Genetic diversity and population differentiation of the Chinese soft-shelled turtle (Pelodiscus sinensis) in three geographical populations

The Chinese soft-shelled turtle (Pelodiscus sinensis) is one of the most important economical chelonians in the world. To understand the genetic variations of the Chinese soft-shelled turtle in China, 62 individuals were sampled from three localities and 18 polymorphic microsatellite loci tested were used to detect genetic diversity and population structure. Results showed that the genetic diversity of the wild P. sinensis was high. Except for the Wuhu populations, the majority of microsatellite loci are not deviation from Hardy–Weinberg equilibrium in the other two populations. AMOVA analysis indicated that genetic variations occurred mainly within populations (97.4%) rather than among populations (2.6%). The gene flow estimates (Nm) among three geographic populations demonstrated that strong gene flow existed (Nm > 1, mean 6). The present study supported that different habitats, breed turtles escaped, multiple paternity and long evolutionary history may be responsible for the current genetic diversity and differentiation in the wild Chinese soft-shelled turtle.     

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.     

Genetic diversities of the giant panda (Ailuropoda melanoleuca) in Wanglang and Baoxing Nature Reserves

Genetic variations in the giant panda populations in Wanglang and Baoxing Nature Reserves were evaluated in this study. Panda feces were collected from these two reserves and DNA samples extracted from the feces were genotyped at 13 microsatellite loci. A total of 130 alleles were identified from the 13 microsatellite loci in 63 giant pandas, including 35 private alleles in Wanglang, 53 private alleles in Baoxing, and 42 alleles shared between the two populations. The mean observed heterozygosity, average number of alleles, average number of allelic richness, and average polymorphism information content were 0.488, 6.2, 3.302, and 0.612, respectively for the Wanglang population and 0.553, 7.6, 4.050, and 0.747 for the Baoxing population. A moderate degree of genetic differentiation (F _st = 0.26) and no gene flow were found between these two populations. W. He and L. Lin contributed equally to this work.     

Genetic diversity and population structure of common bean (Phaseolus vulgaris) landraces from China revealed by a new set of EST-SSR markers

A new set of EST-SSR markers were developed and employed to analyze the genetic diversity and population structure of Phaseolus vulgaris in China. A total of 2452 microsatellites were identified in 2144 unigenes assembled from P. vulgaris ESTs, indicating that merely 6.9% of the 30,952 unigene sequences contained SSRs. Seventeen of 153 randomly designed EST-SSR primer pairs successfully amplified polymorphic products in 31 landraces from six major production provinces of China, with the mean number of alleles per locus of 2.700 and polymorphism information content of 0.378. The observed and expected heterozygosity ranged from 0.100 to 0.954 and 0.081 to 0.558, respectively. Using these markers, both an unrooted neighbor-joining tree and principal coordinates analysis showed that almost all of the landraces were separated according with their regional distribution. Moreover, population structure analysis revealed that all genotypes formed into three distinct clusters (k = 3), suggesting that geographic and climatic factors could provide diverse degrees of selection pressure. Accordingly, germplasm collection and cross breeding among different regions are suggested to accelerate the process of diverse germplasm creation and broaden germplasm resources of Chinese common bean.     

Genetic diversity and distribution patterns of Ecuadorian capuli (Prunus serotina)

Prunus serotina subsp. capuli (Cav.) is an arboreal species with promising economic prospects in the timber, health-food and neutraceutical markets. Despite its cultural and commercial significance, limited information exists with regards to the degree of genetic variation and ecological history of P. serotina in Ecuador. The main objective of this study was to evaluate the degree of genetic diversity and population structure of Ecuadorian P. serotina, as a preliminary step towards understanding the distribution history of this species in Ecuador and establishing germplasm conservation programs. P. serotina samples (217, representing 8 provinces from the Ecuadorian highlands) were characterized using 8 heterologous SSR markers derived from related Prunus species. Expected heterozygosity across samples (H_e = 0.71) reveals a moderate level of genetic diversity for Ecuadorian P. serotina. Nevertheless, simple allele-count analysis indicates that Ecuadorian capuli has a narrower degree of allelic richness relative to collections from the species’ center of origin in North America. Furthermore, pairwise F statistics (0.0069 ≤ Fst ≤ 0.0319) and Nei genetic distance estimates (0.02 ≤ Ds ≤ 0.09) indicate minimal population differentiation within Ecuadorian capuli. However, Bayesian population structure analysis suggests a subtle genetic contrast between germplasm from the Northern and Southern highlands. Certainly, it is of interest to analyze whether this underlying genetic differentiation between the Northern- and Southern-Highland groups is also manifested in morphological, agronomic or other phenotypic characters that could indicate adaptive differences to divergent agro-ecosystems.     

Genetic variability in British populations ofPotamogeton coloratus (Potamogetonaceae)

The partitioning of genetic variability within and between twelve British populations of the anemophilous aquaticPotamogeton coloratus Hornem. was investigated by isozyme analysis. Low levels of variability as measured by P, A and H were found. Calculation of Wright's F statistics revealed a high mean value of the overall inbreeding coefficient, (F_IT = 0.939), which was attributed both to high levels of genetic subdivision among populations (mean F_ST = 0.702) and to a high frequency of inbreeding or clonal growth within them (mean F_IS = 0.796). Only two populations are polymorphic; both inhabit sites with a long post-glacial history as wetlands. Populations of recent origin, as well as some of older vintage, contain only a single multi-locus isozyme genotype, homozygous at all loci except for IDH. A genetic bottleneck following the Devensian glaciation is discussed as a possible cause of the pattern of variation. Evidence for a duplicated IDH locus is presented.     

Genetic diversity and variation in wild populations of dark sleeper (Odontobutis potamophila) in China inferred with microsatellite markers

Twenty-one highly variable microsatellite loci were used to investigate the genetic diversity and variation of Odontobutis potamophila in China. A total of 160 samples from five wild populations (Dangtu, Sheyang, Yuyao, Minjiang and Donxishan) were genotyped. All of the 21 microsatellite loci tested in this study showed polymorphism. The number of allele per locus ranged from 5.05 to 9.90. Locus 87a of Minjiang population had a 259-bp characteristic allele. The average observed heterozygosity and expected heterozygosity ranged from 0.33 to 0.62 and from 0.40 to 0.70, respectively. The pair-wise F_ST tests and NJ trees of the five O. potamophlia populations revealed that Dangtu, Sheyang, Yuyao and Dongxishan were genetically close to one another and distinct from Minjiang. Far genetic distances were observed among populations from distant geographical areas. This result provided guide for the use of O. potamophila breeds and the protection of the species.     

Genetic diversity and structure of Manila clam (Ruditapes philippinarum) populations from Liaodong peninsula revealed by SSR markers

Manila clam (Ruditapes philippinarum) is an important commercially marine bivalve, and its wild populations have been severely declining in the coast of China during the last decade. In this study, a set of 7 genomic simple sequence repeat (SSR), and 5 expressed sequences tag (EST)-derived SSR markers were analyzed on eight wild R. philippinarum populations to assess the genetic diversity and population differentiation. A total of 114 alleles were detected on 12 loci, and the number of alleles per locus in each population ranged from 2 to 11, and allelic richness per locus varied from 2.00 to 10.88 for each sample. The average of observed and expected heterozygosity ranged from 0.386 to 0.550, and from 0.533 to 0.707, respectively. Pairwise F_ST values indicated that all population pairs had significant genetic differentiation (overall F_ST = 0.242, P < 0.01). Cluster analysis using unweighted pair group method with the arithmetic mean (UPGMA) separated the eight populations into two groups. This study will shed light on the domestication and cultivation on population genetic diversity of R. philippinarum, and also provide the foundation for conservation of R. philippinarum germplasm resources in clam breeding practices.     

高原鼠兔四个地理种群的遗传多样性与遗传分化

采用7 个多态微卫星DNA 标记分析了4 个高原鼠兔地理种群(海晏种群、西大滩东种群、西大滩西种群和昆仑山种群)的遗传多样性和遗传分化。采用多态信息含量(PIC)、期望杂合度(H_e )、观测杂合度(H_o)、基因流(N_m )和基因分化系数(F_st )对种群及物种的遗传多样性水平进行分析;计算各种群间的遗传距离(GD)、遗传相似度(GI)以及遗传距离与地理距离的相关系数,并进行UPGMA 聚类分析。研究结果显示,高原鼠兔的遗传多样性在小哺乳动物中处于较高水平, 其H_e 和H_o 的平均值分别为0. 5332 和0. 6003, 其F_st 为0. 0975,即有9. 75% 的变异存在于种群之间,即变异主要存在于种群内部。4 个种群间的杂合度与多态信息含量均无显著差异,说明它们的遗传多样性水平基本相当。海晏种群与其余3 个种群的遗传分化均达到了中度分化水平(F_st = 0.1043),而另3 个种群间几乎没有分化(F_st = 0. 0253)。Mantel test 结果表明地理距离与遗传距离间没有显著的相关性。     

Genetic structure of populations of Calomys laucha (muridae, sigmodontinae) from central Argentina

The genetic structure of populations of the Sigmodontinae rodent Calomys laucha was studied by means of allozyme electrophoresis. This highly opportunistic species is found preferably in periodically perturbed habitats of crop fields in central Argentina, where it can attain very high densities. A total of 17 enzymatic proteins assayed gave information on 25 loci; only four were monomorphic in the seven populations studied. Levels of genetic variability (H_o from 0.144 to 0.171; P_95% from 44% to 56%) were higher than mean values reported for mammals and rodents. These high levels of heterozygosity could be maintained by large populations that do not experience great fluctuations in size, or by a social structure consistent in many small breeding groups that are formed and dissappear every breeding season. Genetic differentiation at a macrogeographical scale (θ=0.018) was low but statistically significant, and showed no correlation with geographic distance between pairs of populations. The pattern of population differentiation found is compatible with a relatively recent range expansion.     

Population structure and mycelial phenotypic variability of the ectomycorrhizal basidiomycete Laccaria bicolor (Maire) Orton

Mating type allele distribution and phenotypic variability were investigated in field populations of Laccaria bicolor. Sporophores associated with Norway spruce (Picea abies), colonized by natural sources of inoculum and growing in a seed orchard, were sampled to obtain dikaryotic strains and assay their phenotypic variability for traits important to the symbiosis. Basid-iospores were also collected for mating type analysis of different mycelia. Four sporophore mating types were identified containing seven A and five B factors. Out-breeding efficiency was estimated at 73.8% and the population was slightly inbred. Crosses with previously characterized L. bicolor strains from two nearby populations identified in total six sporophore mating types and ten A and nine B factors, for an estimated outbreeding efficiency (85.7%) similar to previous studies of more spatially disparate Laccaria spp. populations. Dikaryotic strains were tested for mycelial growth rate, as a measure of their competitive ability, on agar media containing a soluble (NaH₂PO₄), or an insoluble (CaHPO₄) phosphate source. Their ability to solubilize the latter was also tested to assess their relative capacity to access insoluble, inorganic phosphate. In most cases, significant variation was detected among strains from the same site for all variables. On three sites (VC4, VC5 and VC7), each determined previously to possess a uniform mycelial genotype, phenotypic variability was likely due to epigenetic variation among different strains of the same genotype. Possible evidence for dikaryon-monokaryon crosses was observed in vivo on one sample site (VC2) where adjacent mycelia shared two mating factors. The phenotypic variability of different mycelial genotypes reflected their genetic variability observed as mating type allele diversity and underlined the importance of basidiospore dispersal in introducing new genotypes into the population. The reproductive strategies of L. bicolor are discussed and compared to those of other basidiomycete species.     

Genetic diversity and differentiation of masu salmon (Oncorhynchus masou masou) between and within cultured populations inferred from microsatellite DNA analysis

Masu salmon,Oncorhynchus masou masou,is one of the most valuable fishery species that has been introduced to China,though to date no studies on the genetic diversity and genetic relationship among hatchery populations has been performed with molecular markers.We undertook such a study and sampled 120 individuals from three hatchery stocks and analyzed 20 microsatellite loci.All loci were polymorphic and a total of 91 alleles were detected.A relatively low level of genetic diversity was revealed with effective number of allele of 3.1094,3.3299 and 3.1894 and expected heterozygosity of 0.6600,0.6648 and 0.6638 in the three stocks,respectively.Deviations from Hardy-Weinberg equilibrium were found due to heterozygote deficit.Accordingly,evidence of genetic bottlenecks were found in the three stocks.An individual assignment test demonstrated that 85% of individuals were correctly assigned into their original stocks.Pairwise Fst revealed that significant differentiation occurred between these three stocks.The results of the study indicated that disequilibrium of genetic structure and differentiation has occurred in all three stocks.This information collectively provides a basis for measures to avoid of loss of genetic diversity and introgression in Chinese aquaculture.     

Genetic diversity analysis by microsatellite markers in four captive populations of the sika deer (Cervus nippon)

The Chinese sika deer (Cervus nippon) is a rare and vulnerable animal in China for medical use. In this study, the genetic diversity and population genetic structure of 113 Chinese sika deer from 4 populations (Linyi Farm, LF; Linyi Park, LP, Yangzhou Farm, YF; Yangzhou Zoo, YZ) were investigated with 14 microsatellite loci. Eighty-three alleles were detected at the 14 loci in all populations. The expected heterozygosity ranged from 0.257 to 0.863 and the observed heterozygosity from 0.226 to 0.821. The polymorphism information content at different loci ranged from 0.217 to 0.825. The results of the HWE (Hardy–Weinberg equilibrium) tests indicated that only four loci (CEH-5, BL42, Mber70, and CEH-2) were in HWE (P > 0.01). The mean number of alleles per population ranged from 3.21 to 5.64, observed and expected heterozygosities ranged from 0.568 to 0.685, respectively. Positive inbreeding coefficient (F_IS) values were found in every population. F_ST values ranged from 0.101 in the LF to 0.155 in the YZ. The genetic identity ranged from 0.1236 to 0.1645. The genetic distance ranged from 0.4746 to 0.6025. The results of this study indicate moderate genetic variation and polymorphism across the loci. Appropriate breeding strategies should be designed for deer in captivity.     

Genetic variability of Bouteloua gracilis populations differing in forage production at the southernmost part of the North American Graminetum

Bouteloua gracilis (blue grama grass) native populations have been shown to be highly variable, however the genetic basis of this variability has not been well established. Determining the extent of genetic variability within and among plant populations have important repercussions for the management and conservation of species, and in particular for those subjected to intensive use such as forage plants. Using RAPD, this study was undertaken to investigate the genetic variability of four B. gracilis native populations developed in three grasslands and one shrubland at the southernmost part of the North American Graminetum in México. Significant differences in grass aboveground production were found among the study sites, while considerable genetic variation within each of the four blue grama populations evaluated was detected. The molecular analysis, based on 55 individuals, revealed a total of 108 scorable repeatable bands, with 99 of them being polymorphic (overall polymorphism= 91.7%). Within every population each individual was genetically distinct and no population-specific bands (fixed marker differences) were identified. Pair-wise Φ _ST comparisons indicated that the four blue grama populations examined were significantly different in their genetic constitution (P<0.001). AMOVA revealed that most of the genetic variation detected in Bouteloua gracilis was explained by intra- (88.53%), rather than by inter-population (11.47%) differences. UPGMA based on the Φ _ST values indicated that the blue grama population collected from the shrubland displayed the RAPD profiles that most differed among the study sites. Possible causes of these results could reside on intensive grazing reducing, and proper management conserving, the forage production and genetic diversity of blue grama native populations. Our results are consistent with previous studies analyzing population genetic variation in outcrossing grasses and, in particular, with ecological and cytological evidence for a high genetic variability in native populations of B. gracilis. The implications of our findings and prospective studies to be undertaken using molecular tools in the study of blue grama biology and ecology are discussed. This revised version was published online in August 2006 with corrections to the Cover Date.     

Genetic diversity and genetic structure of Northern Goshawk (Accipiter gentilis) populations in eastern Japan and Central Asia

Japanese goshawk was classified as a vulnerable species in the Red Data Book. There have been possibilities of a decrease of genetic diversity accompanied by habitat loss and genetic pollution due to hybridization with escaping imported goshawks. In this paper, genetic diversity, gene flow and conservation of Northern Goshawk (Accipiter gentilis) in Japan are discussed and compared with that in Central Asia. We used 11 newly developed microsatellite markers and also adopted six previously published markers. Genetic diversity was shown to be maintained with 0.58 as mean heterozygosity and 3.95 as mean allelic richness. The degree of genetic differentiation across all populations was low (Nei’s genetic differentiation index = 0.036, Wright’s genetic differentiation index = 0.039), possibly due to gene flow via adjacent regions (average number of migrants = 4.26; 0.68–20.30). However, it is possible that slight differentiation resulted from the short divergence time and/or inflow of escaping imported individuals. We recommend that goshawks in eastern Japan should be managed as a single unit. They do not appear to be under threat genetically at present, but there is the potential for rapid loss of genetic diversity. For future conservation, investigations of dispersal routes and actual conditions of gene flow are also recommended. To prevent further inflow of escaping goshawks into natural populations, it is desirable to reduce importation of goshawks and to enact a regulation obliging purchasers to register imported goshawks. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Genetic variability and bottleneck studies in Zalawadi, Gohilwadi and Surti goat breeds of Gujarat (India) using microsatellites

Indian goat breeds are recognized as an invaluable component of the world's goat genetic resources. Microsatellite pairs were chosen from the list suggested by International Society for Animal Genetics (ISAG) and amplified in two multiplexes (Set-I: 7 microsatellites and Set-II: 11 microsatellites) for automated fluorescence genotyping to assess bottleneck and analyze genetic variability and genetic distances within and between three goat breeds viz. Zalawadi, Gohilwadi and Surti. The observed number of alleles ranged from 4 (Oar JMP-29) to 15 (ILSTS-030 and -034) with a total of 178 alleles and mean of 9.89 alleles across the three breeds. The overall heterozygosity, PIC and Shannon index values were 0.61, 0.60 and 1.50 indicating high genetic diversity. The maximum observed heterozygosity was found in Gohilwadi and minimum in Surti goat breed. The Nei's standard genetic distance was minimum between Zalawadi and Gohilwadi, and maximum between Gohilwadi and Surti. Non-significant heterozygote excess on the basis of IAM, TPM and SMM models, as revealed from Wilcoxon sign-rank tests, along with a normal ‘L’-shaped distribution of mode-shift test, indicated no bottleneck in Zalawadi and Gohilwadi goat populations, whereas mild bottleneck in the recent past for Surti breed. This research on goat genetic diversity in Gujarat state provides valuable information on Zalawadi, Gohilwadi and Surti goat genetic resources, and will assist in developing a national plan for the conservation and utilization of indigenous goat breeds.     

Genetic polymorphisms in three Alpine populations (Visp valleys,Switerland)

Phenotype distributions and allele frequencies of 13 blood proteins are presented for the populations of the three Visp valleys, situated in the Swiss Alps. Blood samples of a total of 883 individuals were electrophoretically analysed. The three populations were statistically compared with each other, and with an additional sample from the literature thought to be representative of the entire Swiss population. Statistical differences are revealed and genetic distances are presented. These results are interpreted in connection with differences between the Visp valleys in topological situation.     

Isolation and characterization of ten polymorphic microsatellite markers for the blue mussel (Mytilus edulis)

In this study, we isolated 10 novel polymorphic microsatellite markers in Mytilus edulis by using the magnetic beads enrichment procedure. The characteristics of these loci were estimated by using a sample of 32 individuals of M. edulis. The number of alleles at 10 polymorphic microsatellite loci ranged from 2 to 15 with an average of 5.667. HO and HE ranged from 0.2667 to 1.0000 (0.6800 in average) and from 0.4723 to 0.9226 (0.6190 in average), The PIC value of 6 loci was more than 0.5, and that of the other 4 was between 0.25 and 0.50, Significant deviation from Hardy–Weinberg Equilibrium was observed at ME8, ME115 and ME153 after Bonferroni correction (P < 0.004, adjusted value), which possibly was due to the presence of null alleles. This study will be useful for the analysis of population genetic diversity, and the management of this important M. edulis resource.     

Genetic diversity and population genetic structure of six dromedary camel (camelus dromedarius) populations in Saudi Arabia

Camels are an integral and essential component of the Saudi Arabian heritage. The genetic diversity and population genetic structure of dromedary camels are poorly documented in Saudi Arabia so this study was carried out to investigate the genetic diversity of both local and exotic camel breeds. The genetic diversity was evaluated within and among camel populations using 21 microsatellite loci. Hair and blood samples were collected from 296 unrelated animals representing 4 different local breeds, namely Majaheem (MG), Maghateer (MJ), Sofr (SO), and Shaul (SH), and two exotic breeds namely Sawahli (SL) and Somali (SU). Nineteen out of 21 microsatellite loci generated multi-locus fingerprints for the studied camel individuals, with an average of 13.3 alleles per locus. Based on the genetic analyses, the camels were divided into two groups: one contained the Saudi indigenous populations (MG, MJ, SH and SO) and the other contained the non-Saudi ones (SU and SL). There was very little gene flow occurring between the two groups. The African origin of SU and SL breeds may explain their close genetic relationship. It is anticipated that the genetic diversity assessment is important to preserve local camel genetic resources and develop future breeding programs to improve camel productivity.     

Genetic structure of introduced European fallow deer (<Emphasis Type="Italic">Dama dama dama</Emphasis>) in Tasmania,Australia

European fallow deer are an introduced species classified as partly protected wildlife in Tasmania, Australia. Current management practices are primarily governed under the Quality Deer Management regime, in which animals are harvested during designated hunting seasons. Among populations, prominent morphological differences have been reported; however, the genetic relationship of these populations has until now been poorly understood. Representative animals were sampled from three key areas across their range and genotyped at ten polymorphic microsatellite loci to investigate genetic diversity, population structure, and genetic bottlenecks. Allelic richness was low in all three populations and ranged between 2.20 and 2.49 alleles/locus. A genetic bottleneck was detected in two of the three populations (P < 0.001). Population differentiation was evident between Lake Echo and Benham (q = 0.122; P < 0.001) and Benham and Connorville (q = 0.110; P < 0.001), but not between Lake Echo and Connorville (q = 0.0235), with individuals being identified as belonging to two genetic clusters. The pattern of population differentiation from the three study populations suggests that deer from the western region of their range are genetically distinct to those from the eastern region. This correlates with morphological variation within Tasmanian fallow deer, in which differences between the regions maybe attributable to geographical barriers.