Toxicity of Chemically Spiked Sediment to the Carpet Shell Clam Ruditapes decussatus Embryos and Larvae

The objective of this research was to assess the toxicity of sediment contaminated with cadmium, DDT, chlorpyrifos, and fluoranthene to embryos and larvae of the European clam Ruditapes decussatus, exposed to two sediment fractions, the whole sediment and elutriate. The percentages of abnormal D-shaped larvae and larval mortality have been investigated. The median effective concentration (EC50) values, reducing 50% of the percentage of D-shaped larvae, in whole sediments and elutriates were, respectively, 1.17 mg/kg and 417.1 μgl^?1 (3.71 μM) for cadmium, 1.66 mg/kg and 97.8 μgl^?1 (0.48 μM) for fluoranthene, 1.71 mg/kg and 384.8 μgl^?1 (1.08 μM) for DDT, and 0.96 mg/kg and 339.5 μgl^?1 (0.96 μM) for chlorpyrifos. The 96h-median lethal concentrations (LC50) reducing larval survival by 50% were 4.04 mg/kg 654.3 μgl^?1 (5.82 μM) for cadmium, 17.41 mg/kg 8666.6 μgl^?1 (42.84 μM) for fluoranthene, 3.93 mg/kg and 457.4 μgl^?1 (1.29 μM) for DDT, and 2.53 mg/kg and 308.06 μgl^?1 (0.87 μM) for chlorpyrifos. Based on EC₅₀ and LC₅₀ comparisons to toxicity data for other marine species, these findings suggest that the R. decussatus embryotoxicity and larvae mortality bioassay were among the most sensitive tools for sediment quality assessment.     

Isolation of Vibrio alginolyticus and Vibrio splendidus from Aquacultured Carpet Shell Clam (Ruditapes decussatus) Larvae Associated with Mass Mortalities

Two episodes of mortality of cultured carpet shell clams (Ruditapes decussatus) associated with bacterial infections were recorded during 2001 and 2002 in a commercial hatchery located in Spain. Vibrio alginolyticus was isolated as the primary organism from moribund clam larvae that were obtained during the two separate events. Vibrio splendidus biovar II, in addition to V. alginolyticus, was isolated as a result of a mixed Vibrio infection from moribund clam larvae obtained from the second mortality event. The larval mortality rates for these events were 62 and 73%, respectively. Mortality was also detected in spat. To our knowledge, this is the fist time that these bacterial species have been associated with larval and juvenile carpet shell clam mortality. The bacterial strains were identified by morphological and biochemical techniques and also by PCR and sequencing of a conserved region of the 16S rRNA gene. In both cases bacteria isolated in pure culture were inoculated into spat of carpet shell clams by intravalvar injection and by immersion. The mortality was attributed to the inoculated strains, since the bacteria were obtained in pure culture from the soft tissues of experimentally infected clams. V. alginolyticus TA15 and V. splendidus biovar II strain TA2 caused similar histological lesions that affected mainly the mantle, the velum, and the connective tissue of infected organisms. The general enzymatic activity of both live cells and extracellular products (ECPs), as evaluated by the API ZYM system, revealed that whole bacterial cells showed greater enzymatic activity than ECPs and that the activity of most enzymes ceased after heat treatment (100°C for 10 min). Both strain TA15 and strain TA2 produced hydroxamate siderophores, although the activity was greater in strain TA15. ECPs from both bacterial species at high concentrations, as well as viable bacteria, caused significant reductions in hemocyte survival after 4 h of incubation, whereas no significant differences in viability were observed during incubation with heat-killed bacteria.     

独龙牛遗传多样性及其种群遗传结构的等位酶分析

采用水平片淀粉凝胶电泳技术,进行３０头独牛牛４１种蛋白质共计４４个遗传座位的等位酶分析,只在Ｔｒ,Ｈｐ,Ａｍｙ,Ｅｓｔ等４个座位发现多态性。每个座位等基因的平均数、多态座位百分比和平均杂合度值分别为Ａ＝１．０９０９、Ｐ＝０．０６８２和Ｈ＝０．０２６２。贡山县和福贡县独龙牛群体从酶基因的角度上看遗传多样性贫乏,可能是分别由小种群引种而来,受到瓶颈效应的作用,并伴随着创立者事件的发生。我们结合独龙牛在     

Uptake and Retention of Vibrio parahaemolyticus in a Cohabitating Population of Ruditapes decussatus and Ruditapes philippinarum Under Experimental Conditions

The presence of Vibrio parahaemolyticus in bivalve mollusc is an important cause of foodborne illnesses, and their levels are influenced by environmental changes, such as temperature and salinity. Clams are common species in estuaries and are used in environmental monitoring programmes. Present study compared the uptake and retention of nonpathogenic V. parahaemolyticus by two species of clam (Ruditapes decussatus and R. philippinarum), cohabitating in a closed system. Results showed no significant differences were found between both species of clams. Bacterial levels are following a similar trend with values between 3.48 and 3.70 log CFU/g for R. decussatus and between 3.15 and 3.49 log CFU/g for R. philippinarum. So, in the absence of water renewal, high and stable levels of V. parahaemolyticus were observed in cultured clams after exposure. Changes in physical parameters should be taken into account to design surveillance programmes in bivalves, and sampling should focus on species that have faster filtration rates at that water temperature since they potentially represent the worst-case scenario.     

Population Genetics of Allozyme Variation in NEUROSPORA INTERMEDIA

Electrophoretically detectable variation in the fungus Neurospora intermedia has been surveyed among isolates from natural populations in Malaya, Papua, Australia and Florida. The principal result is a pattern of genetic variation within and between populations that is qualitatively no different than the well documented patterns for Drosophila and humans. In particular, there is a high level of genetic variation, the majority of which occurs at the level of local populations. Evidence is presented which argues that N. intermedia has a population structure analogous to that of an annual vascular plant with a high level of vegetative reproduction. Sexual reproduction appears to be a regular feature in the biology of the species. Substantial heterokaryon function seems unlikely in natural populations of N. intermedia. Theoretical considerations concerning the mechanisms underlying the observed pattern of variation most likely should be consistent with haploid selection theory. The implications of this constraint upon the theory are discussed in detail, leading to the presentation of a model based upon the concept of environmental heterogenicity. The essence of the model, which is equally applicable to haploid and diploid situations, is a shifting distribution of multiple adaptive niches among local populations such that a given population has a small net selective pressure in favor of one allele or another, depending upon its particular distribution of niches. Gene flow among neighboring populations with differing net selective pressures is postulated as the principal factor underlying intrapopulational allozyme variation.     

湖北3种药用淫羊藿植物等位酶多样性与居群遗传结构

采用超薄平板微型聚丙烯酰胺等电聚焦电泳方法对湖北3种淫羊藿属（Epimedium L．）药用植物：柔毛淫羊藿（E．pubescens Maxim．）、箭叶淫羊藿（Esagittatum（Sieb．＆Zucc．）Maxim．）和巫山淫羊藿（Ewushanense T.S．Ying）的11个自然居群进行了等位酶种内遗传多样性和居群遗传结构以及种间遗传关系的研究。6个酶系统在3种淫羊藿植物中检测到13个酶位点共45个等位基因,分析结果表明：1）3种淫羊藿均具有较高的遗传多样性水平（A=2．6-3．2,P=69．2％-84．6％,Ho=0．274-0．377,HE=0．282-0．369）,远高于多年生草本植物和依靠动物传粉植物的平均水平;2）所有居群都显著偏离Hardy—Weinberg平衡,大多数多态位点固定指数（F）明显偏离于0且正负值各半,暗示该属植物可能具有复杂的繁育系统;3）种内和种间的遗传分化度均较低,分别为GST=0．0246-0．0409和0．0495-0．1213,表明种内居群间存在较高的基因流和种间较近的遗传关系;4）聚类分析表明柔毛淫羊藿与箭叶淫羊藿的亲缘关系更近,这与形态学特征、花瓣演化趋势及系统发育分析等方面的研究的结果相吻合。讨论分析认为3种淫羊藿植物的遗传变异特性是由淫羊藿属植物异交与克隆繁殖的混合繁育系统、多年生的生活特性、古老的进化历史和种子的蚁播特性等多因素共同决定的。     

Spatial and seasonal biomarker responses in the clam Ruditapes decussatus

The clam Ruditapes decussatus is an important resource to preserve in coastal lagoon systems around the Mediterranean including the South Portugal. To assess spatial and temporal biomarker responses to contamination in the species, a multibiomarker approach was conducted using antioxidant enzymes, MFO system phase I and II; acetylcholinesterase, metallothionein (MT), δ-aminolevulinic acid dehydratase and lipid peroxidation (LPO). The condition index (CI), metals and polycyclic aromatic hydrocarbons (PAHs) were also determined. The levels of contaminants were not particularly high and the antioxidant enzymes, acetylcholinesterase (AChE), MT in the digestive gland, and δ-aminolevulinic acid dehydratase (ALAD) do not provide a suitable seasonal and spatial discrimination reversely to that regarding CYP450, glutathione-S-transferase (GST), MT in the gills, and LPO in both tissues. However, even those could vary with natural variables that may act as confounding factors. Thus, seasonal variability and natural range of biomarker responses must be carefully and accurately taken into account in ecotoxicological approaches of environmental quality assessment programmes.     

Allozyme Variation in a Natural Population of the Nile Crocodile

Blood samples were collected for allozyme studies from 92 Crocodylusniloticus from the Runde River in Gonarezhou National Park,southern Zimbabwe. Two (glucose phosphate isomerase and erythrocyteacid phosphatase) of 27 protein coding loci were polymorphicwhen examined by starch-gel electrophoresis. This amount ofvariability is similar to that found in another crocodilian,Alligator mississippiensis and is not unusually low as has beenfound in a number of large vertebrates. In a single semi-isolatedpopulation, allele frequencies at both polymorphic loci werein Hardy-Weinberg equilibrium suggesting a random mating patternwith no severe bottleneck effect in the founding of this population.Population F-statistics suggest that panmixia exists withinand among the three main breeding sites studied.     

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.     

胡卢巴等位酶变异和遗传多样性研究

采用聚丙烯酰胺凝胶电泳技术,对33份胡卢巴(Trigonella foenum-graecum L.)种质资源的5个酶系统 24个酶位点的变异和遗传多样性进行初步分析.结果表明:参试胡卢巴的遗传多样性水平较高,物种水平上的遗传多样性参数:多态位点百分数(P)为75.0%,平均每位点的等位基因数(A)为1.75,平均期望杂合度(He)为0.352;种源水平上的平均遗传多样性参数:P=70.6%,A=1.87,He=0.422.各种质资源间基因分化系数(GST)为0.026;基因流(Nm)的平均值为26.14,表明胡卢巴不同种质资源间基因分化水平低,基因交流频繁.聚类分析结果显示,来自中国不同地区的胡卢巴亲缘关系较近,而国外胡卢巴和国内胡卢巴的亲缘关系相对较远.     

Pathogenicity Variation and Population Genetic Structure of Plasmopara viticola in China

Viticulture in China, like in many other major grape‐growing countries around the world, is severely affected by downy mildew (DM) disease caused by Plasmopara viticola (Pv). However, little has been known about the pathogenicity and genetic structure of the pathogen distributed in China. In this study, 206 single‐sporangiophore Pv strains were isolated from Pv‐infected leaves collected from the most important grape‐growing regions in China. Among them, 29 strains, isolated from a majority of sampled regions and from the hosts with different DM resistance, were tested for their pathogenicity by inoculating into six grape cultivars with different levels of DM resistance. Significant difference in pathogenicity was observed among these strains. Seven pairs of SSR primers selected from previous reports were used for genetic studies of these 206 Pv strains. A total of 64 alleles and 193 genotypes were identified, suggesting that oosporic infection resulted from sexual reproduction made the major contributions to the disease epidemics during the growing season. Analysis of molecular variance (AMOVA) and principal coordinate analysis (PCoA) showed that most of genetic variations were within populations. In addition, low levels of pairwise FST value (ranged from 0.02 to 0.07) and high levels of gene flow were detected between populations. Results from this study suggest that long‐distance dispersals of Pv oospore occur in China.     

Population Structure in Daphnia Obtusa: Quantitative Genetic and Allozymic Variation

Quantitative genetic analyses for body size and for life history characters within and among populations of Daphnia obtusa reveal substantial genetic variance at both hierarchical levels for all traits measured. Simultaneous allozymic analysis on the same population samples indicate a moderate degree of differentiation: G(ST) = 0.28. No associations between electrophoretic genotype and phenotypic characters were found, providing support for the null hypothesis that the allozymic variants are effectively neutral. Therefore, G(ST) can be used as the null hypothesis that neutral phenotypic evolution within populations led to the observed differentiation for the quantitative traits, which I call Q(ST). The results of this study provide evidence that natural selection has promoted diversification for body size among populations, and has impeded diversification for relative fitness. Analyses of population differentiation for clutch size, age at reproduction, and growth rate indicate that neutral phenotypic evolution cannot be excluded as the cause.     

Allozyme Variation and the Genetic Structure of Populations of the Rare Sedge Carex misera (Cyperaceae)

Abstract Carex misera is a rare sedge, endemic to rocky outcrops and mountain summits within the southern Appalachian Mountains from northern Georgia to northern North Carolina. We assessed allozyme diversity for 406 individuals from nine populations over most of the geographic range. Twenty-seven putative loci were assayed and eight (30%) were found to be polymorphic. Nei's gene diversity statistics ( H _T =0.043, H _S =0.019, G _ST =0.551) indicated low levels of variation but relatively highly differentiated populations, suggesting little gene flow. Significant deviations from genotypic expectations under Hardy-Weinberg equilibrium, high positive fixation indices, and the existence of small genetic neighborhoods within populations suggest that at least some inbreeding occurs. Cluster analysis of Nei's genetic identity statistics and principal component analysis of allele frequency data showed high similarity among the six southern populations with the two northern populations more differentiated from them and from each other. These results suggest that preservation of the northern populations is necessary to conserve the already low levels of genetic diversity within the species.     

Genetic Variation and Population Structure of Oriental Migratory Locust, Locusta migratoria manilensis, in China by Allozyme, SSRP-PCR, and AFLP Markers

Allozyme analysis, microsatellite primer PCR (SSRP-PCR), and amplified fragment length polymorphism (AFLP) techniques were used to assess genetic diversity and population structure of the Chinese oriental migratory locust, Locusta migratoria manilensis. A total of 299 PCR markers (67 SSRPs and 232 AFLPs) were detected in eight populations, of which 98.7% were polymorphic markers. The proportion of polymorphic loci (95.5–98.8%) by SSRP+AFLP markers indicated no significant differences between populations, and all populations exhibited a similar level of variability; results of the allozyme analysis demonstrated that 19 loci gave rise to a lower level of polymorphism (55.6–66.7%). The genetic distances between the populations were relatively low. Shannon’s index and Nei’s gene diversity showed low differentiation among the populations. Allozyme analysis, however, reflected greater similarity and smaller differentiation between the populations than those shown by SSRP and AFLP markers. Neighbor-joining dendrograms derived from both the allozyme and SSRP+AFLP markers showed that the genetic distances among Chinese oriental migratory locust populations were not greatly influenced by geographic distance and breeding habitats.     

Seasonal Variation of Metals in Seawater, Sediment, and Manila Clam Ruditapes philippinarum from China

Concentrations of trace metals (Cu, Pb, Zn, Cd, Cr, Hg, and As) were determined for the first time in seawater, sediment, and Manila clam from Deer Island, Liaoning Province, China. The seawater, sediment, and clam samples were collected seasonally at three clam farming sites around Deer Island during 2010–2011. The average concentrations of Cu, Pb, Zn, Cd, Cr, Hg, and As in the seawater samples were 4.16, 0.72, 5.88, 0.45, 2.51, 0.03, and 1.02 μg/l, respectively. The seasonal variations of trace metals in seawater showed a significant difference in the concentrations of Cu, Pb, Zn, Hg, and As among seasons. The average concentrations of Cu, Pb, Zn, Cd, Cr, Hg, and As in the sediment samples were 6.43, 13.80, 53.08, 1.10, 36.40, 0.05, and 4.78 mg/kg dry weight, respectively. Trace metal concentrations in sediment seasonally varied significantly except for Cd and Hg. The average concentrations of Cu, Pb, Zn, Cd, Cr, Hg, and As in the clam samples were 11.28, 0.61, 92.50, 0.58, 3.98, 0.03, and 1.98 mg/kg dry weight, respectively. Concentrations of Cu, Zn, Cd, Cr, and As in Manila clam showed marked seasonal fluctuations with significant difference. Cu and Zn were the metals with the highest mean biosediment accumulation factor values in Manila clam. Besides, significant correlations for the concentrations of Cu and Zn relative to their concentrations in sediment were also found. Such differences in regression analyzes may be explained by differential bioaccumulation of essential and xenobiotic metals. Concentrations of trace metals in Manila clam did not exceed the maximum established regulatory concentrations for human consumption. Moreover, the calculations revealed that the estimated daily intake values for the examined clam samples were below the internationally accepted dietary guidelines and the calculated hazard quotient values were well less than 1, thus strongly indicating that health risk associated with the intake studied metals through the consumption of Manila clam from Deer Island was absent.     

Allozyme Variation and the Genetic Structure of Populations of Trochodendron aralioides, a Monotypic and Narrow Geographic Genus

Trochodendron aralioides Siebold & Zucc., a primitive angiosperm that is insect-pollinated, has wind-dispersed seeds and grows only in eastern Asia. Nineteen populations were analyzed, including 16 from Taiwan, two from the main islands of Japan and one from Iriomote Island in the Ryukyu Islands. Genetic variability (0.133) at the species level was more similar to that of a narrow geographic species than an endemic species. Based on genotype frequencies, mating within populations was non-random (F _{I s}=0.065) and there was significant genetic differentiation (F _ST =0.164) among populations. Genetic diversity was largely within, rather than among, populations (H _s =0.132, 85.14%). Bisexual flowers of T. aralioides exhibit synchronized dimorphism. The protogynous and protandrous morphs are self-incompatible, which probably promotes outcrossing and contributes to the high levels of heterozygosity within populations. Using a maximum likelihood tree, populations of T. aralioides were separated into two distinct clusters: Japan and Taiwan/ Iriomote Island. Populations of T. aralioides on Iriomote Island and in northern Taiwan exhibited a high degree of genetic similarity. The isolation-by-distance model does not fit populations in Taiwan, but suitably describes the relationship between populations of T. aralioides in Japan and Taiwan. Received 28 April 2000/ Accepted in revised form 13 December 2000     

Population Genetic Structure of Endemic and Endangered Yellow Catfish, Horabagrus brachysoma, Using Allozyme Markers

The allozyme variation and population genetic structure of Horabagrus brachysoma in three natural populations from the southern part of the Western Ghats region, India, were investigated by polyacrylamide gel electrophoresis. Variations at 14 loci from 14 enzyme systems were analyzed. The allozyme analysis revealed a high level of genetic variation in this species, with an average of observed alleles per locus of 2.357 and observed heterozygosity of 0.178. The positive value of the fixation index (FIS=0.507) implied a significant deficiency of heterozygosity at the population level. The highly significant probability (P<0.0001) for the overall loci suggested that the three sample sets were not part of the same gene pool.     

Sequence of the Small Subunit Ribosomal RNA Gene of Perkinsus atlanticus-like Isolated from Carpet Shell Clam in Galicia, Spain

Parasites identified as Perkinsus atlanticus have been reported infecting carpet shell clams in Galicia (northwest Spain). We have sequenced the 18S ribosomal RNA gene of in vitro cultured Perkinsus atlanticus-like or hypnospores from diseased clams, and compared it with the same genomic region from P. marinus and Perkinsus sp. We have also compared the sequence of internal transcribed spacer (ITS) 1, ITS 2, and 5.8S rRNA from our isolate with the P. atlanticus GenBank sequence. The phylogenetic analysis of our cultured parasite based on the 18S gene led us to conclude that this isolate is not related to the genus Perkinsus but to the protists Anurofeca, Ichthyophonus, and Psorospermium, located near the animal-fungal divergence. These last two genera have been included, together with Dermocystidium, in the newly described DRIPs (Dermocystidium, rossete agent, Ichthyophonus, and Psorospermium) clade, recently named Mesomycetozoa. Received October 25, 1999; accepted February 11, 2000.     

Genetic Structure of the Han Chinese Population Revealed by Genome-wide SNP Variation

Population stratification is a potential problem for genome-wide association studies (GWAS), confounding results and causing spurious associations. Hence, understanding how allele frequencies vary across geographic regions or among subpopulations is an important prelude to analyzing GWAS data. Using over 350,000 genome-wide autosomal SNPs in over 6000 Han Chinese samples from ten provinces of China, our study revealed a one-dimensional “north-south” population structure and a close correlation between geography and the genetic structure of the Han Chinese. The north-south population structure is consistent with the historical migration pattern of the Han Chinese population. Metropolitan cities in China were, however, more diffused “outliers,” probably because of the impact of modern migration of peoples. At a very local scale within the Guangdong province, we observed evidence of population structure among dialect groups, probably on account of endogamy within these dialects. Via simulation, we show that empirical levels of population structure observed across modern China can cause spurious associations in GWAS if not properly handled. In the Han Chinese, geographic matching is a good proxy for genetic matching, particularly in validation and candidate-gene studies in which population stratification cannot be directly accessed and accounted for because of the lack of genome-wide data, with the exception of the metropolitan cities, where geographical location is no longer a good indicator of ancestral origin. Our findings are important for designing GWAS in the Chinese population, an activity that is expected to intensify greatly in the near future.     

Disentangling the Population Structure and Evolution of the Clam Pathogen Vibrio tapetis

Vibrio tapetis is a fastidious slow-growing microorganism that causes the Brown Ring Disease in clams. Recently, two subspecies for this bacterial pathogen have been proposed. We have developed a multilocus sequence typing scheme and performed evolutionary studies of V. tapetis population using the great majority of isolates of V. tapetis obtained worldwide until now (30 isolates). V. tapetis constitutes a high polymorphic population, showing low diversity indexes and some genetic discontinuity among the isolates. Mutation events are more frequent than recombination, although both are approximately equally important for genetic diversification. In fact, the divergence between subspecies occurred exclusively by mutation but the diversity observed among isolates of the same subspecies appeared to be generated mostly by recombination. Between the subspecies, genetic distance is very high and almost no recurrent gene flow exists. This pathogen displays a non-clonal population structure with an ancient spatial segregation population and some degree of geographical isolation, followed by a population expansion, at least for V. tapetis subsp. tapetis. A database from this study was created and hosted on publmlst.org (http://pubmlst.org/vtapetis/).