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.     

Genetic differentiation among populations ofArabis serrata (Brassicaceae) along its geographic distribution

Levels and distribution of genetic variation were investigated in ten populations of the perennialArabis serrata distributed along a latitudinal gradient throughout Japan. Populations of this endemic species occupy predominantly three types of habitats: limestone and derived soils, volcanic and disturbed sites. Previous studies showed that plants ofA. serrata are differentiated in morphological and ecological traits under both natural conditions and common garden experiments suggesting genetic differentiation among populations. To assess the degree of genetic differentiation under different habitats ofA. serrata populations, we analyzed the isozyme genetic structure. Ten populations, located in mountains of central and northern Honshu and Hokkaido, were analyzed by starch gel enzyme electrophoresis. Fourteen loci of eight enzymes were resolved and six loci were monomorphic for all the populations. Populations sampled maintain low levels of genetic variation (P=0.16;H=0.05;A=1.16) compared to that maintained by other outcrossing seed plants. In some cases, few or no heterozygous individuals were detected, and consequently, mean observed heterozygosity was zero or near zero. Six (29%) of the fixation indices,F, estimated deviated significantly from Hardy Weinberg genotypic expectations indicating a deficiency of heterozygotes in most of the cases. The mean genetic identity (Nei'sI) between population pairs was 0.852 and indicates a moderate level of genetic differentiation among populations.Arabis serrata has most of its genetic variation distributed among rather than within populations. The among-population component of the total genetic diversity (G _ST mean value) was 0.416, indicating genetic differentiation between populations. There groups of populations were recognized in an unrooted tree generated by the Neighbor-Joining method. These results suggest groups of populations differentiated regionally. Estimates of interpopulational gene flow (Nm) were very variable (range 0.049–3.718) with a meanNm=1.203 for all populations.     

Genetic variation and phylogeographic history of <Emphasis Type="Italic">Picea likiangensis</Emphasis> revealed by RAPD markers

Repeated cycles of retreat and recolonization during the Quaternary ice ages are thought to have greatly influenced current species distributions and their genetic diversity. It remains unclear how this climatic oscillation has affected the distribution of genetic diversity between populations of wind-pollinated conifers in the Qinghai-Tibetan region. In this study, we investigated the within-species genetic diversity and phylogenetic relationships of Picea likiangensis, a dominant forest species in this region using polymorphic DNA (RAPD) markers. Our results suggest that this species has high overall genetic diversity, with 85.42% of loci being polymorphic and an average expected heterozygosity (H _E) of 0.239. However, there were relatively low levels of polymorphism at population levels and the differences between populations were not significant, with percentages of polymorphic bands (PPB) ranging from 46.88 to 69.76%, Nei’s gene diversity (H _E) from 0.179 to 0.289 and Shannon’s indices (Hpop) from 0.267 to 0.421. In accordance with our proposed hypothesis, a high level of genetic differentiation among populations was detected based on Nei’s genetic diversity (G _ST = 0.256) and AMOVA analysis (Phi _st = 0.236). Gene flow between populations was found to be limited (Nm = 1.4532) and far lower than reported for other conifer species with wide distribution ranges from other regions. No clusters corresponding to three morphological varieties found in the south, north and west, respectively, were detected in either UPGMA or PCO analyses. Our results suggest that this species may have had different refugia during the glacial stages in the southern region and that the northern variety may have multiple origins from these different refugia.     

Genetic variability in European black grouse (<Emphasis Type="Italic">Tetrao tetrix</Emphasis>)

We studied microsatellite genetic variation in 14 different geographic populations of black grouse (Tetrao tetrix) across the European range. Populations were grouped in three different fragmentation categories: isolated, contiguous and continuous, respectively. Genetic diversity, measured as observed heterozygosity (H _O), expected heterozygosity (H _E) and allelic richness, were lower in isolated populations as compared to the other two categories that did not differ amongst one another. These results imply that lowered genetic variability in black grouse populations is negatively affected by population isolation. Our results suggest that the connectivity of small and isolated populations in Western Europe should be improved or else these face an increased risk of extinction due to genetic and demographic stochasticity.     

Population structure of an endangered frog (<Emphasis Type="Italic">Babina subaspera</Emphasis>) endemic to the Amami Islands: possible impacts of invasive predators on gene flow

The otton frog (Babina subaspera) is an endangered species endemic to the Amami Islands, Japan. High predation pressure from an introduced carnivore, the mongoose, has caused declines in the frog populations and created a large habitat gap around an urban area. To promote effective conservation, we investigated the genetic status of the species and examined the effect of the habitat gap on gene flow among populations. Using five polymorphic microsatellite loci and mitochondrial DNA sequences, we investigated genetic diversity, genetic structure and gene flow in B. subaspera populations on the islands of Amami-Oshima and Kakeroma-jima. The expected heterozygosity (H _E) within each locality was generally high (range: 0.67–0.85), indicating that B. subaspera maintains high genetic diversity. However, genetic differentiation was observed, and the two populations, TAG and KAR, showed little gene flow with other populations. The clustering and F _ST analyses also predicted that these two populations were clearly distinct. According to the mitochondrial DNA analysis, the observed genetic differentiation occurred relatively recently. Possible barriers such as mountain ridges, rivers or roads did not result in genetic separation of the populations. These data support the hypothesis that the habitat gap created by an introduced predator prevented the gene flow among B. subaspera populations. When developing conservation strategies for B. subaspera, focus should be directed to these two isolated populations; careful monitoring of population size and genetic diversity should be conducted along with the mongoose elimination project ensues.     

Allozyme Diversity and Population Genetic Structure of Pinus densata Master in Northwestern Yunnan, China

We investigated the levels and patterns of genetic diversity of Pinus densata Master in Yunnan. Horizontal starch-gel electrophoresis was performed on macrogametophytes collected from nine populations in northwestern Yunnan, China. Compared with other gymnosperm species, P. densata has higher mean values for all measures of genetic diversity. Allozyme polymorphism (0.99 criterion) was 97.0% and 71.4% at the species and population levels, respectively. The average number of alleles per locus was 3.1 and 2.0 at the species and population levels. Mean expected heterozygosity was substantially higher in P. densata than average values investigated for other gymnosperms both at the population (H _ep = 0.174±0.031) and at the species (H _es = 0.190) levels. Of the total genetic variation, less than 12% was partitioned among populations (G _ST = 0.112). Our allozyme survey supports the suggestion that the observed higher diversity in P. densata may be attributed partly to its hybrid origin between two genetically distinct species, P. yunnanensis and P. tabulaeformis. In addition, we suggest that introgression would give rise to the increase in genetic diversity occurring in P. densata.     

基于微卫星DNA的神农架川金丝猴遗传结构研究

川金丝猴(Rhinopithecus roxellana)是我国特有珍稀濒危物种,了解其种群遗传结构和关键影响因素,对该物种的保护具有重要意义。以我国分布最东端的湖北神农架川金丝猴种群为研究对象,基于非损伤性DNA技术和微卫星DNA遗传标记等分子生物学方法及景观遗传参数,探讨了神农架川金丝猴的遗传多样性和遗传结构,旨在为川金丝猴的研究及川金丝猴种群的可持续发展提供理论基础。利用12个多态性微卫星位点,在455份川金丝猴粪便样品中,共检测到62个微卫星等位基因;共鉴定出316个不同川金丝猴个体;种群的平均期望杂合度、平均观察杂合度和多态性信息含量分别为0.626、0.559和0.650;群体间的Nei's遗传距离为0.046—0.139,分化系数为0.015—0.046。结果表明与其他地区川金丝猴种群相比,神农架川金丝猴种群具有较低的遗传多样性水平,种群内部存在遗传分化趋势;结合景观参数分析表明地理距离不是影响神农架川金丝猴群体间遗传距离的主要因素,而生境中的灌丛和草地以及人类活动干扰可能是影响川金丝猴遗传交流的主要因素。     

A cline of allozyme variation inAbies mariesii

Genetic variation at 22 allozyme loci was examined for 1,003 trees from 11 isolated natural populations ofAbies mariesii covering all except the southernmost region of its geographic range. Genetic diversity within species (H _es=0.063) was low compared to many other long-lived woody species. Most of the genetic variation is found within populations (G _ST=0.144) despite their isolated distribution. Genetic distance between populations was positively correlated with geographic distance. Genetic diversity within populations was generally low (meanH _ep=0.054), but varied across populations in a clinal fashion such that genetic variation decreased with increasing latitude. These genetic characteristics may reflect the distribution history of this species.     

Microsatellite analysis of genetic diversity in the Chinese alligator (<Emphasis Type="Italic">Alligator sinensis</Emphasis>) Changxing captive population

Chinese alligator (Alligator sinensis) is a critically endangered species endemic to China. In this study, the extent of genetic variation in the captive alligators of the Changxing Reserve Center was investigated using microsatellite markers derived from American alligators. Out of 22 loci employed, 21 were successfully amplified in the Chinese alligator. Sequence analysis showed loci in American alligators had a bigger average size than that of the Chinese alligators and the longest allele of an individual locus almost always existed in the species with longer stretch of repeat units. Eight of the 22 loci were found to be polymorphic with a total of 26 alleles present among 32 animals scored, yielding an average of 3.25 alleles per polymorphic locus. The expected heterozygosity (H _E) ranged at a moderate level from 0.4385 to 0.7163 in this population. Compared to that in the American alligators, a lower level of microsatellite diversity existed in the Changxing population as revealed by about 46% fewer alleles per locus and smaller H _E at the homologous loci. The average exclusion power and the ability to detect shared genotypes and multiple paternity were evaluated for those markers. Results suggested that when the polymorphic loci were combined, they could be sensitive markers in genetic diversity study and relatedness inference within the Chinese alligator populations. The level of genetic diversity present in the current Changxing population indicated an important resource to complement reintroductions based on the individuals from the other population. In addition, the microsatellite markers and their associated diversity characterized in this population could be utilized to further investigate the genetic status of this species.     

Analysis of molecular genetic diversity and population structure in Amaranthus germplasm using SSR markers

We assessed the molecular genetic diversity and population structure of Amaranthus species accessions using 11 simple sequence repeat markers. A total of 122 alleles were detected, and the number of alleles per marker (N_A) ranged from 6 to 21 with an average of 11.1 alleles. The frequency of major alleles per locus ranged from 0.148 to 0.695, with an average value of 0.496 per marker. The overall polymorphic information content values were 0.436–0.898, with an average value of 0.657. The observed heterozygosity (H_O) and expected heterozygosity (H_E) ranged from 0.056 to 0.876 and from 0.480 to 0.907, with average values of 0.287 and 0.698, respectively. The average H_O (0.240) was lower than the H_E and gene flow (Nm), and showed substantial genetic variability among all populations of amaranth accessions. The sample groupings did not strictly follow the geographic affiliations of the accessions. A similar pattern was obtained using model-based structure analysis without grouping by species type. Knowledge of the genetic diversity and population structure of amaranth can be used to select representative genotypes and manage Amaranthus germplasm breeding programs.     

Isolation and characterization of first microsatellite markers for the noble crayfish, <Emphasis Type="Italic">Astacus astacus</Emphasis>

Noble crayfish (Astacus astacus) is listed as vulnerable by the IUCN Red List of Threatened Species in Europe. However, very little is known about genetic diversity and structuring of noble crayfish populations, mainly because of the lack of informative genetic markers. We describe the isolation and characterization of the first microsatellite markers for this species, which were obtained by screening 4,000 recombinant clones. Eight loci revealed polymorphisms in a panel of 172 individuals from seven populations in Northern Europe. Number of alleles per locus ranged from two to 10 (average 4.4) and heterozygosity levels among populations varied from 0 to 0.80 for H _o and from 0 to 0.72 for H _e.     

Microsatellite loci for studies on population differentiation and connectivity of the red‐bellied yellow tail fusilier,Caesio cuning (Caesionidae)

Ten polymorphic microsatellites were isolated from the red‐bellied yellow tail fusilier Caesio cuning, a reef‐associated fish which occurs widely in the Indo‐Pacific region. The species is exploited by both small‐scale and commercial fisheries. Fifty individuals from six populations were genotyped using primers that reliably amplified 10 polymorphic loci. The number of alleles per locus ranged from three to 11. Observed heterozygosity (H_O) and expected heterozygosity (H_E) ranged between 0.400 to 0.880 and 0.337 to 0.843, respectively. These microsatellite loci may be used to study population structure, genetic diversity and connectivity of C. cuning in the range of its distribution.     

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     

Microsatellite analysis of the natterjack toad (Bufo calamita) in Denmark: populations are islands in a fragmented landscape

The European natterjack toad (Bufo calamita) has declined rapidly in recent years, primarily due to loss of habitat, and in Denmark it is estimated that 50% of the isolated populations are lost each decade. To efficiently manage and conserve this species and its genetic diversity, knowledge of the genetic structure is crucial. Based on nine polymorphic microsatellite loci, the genetic diversity, genetic structure and gene flow were investigated at 12 sites representing 5–10% of the natterjack toad localities presently known in Denmark. The expected heterozygosity (H _E) within each locality was generally low (range: 0.18–0.43). Further analyses failed to significantly correlate genetic diversity with population size, degree of isolation and increasing northern latitude, indicating a more complex combination of factors in determining the present genetic profile. Genetic differentiation was high (overall θ = 0.29) and analyses based on a Bayesian clustering method revealed that the dataset constituted 11 genetic clusters, defining nearly all sampling sites as distinct populations. Contemporary gene flow among populations was undetectable in nearly all cases, and the failure to detect a pattern of isolation by distance within major regions supported this apparent lack of a gene flow continuum. Indications of a genetic bottleneck were found in three populations. The analyses suggest that the remaining Bufo calamita populations in Denmark are genetically isolated, and represent independent units in a highly fragmented gene pool. Future conservation management of this species is discussed in light of these results. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Population genetic structure of Ceriops tagal (Rhizophoraceae) in Thailand and China

Knowledge of the amount and patterns of genetic variation within and among populations of mangrove trees is essential for devising optimum genetic management strategies for their conservation and sustainable utilization. Ceriops tagal is a widespread viviparous mangrove. Genetic diversity in the species was examined with inter-simple sequence repeat (ISSR). Nine natural populations were collected from Thailand and China. The estimates of genetic variation were extremely low (H_T = 0.0179 ± 0.005, H_S = 0.0084 ± 0.001), and only 47% of the total gene diversity was maintained within populations (G_ST = 0.529). The eastern coastal populations of Thailand were more similar to populations from China than to populations from the western coastline of Thailand. A high level of Nei's genetic identity exists between populations of C. tagal (I = 0.989), suggesting their common ancestry. The low levels of genetic diversity in the species may result from a series of genetic bottlenecks during several glacial epochs.     

Strong genetic differentiation of the East-Himalayan <Emphasis Type="Italic">Megacodon stylophorus</Emphasis> (Gentianaceae) detected by Inter-Simple Sequence Repeats (ISSR)

Megacodon stylophorus (Clarke) Smith is a perennial alpine herb endemic to the species-rich eastern Himalayan region. Its populations are locally scattered as isolated patches throughout this region. Genetic variation within and among six populations of this species was assessed using ISSR fingerprinting with 13 primers. High levels of genetic diversity exist within species (P = 69.83%, H_T = 0.1949 and H_sp = 0.3047), while the within-population diversity is low (P = 11.21%, H_E = 0.0532 and H_pop = 0.0792). Extraordinarily high levels of genetic differentiation were detected among populations based on various statistics, including Neis genetic diversity analysis (72.7%), Shannons diversity index (74.01%) and AMOVA (80.70%). That is, populations shared low levels of genetic identity (I = 0.8203 ± 0.0430). This genetic structure was probably due to severe genetic drift of the small-sized patchy populations resulting from postglacial habitat fragmentations. The observed genetic structure of the populations implies that as many populations as possible should be considered for any in situ and ex situ conservation practice on this species.     

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.     

北沙柳群体遗传多样性和遗传结构分析

以内蒙古北沙柳(Salix psammophila)国家种质资源库内9个群体(P1~P9)288个无性系为实验材料,利用TP-M13-SSR技术,选取22对具有多态性EST-SSR北沙柳引物,采用毛细管电泳对PCR产物进行检测,分析北沙柳遗传多样性、分化程度和群体遗传结构,为北沙柳种质资源库遗传管理、无性系鉴定、品种选育、遗传改良和构建指纹图谱提供理论依据。结果显示:(1)22对EST-SSR引物共检测到222个等位基因,各位点平均等位基因数(A)为10,四倍体基因型丰富度(G)和特异基因型(G1)总和分别为1 460和802个,平均特异基因型比率(P1)和种质鉴别率(P2)分别为45.86%和13.21%。(2)9个群体平均等位基因数(A)为7.475,基因型丰富度(G)为15.586,观察杂合度(Ho)和期望杂合度(He)分别为0.577和0.638。以期望杂合度He为标准,北沙柳群体遗传多样性水平最低的是P1和P9。(3)北沙柳群体遗传分化系数仅为0.02,AMOVA分子变异分析显示,北沙柳群体大部分遗传变异来自群体内(97%),群体间变异仅为3%。(4)三维主成分、聚类和Structure群体遗传结构分析显示,9个群体被划分为2个组,Mantel检验表明北沙柳遗传距离与地理距离极显著相关(r=0.684 P0.001)。研究表明,北沙柳种质资源具有丰富的遗传多样性,这是其具有耐旱、耐寒、耐高温、耐沙埋和抗风蚀等适应性较强的分子基础;北沙柳的遗传变异集中在群体内;分布区群体呈现由中心向边缘群体扩张分化的趋势。     

Dissimilar patterns of genetic variation in two insular endemic plants sharing species characteristics,distribution, habitat,and ecological history

Camssonia guadalupensis ssp. clementina (Onagraceae) and Cryptantha traskiae (Boraginaceae) share many species characteristics that affect levels and pattern of genetic variation. In addition, they have a similar distribution, are found in the same habitat, and share ecological history by virtue of co-occurring at nearly all of the locations at which they are found. All populations of the two taxa on San Clemente Island were surveyed for genotypes at 16 allozyme loci, revealing generally low levels of genetic variation. However, Cam. g. clementina has more genetic variation than Cryp. traskiae at the taxon level (P = 37.5 versus 18.8, A = 1.69 versus 1.31, and H_E = 0.088 versus 0.003) and significantly more alleles and higher heterozygosity within populations (A = 1.09 versus 1.03, A_E = 1.02 versus 1.00; H_O = 0.013 versus 0.001 and H_E = 0.017 versus 0.003). Some populations of each taxon are monomorphic at all loci. Much greater differentiation among populations occurs in Cam. g. clementina (G_ST = 0.810) than in Cryp. traskiae (G_ST = 0.042). Locations of the more variable populations of each taxon do not coincide, and the pattern of genetic similarity of localities differs in the two taxa. Striking population genetic differences exist between these taxa despite shared species characteristics, distribution, habitat, and recent history.