中国近海带鱼Trichiurus japonicus的命名和分类学地位研究

带鱼属(Trichiurus)鱼类是中国最重要的海洋渔业捕捞对象之一。然而,有关中国南北沿海均有分布的这种带鱼(简称中国近海带鱼)应取何名、属于何种及其系统进化过程等问题仍未有统一的认识和定论。本研究通过测定中国近海带鱼14个群体共计166个个体的线粒体16S r RNA基因序列,分析该物种与中国近海其他3种带鱼属鱼类的序列变异,比较该种带鱼与世界其他带鱼属有效种的形态差异,综合探讨其命名、分类地位及系统进化过程。基于Kimura双参数模型计算,中国近海带鱼(Tsp-CH)与台湾(Tj-WT)及日本(Tj-JP)的带鱼(Trichiurus japonicus)的组间净遗传距离(0.000 7~0.002 1)远低于带鱼属内其他种间的净遗传距离(0.065 6~0.082 0),也明显低于高鳍带鱼(Trichiurus lepturus)地理群体间的遗传距离(0.010~0.016);分子变异分析(AMOVA)和FST分析均表明这三组带鱼组间遗传分化不显著。结果表明,中国近海带鱼与来自台湾及日本的带鱼(T.japonicus)的遗传分化处于种内水平。采用邻接法构建的分子系统树显示,不同地理来源的带鱼(T.japonicus)(即包括Tsp-CH,Tj-WT,Tj-JP)与高鳍带鱼(T.lepturus)、南海带鱼(Trichiurus nanhaiensis)、短带鱼(Trichiurus brevis)等3种带鱼属鱼类互为单系,在属内各自形成独立的进化分支。结合分子数据和形态学比较研究资料,本研究确认中国南北沿海均有分布的这种带鱼是Trichiurus japonicus Temminck et Schlegel,1844,它在种的分化、形成、分布及形态上与世界其他带鱼属鱼类存在系列差异。     

基于COXI基因的太平洋西岸文昌鱼地理种群分析

文昌鱼是进化发育研究的重要模式动物,目前实验材料均采自野外.因此,对其进行正确的物种鉴定和地理种群的遗传分化分析十分必要.该研究扩增并测定了COX 1基因部分序列,结合NCBI数据库中的COX 1序列信息,对太平洋西岸文昌鱼的种类和地理种群分化情况进行了分析.结果表明,马来文昌鱼(Branchiostoma malayanum)、白氏文昌鱼(B.belcheri)和日本文昌鱼(B.japonicum)这3个种之间的遗传差异很大,再次证实3个物种的有效性,同时提出应当审慎对待NCBI数据库中文昌鱼的种名标注;太平洋西岸文昌鱼属Branchiostoma的3种文昌鱼群体遗传多样性均处于较高水平,同一物种的不同地理种群间没有出现明显的遗传分化,反映了海洋动物的基因交流较容易,不同海域隔离较弱.     

不同地理种群美洲斑潜蝇及近缘种的rDNA-ITS1序列分析和比较

【目的】通过对美洲斑潜蝇Liriomyza sativae Blanchard 不同地理种群及近缘种间的核糖体DNA第一内转录间隔区（rDNA-ITS1）进行比较,分析美洲斑潜蝇不同地理种群间的遗传分化情况,并为美洲斑潜蝇与近缘种间提供分子鉴别标记。【方法】用PCR产物直接测序法及克隆测序法对我国美洲斑潜蝇8个地理种群的rDNA-ITS1序列进行测序,并调用GenBank中3个近缘种的rDNA-ITS序列,运用软件MEGA3.1对美洲斑潜蝇不同地理种群及近缘种间的rDNA-ITS1序列进行分析。【结果】美洲斑潜蝇8个地理种群间的分化程度较低,只有8个变异位点,遗传距离都在0.02以下,但4个近缘种间的碱基差异显著,遗传距离为0.149～0.390,有126个变异位点,12个美洲斑潜蝇特异性识别位点。【结论】虽然基于rDNA-ITS1序列所显示的美洲斑潜蝇各地理种群之间的遗传分化很小,但是其分化趋势与地理分布基本相吻合;得到的12个特异性识别位点不仅可以作为美洲斑潜蝇与其近缘种间鉴别的分子标记,而且可为今后设计鉴别性PCR引物提供重要的参考依据。     

亚洲玉米螟不同地理种群基于COⅠ基因序列初步分析

本研究通过对我国亚洲玉米螟Ostrinia furnacalis(Guenée)6个地理种群的线粒体DNACOⅠ基因进行测序,运用分子进化遗传分析软件MEGA5对序列进行对比和同源性分析,并建立系统发育关系。结果表明,COⅠ基因在6个地理种群中进化具有一定的差异,平均遗传距离为0.013;进化树显示,亚洲玉米螟的三亚种群、广州种群与南昌种群聚为一支,然后与泰安种群聚为一支,再与哈尔滨种群聚为一支;而廊坊种群另聚成一支。遗传分歧度与系统发育进化关系均表明不同地理种群的遗传分化与地理距离之间具有一定的相关性。     

安徽长江流域黄鳝6个地理种群的遗传变异研究

采用线粒体细胞色素b(Cyt b)为分子标记,研究了安徽长江流域黄鳝6个地理种群(当涂、无为、繁昌、贵池、怀宁和望江)共180尾个体的遗传变异关系。结果显示,在1087 bp序列中共检测到变异位点101个,单倍型68个,碱基组成中A+T的含量大于G+C的含量。6个地理种群的单倍型多样性(0.623~0.940)较高,核苷酸多样性(0.001 78~0.019 04)较低。群体分化指数(Fst:0.026 12~0.947 07)、基因流(Nm:0.027 94~18.6400)和分子变异分析(AMOVA)结果表明,安徽长江流域黄鳝一些地理种群间存在着明显的遗传分化。单倍型系统进化树和进化网络图表明:6个地理种群分为2个大的进化支,当涂与繁昌种群为一支,其余4个种群为另一支。地理隔离和黄鳝有限的迁移能力可能是造成种群遗传分化的原因。     

星豹蛛不同地理种群COⅠ基因序列差异初步分析

星豹蛛广泛分布于我国南北各省的农田、果园、菜田及森林等生态系统中,是农林害虫的重要天敌。本文测定了采自山西临汾、运城、晋中和忻州4个地区的星豹蛛地理种群细胞色素氧化酶亚基Ⅰ(COⅠ)基因部分序列(932bp),并对此序列及从NCBI网站GenBank上下载的采自国内10个省市星豹蛛相应序列一并进行遗传多样性研究,分析了碱基组成和变异情况以及核苷酸序列差异,采用距离矩阵邻接法和最大简约法构建了不同的分子系统树,得到了相似的拓扑结构,从分子水平初步探讨了星豹蛛不同地理种群的遗传结构。结果表明,星豹蛛地理种群间的COⅠ序列同源性达98%～100%,显示出较大的遗传差异。序列比对后从供试14个COⅠ序列中共检测出41个变异位点和6个单倍型,系统发育分析结果表明种群间存在一定的遗传分化。综合分析,星豹蛛不同地理种群之间的遗传差异较大,遗传多样性水平较高,进一步从分子遗传学角度证明了星豹蛛成为我国广布种的原因。     

基于线粒体 Cyt b 基因的柴达木盆地子午沙鼠的遗传多样性与种群结构分析

对采集自柴达木盆地4个子午沙鼠种群的线粒体Cyt b部分序列进行测序,分析其遗传多样性和种群间系统进化关系。结果显示：冷湖-苏干湖种群的遗传多样性最高（Hd = 1.000;π = 0.00530）,花土沟种群的遗传多样性最低（Hd = 0.750;π = 0.00255）。分子变异分析结果显示61.68%的变异来自种群内,38.32%的变异来自种群间。其中, 冷湖-苏干湖种群与其他种群之间的遗传分化水平相对较低,格尔木种群与其他种群之间有较高水平的遗传分化。系统进化分析显示柴达木盆地子午沙鼠以冷湖-苏干湖为发源地沿盆地周边自西向东扩散,各种群之间存在广泛的基因交流。由于地理阻隔,格尔木种群与其他种群间基因交流较少。各地理种群间遗传距离与地理距离不相关。青藏高原大湖期是柴达木盆地各种群之间产生遗传分化的主要原因。     

高原鼢鼠线粒体谱系地理学和遗传多样性

高原鼢鼠是一类地下独居啮齿动物,为青藏高原特有种之一。为研究该物种的谱系地理学和遗传多样性,本文测定了采自青藏高原东部3个地理种群8个小种群共37个个体的线粒体D-loop区序列变异。在长度为627bp的序列中,共发现50个变异位点,定义了26种单倍型。该物种的单倍型多样性（Haplotype diversity,H）较高和核苷酸多样性（Nucleotide diversity,πn）较低。谱系分析得到3个稳定的分支,分别与采集的地理种群相吻合：同一地理种群内单倍型之间遗传差异小,而不同地理来源的单倍型之间存在较大区别。距离隔离分析表明高原鼢鼠的遗传分化与地理距离呈正相关。AMOVA分析同样表明地理种群之间存在显著差异：地理种群间变异占遗传变异的80.45%。高原鼢鼠的这种遗传结构特点可能主要是由于第四纪气候变迁、该物种稳定的地下生活环境和有限的迁移能力造成的。     

三化螟COⅠ序列分析及DNA条形码研究

三化螟Scirpophaga incertulas是水稻的重要害虫之一。本研究通过对三化螟3个地理种群线粒体COⅠ基因的序列分析,初步探讨了中国三化螟种群间的遗传分化。36个三化螟样本共得到了9个单倍型,其中有17个变异位点,占总位点数的3.13%。系统进化分析表明,来源于各地理种群的单倍型散布在不同的进化支上,缺乏明显的地理分布格局。联合网上公布的相关物种序列进行的遗传分析表明,线粒体COⅠ基因能够对三化螟进行准确的物种鉴定。     

基于线粒体COI序列变异的高原鼢鼠种群遗传分化研究

基于线粒体COI基因序列对高原鼢鼠7个地理种群的遗传多样性、遗传分化和基因流进行分析,158条COI基因序列中发现了570个变异位点,界定了54个COI单倍型。总体单倍型多样性指数Hd为0.911,种群单倍型多样性在0.278—0.964之间,高原鼢鼠的种群遗传多样性较高。群体总的遗传分化系数Fst为0.611,群体间的基因流Nm在-0.020—3.700之间,部分地理种群之间的遗传分化程度高,基因流弱。AMOVA分子变异分析显示,高原鼢鼠的遗传变异主要来自种群之间(77.56%),种群内部的遗传变异较低(22.44%)。中性检验(P0.01)与错配分析显示高原鼢鼠种群经历了群体扩张事件。IBD未检测到地理距离与种群间遗传距离的显著性相关关系(R2=0.124,P=0.118)。综合分析认为,高原鼢鼠不同地理种群间遗传分化的原因除地理隔离外,还与迁移扩散方式、进化过程和其他环境因素有关。     

台湾海峡夏秋季游泳动物资源分布及群落结构

根据夏季和秋季在台湾海峡进行的底拖网调查数据,分析了台湾海峡游泳动物资源密度指数分布及群落结构.结果表明,台湾海峡夏季平均资源密度指数高于秋季,分别为8.50和6.94kg·h^-1;夏秋季出现游泳动物种类分别为80种和91种,秋季丰富度、多样性、均匀度均高于夏季,夏秋季平均多样性指数分别为2.0466和2.3964;相对重要性指数IRI大于200的优势种夏季有5种,为带鱼、发光鲷、短尾大眼鲷、花斑蛇鲻、中国枪乌贼,秋季有6种,为带鱼、七星底灯鱼、刺鲳、中国枪乌贼、蓝圆_鲹、鹿斑鲾;夏季优势种的聚集强度比秋季强.     

东海带鱼和小型鱼类空间异质性及其空间关系

根据2001年秋季东海区121个调查站位的调查资料,以变异函数为工具,分析带鱼和7种小型鱼类(黄鲫、棘头梅童鱼、鳄齿鱼、六丝钝尾虎鱼、发光鲷、七星底灯鱼和细条天竺鲷)的空间异质性及其空间关系.结果表明,带鱼的变异函数曲线与细条天竺鲷、六丝钝尾虎鱼和发光鲷的曲线极为相似,对不同距离的变异函数值进行相关分析,带鱼与上述3种小型鱼类均达到极显著相关水平(P<0.01).黄鲫和棘头梅童鱼的变异函数表现出纯金块效应,而其它几种鱼都可拟合为球状或指数模型,并且都具有较强的空间自相关特性,其中细条天竺鲷、六丝钝尾虎鱼和发光鲷的变程也都接近或超过带鱼265km的变程,带鱼与这3种小型鱼类之间具有较强的空间追随关系,因此它们是带鱼的主要摄食对象.     

Feeding habits and ontogenetic diet shifts of hairtail, Trichiurus margarites, in the Beibu Gulf of the South China Sea

The monthly and ontogenetic variations in diet of hairtail Trichiurus margarites Li (1992) [20] (Perciformes, Trichiuridae) were examined in the Beibu Gulf of the South China Sea from October 2008 to September 2009. Stomachs of 666 hairtail ranging in size from 121 mm to 561 mm pre-anal length (PL) were sampled monthly from commercial fish catches. Fish were the primary prey, with Decapterus maruadsi (Perciformes, Carangidae) averaging 23% by number, 34% by weight, and 49% by Index of Relative Importance (IRI). Other important prey in the diet included the small benthic fish, Bregmaceros rarisquamosus and Bregmaceros nectabanus (Gadiformes, Bregmaceroridae) and the decapod shrimp, Acetes chinensis, with IRI percentages of 8%, 4%, and 3%, respectively. Low rates of cannibalism and predation on 30 additional species of prey were observed. Trophic diversity (Brillouin Index, H_z) was moderate throughout the year. Mean feeding intensity (Repletion Index, RI) varied considerably by month and increased with the gonad maturity stages of hairtail; conversely, the proportion of empty stomachs decreased with maturity stages, from 60.9% empty at Stage I to 41.6% empty at Stage VI. Prey weight and numbers differed significantly among the 14 PL size classes and increased with body size. Cluster analysis of prey IRI values also indicated differences in the feeding habits of hairtail by size class. Understanding the monthly and ontogenetic changes in hairtail diet may assist in the development and improvement of marine ecosystem modeling for the Beibu Gulf, South China Sea.     

应用高通量测序技术对我国东海带鱼肠道菌群的研究

带鱼（Trichiurus spp.）是我国东海区重要的经济鱼类,通过研究分析我国东海带鱼肠道内容物的菌群结构,了解其所携带的自身特有的病原微生物情况。采集我国东海海域捕获的带鱼,提取肠道内容物DNA,采用Ion S5TM XL高通量测序平台和生物信息学分析方法,构建10个样本的16S rRNA V3-V4区基因测序文库。结果显示,10个样本共得到 1 221 个OTU（operational taxonomic unit）,分属28个菌门345个菌属。从门水平上看,柔膜菌门（Tenericutes）和变形菌门（Proteobacteria）丰度较高,分别为51.30%和29.58%;从属水平上看,支原体属（Mycoplasma）和弧菌属（Vibrio）占比较高,相对丰度分别为50.95%和13.79%。研究结果提示我国东海带鱼肠道内容物微生物菌群中支原体属含量可能较高,在食品加工过程中存在交叉污染的可能,相关生产过程需提高警惕并采取一定控制措施,同时为新病原的发现和防控提供了参考。     

A spatial analysis of trophic composition: a case study of hairtail (<Emphasis Type="Italic">Trichiurus japonicus</Emphasis>) in the East China Sea

The spatial distribution of fish on feeding grounds is an important factor in determining their prey composition. Of the factors that may influence the spatial distribution on the feeding ground and subsequent diet composition is the fish maturation stage. Using hairtail (Trichiurus japonicus) as an example, we evaluated the impacts of gonad development stage on diet composition. Hairtail supports one of the most valuable and largest fisheries in the East China Sea. As one of the top predators, it plays an important role in the ecosystem. We analyzed hairtail stomach samples collected on their feeding grounds from a fisheries-independent survey program in September 2005. Our analyses suggest that females in their third maturity stage tended to feed more intensively. Fish were the most important preys for hairtail, accounting for 72.6% of the total stomach contents in weight. The four most important fish species were juvenile hairtail (25.2%), Japanese scad (11.4%), Japanese jack mackerel (7.7%), and small yellow croaker (5.9%), suggesting strong cannibalism. A cluster analysis suggests that hairtail could be divided into three groups in their spatial distribution based on their diets: one group with similar percentages of fish and crustacean preys mainly distributed in the south of East China Sea far from the coast; one group mainly consuming fish and distributed over the north of East China Sea near the coast; and the third group consuming mainly crustacean species mainly distributed in the open sea. We hypothesize that gonadal development stage of hairtail may determine their movement from spawning ground to feeding ground, and subsequently spatial distribution on the feeding ground, which in turn results in different feeding intensities and prey compositions. Handling editor: Robert Bailey     

气候环境因子和捕捞压力对南海北部带鱼渔获量变动的影响

带鱼(Trichiurus japonicas)是南海北部的重要经济鱼类,其渔获量的变化不仅与捕捞压力有关,还与气候环境变化有关.为了研究气候变化和捕捞对南海北部带鱼渔获量变动的影响,使用长时间序列渔业统计资料和气候变化数据对1956-2006年的南海北部带鱼渔获量变动进行了分析.南海北部的带鱼渔获量变化可划分成因捕捞效应所产生的趋势变化和因气候环境变化所导致的渔获量变动.捕捞效应所产生的趋势变化可用Fox模型拟合,Fox模型拟合结果显示南海北部带鱼渔获量与捕捞努力量关系显著(P＜0.01),说明捕捞压力的增长显著影响到南海北部带鱼渔获量的变化.移除捕捞效应所产生的趋势变化后,渔获量变动与中国南方降雨、南海北部海表水温、南海北部夏季季风以及南海北部冬季季风等气候因子呈显著正偏相关(P＜0.04),与热带气旋影响指数呈显著负偏相关(P＜0.03),这种相关说明南海北部带鱼渔获量变动还受气候环境因子的影响.南海北部带鱼渔获量可用捕捞努力量和气候变量来拟合,且拟合效果显著(R2=0.958,P＜0.01),表明南海北部带鱼渔获量的变动归因于捕捞压力的单调增长和气候环境的变化.在南海北部的捕捞压力维持在现有水平下,未来的气候变化和人类活动引起营养盐的增加都可能有利于南海北部带鱼渔业产量的增加,且由于未来极端天气事件的频繁发生,可能还会引起带鱼渔获量的变动幅度加剧.     

Multiplex genotyping based on the melting temperature of a single locked nucleic acid probe

Locked nucleic acid (LNA) is a modified RNA nucleotide that can be incorporated at specific positions to generate probes with the desired length, melting temperature (T_M), and specificity. Here, we describe a method of multiplex genotyping based on dramatic shifts in the T_M of a single dual-labeled LNA probe. Using this method, two varieties of the hairtail fish Trichiurus lepturus can be distinguished from each other, as well as from Trichiurus japonicus, based on a 1- to 2-bp difference in a fragment of mitochondrial cytochrome oxidase subunit 1. The shift in T_M was 15 °C for a 1-bp mismatch and 27 °C for a 2-bp mismatch, indicating remarkable specificity. We anticipate that the method will be widely useful in applications such as species identification that require accurate, multiplex, and efficient detection of DNA polymorphisms.     

利用SLAF-seq技术开发带鱼(Trichiurus japonicus)微卫星标记以及跨物种扩增检测

带鱼(Trichiurus japonicus)是广泛分布于东亚大陆架海域的暖温性近底层鱼类,长期位居我国单鱼种渔获量第一位。自上世纪70年代以来,持续过度捕捞和海洋环境变化导致中国近海带鱼资源基础和遗传多样性受到严重影响,但有关带鱼种群的微卫星DNA标记研究却较为缺乏,不利于该物种遗传资源评估和保护。为此,本研究采用基于高通量测序平台的SLAF-seq技术,从带鱼的195 308个SLAF标签中识别出25 704个二至六碱基重复微卫星位点。经过引物扩增验证,最终筛选出36个具有多态性的微卫星标记。各位点等位基因数4～35,均值14.47。观测杂合度0.214～1.000,期望杂合度0.456～0.979,均值分别为0.620和0.803。所有位点的多态信息含量值均大于0.25。经Bonferroni校正,21个位点符合哈迪-温伯格平衡,且各位点间不存在连锁不平衡。这21个多态性微卫星标记可为带鱼的种群遗传资源研究提供新的有效分子标记和技术支撑。Bottleneck分析结果表明,宁波近海带鱼群体未检测到近期的遗传瓶颈效应,这可能与目前东海区带鱼野生群体数量还比较庞大、遗传变异仍然较为丰富有关。跨物种扩增结果显示,分别有12、16、4和3个带鱼微卫星标记在带鱼属(Trichiurus)、沙带鱼(Lepturacanthus savala)、窄颅带鱼(Tentoriceps cristatus)及小带鱼(Eupleurogrammus muticus)中具有较好的通用性,这些微卫星标记为今后带鱼科相应属、种的系统进化关系研究提供新的分析手段和契机。     

Trophic interactions and the diet composition of sympatric finfish predators in the tropical demersal ecosystem in the Bay of Bengal

The dietary composition, foraging strategies, and interspecific trophic interactions were identified for four major demersal carnivorous finfishes, namely, croaker Otolithes ruber, hairtail Trichiurus lepturus, threadfin bream Nemipterus japonicus, and lizardfish Saurida undosquamis, along the north-western part of Bay of Bengal from 2014 to 2016. Two species, Trichiurus lepturus and Saurida undosquamis, were identified as finfish feeders due to the high number of teleost (clupeids and engraulids) prey. One species, Nemipterus japonicus, had a significantly different diet of metapenaeids and charybdids, and was identified as a shellfish feeder. The final species, Otolithes ruber, preyed equally on crustaceans and teleosts, and was identified as a shellfish-finfish feeder. The feeding activity of all four species was lower during peak spawning periods and tended to increase with maturity. Feeding preferences varied with seasons. The trophic level ranged from 3.49 to 4.01, classifying the four species as medium-carnivores or meso-predators. Niche breadth ranged from 0.170 to 0.421, with seasonal and ontogenetic variations. Individual or subgroup specialization was observed on dominant prey, but intraspecific diet variations indicated all four species to be opportunistic predators. There was substantial prey overlap for Saurida undosquamis with Otolithes ruber and Trichiurus lepturus, which increased ontogenetically and coincided with their peak spawning. Sharing of abundant prey resources together with temporal and ontogenetic resource partitioning at intra- and interspecific levels possibly lowered dietary competition, thereby facilitating the coexistence of these demersal predators. This study provides new information on feeding interactions from a tropical demersal ecosystem that can be applied for the ecosystem-based management of trawl fisheries.     

Genetic Variation at the Mitochondrial 16S rRNA Gene among Trichiurus lepturus (Teleostei:Trichiuridae) from Various Localities: Preliminary Evidence of a New Species from West Coast of Africa

The taxonomic classification of large head hairtail (Trichiurus lepturus) is controversial because of similar body appearance and silvery coloration. Ten samples of T. lepturus caught off the west coast of Africa and 43 samples of T. lepturus caught off the western Atlantic coast and Indo-Pacific waters were used for sequence comparison of mitochondrial DNA encoded partial 16S ribosomal RNA(16S rRNA) gene. Ten samples of T. japonicus (obtained from various parts of southern Japan) were also included in the comparative analysis. For the 509 bp sequence determined, 58 sites were variable, of which 53 were parsimony informative. Phylogenetic analyses using maximum parsimony, maximum likelihood and Bayesian algorithm with Eupleurogrammus muticus as outgroup, showed that the haplotypes of T. lepturus obtained from the West coast of Africa, Indo-Pacific and Western Atlantic coast constituted clearly distinct and well supported lineages without any sharing and overlapping between them. Previous morphological analyses and this genetic study strongly indicate that the morphotypes of T. lepturus obtained from the West African coast are genetically distinct and probably represents a separate species.