Molecular identification of hairtail species (Pisces: Trichiuridae) based on PCR-RFLP analysis of the mitochondrial 16S rRNA gene

A rapid PCR-RFLP analysis was designed to identify 3 closely related species of hairtails: Trichiurus lepturus, T. japonicus, and Trichiurus sp. 2, basing on partial sequence data (600 bp) of the mitochondrial DNA encoding the 16S ribosomal RNA (16S rRNA) gene. Restriction digestion analysis of the unpurified PCR products of these 3 species, using EcoRI and VspI endonucleases, generated reproducible species-specific restriction patterns showing 2 fragments (250 bp and 350 bp) for T. lepturus in EcoRI digestion and 2 fragments (196 bp and 404 bp) for T. japonicus in VspI digestion, whereas no cleavage was observed for Trichiurus sp. 2 in both EcoRI and VspI digestions. The PCR-RFLP technique developed in this study proved to be a rapid, reliable and simple method that enables easy and accurate identification of these 3 closely related species of the genus Trichiurus.     

Biochemical systematics of Trichiurus lepturus and T. japonicus (Perciformes,Trichiuridae) from Taiwan Strait

Two morphological different species of hairtails, Trichiurus lepturus and T. japonicus were compared by starch gel electrophoresis. Isozyme patterns of eight metabolic enzymes and general muscle proteins using extracts of eye, muscle, liver and heart revealed 16 loci. The polymorphic loci were sAAT-1, GPI-A, GPI-B, IDHP-1 and PGM-2 for at least one of the two species. There were no fixed allelic isozyme patterns to differentiate among them. NEI's genetic identity (I) between the two species was calculated. An I index of 0.986 suggests that the two morphologically different hairtails belong to the same species, Trichiurus lepturus.     

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。     

高鳍带鱼遗传变异及与近缘种间的系统进化关系

高鳍带鱼Trichiurus lepturusLinnaeus,1758分布广泛、形态多变,与近缘种间辨别困难,在其种群鉴别、物种分类及系统进化上争议较大。本项研究通过测定采自海南三亚外海高鳍带鱼疑似种11个个体的线粒体16S rRNA基因部分序列,结合已报道的该物种其它地理种群及其近缘种的同源序列,采用生物软件对碱基组成和序列变异进行分析,计算Kimura双参数净遗传距离和分歧时间,进行分子变异分析(AMOVA)和分化固定指数(FST)计算,并以小带鱼Eupleurogrammus muticus为外群构建NJ、ML系统树,综合探讨世界范围内高鳍带鱼的遗传变异及与近缘种间的系统进化关系。根据所得分子数据并结合形态学研究结果得出如下结论:1)采自海南三亚外海的带鱼是高鳍带鱼T.lepturusLinnaeus,1758,该物种在中国南海和东海南部有分布;2)海南三亚外海、非洲西岸和大西洋西岸的高鳍带鱼是同一个物种的3个地理种群,彼此间遗传分化显著;3)高鳍带鱼是带鱼属中最新演化的种类,与日本带鱼T.japonicus、带鱼未定种Trichiurussp.2具有较近的亲缘关系;短带鱼T.brevis则是比它们原...     

基于空间自相关的东海带鱼聚集特征年代际变化

海洋鱼类通常以集群的形式分布在特定空间内,具有高度的空间异质性特征.基于1971—2011年中国机轮拖网渔业捕捞统计及底拖网科学调查获取的东海带鱼数据,并结合夏季研究水域内海表温度及黑潮区PN断面表层盐度数据,利用空间统计方法对东海带鱼资源的聚集特征进行年代际分析.全局自相关性分析显示,1971—2011年Moran I指数先减小再增大且均为正值,表明东海带鱼聚集性呈先减弱再增强的趋势;PN断面表层盐度均值变化趋势与之相反.局部自相关性分析显示,除1971年带鱼热点分布受作业水域范围限制而集中在中部外,1981—2011年带鱼分布热点区域呈现先向南部外海移动,随后逐步向北部外海移动的格局,且相应的热点分布范围亦呈现先集中后扩散的趋势.带鱼热点分布区域随海表温度第一模态变化做适应性移动,且均靠近黑潮北分支左侧水域.     

基于Beverton－Holt模型的东海带鱼资源利用与管理

根据1959-2003年收集的东海带鱼年龄组成、肛长等生物学资料,对东海带鱼群体的利用结构进行了分析,并利用Beverton-Holt模型的单位补充量渔获量理论,分析和探讨了东海带鱼资源的合理利用.结果表明:1)东海带鱼渔获群体组成低龄化趋势明显,渔获年龄由20世纪50年代末期的0～6龄缩小为21世纪初的0～4龄,主要组成群体为0龄和1龄鱼,2龄鱼的比例由50年代末期的12.84%下降到21世纪初的6.91%,3龄鱼的下降幅度更大,由原来的4.92%下降为0.57%,渔获年龄组成进一步简单化.2)2000-2003年东海带鱼的年平均开发率E为0.864,远超过现行渔业下的最适开发率0.51,东海带鱼资源处于过度捕捞状态.3)增加东海带鱼单位补充量渔获量(YM/R)最有效的方法是提高其开捕年龄,若将带鱼开捕年龄tc由目前的0.5龄提高到1龄,其单位补充量渔获量可比2003年增加55.38%;若tc提高到1.5龄,其单位补充量渔获量可增加100.81%;若tc提高到2龄,其单位渔获量可增加130.52%;如果提高到2.75龄,其单位补充量渔获量将出现最大值,可增加145.23%左右.在当前大幅降低捕捞强度有较大困难的情况下,建议采取逐年、逐步提高带鱼开捕规格并适当降低其捕捞强度,以更好地恢复东海带鱼资源.     

北部湾带鱼的摄食习性

2008年8月至2009年9月,对北部湾带鱼逐月渔获物胃含物进行鉴定和统计分析,研究其摄食习性.结果表明：北部湾带鱼捕食种类包括鱼类、头足类、底栖甲壳类以及浮游动物等,属于广食性动物.优势种类有少鳞犀鳕(37.99%)、蓝圆鲹(16.42%)和中国毛虾(10.03%).蓝圆鲹和尖吻小公鱼全年在全湾带鱼的食物中均有出现,是重要的饵料指标种类.摄食强度与饱满指数的季节差异十分显著(P<0.001),食物多样性无显著季节性差异(P>0.05),秋季最高,全年平均为1.97.聚类分析表明,北部湾带鱼在达到50%性成熟肛长值(190 mm)时,饵料由幼鱼的以小型浮游动物、中上层鱼类及甲壳类为主向成鱼的以较大型鱼类和头足类为主转换.     

北部湾带鱼的摄食习性

2008年8月至2009年9月,对北部湾带鱼逐月渔获物胃含物进行鉴定和统计分析,研究其摄食习性.结果表明：北部湾带鱼捕食种类包括鱼类、头足类、底栖甲壳类以及浮游动物等,属于广食性动物.优势种类有少鳞犀鳕(37.99%)、蓝圆鲹(16.42%)和中国毛虾(10.03%).蓝圆鲹和尖吻小公鱼全年在全湾带鱼的食物中均有出现,是重要的饵料指标种类.摄食强度与饱满指数的季节差异十分显著(P<0.001),食物多样性无显著季节性差异(P>0.05),秋季最高,全年平均为1.97.聚类分析表明,北部湾带鱼在达到50%性成熟肛长值(190 mm)时,饵料由幼鱼的以小型浮游动物、中上层鱼类及甲壳类为主向成鱼的以较大型鱼类和头足类为主转换.     

Evolutionary and biogeographical patterns within the smelt genus Hypomesus in the North Pacific Ocean

Aim We address questions about trans‐Pacific distributions of marine organisms and the North Pacific Ocean as a centre of marine biodiversity through a phylogenetic and biogeographical study of a pan‐Pacific genus of Northern Hemisphere smelts (Hypomesus, Pisces: Osmeridae). Location North Pacific Ocean. Methods Relationships of the five species of Hypomesus from throughout the North Pacific were reconstructed through maximum likelihood and Bayesian phylogenetic analyses of sequence data from two mitochondrial (cytb, 16S) and three nuclear (ITS2, S71, RAG1) gene regions of five to 25 individuals per species, totalling 3588 characters. The resulting phylogenies were used to test hypotheses of species relationships and geographical origins using both dispersal‐based and maximum likelihood methods for inferring ancestral areas (lagrange ). Cytb sequence divergence and a Bayesian approach (beast ) were used to estimate the timeframe of Hypomesus evolution, which was compared with work on similarly distributed taxa. Results Hypothesized trans‐Pacific Ocean relationships based on lateral line scale counts were not supported by the phylogeny, suggesting parallel evolution of this phenotype, although we found one such relationship between the western H. japonicus and the two eastern Pacific species (H. pretiosus and H. transpacificus). Dispersalist approaches rejected an early proposal of a double‐compression vicariant mechanism as well as an eastern Pacific origin. Results from the lagrange analysis suggested a more widespread ancestor, although also supporting a role for the western Pacific. Divergence estimates suggested that most splits between species occurred in the mid‐Miocene, and the most recent speciation event, between the eastern Pacific species, occurred in the Pliocene to early Pleistocene. Main conclusions Our molecular data indicate that the character historically used to define relationships within Hypomesus, lateral line scale count, does not reflect ancestry within the genus. Biogeographical reconstructions suggest an important role for the western North Pacific in the diversification of Hypomesus. While uncertainty remains over the date of origin for this genus, estimates place the divergences during periods of climatic cooling that have been important in generating diversity in a number of similarly distributed organisms. Additional comparative data will provide further insight into the relative importance of the western region in generating diversity in the North Pacific Ocean.     

Modeled distributions of Aedes japonicus japonicus and Aedes togoi (Diptera: Culicidae) in the United States,Canada, and northern Latin America

The Asian bush mosquito, Aedes japonicus japonicus, and the coastal rock pool mosquito, Aedes togoi, are potential disease vectors present in both East Asia and North America. While their ranges are fairly well‐documented in Asia, this is not the case for North America. We used maximum entropy modeling to estimate the potential distributions of Ae. togoi and Ae. j. japonicus in the United States, Canada, and northern Latin America under contemporary and future climatic conditions. Our results suggest suitable habitat that is not known to be occupied for Ae. j. japonicus in Atlantic and western Canada, Alaska, the western, midwestern, southern, and northeastern United States, and Latin America, and for Ae. togoi along the Pacific coast of North America and the Hawaiian Islands. Such areas are at risk of future invasion or may already contain undetected populations of these species. Our findings further predict that the limits of suitable habitat for each species will expand northward under future climatic conditions.     

A Review of the Sipunculan Genus Thysanocardia Fisher

The taxonomy of the sipunculan taxon Thysanocardia Fisher is reviewed. Originally erected as a subgenus of Golfingia Lankester, the status of Thysanocardia is here elevated to the level of a genus. Of the 17 species currently recognised within this genus, most of which were originally described from single specimens, only three are considered sufficiently distinct as to warrant specific status, namely T. catherinae (Grube), T. procera (Möbius) and T. nigra (Ikeda). T. catherinae is the most widespread of these species being distributed in the western North Atlantic, South Atlantic and western Indian Ocean, whilst T. procera is confined to the north-eastem region of the North Atlantic and T. nigra chiefly to the North Pacific Ocean.     

A new species of Osedax (Annelida: Siboglinidae) associated with whale carcasses off Kyushu, Japan

A new whale-bone-eating polychaete species of the genus Osedax was found on sperm whale carcasses submerged off Cape Nomamisaki, Kyushu, Japan, at a depth of approximately 200 m. The new species, Osedax japonicus, is the fourth known species of the genus Osedax and the first species from the western Pacific. Female O. japonicus specimens (1) form dense clusters on whale carcasses; (2) have a body composed of crown, trunk, and root structure; (3) lack a digestive tract; and (4) have bacterium-like particles in the tissue of the root structure. Osedax japonicus shares all these characteristics with O. rubiplumus and O. frankpressi, and items (1) to (3) with O. mucofloris. Osedax japonicus is easily distinguished from the other three known species by oviduct morphology, body length, and palp coloration in females. No males of O. japonicus have yet been found.     

基于线粒体COⅠ和16S rRNA基因序列比较分析东海带鱼群体遗传多样性

测定了东海带鱼(Trichiurus lepturus Linnaeus)三个群体(命名为A: 122°32′E 29°55′N、B: 123°30′E 26°75N; C: 124°24′E 27°26′N)72个个体的线粒体DNA16S rRNA和COⅠ基因序列,通过单基因序列和联合序列分析, 研究了东海带鱼群体的遗传变异情况。分别得到1130 bp的COⅠ基因序列片段和554 bp的16S rRNA序列片段, 其中COⅠ基因片段的T、C、A、G含量分别为29.0%、28.9%、24.4%和17.7%; 16S rRNA基因片段的T、C、A、G含量分别为22.7%、27.6%、28.0%和21.7%。基于线粒体16S rRNA、COⅠ和16S+COⅠ基因序列分析, 72个个体中分别确定43个, 8个和49个单倍型, 存在单倍型共享现象。群体的单倍型多样性指数为0.9766—0.9992, 显示了群体内的单倍型较为丰富。3个群体间各序列平均核苷酸差异数(K)在5.111—9.024和0.0045—0.0076, 核苷酸多样性指数(π)为0.0048—0.0084, 显示不同带鱼群体遗传多态性丰富。使用邻接法构建的分子进化树揭示同一群体内大部分个体聚在一起。分析结果表明, 群体A遗传背景比群体B、群体C较为丰富, 群体内部个体差异大于群体间差异, 群体间基因交流频率较高, 遗传分化不明显, 初步判定东海带鱼3个群体的遗传多样性偏低。     

Low worldwide genetic diversity in the basking shark (Cetorhinus maximus)

The basking shark (Cetorhinus maximus) is found in temperate waters throughout the world's oceans, and has been subjected to extensive exploitation in some regions. However, little is known about its current abundance and genetic status. Here, we investigate the diversity of the mitochondrial DNA control region among samples from the western North Atlantic, eastern North Atlantic, Mediterranean Sea, Indian Ocean and western Pacific. We find just six haplotypes defined by five variable sites, a comparatively low genetic diversity of pi=0.0013 and no significant differentiation between ocean basins. We provide evidence for a bottleneck event within the Holocene, estimate an effective population size (Ne) that is low for a globally distributed species, and discuss the implications.     

Divergence of two forms of Triphoturus in the eastern Pacific based on mtDNA cytochrome b gene sequences and larval morphology

Divergence between two eastern Pacific forms of Triphoturus , currently considered to belong to the same species was tested by DNA sequences of the cytochrome b gene (DNA obtained from larvae collected in northern Chile and from adults in the Southern California Bight) and examination of larval characters. The number of apparently fixed substitutions (12 among 31 variable sites, out of 1001 bases) was high and the pattern of mid‐lateral trunk pigmentation in larvae also differed consistently between the two forms. The results support the separate species status for T. mexicanus (North America) and T. oculeus (Central‐South America).     

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.     

Origin, diversification, and historical biogeography of the genus Trachurus (Perciformes: Carangidae)

We addressed phylogenetic relationships in the genus Trachurus using cytochrome b gene and D-loop sequences. The trees showed five groups: (1) the Southwest Pacific species (T. japonicus, T. novaezelandiae, and T. declivis); (2) The Mediterranean Sea and Eastern Atlantic species (T. mediterraneus); (3) The Atlantic Ocean species (T. lathami and T. trecae); (4) Eastern Atlantic species (T. trachurus and T. capensis); and (5) a group of highly mobile pelagic species, two from the Eastern Pacific (T. symmetricus and T. murphyi) and one from the Eastern Atlantic (T. picturatus). The phylogeny based on Cyt b, supports the molecular clock hypothesis and our results agree with the reported fossil indicating that the origin of this genus occur when the Thetys Sea closed (around 18.4 MYA). In addition, a very slow neutral substitution rate is reported identified only two periods of maximum diversification: the first occurring between 18.4 and 15.0 MYA and the second between 8.4 MYA and present day.     

At-sea distributions and abundance of tropicbirds in the eastern Pacific

During spring and autumn 1980–95, we surveyed Red-tailed Phaethon rubricauda , White-tailed P. lepturus and Red-billed Tropicbirds P. aethereus at sea in the Pacific between the coast of the Americas and 176°W. For the Pacific, we had complete coverage of the range of aethereus , but only partial coverage of that of rubricauda and lepturus . Six areas of higher density were indicated: three of rubricauda , two of lepturus and one of aethereus . After pooling data across years, the 'abundance' (total number including subadults and adults) estimate for rubricauda was 81 700 (boreal spring) and 86 500 (boreal autumn) birds. Abundance of each of the three rubricauda subpopulations differed between seasons by about 50% despite seasonal consistency when populations were grouped. Furthermore, high densities of rubricauda occurred at the edge of our study area, indicating that neither of the seasonal estimates for this species could be considered as total numbers. Abundance estimates of lepturus during the non-breeding season (when these birds had dispersed from colonies) were 11 000 and 41 500 birds for northern and southern populations, respectively. Estimated abundance of aethereus during the boreal spring was 26 700 birds, and 33 400 during the boreal autumn. Because tropicbirds are attracted to survey vessels, we also estimated the abundance after excluding those recorded as flying in a steady direction, or having been attracted to the ship. Considering only stationary birds (i.e. those that could not have been attracted), our minimum estimates were 41 000 rubricauda , 15 750 aethereus , 28 000 southern lepturus and 6400 northern lepturus .     

Spatial and environmental determinants of the distribution of Striped Marlin (Kajikia audax) in the western and central North Pacific Ocean

Striped Marlin is a highly migratory species distributed throughout tropical and temperate waters in the North Pacific Ocean. The habitat characteristics of Striped Marlin in the western and central North Pacific Ocean were examined using generalized additive models by modelling fishery catch-rates as a function of remotely-sensed environmental covariates, including sea surface temperature (SST), chlorophyll-a concentration (CHL), mixed layer depth (MLD) and sea height anomalies (SHA). SST explained the largest proportion of the deviance, and is therefore considered the best predictor for the habitat of Striped Marlin. Spatial distributions of the relative density of Striped Marlin indicated that there is a seasonal north–south migration, and that the highest densities occur in the central North Pacific Ocean. The preferred habitat characteristics of Striped Marlin in high density areas were identified as SST between 23 and 26 °C, MLD within 30 m depth, and CHL around 0.08 mg m^?3, while no preferred range was found for SHA. The results of this study could improve our understanding of Striped Marlin spatial distributions and habitat characteristics.