南极鱼类DNA条形码及分子系统进化研究

本文采用COI基因兼并引物对15种36个南极鱼类DNA进行扩增测序,并结合Gen Bank已有序列进行联配分析,对南极鱼2科22属43种共97条COI基因片段(539 bp)进行序列比较和系统发生关系研究,探索了DNA条形码技术在辅助鱼类物种鉴定和分类中的适应性与可行性。结果分析表明,43种南极鱼科和鳄冰鱼科的鱼类COI基因的平均碱基组成为T:31.9%、G:18.3%、A:22.2%和C:27.6%,具有明显的碱基偏倚性。南极鱼类的种间平均距离为0.157,种内平均遗传距离为0.002,种间平均遗传距离是种内平均距离的79倍;系统分析结果显示,除南极小带腭鱼(Cryodraco antarcticus)和罗斯海小带腭鱼(Cryodraco atkinsoni)外,其余的鱼类皆能够形成独立的分支,且与形态学分支一致。由此可见,DNA条形码对南极鱼亚目鳄冰鱼科和南极鱼科鱼类能够进行有效的物种鉴定,基于COI基因所建的NJ(neighbor-joining)树对物种分类具有较为准确的辨识力。系统发生关系表明,DNA条形码可以对除南极小带腭鱼(Cryodraco antarcticus)和罗斯海小带腭鱼(Cryodraco atkinsoni)外的南极鱼物种进行鉴定,不仅可以作为形态学的辅助手段为南极鱼分类系统的必要补充和佐证,并且可以用于探讨南极鱼类近缘种的系统发育关系。     

鳅科鱼类DNA条形码分析及泥鳅和大鳞副泥鳅的分子鉴定

采集了23种鳅科鱼类89尾个体的线粒体COI基因5端序列,分析了碱基组成以及不同鳅科鱼类之间的种间遗传距离和种内遗传距离。结果显示,鳅科鱼类的种间遗传距离显著大于种内遗传距离,表明以COI作为鳅科鱼类DNA条形码进行品种鉴定具有一定的可行性。在建立鳅科鱼类DNA条形码的基础上,设计了主要物种泥鳅(Misgurnus anguillicaudatus)和大鳞副泥鳅(Paramisgurnus dabryanus)特异性引物,结果显示,该引物具有较高的特异性和灵敏度,能够实现对泥鳅、大鳞副泥鳅及其混合样品的物种鉴定。     

DNA 条形码在鲱形目鱼类物种鉴定和系统进化分析中的应用

采用PCR特异性扩增获得中国近海鲱形目(Clupeiformes)2科6属7种的48条线粒体COI基因序列,结合从Gen Bank筛选出的4科40属83种的COI基因序列225条,对鲱形目鱼类的COI条形码基因特征、种内与种间遗传距离及其分子系统进化关系进行了分析,探索了DNA条形码技术在辅助鱼类物种鉴定和分类中的适应性。结果表明,4科41属90种273条COI基因序列的平均碱基组成为T:28.3%、C:28.3%、A:24.2%、G:19.2%,碱基组成表现出明显偏倚性。鲱形目鱼类种间的平均遗传距离为0.131,种内平均遗传距离为0.003,种间距离为种内距离的41倍;系统学分析结果显示,97.8%的鱼类在系统进化树上均为单系。可见,鲱形目鱼类DNA条形码符合物种鉴定的要求,且基于COI基因所建的NJ树对物种分类具有较为准确的辨识力。系统进化分析结果表明,COI基因不仅能够解决低阶分类单元的系统进化关系,对于高阶分类单元的系统分析研究结果也有一定参考价值。     

不同DNA条形码基因在帘蛤目贝类分类鉴定中的比较分析

DNA条形码基因已经广泛应用在海洋贝类的分类鉴定、系统发育进化、种群遗传分析等领域的研究。为进一步研究评估不同DNA条形码基因在海洋贝类鉴定中的作用,本研究利用从Gen Bank数据库随机下载的帘蛤目COI、16S r RNA、18S r RNA和28S r RNA基因序列,通过传统距离法和单系聚类法结合分析,比较了上述DNA条形码基因在鉴定物种及系统发育进化中的鉴定效率,并以本实验室已获得的部分贝类DNA序列进行了验证。结果表明,根据"10倍法则"和"2%"阈值标准,本研究中COI能够鉴定57.1%物种,16S r RNA能够鉴定60.9%,18S r RNA鉴定16.7%,而28S r RNA无法有效鉴定;多数种COI和16S r RNA基因序列的种间遗传距离和种内遗传距离存在"条形码间隙",而18S r RNA和28S r RNA序列的种间和种内的遗传距离存在显著重叠,没有明显"条形码间隙";聚类分析结果表明,基于COI基因序列,87.9%的个体与同种聚为单系,以16S r RNA序列,65.6%的个体与同种聚为单系,未聚成单系的个体则形成姐妹系,未出现不同种聚为单系现象,能够呈现与形态分类基本一致的系统发生关系;但18S r RNA和28S r RNA呈现的聚类关系相对混乱。相对而言,在鉴定帘蛤目物种时,COI和16S r RNA都能够作为条形码基因,且COI有效性更高,18S r RNA和28S r RNA基因由于种内变异较大,不适于作为条码基因。研究结果为科学选用DNA条形码基因进行帘蛤目贝类的鉴定提供了参考资料。     

线粒体COI基因条形码在鲿科鱼类物种鉴定中的应用

为了探讨线粒体COI基因作为DNA条形码在中国鲿科(Bagridae)鱼类物种鉴定中的有效性,以及系统发育中的适用性,本研究对4属11种鲿科鱼类进行PCR扩增,获得48条线粒体COI基因序列,同时从Gen Bank筛选获得8种鲿科鱼类的12条COI基因序列进行分析。19种鲿科鱼类的COI基因序列特征显示:长度为674 bp的COI序列片段平均碱基组成为24.82%A,30.44%T,27.10%C和17.64%G,碱基组成呈现明显的AT偏倚性(55.26%),具有硬骨鱼类的线粒体COI基因的碱基组成的典型特征。核苷酸位点中有变异位点226个,简约信息位点195个,单一信息位点31个,转换颠换比为3.35。19种鲿科鱼类的种内、种间和属间平均遗传距离分别为0.0041、0.1136和0.1268,种间遗传距离平均为种内遗传距离的27.7倍。在本研究中,鲿科鱼类所有的物种均形成单系,在物种鉴别上与形态学分类结果基本一致,然而鲿科的4个属中只有鱯属形成单系,黄颡鱼属、属和拟鲿属均未形成单系,其进化地位需要进一步研究。线粒体COI基因作为条形码可有效对鲿科鱼类进行物种鉴定,也为鲿科的系统发育提供了参考。     

鲉形目鱼类DNA条形码分析及鲉科DNA条形码电子芯片建立

为建立鲉形目内各物种的快速鉴别方法,本研究扩增了我国47个鲉形目物种并下载了Gen Bank上收录的鲉形目共计23科85属233种873条细胞色素C氧化酶I基因(COI)序列,分析该基因结构特性。结果表明,鲉形目DNA条形码基因的碱基变异中,不变位点508个,占总位点数的82.1%;转换位点70个,颠换位点41个,分别占总位点数的11.3%和6.6%;种内遗传距离为0~0.019,平均遗传距离为0.003?0.0034;属内种间遗传距离为0.003~0.258,平均值为0.086?0.038;基于233个物种的COI序列构建的系统进化树显示,227个物种(97.4%)能聚为独立分支,且具有较高支持度。在此基础上以鲉科11属39种鱼类的DNA条形码为例,筛选出25个种的37个特异性探针,以此探针对鲉科鱼类进行物种快速鉴定成功率为64.1%,研究结果表明DNA条形码芯片用于鲉科的鉴定具有一定的可行性。     

基于DNA条码基因的鳢科鱼类系统进化与物种鉴定

鳢科(Channidae)鱼类在亚洲分布广泛,其中中国的土著种类是重要养殖品种,国外很多种类主要作为观赏鱼引进我国。本研究利用线粒体COΙ基因序列,对分布于我国的鳢科鱼类不同种群样本序列,及在Gen Bank中获得其他鳢科鱼类的序列进行分析,探讨其作为DNA条形码基因对鳢科进行物种鉴定和系统进化分析的可行性。通过对本研究采集的149个鳢样本和122条Gen Bank中已有序列进行分析,结果显示,所研究的鳢科鱼类的COΙ基因576 bp片段中不存在碱基插入缺失现象,其平均碱基含量A+T(51.4%)高于G+C含量(48.6%),存在偏倚性;多态位点占47.2%。利用Mega 6.0软件基于Kimura’s 2-parameter模型计算25种鳢种内平均遗传距离为0.028,其中巴卡鳢(Channidae barca)种内遗传距离最大,为0.137,超过了某些种间遗传距离;种间遗传距离为0.030~0.302,平均为0.217。其中最大距离0.302为饰鳍鳢(Channidae ornatipinnis)和黑体鳢(Channidae melasoma)之间,甚至超过了与外群之间的距离。利用邻接法(Neighbour-Joining,NJ)和最大似然法(Maximum Likelihood Tree,ML)分别构建系统进化树,同种个体获得较高支持率,而不同种间的关系支持率较低,同时发现存在由多个种组成的巴卡鳢和南鳢复合支系。本研究表明,进行我国土著鳢科鱼类物种鉴定时COI基因是有效的工具,而进行外来观赏鱼鉴定,尤其是巴卡鳢、斯氏鳢等物种进行鉴定时,需结合多方面信息;COI基因不适合鳢科鱼类种间遗传进化关系的研究。     

DNA条形码在西藏水系裂腹鱼亚科鱼类鉴定中的研究

为确定DNA条形码技术在西藏水系裂腹鱼亚科(Schizothoracinae)物种鉴定中的可行性,利用西藏水系所采集260尾裂腹鱼亚科样本,测定其线粒体细胞色素C氧化酶亚基1(COI)基因片段序列,计算遗传距离,构建系统发育树,并与GenBank中相关序列进行比对。260个样本经检测均获得有效COI基因扩增片段,COI基因碱基组成偏倚明显,A+T含量为54.74%,显著高于G+C含量(45.26%)。基于Kimura双参数模型计算遗传距离,遗传距离阈值设置为0.02时,260个样本可被鉴定到种的为249尾样本,11尾由于样本量少,数据库中存在多个命名,只鉴定到属,其中与形态学鉴定一致的179尾样本,一致率为68.8%,裂腹鱼亚科裸鲤属(Gymnocypris)不能通过COI基因鉴定到种,拉萨裂腹鱼(Schizothoracinae)、异齿裂腹鱼(S.schizothorax o#x02BC;connori)、巨须裂腹鱼(S.macropogon)3个种之间的遗传距离阈值以0.02不能有效鉴别,而遗传距离阈值以0.01作为这3个种的鉴定标准,可达到有效鉴别的目的。基于邻接法构建系统发育树,裂腹鱼亚科鱼类形成一个支持率较高的单系群,Bootstrap检验支持率为99%,系统进化树聚类方式与以遗传距离值为标准的鉴定结果一致,很好地反映了水系物种间的地理和历史联系。     

基于COI和16S rRNA的库页岛马珂蛤遗传多样性和分子系统进化研究

本研究以库页岛马珂蛤(Pseudocardium sachalinense)为研究对象,讨论COI和16S rRNA两种DNA条形码在贝类的遗传多样性、分子进化和种类鉴定的适用性,并利用两种条形码评估库页岛马珂蛤的遗传多样性。本文在获得库页岛马珂蛤线粒体全基因组的基础上,测序获得库页岛马珂蛤群体的COI和16S rRNA序列,发现COI基因核苷酸多样性为0.00195,高于16S rRNA核苷酸多样性(0.00073)。基于COI基因的单倍型多样性为0.76,大于16S rRNA的单倍型多样性(0.318)。其次,用全线粒体基因组构建8种贝类的系统进化树为参考,发现基于COI和16S rRNA的系统进化树与参考一致,提示这两种条形码片段可用于推断贝类的分子进化关系。最后,分别对马珂蛤科和帘蛤科15属17种贝类的COI基因和16Sr DNA进行序列比较,发现COI基因和16S rRNA的种间遗传距离均是种内距离的62倍。以上结果说明,16S rRNA与COI基因一样,能有效地构建马珂蛤科和帘蛤科的系统发育关系和物种鉴定,但在分析库页岛马珂蛤的遗传多样性时利用COI基因比16S rRNA能发现更多的遗传变异。     

DNA条形码技术在藻类分类学中的研究现状与展望

本文在对DNA条形码(DNA barcode)技术的发展进程的分析归纳的基础上,总结已发表的各门藻类的DNA条形码序列,并未确定一条通用DNA条形码。认为目前藻类DNA条形码的研究重点仍是加快开发新的DNA条形码片段并对其进行评价,为寻找理想的通用DNA条形码提供理论支持。现阶段较为常用的DNA条形码基因主要包括ITS、COI、rbcL等基因,几种常用基因片段的各自存在优缺点,本文对各片段的主要问题进行了分析。其中原核蓝藻的ITS基因和藻胆蛋白基因可考虑作为首选DNA条形码,真核藻类主要考虑ITS和rbcL基因,很难找到像动物COI基因可在物种鉴定中广泛通用的DNA条形码。不同基因片段间互补应用,并与传统形态学鉴定方法相结合可有效提高近缘藻类分类的准确性。并综述了藻类DNA条形码研究的新进展,展望了其应用前景。     

Competitive interactions between native and exotic salmonids: a combined field and laboratory demonstration

Abstract –  We studied the impact of two exotic salmonid species (brook trout, Salvelinus fontinalis and rainbow trout, Oncorhynchus mykiss ) on native brown trout ( Salmo trutta fario ) habitat, growth and survival. Habitat selection and vertical distribution between young-of-the-year of the three species were examined in a stream aquarium under different sympatric and allopatric combinations. In addition, similar species combinations were introduced in a Pyrenean mountain stream (southwest France) in order to extend laboratory results to growth and apparent survival. Both laboratory and field results indicated that rainbow trout significantly affected native brown trout habitat selection and apparent survival. On the contrary, brown trout habitat, growth and apparent survival were hardly affected by brook trout. These results support the idea that rainbow trout negatively influence native brown trout, and that competition could influence the outcome of fish biological invasions in freshwater ecosystems.     

Methanol as cryoprotectant and the suitability of 1.2 ml and 5 ml straws for cryopreservation of semen from salmonid fishes

For salmonid semen, the cryoprotective action of 10% methanol was compared with a 5% dimethyl sulphoxide (DMSO), 1% glycerol mixture, until now one of the most effective cryoprotectants. In Oncorhynchus mykiss (Walbaum), Salmo trutta L. f. fario, Salmo trutta L. f. lacustris and Salvelinus alpinus (L.), semen cryopreserved with both cryoprotectants yielded post-thaw fertilization rates of 90-100% of control with untreated semen at sperm-to-egg ratios of 1.8 × 10⁶-2.4 × 10⁶ spermatozoa per egg. However, at sperm-to-egg ratios of 0.9 × 10⁶-1.2 × 10⁶ spermatozoa per egg, semen cryopreserved with methanol had significantly higher fertilization rates than semen frozen with the DMSO/glycerol mixture. In other studies we obtained similar data for Coregonus sp., Salvelinus fontinalis (Mitchill), Thymallus thymallus (L.) and Hucho hucho (L.), proving that methanol is the most effective and generally applicable cryoprotectant for semen of the studied salmonid species. To facilitate the insemination of large egg batches we investigated the suitability of 1.2 ml and 5 ml straws for deep freezing of semen of Oncorhynchus mykiss, Salmo trutta f. fario, Salmo trutta f. lacustris and Salvelinus alpinus. With 1.2 ml straws the fertilization rates were similar to 0.5 ml straws when using lower freezing and higher thawing temperatures. The 5 ml straws resulted in a fertilization success of only about 40% of fresh semen control.     

Using allometry with fish size to estimate production to biomass (P/B) ratios of salmonid populations

Abstract – The ratio of annual production rate to average biomass ( P / B ) is sometimes used as a shortcut method of estimating production if biomass is known. P / B ratios vary among salmonid populations in different areas depending on the species, fish size and growing conditions. The hypothesis that annual P / B ratios for salmonid populations can be predicted from the allometric equation: P / B  =  a W ^−0.35 was investigated in this study. The allometric coefficient (−0.35) was obtained from the literature, and W was the average weight (g) of fish in the population. Plots of P / B versus fish weight for three species of salmonids, Salvelinus fontinalis , Salmo trutta and Salmo salar , showed a declining trend, with a slope consistent with the hypothesis. The coefficient a of the allometric equation was species and habitat dependent. The efficacy of using the allometric formula to estimate the P / B ratio of specific salmonid populations is examined.     

Divergence of Salvelinus species from northeastern Asia based on mitochondrial DNA

Abstract –  Phylogenetic analysis of charrs of the genus Salvelinus was performed using PCR-RFLP analysis of mitochondrial DNA (mtDNA). Three fragments of mtDNA (ND1/ND2, ND5/ND6 and Cyt b /D-loop) were amplified by PCR and examined for restriction site variation using 13 restriction endonucleases. Analysis of 313 sites of over 7672 bp of charr mtDNA was conducted. Six phylogenetic lineages of the mtDNA were revealed, corresponding to six separate charr taxa: Salvelinus leucomaenis Pallas; Salvelinus levanidovi Chereshnev, Skopetz & Gudkov; Salvelinus taranetzi Kaganovsky; Salvelinus malma krascheninnikovi Taranetz; Salvelinus malma malma Walbaum and Salvelinus alpinus alpinus . The Levanidov ( S. levanidovi ) and white-spotted ( S. leucomaenis ) charrs represented the most divergent lineages. These are probably closest to a common ancestor of the genus. Salvelinus taranetzi was the next divergent lineage. Salvelinus malma krascheninnikovi was placed between S. leucomaenis and S. taranetzi . Salvelinus malma malma and S. a. alpinus were sister taxa, and were on the last branch to diverge. The divergence between S. m. malma and S. a. alpinus inferred from mtDNA nucleotide sequences was 1.1%; between S. m. malma and S. taranetzi 2.8%; between S. m. malma and S. m. krascheninnikovi 4%; between S. taranetzi , S. m. krascheninnikovi and S. a. alpinus 2.8%. Salvelinus levanidovi and S. leucomaenis were almost equally remote from the other charrs by some 9% and 7%, respectively. The extent of genetic differences between the northern S. m. malma populations and the European S. a. alpinus populations indicates that they diverged recently. The existence of many putative charr species with different divergence times in northeastern Asia suggests that this region may be one of the centres of speciation of the genus Salvelinus .     

Brown trout, Salmo trutta L.: a new species for intensive marine aquaculture

Abstract. Strains of two salmonid species, brown trout, Salmo trutta L., and Atlantic salmon, Salmo salar L., were compared for the purpose of marine aquaculture. Survival rate, growth and sexual maturation rate were investigated. Brown trout performances were good and allowed for intensive production.     

Proliferative kidney disease and renal myxosporidiosis in juvenile salmonids from rivers in England and Wales

The results from a survey for proliferative kidney disease (PKD) and renal myxosporidiosis in wild salmonids from rivers in England and Wales are presented. One hundred and eighty-five salmon, Salmo salar , 235 brown trout, Salmo trutta , 16 charr, Salvelinus alpinus, and five grayling, Thymallus thymallus, were obtained from 23 locations on 16 rivers between July and October 1997. They were examined for the presence of clinical PKD and for histological evidence of infections with Tetracapsula bryosalmonae and other renal myxozoans. Prevalence of infection with T. bryosalmonae detected histologically in brown trout varied from 11 to 43% in enzootic rivers and was only found in salmon in two rivers at low prevalence. Nephromegaly was positively associated with PKD in brown trout but in salmon mild nephromegaly was only associated with infection with an unidentified Chloromyxum sp.     

Detection of Renibacterium salmoninarum in salmonid kidney samples: a comparison of results using double-sandwich ELISA and isolation on selective medium

Abstract A total of 1239 kidney samples from four species of salmonid fish, Atlantic salmon, Salmo salar L., brown trout, Salmo trutta L., Arctic charr, Salvelinus alpinus (L.), and rainbow trout, Oncorhynchus mykiss (Walbaum), were screened for Renibacterium salmoninarum using double-sandwich ELISA and bacterial isolation. For bacterial isolation, samples were homogenized, washed, plated onto S-KDM and incubated for 12 weeks. Samples for ELISA were kept frozen until tested. After thawing, 25% homogenates in PBS were heated at 100°C for 15 min in the presence (2.5% v/v) of HemoDe solvent (terpene and butylated hydroxyanisole) and then centrifuged. The supernatant was tested with polyclonal antibodies against whole bacterium in a double-sandwich ELISA. In seven out of 12 groups tested, all samples were negative in both tests. Positive ELISA results occurred in five groups. Renibacterium salmoninarum was isolated on SKDM from samples in four out of these five groups. The ELISA test gave significantly higher numbers of positive samples in three out of the four groups showing positive results in both tests.     

The occurrence of proliferative kidney disease (PKD) in cultured and wild fish: further investigations

Abstract. In an investigation of the occurrence of proliferative kidney disease (PKD) in freshwater fish other than rainbow trout, 18 species of wild fish and seven species of fish raised in cultivation wore sampled from waters where the disease occurred annually in rainbow trout, Oncorhynchus mykiss (Richardson). Results revealed that certain wild stocks of brown trout. Salmo trutta L., grayling, Thymallus thymallus L., and pike, Esox lucius L., were infected with PKD, as were cultivated Atlantic salmon, Salmo salar L., parr, brown trout and char, Salvelinus alpinus (L.). Microscopical examination revealed the presence of the PKX cell in these species and also intraluminal protozoa possibly related to the PKX cell, which were not found in the rainbow trout. Other species of freshwater fish had myxosporidan infections but, unlike PKD infection, there was little host/parasite tissue response. The PKX cell as a myxosporidan stage is discussed and the presence of the disease in wild fish is reported.     

Real-time PCR detection of Parvicapsula pseudobranchicola (Myxozoa: Myxosporea) in wild salmonids in Norway

The myxozoan genus Parvicapsula contains 14 species infecting fish, some of which are known to cause severe disease in farmed and wild salmonids. Parvicapsula pseudobranchicola infections were first reported from seawater-reared Atlantic salmon, Salmo salar, in Norway in 2002 and have since then been an increasing problem. The present study describes a Taqman real-time PCR assay for specific detection of P. pseudobranchicola. The Taqman assay targets the 18S rRNA gene of P. pseudobranchicola and is able to detect as few as ten copies of the target sequence. Using the described assay, P. pseudobranchicola was detected in both farmed and wild salmonids, indicating that wild Atlantic salmon, sea trout, Salmo trutta, and Arctic char, Salvelinus alpinus, may be natural hosts of the parasite. Parvicapsula pseudobranchicola was found in samples from wild salmonids in the far south and the far north of Norway, displaying a wide geographic range of the parasite. Farmed salmonids showed P. pseudobranchicola infection levels many folds higher than that observed for wild sea trout, indicating that farmed Atlantic salmon are subjected to an elevated infection pressure compared with wild salmonids.     

Assessing perturbation of river fish communities in the Iberian Ecoregion

Abstract  A spatially based approach was used to analyse the response of fish-based metrics to human impacts in the Iberian Peninsula. A fish-based typology was established that distinguished one salmonid type (fish assemblages dominated by Salmo trutta fario L.), two mixed types ( S. trutta fario associated with different cyprinids) and six cyprinid types (dominated by different species of barbel [ Barbus spp.], nase [ Chondrostoma spp.] or chub [ Leuciscus spp.]). These types broadly correspond to different forms of ecosystem functioning, ranging from the cold, northern and high altitude sections to warmwater, lowland and southern sections. Twenty metrics were identified that responded to disturbance – four to 14 per fish type. The highest correlations were −0.795 for abundance of Squalius sp. and segment (localised) disturbance and 0.754 for abundance of limnophilic specimens and water quality disturbance. Disturbance of segment, habitat and hydrological regime yielded more metric responses in western Iberian fish types, while that of habitat and water quality gave more in north-eastern Iberian fish types. Global (catchment scale) disturbance generally gave more responsive metrics and higher correlations than partial disturbances. All guilds were represented and a number of metrics were responsive across fish types – namely native species, alien abundance, water column (natives), eurytopic and invertivorous (natives). However, several metrics were only reactive in one or a few types, such as benthic and S. trutta fario in north-western mixed fish type. Different trends in metric reaction occurred for total abundance in north-western mixed fish type, and for eurytopic and phytophilic (natives) in the north-eastern fish types.