应用环境DNA技术对邵伯湖浮游动物物种检测的初步研究

为掌握邵伯湖浮游动物物种组成,利用环境DNA技术于2018年11月对其浮游动物群落进行了监测。在邵伯湖15个采样点同步进行了水样采集,抽滤后进行了DNA提取,利用线粒体DNA 12S r RNA引物进行PCR扩增,并进行了高通量测序。结果显示,从二代测序的1114482条DNA序列中,比对得到浮游动物OTUs数68个。利用宏条形码共检出浮游动物22种(隶属于14科18属),邵伯湖浮游动物功能群以轮虫滤食者RF为主,各样点浮游动物α和β多样性的各项指数较为均匀,表明邵伯湖各区域的浮游动物多样性水平较接近。环境DNA技术适用于浅水湖泊浮游动物群落监测,在现阶段的淡水浮游动物资源监测中,该技术宜与传统的监测方法结合使用。     

长江中游常见鱼类DNA条形码研究及其电子芯片分析

为建立长江中游常见鱼类的快速鉴别方法,文献调研了7目11科50属64种鱼类名录,GenBank共获取168条线粒体细胞色素c氧化酶I (COⅠ)序列,分析了序列特征、不同阶元Kimura-2-paramater(K2P)遗传距离及系统进化关系。结果显示,64种鱼类的种间遗传距离(平均值为0.084)明显大于种内(平均值为0.0079),NJ树上不同物种均能以较高支持度聚类成独立分支,以线粒体COⅠ序列作为DNA条形码可准确鉴定所研究鱼类;综合利用分子生物学软件筛选物种特异性探针,最终43种鱼类可筛选出112条物种特异性探针,物种识别率为67.2%。本研究验证了DNA条形码芯片技术在长江中游鱼类物种鉴定的可行性,可为该地区鱼类物种多样性保护提供技术支持。     

基于环境DNA metabarcoding的西轩岛近海鱼类多样性研究

鱼类多样性的保护对于生态系统的科学管理和资源的可持续利用至关重要。环境DNA metabarcoding技术的出现和应用为水生生物的调查与监测带来了强有力的技术革新。本研究以浙江舟山近海岛屿——西轩岛为例，设计了4个不同采样站位，先后于2019年2月(冬季)、5月(春季)和11月(秋季)共采集水样12个，通过环境DNA提取、扩增、高通量测序以及生物信息学分析，对西轩岛近海鱼类多样性进行了分析，同时评估了鱼类多样性的时空差异。结果显示，共监测到鱼类33种，隶属于12目26科32属，其中，鲈形目(Perciformes)种类最多，共19种，约占所有种类的57.6%。不同采样季节的多样性指数和均匀度指数均存在显著差异，表明季节可能是影响西轩岛近海鱼类多样性的因素之一。综合时间和空间分析的结果显示，在繁殖季节且远离舟山本岛一侧的采样点监测到的鱼种数量更多。通过比对之前传统渔业资源调查的结果发现，不同季节优势种存在较大变化，可能与采样点数量较少且集中有关。进化树富集结果显示，各季节的优势鱼种与传统调查手段的结果有较大差异，表明目前环境DNA仍不能完全替代传统调查方法，但可以将环境DNA方法与传统的调查方法相结合，以确保监测结果的准确性和可靠性。     

应用RAPD技术分析雅砻江5种裂腹鱼类的亲缘关系

利用随机扩增多态DNA(RAPD)技术对雅砻江流域的2属5种(亚种)裂腹鱼类的亲缘关系进行了初步分析.采用筛选确定的20个扩增效果好的引物进行扩增,检测出214个位点.遗传距离和用UPG-MA法聚类得到的聚类图反映的5种裂腹鱼类的亲缘关系,与形态学分类方法所得结果基本一致.说明RAPD技术可有效用于这几种裂腹鱼类亲缘关系的研究.     

LAMP法在水产动物病原快速检测中的应用

近年来,一种新的恒温核酸扩增方法LAMP法(loop-mediated isothermal amplification),即环介导等温扩增法已经被开发利用。它采用能特异识别靶序列上6个位点的4条引物及一种具有链置换活性的DNA聚合酶(Bst DNA polymerase),在恒温条件(60~65℃),不到1h的时间里进行核酸扩增,其扩增效率可达到109~1010个数量级,具有特异性强、等温灵敏、操作简单、产物易检测等优点。LAMP法已经被用来快速检测水产动物病原(细菌、病毒、寄生虫)。文章就LAMP法的反应原理、引物设计及其在水产动物病原快速检测中的应用等做简要的综述。     

草鱼线粒体细胞色素b基因的克隆与序列分析

用DNAExtractionKit提取草鱼(Ctenopharyngodonidella)肝脏的总DNA,合成特异引物,进行PCR扩增。扩增产物经琼脂糖电泳检测、纯化后克隆到pGEM Teasyvectorsystem的T载体上,筛选转化子,提取质粒,酶切鉴定。重组质粒序列测定的结果显示克隆了草鱼线粒体细胞色素b(cytb)基因1140个碱基及两侧部分序列共1254bp。用DNA分析软件VectorNTI6.0比较草鱼与GenBank中18种鱼类cytb的序列,显示草鱼与它们的cytb基因具有较高的同源性;根据草鱼与这18种鱼的cytb基因序列同源性所建立的进化树,与传统的分类地位基本吻合。     

鱼类环境DNA研究中通用引物的筛选验证

为了筛选一个通用性和适用性良好的能够运用于环境DNA(eDNA)研究的鱼类引物,从相关文献中选取了鱼类线粒体基因组部分片段的5对引物,分别对线粒体D-loop区、16S rRNA基因、COI基因以及Cytb基因部分片段进行扩增。对千岛湖48种鱼类基因组DNA进行扩增后比较发现,引物16s和COI均可以取得良好的扩增效果,通用性优于其他几对引物。引物16s的扩增产物经凝胶电泳检测均出现明亮的目的条带,引物COI则有3种鱼的条带经凝胶电泳检测亮度较暗。利用上述引物对环境样品eDNA扩增时发现,只有16s和COI的引物具有良好的扩增效果,能够得到明显单一的亮带。对该两种引物的PCR产物克隆后测序比对发现,16s的PCR产物均为千岛湖常见鱼类物种的基因片段,COI的PCR产物则为细菌COI基因的部分片段。综上,我们认为引物16s在通用性和适用性上都更为适合作为鱼类群落结构eDNA研究的通用引物。     

秋季济南地区鱼类群落结构及其与环境因子的关系

于2014年和2015年秋季对济南地区23个采样点的鱼类群落结构和环境因子特征进行了野外调查。结果表明:两年调查中采集到鱼类分别为5目25种和6目28种,各采样点鱼类个体数量平均值为45.61尾和66.48尾,香农威纳指数分别为1.45和1.81,均匀度指数分别为0.72和0.74。典范对应分析表明,2014年影响鱼类群落结构的主要环境因子是水温和总氮;2015年影响鱼类群落结构的主要环境因子是总磷和总氮。     

巨魾野生群体遗传多样性的RAPD分析

巨魾(Bagarius yarrelli)为云南特有的经济鱼类,利用随机扩增多态性DNA(RAPD)技术对元江下游的河口巨野生群体进行了遗传多样性分析,在50条随机引物中筛选出19条多态性较好的引物,通过PCR扩增,19条引物在巨群体中共检测到67个位点,其中多态性位点66个,平均多态性位点比率为98.51%,个体间平均遗传相似系数为0.890 9,个体间平均遗传距离为0.117 6;群体Nei's基因多样性指数为0.291 6,Shannon信息指数为0.426 9,结果表明巨野生群体具有较高的遗传多样性。     

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。     

环境DNA分析技术—一种水生生物调查新方法

掌握珍稀濒危和外来入侵物种的分布状况对于物种保护和管理十分重要。环境DNA(Environmental DNA)分析通过收集、分离和分析环境样品中的DNA来检测物种是否存在,是一种低耗、高效、高灵敏度的无损伤性物种监测新技术(e DNA)。本文综述了环境DNA技术的发展、分析方案、优势及存在的问题,主要综述了该方法在外来入侵物种足迹追踪、濒危珍稀水生生物资源调查和物种多样性分析中的研究现状,并对环境DNA分析技术在生物多样性保护研究中的应用前景进行了展望。     

三都澳大型底栖动物种类组成特点

根据2009年5月至2010年2月期间共9个航次在三都澳水域采集的底泥样品,分析三都澳大型底栖动物种类组成特点及其与养殖活动之间的关系.结果表明,三都澳水域底泥样品中共出现大型底栖动物119种,其中多毛类动物种类数量优势明显,达65种,占总种类数54.62％；甲壳动物和软体动物也是此水域常见类群,种类数分别为21种(占...     

Use of focal species in marine conservation and management: a review and critique

1. Focal species (i.e. indicators, keystones, umbrellas, and flagships) have been advocated for the management and conservation of natural environments. 2. The assumption has been that the presence or abundance of a focal species is a means to understanding the composition and/or state of the more complex community. 3. We review the characteristics of focal species, and evaluate their appropriateness and utility judged against conservation objectives. 4. It appears that indicator species (of both composition and condition) may be of greatest general utility, and that several types of focal species may exhibit useful indicator properties. Copyright © 2001 John Wiley & Sons, Ltd.     

On species and speciation with reference to the fishes

The nature of species and the processes in which they participate are subjects of continuing debate among evolutionary biologists. I begin by examining how ichthyologists treat species empirically. Such treatments provide a pattern of species and their relationships over time and space. I suggest that this empirical record points to a predominant mode of speciation: vicariant, Model I, allopatric speciation. I also suggest that species are real and that they are individuals. There is a single species concept, the evolutionary species concept (ESC), that best captures the way we think about fish species. This concept is also well integrated with the manner in which species are treated in Phylogenetic Systematics and with the philosophical concept that species are particulars rather than universals.     

黄河口及其邻近水域浮游动物群落结构特征及其季节变化

根据2013年8月、10月和2014年2月、5月在黄河口及其邻近水域4个航次的调查数据,分析了该海域浮游动物的种类组成、数量变动、优势种、种类多样性及其季节变化。本次黄河口及其邻近水域调查共鉴定浮游动物43种,其中原生动物、毛颚动物、尾索动物和栉水母各1种,刺胞动物8种,浮游甲壳类18种,浮游幼体及鱼卵、仔稚鱼共13种(类)。浮游动物的平均丰度为2115.64 ind/m~3,不计夜光虫的平均丰度为95.93 ind/m~3,其中浮游甲壳类占71.43%。浮游动物丰度存在显著的季节变化,数量高峰出现在春季(5月),其次为冬季(2月)、秋季(10月)和夏季(8月)。毛颚动物强壮箭虫(Sagitta crassa)和双刺纺锤水蚤(Acartia bipinnata)、小拟哲水蚤(Paracalanus parvus)等桡足类为夏、秋、冬三个季节的主要优势种,夜光虫(Noctiluca scintillans)为春季的绝对优势种。浮游动物群落物种丰富度指数(D)、Shannon-Wiener指数(H')和均匀度指数(J')的变化趋势一致,表现为夏秋季高,冬春季低。黄河口及其邻近水域浮游动物的群落结构特征具有明显的季节变化;桡足类和浮游幼体是主要类群,对该水域浮游动物的数量变动及种类多样性的变化具有较大影响。     

Population crash in Lesotho's endemic Maloti minnow Pseudobarbus quathlambae following invasion by translocated smallmouth yellowfish Labeobarbus aeneus

1. A genetically distinct population of the Maloti minnow Pseudobarbus quathlambae (Lesotho's only endemic fish) is known only from the Mohale catchment, and was formerly abundant in the Senqunyane, Bokong and Jorodane rivers which flow into Mohale Reservoir.
2. Situated ~4 km downstream of Mohale Reservoir, the Semongkoaneng waterfall has historically prevented larger fish species from moving upstream into areas inhabited by P. quathlambae. After the filling of the Mohale Reservoir in 2003, an inter‐basin transfer (IBT) linking it to Katse Reservoir was opened and in 2006 the smallmouth yellowfish Labeobarbus aeneus, a larger more aggressive species, was recorded in the reservoir, presumably introduced via the IBT.
3. The objectives of the present study were to: (1) establish whether any additional non‐native fish species were present in the Mohale catchment; (2) ascertain whether L. aeneus has dispersed into the rivers flowing into Mohale Reservoir; and (3) gauge whether the Mohale population of P. quathlambae is in decline. Twenty‐eight sites situated on major rivers flowing into the reservoir, and four sites in the reservoir itself, were surveyed to evaluate changes in fish populations and habitat quality.
4. Results indicate that P. quathlambae has all but disappeared from its natural range: only five individuals were recorded in the Jorodane and Bokong rivers, and none were recorded in the Senqunyane River – a former stronghold for the species. On the other hand, L. aeneus was recorded in all three rivers and is probably responsible for the decline of the P. quathlambae population, given that there does not appear to have been major deterioration in habitat conditions. Another non‐native fish, the Orange River mudfish Labeo capensis, was recorded in the Mohale catchment for the first time. Urgent conservation action is required to prevent the Mohale lineage of P. quathlambae from becoming extinct.

Copyright © 2016 John Wiley & Sons, Ltd.     

Species concepts and speciation of fishes: concluding remarks

The definition of the species category has stimulated more debate than perhaps any other topic in the biological sciences. There are currently more than 22 different species concepts and the debate continues on which concepts apply to all organisms, which concepts are operational and which concepts should be used in specific circumstances. The first major division of the types of concepts depends on whether one views species as constructs that exist for ordering biodiversity and information retrieval (i.e. classes), or views species as ontological individuals that exist in nature. If species are categories that can be defined, then theoretically, a single species can arise more than once in different places or at different times. If, on the other hand, species are individuals, then they are historical events, monophyletic and each species is unique.     

广西桂林青狮潭水库鱼类物种组成及多样性分析

2015年4月至2016年1月按季度对青狮潭水库库区鱼类资源进行了调查,采集鱼类样本3 750尾(153.28kg),经鉴定有鱼类32种,隶属于5目12科27属,其中以鲤形目鱼类为主,分别占总物种数和总个体数的53.13%和61.92%。相对重要性指数分析表明,鲫(Carassius auratus)、■(Hemiculter leucisculus)和鲤(Cyprinus carpio)为优势种;鱼类多样性分析结果显示,各季节丰富度指数(D)为2.58~3.52,Shannon-Wiener多样度指数(H')为1.62~1.92,Pielou种类均匀度指数(J')为0.53~0.63,其中夏季多样性最高、冬季相对较低;空间上,鱼类多样性呈现从河流入库口、近岛水区向湖心降低趋势。聚类及相似性分析(ANOSIM)表明,鱼类群落组成时空差异不明显。     

An introduction to species concepts and speciation of fishes

More than 22 different species concepts have been proposed. The concepts in general reflect the philosophical outlook, particular expertise, and the groups on which the authors are working. The full‐length papers in this special issue dedicated to species concepts relative to fishes are based on presentations by the authors at the 2001 annual meeting of the American Society of Ichthyologists and Herpetologists at University Park, Pennsylvania, USA and generated much discussion on the topic of what constitutes a species.     

Heads you win,tails you lose: Life‐history traits predict invasion and extinction risk of the world's freshwater fishes

1. Freshwater fishes have the distinction of being both a highly imperilled taxonomic group as well as one that has produced many invasive species with widespread ecological impacts. Faced with the difficult task of identifying those species with the greatest need for management action, ecologists have turned to using predictive suites of ecological and life‐history traits to provide reasonable estimates of fish invasion and extinction risk. Whether traits associated with invasiveness are the inverse of those associated with imperillment, known as the ‘two‐sides‐of‐the‐same‐coin’ hypothesis, remains unclear.
2. A global trait analysis (including maximum total body size, longevity, size at maturation, age at maturation, fecundity and egg size) for 6293 freshwater fishes was conducted to examine the trait correlates of species proneness to invasion or extinction. A meta‐analytical procedure was deployed using univariate and multivariate trait analyses that accounted for the effects of shared phylogeny.
3. Mean trait differences (measured as Hedges' d effect size) were found between invasive and threatened species when compared with native species, thus supporting the two‐sides‐of‐the‐same‐coin hypothesis for freshwater fish. Invasive species were characterized by larger body size, greater longevity, delayed maturation and higher fecundity than threatened species. Furthermore, invasive species were found to display greater trait variability compared with threatened species, suggesting that different traits may be selected at different stages of the invasion process (from pathway entrainment to establishment) whereas more specific trait combinations may predispose species to higher extinction risk.
4. The present study demonstrated a strong trait basis to global‐scale invasion risk and extinction vulnerability for freshwater fishes. Given that both time and resources are too limited for detailed species‐by‐species assessments, the results suggest that trait correlates provide a reasonable estimate of invasion and extinction risk that can inform more targeted and proactive conservation strategies.