巨蛎属牡蛎DNA序列的比较及鉴定

【目的】了解巨砺属牡蛎的系统关系和种类区分。【方法】对我国沿海分布的7种巨砺属牡蛎(香港牡蛎、有明牡蛎、熊本牡蛎、岩牡蛎、艾氏牡蛎、太平洋牡蛎、葡萄牙牡蛎)的线粒体DNA片段(COI、12S、16S和tRNAs),以及核糖体RNA基因转录间隔子序列(ITS-1、ITS-2和ITS)进行分子系统学研究。【结果】无论种间或种内,tRNAs序列差异最大,亚种内TS1序列差异最大;tRNAs和COI序列较其它序列变异更快,种间变异与种内变异之间有明显的条形码间隙;12S、16S、ITS和ITS2的种间变异与种内变异无重叠及条形码间隙;ITS1的种间变异与种内变异出现重叠。在亚种层面,12S、ITS、ITS1和ITS2的亚种间变异与亚种内变异出现重叠;16S的亚种间变异与亚种内变异无重叠及条形码间隙;tRNAs与COI序列亚种间变异与亚种内变异之间有明显的条形码间隙,有利于区分亚种。【结论】tRNAs和COI序列可用于种及亚种的鉴定。     

Sequences Characterization of Microsatellite DNA Sequences in Pacific Abalone(Haliotis discus hannai)

1 Introduction Microsatellites or simple sequence repeats (SSRs) are tandemly repeated motifs of one to six bases found in all prokaryotic and eukaryotic genomes analysed to date (Zane et al., 2002). Due to their hyper-variable and co-dominant nature, relatively high abundance and random distribution in the genome, microsatellites are among the most efficient class of molecular markers. Such repeats display high polymorphism because of variation in repeat length and can be rapidly analysed t…     

Using DNA damage to monitor water environment

DNA damage of aquatic organisms living in polluted environments can be used as a biomarker of the genotoxicity of toxic agents to organisms. This technique has been playing an important role in ecotoxicologlcal study and environmental risk assessment. In this article, main types of DNA damage caused by pollutants in water environments were reviewed; methods of detecting DNA damage were also documented for water environmental monitoring.     

In two waters: contemporary evolution of lagoonal and marine white seabream (Diplodus sargus) populations

Brackish water ecosystems are often exposed to wide variations in environmental variables, including temperature and salinity, which may cause strong selective pressures on organisms modifying the genetic patterns of species. The aim of this work was to test whether there is a ‘divergence-with-gene flow’ in coastal lagoon populations of white seabream (Diplodus sargus) (Ria Formosa, S Portugal and Mar Menor, SE Spain) respect to four marine populations, by using partial sequences of cyt b mitochondrial gene and information from nine microsatellite loci. Genetic diversity was highest in both coastal lagoons (Mar Menor and Ria Formosa) considering mitochondrial and nuclear markers. Although some of F_ST population pairwise comparisons were not significant, analyses of molecular variance (AMOVAs) detected differences between groups (coastal lagoon and marine) close to significance. Also, only two haplotypes (Cytb-17 and Cytb-18) were detected in both coastal lagoon sampling sites and these localities (Mar Menor and Ria Formosa) showed the highest number of singletons, some of them with a high number of mutations, as has been already described for other Mar Menor populations (Pomatochistus marmoratus and Holothuria polii). Also, several tests detected significant positive and balancing selection considering mtDNA and microsatellite data. These data support the hypothesis of selection as one of the drivers of the genetic differences found between coastal lagoon and marine populations. The life strategy adopted by Diplodus sargus in coastal lagoons allows it to decrease its mortality rate and improve the heritability of its genes. Also, the increase time spent in coastal lagoons with different temperatures and salinities favours the fitness selection and the maintenance of exclusive haplotypes and genotypes in coastal lagoon inhabitants favouring the ‘divergence-with-gene-flow’.     

West versus East Mediterranean Sea: origin and genetic differentiation of the sea cucumber Holothuria polii

We studied the genetic structure of the sea cucumber Holothuria (Roweothuria) polii (Delle Chiaje 1823) by analysing the mitochondrial DNA variation in two fragments of cytochrome oxidase I (COI) and 16S genes. Individuals were collected in seven locations along the Mediterranean Sea, which cover a wide range of the species distribution. We found high haplotype diversity for COI and moderate diversity for 16S, and low nucleotide diversity for both genes. Our results for the COI gene showed many recent and exclusive haplotypes with few mutational changes, suggesting recent or ongoing population expansion. The Western and Eastern Mediterranean populations exhibited slight but significant genetic differentiation (COI gene) with higher genetic diversity in the East. The most ancient haplotype was not present in the westernmost sampling location (SE Spain). The oldest expansion time was observed in Turkey, corresponding to mid‐Pleistocene. Turkey had also the highest genetic diversity (number of total and exclusive haplotypes, polymorphisms, haplotype and nucleotide diversity). This suggests that this region could be the origin of the subsequent colonizations through the Mediterranean Sea, a hypothesis that should be assessed with nuclear markers in future research.     

Induction of DNA strand breaks in the mussel (Mytilus trossulus) and clam (Protothaca staminea) following chronic field exposure to polycyclic aromatic hydrocarbons from the Exxon Valdez spill

In 2002, 13 years after the Exxon Valdez spill, mussels and clams were examined for lingering oil exposure and damage. Known oil patches were sampled at four locations, and compared to nearby reference areas (same bay), and were also compared to "hot reference" sites to verify the methods used (Cordova harbor and fresh diesel spill at Port Chalmers). Passive samplers deployed for a month at the sites, along with tissue samples, confirmed that the oiled sites were oiled (fingerprinting back to Exxon Valdez oil) and that reference sites were clean. The highest PAH loads were detected in sub-surface interstitial waters at oiled sites. Exposure at the surface was generally low level, and probably intermittent. DNA damage was assessed in blood cells using sensitive comet analyses. DNA strand breakage was detected in both mussels and clams, with the highest level of damage detected at "hot reference" sites of Cordova harbor and Port Chalmers. Bioavailability and DNA damage at the oiled sties was low, indicating there has been substantial progress in recovery from the spill 13 years before, yet low level bioavailability and damage were still detectable.     

用于构建生物系统发育树的古DNA序列

主要综述了古 DNA研究进展以及结合古 DNA序列和基因库中的数据构建系统发育树。这些研究能解决许多有关演化生物学、考古学、人类演化及迁移、动植物的家养和驯化过程及早期农业的发展、考古点的动植物残骸的精确鉴定及地质演化等问题。另外 ,还列举了一些重要的实例