Yangtze River and two largest Chinese freshwater lakes. The factors that may result in genetic divergence and significant reduction of the observed heterozygosity were discussed.     

元江鲤种群遗传多样性

选择12对微卫星标记检测了于2011年采集自元江(红河上游中国江段)5个样点192尾鲤的群体遗传多样性.共检测到201个等位基因,每个位点等位基因2-27个.各群体各位点平均等位基因(NA)12.25-14.67个,平均有效等位基因(NE)8.28-9.73个,平均观察杂合度(Ho)o.7765-0.8037,平均期望杂合度(HE)0.7761-0.8080,平均多态信息含量(PIC)0.7534-0.7843.元江鲤种群192个个体各位点NA、NE、Ho、HE、PIC分别为16.50、11.26、0.7927、0.8049、0.7966,种群遗传多样性水平高.元江鲤群体之间遗传分化小,可作为一个种群管理单元进行管理.增殖放流要防止遗传多样性丧失.     

Microsatellite diversity and population genetic structure of redfin culter ( Culter erythropterus ) in fragmented lakes of the Yangtze River

Redfin culter (Culter erythropterus) is a small lethic freshwater fish and widely distributed in the adjacent lakes of the Yangtze River of China. Five microsatellite loci were applied to investigate the genetic variation and population structure of redfin culter from seven lakes in the middle-and-lower reaches of the Yangtze River. The gene diversity was high among the populations (H > 0.9), the average number of alleles among seven populations was low with a range from 2.00 to 3.87. The mean observed (H _O) and expected (H _E) heterozygosity ranged from 0.111 to 0.419 and from 0.162 to 0.750, respectively. Significant deviations from Hardy-Weinberg Equilibrium expectation were found in 50% of the total locus-population combination tests in which heterozygote deficits were apparent. The analysis of molecular variance (AMOVA) indicated that the percentage of variance among and within these populations were 6.18 and 93.82, respectively. The Fst values (0.062, P < 0.001) among studied populations indicated that there were significant genetic differentiations among redfin culture populations from the scattered lakes with different connections to the Yangtze River. These results are useful for the evaluation and conservation of small freshwater fishes. The factors that may be involved in low intra-population polymorphism and the pattern of the population genetic structure of redfin culter from the Yangtze River were discussed. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Handling editor: C. Sturmbauer     

Population genetics of wild Siniperca knerii Garman, 1912 in China as evaluated by microsatellites

The Chinese perch Siniperca knerii Garman, 1912 is an endemic perciform freshwater fish species mainly distributed in the Yangtze River and the Pearl River of China. To evaluate their genetic diversity in these rivers, microsatellite markers were used to assess the genetic structure and genetic variability among nine wild populations of S. knerii. In this study, the 12 loci used were polymorphic, with observed heterozygosity (Ho) ranging from 0.4079 to 0.8886 and polymorphism information content (PIC) ranging from 0.4511 to 0.7146. Results showed that six populations from the Yangtze River had a higher genetic diversity than those from the three Pearl River populations. The Bayesian STRUCTURE analysis recovered genetic clusters that matched localities perfectly or the kind of ecology environment with a significant Fst between them. The findings of this research should provide useful information for management and conservation of S. knerii stocks.     

Microsatellite variability and heterozygote excess in Elymus trachycaulus populations from British Columbia in Canada

Microsatellite markers were used to assess the genetic diversity and population structure in four populations of Elymus trachycaulus from British Columbia and one population of Elymus alaskanus from Northwest Territories. Fourteen microsatellite loci were used in this study. Our results indicated that E. trachycaulus is highly polymorphic, with an average percentage of polymorphic loci of 96.5% over the four populations. Average expected heterozygosity values (H_E or gene diversity) varied from 0.418 to 0.585 with a mean of 0.497. Most of the genetic variation was found within populations (85%) and the differentiation among populations was found to be 15% (F_st = 0.15). Interpopulation genetic distances corresponded well with the geographic distance between the population sites of origin, as well as morphological characteristics. Tests for Hardy–Weinberg equilibrium (HWE) for all loci and all populations revealed that all loci significantly differ from HWE. Subsequent analysis indicated that departure from HWE at some loci was due to an excess of heterozygotes. Possible explanations for heterozygote excess are discussed. The most likely reason for observed heterozygote excess could be due to the polyploidy nature of the species.     

Genetic diversity and differentiation of Daphnia galeata in the middle and lower reaches of the Yangtze River,China

Mitochondrial 16S rDNA and CO I gene were used as molecular markers for the analysis of the genetic diversity and differentiation of Daphnia galeata populations in nine water bodies in the middle and lower reaches of the Yangtze River. In the combined 16S rDNA and CO I gene sequences, 54 variable sites and 44 haplotypes were observed among 219 individuals belonging to nine D. galeata populations. Average haplotype diversity and nucleotide diversity were, respectively, 0.72% and 0.56%. The F‐statistics (F_ST) value of the D. galeata populations was 0.149. According to the results of the neutral test, D. galeata in the middle and lower reaches of the Yangtze River had experienced a bottleneck effect in the history. Molecular variance analysis indicated that the genetic differentiation of the D. galeata populations mainly occurred within populations (85.09%). Greater genetic differentiations of D. galeata among individuals within populations appeared in the populations from the Huaihe River basin, whereas smaller genetic differentiations occurred in the populations from the middle reaches of the Yangtze River. Strong gene flows were all observed between Group I (four populations from the middle reaches of the Yangtze River) and Group ΙΙ (three populations from the middle and lower reaches of the Yangtze River), and Group ΙΙΙ (two populations from the Huaihe River basin). The effective migration rates (M) were 851.49 from Group I to Group ΙΙ and 685.96 from Group I to Group ΙΙΙ, respectively. However, no significant relationship was observed between the genetic differentiation and geographical distance of the nine populations (r = .137, p > .05). Results suggested that the genetic differentiation of D. galeata in the water bodies in the middle and lower reaches of the Yangtze River resulted mainly from geographical isolation.     

Isolation and characterization of polymorphic microsatellite loci from Yellowcheek (Elopichthys bambusa)

Nine yellowcheek (Elopichthys bambusa) microsatellite loci were isolated using the fast isolation by AFLP of sequences containing repeats (FIASCO) protocol. Three to eight alleles per locus were detected in 29 samples collected from five populations of E. bambusa. The mean number of alleles was 5.6 ± 1.9 and the level of observed heterozygosities ranged from 0.415 to 0.843. These are the first microsatellite loci characterized from E. bambusa that can be used for estimating genetic diversity, population structure and parentage analysis.     

Allozyme variation of the endangered endemic plant Myricaria laxiflora: Implications for conservation

Myricaria laxiflora, a riparian plant that naturally occurs in the riverbanks of the Yangtze River Valley, has become extinct across its entire geographical distribution range in the wild due to the construction of the Three Gorges Dam. The allozyme variation of M. laxiflora populations was investigated in the present study. Mean number of alleles per locus (A) was 2.35, and the observed heterozygosity (H_o) and expected heterozygosity (H_e) were 0.35 and 0.30, respectively. Six populations showed significant excesses of heterozygotes based on the examination of a multilocus fixation index (F_IS). The population genetic divergence of M. laxiflora is high (G_ST = 0.144 and ?_B = 0.131) and the analysis of molecular variance analysis shows that 19.71% of the total genetic variation is caused by the difference between populations. Based on the obtained genetic information, six management units have been identified, all of which are expected to enhance the effective management of the remaining and transplanted individuals of this endangered species in the future.     

Assessment of genetic diversity and chemical composition among seven black locust populations from Northern China

Black locust (Robinia pseudoacacia L.) is one of the important biomass sources used to produce bioenergy and bioethanol. In this study, we examined variations in chemical composition as well as genetic diversity and differentiation among 165 black locust plants from seven populations in five provinces (Beijing, Hebei, Gansu, Shanxi, Shandong) of Northern China using microsatellite markers(SSR). The contents of cellulose, hemicellulose, lignin varied widely among seven populations. Of the microsatellite markers analysed, 14 showed polymorphisms, and 45 alleles were identified. The polymorphism information content (PIC) ranged from 0.2885 (Rops4) to 0.6837 (Rp200), and most of the microsatellite loci had PIC values > 0.5. Expected heterozygosity (He), observed heterozygosity (Ho), and Shannon's information index (I) detected relatively high genetic variation among populations. The percentage of polymorphic loci in three populations was 100%, and the average among all populations were 95.92%. Analysis of molecular variance (AMOVA) indicated that the degree of genetic differentiation among the seven populations was low (G_ST = 0.058; N_m = 4.05), and chemical compositions had no relationship with genetic or geographic distance. This study demonstrates that microsatellite markers efficiently assess of genetic diversity and genetic differentiation in black locust populations, and all seven populations exhibit high genetic diversity. The population from Feixian has the potential to be lingo-cellulosic biomass for bioenergy and bioethanol.     

Genetic diversity of Astragalus nitidiflorus, a critically endangered endemic of SE Spain,and implications for its conservation

Inter-simple sequence repeats (ISSR) markers were used to assess the genetic diversity and population structure in five populations of Astragalus nitidiflorus, a critically endangered species endemic to southeast Spain. Eight primers amplified 78 bands with 40 (51.3%) being polymorphic. Statistical results indicated a low genetic diversity at the population and species level, with percentages of polymorphic bands (PPB) ranging from 28.2 to 37.2% (an average of 31.8%), and means of gene diversity (H_E) of 0.129 and 0.171 respectively. The Shannon’s index (SI) ranged from 0.160 to 0.214 at the population level and was 0.260 at the species level. A low level of genetic differentiation among populations was detected, based on the Shannon’s information index (0.297), the coefficient of genetic differentiation between populations (G_ST = 0.2418) and AMOVA analysis (Φ_ST = 0.255). The estimated gene flow (Nm) was 0.789. The high genetic connectivity found among populations of A. nitidiflorus is an evidence of a recent habitat fragmentation. In addition, a bottleneck event in the past has been revealed, with a subsequent reduction of population size and a loss of genetic variation. Based on these results, the conservation strategy of A. nitidiflorus was proposed.     

Sequence Polymorphism and Geographical Variation at a Positively Selected MHC-DRB Gene in the Finless Porpoise (Neophocaena phocaenoides): Implication for Recent Differentiation of the Yangtze Finless Porpoise?

Sequence polymorphism at the MHC class II DRB locus was investigated in three finless porpoise (Neophocaena phocaenoides) populations in Chinese waters. Intragenic recombination and strong positive selection were the main forces in generating sequence diversity in the DRB gene. MHC sequence diversity changed significantly along the study period. Significant decrease in heterozygosity and lost alleles have been detected in the Yangtze River population and South China Sea population since 1990. Furthermore, there is a trend of increasing population differentiation over time. Especially, the genetic differentiation between the Yangtze River population and the Yellow Sea population was very low prior to 1990 (F _ST = 0.036, P = 0.009), but became very significant after 1990 (F _ST = 0.134, P < 0.001), suggesting a recent augmentation of genetic differentiation between both populations probably in a relatively short-term period. Porpoises from the Yangtze River displayed divergent frequencies of shared and private alleles from those displayed by two marine populations, which suggest that the former riverine population has been under a different selection regime (characteristic of a fresh water environment) than that of its marine counterparts.     

Genetic diversity within and among populations of the endangered and endemic species Primula merrilliana in China

Primula merrilliana Schltr. is an endangered and narrowly-distributed endemic species of southern Anhui Province in China. In this study, the level of genetic variation and the pattern of genetic structure in six natural populations of P. merrilliana were assessed by using ISSR (inter-simple sequence repeats) markers. Based on ten primers, 137 clear and reproducible DNA fragments were generated, of which 109 were polymorphic. The statistical results indicated that there was a relatively low genetic diversity within populations, and a high genetic differentiation among populations (G_ST = 0.53, Φ_ST = 0.49). The level of population genetic diversity was correlated to habitat type and the gene flow (N_m) was low with only 0.45. The unexpected genetic structure of P. merrilliana may be explained by limited gene flow that was caused by habitat fragmentation and limited seeds and pollen dispersal ability, self-compatible breeding system and biennial life form.     

Genetic Variation Analysis within and among Six Varieties of Common Carp (Cyprinus carpio L.) in China Using Microsatellite Markers

Five microsatellites were used to study the genetic diversity and genetic structure of one wild and five domestic varieties of common carp in China (the Yangtze River wild common carp, Xingguo red carp, purse red carp, Qingtian carp, Russian scattered scaled mirror carp and Japanese decorative carp). All loci in this study showed marked polymorphism with the number of alleles ranging from 4 to 13. Domestic varieties (except Xingguo red carp) showed less genetic diversity than the Yangtze River wild common carp in terms of allelic diversity. Population differentiation was assessed and each combination of populations displayed significant differentiation (P < 0.05) with the exception of that between the Yangtze River wild common carp and Xingguo red carp. Genetic distance analysis (Nei's standard genetic distance and pairwise F _st distance) showed that the largest distance was between Russian scattered scaled mirror carp and the Yangtze River wild common carp and the smallest distance was between the Yangtze River wild common carp and Xingguo red carp. However, among six populations Japanese decorative carp displayed the highest level of variability in terms of heterozygosity.     

Genetic diversity of the threatened aquatic plant Ottelia alismoides in the Yangtze River

Ottelia alismoides is a threatened submerged macrophyte in China. Genetic variation and population structure of 11 O. alismoides populations from lakes in mid-lower reaches of the Yangtze River were assessed by inter-simple sequence repeat (ISSR) markers. Eleven primer combinations produced a total of 130 unambiguous bands of which 57 (43.9%) were polymorphic. O. alismoides exhibited a very low level of intra-population genetic diversity (P_p = 13.0%, H_E = 0.042, I = 0.063). The main factors responsible for that were its short life history and high degree of autogamy in the reproductive system of the species. The F statistics calculated by different approaches consistently revealed a high genetic differentiation among populations, contributing >55% of the total gene diversity. The evident population structure of O. alismoides could be due to self-fertilizing reproduction, restricted gene flow and genetic drift. Estimates of gene flow by F_ST and coalescent-based simulation analysis indicated a restricted recurrent gene exchange among populations (Nm = 0.180, M = 0.190). Genetic drift played a more important role than gene flow in the current population genetic structure of O. alismoides because its habitat range was fragmented and highly influenced by environment changes. The results are discussed in relation to both in situ and ex situ conservation efforts of the species. A conservation strategy for conserving all extant populations to maximize genomic representation of the species is recommended.     

Genetic diversity and population structure of a cyprinid fish (Ancherythroculter nigrocauda) in a highly fragmented river

In this study, samples of Ancherythroculter nigrocauda, an endemic fish in the upper Yangtze River, were collected above and below dams in the Longxi River, a tributary of the upper Yangtze River, China, to investigate the genetic impacts of dams. The mitochondrial cytochrome b gene (cyt b) and 13 microsatellite (SSR) loci were used to analyze whether dams have resulted in loss of genetic diversity of the two fragmented populations or caused genetic differentiation between them. The results showed that the haplotype diversity (0.488; 0.486), nucleotide diversity (0.084%; 0.082%) and average expected heterozygosity (0.652; 0.676) of the two populations were all at a low level, and recent bottlenecks were detected. However, there was no genetic differentiation detected by the low genetic differentiation index (F_st, cyt b: ?0.1677, p = 0.99707; SSR: 0.00259, p = 0.81427). Besides, 11 pairs of half‐sibling relationship were found between the two populations indicating that there were individual movements and gene flow between them. This could be the larvae moving from upstream to downstream when water spilled over dams in flooding season. Therefore, our analysis showed that the dams have caused a loss of genetic diversity of the populations of A. nigrocauda in the Longxi River, blocked the active upstream movement but allowing passive downstream drift of larvae.     

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 of two Southern African cichlids (Oreochromis andersonii and O. macrochir) in the Zambezi and Congo River basins

Oreochromis andersonii and O. macrochir are two important cichlid species native to Southern Africa. We describe in this paper their genetic population structure in the Upper Zambezi River, Kafue River, and Lake Bangweulu representing part of the Congo and Zambezi River Basins. Microsatellite genetic markers were employed to analyse the genetic population structure of the two species using 177 tissue samples. The average allele richness of O. andersonii was higher in the Zambezi River (10.500) than in the Kafue River (9.583) though not statistically different. For O. macrochir, it was highest in the Zambezi River (11.170) followed by the Kafue River (9.781) and least in Lake Bangweulu (7.067) and their differences were significant. The gene diversity indices; gene diversity (hs), observed heterozygosity (H_O), expected heterozygosity (H_E) were high and similar in O. andersonii populations. However, in O. macrochir H_E was significantly lower in Lake Bangweulu (0.678) compared to the Kafue River (0.799) and Zambezi River (0.802) populations. Population differentiation estimated by R_ST and D_EST revealed high differentiation in both species (R_ST = 0.598, D_EST = 0.777 for O. andersonii; R_ST = 0.379, D_EST = 0.710 for O. macrochir). The highest source of variation was among populations (84.71%) for O. andersonii and within populations (67.09%) for O. macrochir. Comparisons of population pairs revealed a close genetic similarity between the Zambezi River and Lake Bangweulu populations of O. macrochir. Bottlenecks were observed in both species using the Two-Phase Model (T.P.M.) indicative of a recent genetic loss or reduction in effective population size. Though our results indicate that the populations of both species still maintain sufficiently high levels of genetic diversity in the sampled areas, the bottlenecks observed are a source of concern. We recommend a more robust study of genetic diversity of these species in all sections of these river systems and that some key conservation sites should be identified to protect the gene pool of these native species.     

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 of the traditional Chinese medicinal plant Ypsilandra thibetica (Melanthiaceae): Applications for conservation

Twelve microsatellite markers were developed to determine the genetic diversity and genetic structure of Ypsilandra thibetica, represented by a total of 90 individuals from six natural populations. All twelve microsatellite loci were polymorphic, and the results indicated that a high genetic diversity was present within populations (mean R_S = 4.996; mean H_E = 0.615), with high levels of genetic structure (mean F_ST = 0.165; mean F_IS = 0.692) among populations. This pattern is likely attributable to consanguineous mating, and this hypothesis is supported by a low relatedness coefficient. Our study suggested that environment factors might restrict gene flow among populations. In addition, physical distances between populations were not related to genetic distances, implying that ancestral populations might have been distributed over a wider area. These results suggest that Y. thibetica should be a high priority for conservation managers.     

Genetic diversity of the endangered Chinese endemic herb Dayaoshania cotinifolia (Gesneriaceae) revealed by simple sequence repeat (SSR) markers

Dayaoshania cotinifolia W.T. Wang is a critically endangered perennial herb endemic to southern China. Simple sequence repeat (SSR) markers were employed to assess genetic diversity in two populations of D. cotinifolia. Eight primer pairs generated a total of 36 alleles, with a mean of 4.5 alleles per locus. The expected heterozygosity (H_e = 0.416) and observed heterozygosity (H_o = 0.508) indicated a moderate level of genetic diversity, though the genetic differentiation between the populations was low (F_st = 0.014), a result that was supported by a higher gene flow (N_m = 18.000). No severe bottleneck effect was detected in the two populations. Thus, the endangered status of this species is most likely due to anthropologic effects rather than a lack of genetic diversity. In situ conservation strategies should be promoted, and the sizes of the populations should be increased through artificial breeding.