Discrimination between Icelandic cod (Gadus morhua L.) populations from adjacent spawning areas based on otolith growth and shape

Studies on Atlantic cod (Gadus morhua L.) have demonstrated extensive variation in life history characteristics among populations exposed to different environmental conditions. In Iceland, cod sampled from adjacent spawning areas, within the main spawning area at the southwest coast, exhibit variation in vital life history characteristics. In this study, we investigated the stock structure of Icelandic cod on the main spawning grounds to discriminate between these adjacent spawning groups by using otolith growth and shape. Otolith growth was based on annual increment width estimated for the major age groups (6–7 year olds) of the spawning stock. Otolith shape was determined using Fourier analysis and compared among cod sampled from the different spawning areas with stepwise canonical discriminant analysis (CDA). We found significant differences in growth and otolith shape between adjacent spawning groups of cod where those sampled close to the coast differed from those that were sampled further out on the bank and continental shelf. Our results suggest that these cod may belong to different populations and the large and fast growing cod spawning in the coastal area may need special protection given their significance to the overall productivity of the stock.     

The spatial distribution of cod (Gadus morhua L.) spawning grounds in the Kattegat, eastern North Sea

Similar to many other commercial marine fish species, Atlantic cod (Gadus morhua L.) migrate towards specific sites at spawning. These temporal aggregations are generally the most targeted by the commercial fishery. The Kattegat cod has undergone a substantial reduction over the past 25 years and both stock size and spawning stock biomass have remained at very low levels since the end of the 1990s. There is, therefore, an urgent need to map and document spawning grounds still in use. In the present study, spawning sites of Atlantic cod were identified in the Kattegat using a combination of commercial and fishery independent data from 1996 to 2004. Moreover, putative spawning and non-spawning areas were also sampled before and during the reproductive season between 2002 and 2006, and the proportion of mature females together with the individual physiological status were used to validate and strengthen the spatial analyses.

The spatial analyses identified several spawning areas in the region and two areas in the southeastern part of the Kattegat which appeared to be the most important. The results showed the presence of cod spawning aggregations, although reduced in size, in areas that have been utilized for more than 25 years according to historical information. Some local spawning grounds may have also disappeared. The proportion of mature females was higher in putative spawning than in non-spawning areas (p < 0.001) and females from spawning areas had higher gonadosomatic (p < 0.05) and hepatosomatic (p < 0.001) indices than those from non-spawning areas.

Knowledge of stock spatial and temporal distribution is essential in designing recovery strategies for depleted fish populations. The unambiguous stability of the locations of spawning aggregations over time, as shown in this study, represents a useful aid in order to efficiently implement a recovery plan for the collapsing cod stock in this area.     

南海北部底拖网渔业资源的数量变动

根据2014—2015年南海北部底拖网渔业调查数据,对带鱼 (Trichiurus japonicus) 的渔获率、群体结构、性比与性腺发育、生长及死亡参数等进行了研究。结果表明：1) 2014—2015年南海北部带鱼肛长频率分布为单峰型,优势肛长组为160~190 mm,雌、雄个体的肛长组成无显著差异 (P>0.05);2) 春季雌性个体占比较大,4个季度雌雄比与1∶1均有显著差异 (P<0.05);性成熟度以Ⅱ期为主,占比高达74.2%;最小性成熟肛长为113 mm,50%性成熟肛长 (L₅₀) 为241.5 mm;3) 电子体长频率分析法评估的带鱼渐近肛长为585 mm,生长系数为0.2 a⁻¹,总死亡系数为1.172,自然死亡系数为0.475,开发率为0.59。虽然带鱼当前仍处于过度捕捞状态,但个体平均肛长有恢复迹象。

     

Exploring connectivity between spawning and nursery areas of Mullus barbatus (L., 1758) in the Mediterranean through a dispersal model

Connectivity between spawning and nursery areas plays a major role in determining the spatial structure of fish populations and the boundaries of stock units. Here, the potential effects of surface current on a red mullet population in the Central Mediterranean were simulated using a physical oceanographic model. Red mullet larvae were represented as Lagrangian drifters released in known spawning areas of the Strait of Sicily (SoS), which represents one of the most productive demersal fishing‐grounds of the Mediterranean. To consider the effect of inter‐annual variability of oceanographic patterns, numerical simulations were performed for the spawning seasons from 1999 to 2012. The main goal was to explore connectivity between population subunits, in terms of spawning and nursery areas, inhabiting the northern (Sicilian‐Maltese) and southern (African) continental shelves of the SoS. The numerical simulations revealed a certain degree of connectivity between the Sicilian–Maltese and the African sides of the SoS. Connectivity is present in both directions, but it is stronger from the Sicilian–Maltese spawning areas to the African nurseries owing to the marine circulation features of the region. However, because the majority of the larvae are transported to areas unsuitable for settlement or outside the SoS, the dispersal process is characterized by a strong loss of potential settlers born in the spawning areas. These results are in agreement with the low genetic heterogeneity reported for this species in the Mediterranean Sea and support the existence of a metapopulation structure of red mullet in the SoS and the adjacent areas.     

Population structure of bigeye tuna (Thunnus obesus) in the Indian Ocean inferred from mitochondrial DNA

Population structure of bigeye tuna (Thunnus obesus) in the Indian Ocean, Western Pacific Ocean and Eastern Atlantic Ocean were investigated using mitochondrial (mt) DNA sequence data. A total of 380 specimens were sampled from four regions in the Indian Ocean (Cocos Islands, Southeastern Indian Ocean, Southwestern Indian Ocean and Seychelles), and one region each from the Atlantic (Guinea) and the Western Pacific Oceans, respectively. The reconstructed neighbor-joining phylogeny based on the first hypervariable region (HVR-1) of the mitochondrial control region sequence data showed that haplotypes from the Indian and the Western Pacific Oceans could be grouped into two clades (Clades I and III), whereas in the Atlantic Ocean, two divergent clades (Clades I and II) coexisted. A single stock of bigeye tuna in the Indian Ocean was supported by hierarchical AMOVA tests and pairwise Φ_ST analyses. Clade I was the dominant population in the Indian and the Western Pacific Oceans which consisted of more than 96% of the specimens and Clade II was a specific group exclusively restricted to the Atlantic Ocean which made up 77% of its specimens. A new minor Clade, Clade III was discovered in the Indian and the Western Pacific Ocean. Overall, these analyses indicated that bigeye tuna of the Indian Ocean constituted a single panmictic population.     

欧洲鳗鲡血清免疫球蛋白纯化及其结构分析

应用亲和层析技术提纯欧洲鳗鲡免疫球蛋白（Ig）,并对欧鳗Ig的结构和抗原性进行分析。层析结果表明：Ig蛋白呈现一个锐形曲线,蛋白峰与抗原活性峰高度重叠。SDSPAGE分析表明：欧鳗Ig重链分子量为68 kD,轻链有3条,分子量分别为21 kD、23 kD和26 kD。凝胶电泳结果显示：在非变性非还原条件下,欧鳗Ig有790 kD和350 kD 2条蛋白带,在变性非还原条件下有790 kD、593 kD和350 kD 3条蛋白带。Western-blotting试验证实：兔抗欧鳗Ig能识别欧鳗Ig的多种不同聚合体和Ig的重链,但不能识别Ig的轻链。结论：欧鳗Ig在自然条件下可能以四聚体和二聚体的形式存在,这与其它硬骨鱼的Ig形式有差异。欧鳗Ig链间二硫键不健全,在SDS作用下可解聚产生多种不同分子量的聚合体,首次揭示欧鳗Ig的轻链有3种异型。     

刺参(Apostichopus japonicus)重要经济性状相关SNP标记的验证分析

本研究在前期构建的刺参(Apostichopus japonicus)高密度遗传连锁图谱和QTL分析的基础上,筛选出26个与体长、体重、体宽、棘刺总数、抗病力相关的SNP位点,设计出可用于HRM检测的SNP扩增引物13对。在扩大群体中利用HRM小片段法对这13个刺参重要经济性状相关的候选SNP位点进行分型和多态性检测,并结合扩大群体的相关性状数据进行了QTL位点验证。多态性结果显示,13个位点中有3个单态性位点,其余10个多态性位点中有3个位点为低等位多态性,7个位点为中等位多态性。10个多态性位点的最小等位基因频率(MAF)介于0.016(SNP113)~ 0.332(SNP160)之间,平均值为0.173;各位点的观测杂合度(Ho)介于0.031(SNP113)~0.818(SNP9)之间,平均值为0.433;期望杂合度(He)介于0.031(SNP113)~0.834(SNP9)之间,平均值为0.402;多态信息含量(PIC)介于0.030(SNP113)~0.393(SNP160)之间,平均为0.248,有6个位点偏离Hardy- Weinberg平衡。QTL验证结果表明,SNP40和SNP160位点为与生长(体长、体重、体宽)相关的位点,各位点的优势基因型分别为SNP40(CC)和SNP160(AA);SNP88、SNP112和SNP126这3个位点为与抗病力相关的位点,各位点的优势基因型为SNP88(CC)、SNP112(AA)和SNP126(TT)。基于这5个位点构建生长和抗病二倍型,发现二倍型K1(CC AA TT)抗病力最强,S1(CC AA)、S3(CC AC)在生长方面优势显著,相关研究结果可为分子标记辅助育种在生产中应用提供基础数据。     

银鲳形态特征与DNA条形码研究

鲳属鱼类广泛分布于中国沿海,为重要经济鱼种,鲳属鱼类因外部形态存在较大的相似性,分类一直存在分歧。本研究于2010年10月—2012年9月采集科威特(科威特北部海域)、巴基斯坦(松米亚尼湾、奥尔马拉和伯斯尼)、北部湾和台湾近海的银鲳样品,对其形态特征进行重新描述,并对其DNA条形码开展了研究。银鲳的主要形态特征为背鳍Ⅶ-Ⅷ-39～43;胸鳍21～29;臀鳍Ⅴ-Ⅵ-35～41;尾鳍26～28。鳃耙细弱、稀疏,2～3 8～9=10～12。头部后上方侧线管的横枕管丛和背分支丛后缘呈浅弧形,腹分支丛较背分支丛略长,向后延伸未达背鳍起点,呈峨眉状。脊椎骨数37～38。结合GenBank中所有拉丁学名为Pampus argenteus的COⅠ基因进行同源序列比较发现,所有个体单倍型明显分为4个组群,而从氨基酸遗传差异和组群间遗传距离可以看出,4个组群应为不同的有效种;GenBank中只有FJ384702与本研究序列结果相近。本研究描述了银鲳形态特征,并给出其正确的COⅠ基因DNA条形码序列,为深入开展鲳属鱼类的分类研究奠定了基础。     

鲤胰蛋白酶原基因的电子克隆及生物信息学分析

为深入研究胰蛋白酶在鱼类中的生理功能和作用机制,利用生物信息学的方法,成功获得了鲤3种胰凝乳蛋白酶原cDNA序列(ccTRP1、ccTRP2和ccTRP3)并对其进行了序列分析。结果表明,三者均含有一个长度为729bp的开放阅读框(open reading frame,ORF),编码由242个氨基酸组成的胰蛋白酶原,其中包括15个氨基酸组成的信号肽和5个氨基酸(LDDDK)组成的激活肽。总平均亲水性GRAVY(grand average of hydropathicity)分析表明,三者均是亲水性蛋白。氨基酸比对结果显示,三者具备胰蛋白酶原的保守结构特征,如含有催化三联体氨基酸(His-57、Asp-102和Ser-195),12个半胱氨酸,位于底物结合口袋底部Asp-189和口袋开口处的Gly-216、Gly-226等。同时,鲤3种胰蛋白酶之间具有90%以上的同源性。进化树结果显示,鲤3种胰蛋白酶均属于Group I(阴离子型胰蛋白酶),且三者的进化距离不一致。     

Age determination and growth of juveniles of the European hake,Merluccius merluccius (L., 1758), in the northern Tyrrhenian Sea (NW Mediterranean)

The aim of the present study was to provide an estimation of growth of juvenile European hake, Merluccius merluccius (L., 1758) (OSTEICHTHYES; MERLUCCIIDAE), by means of the analysis of otolith daily increments. Hake specimens were collected during trawl surveys carried out in the northern Tyrrhenian Sea (NW Mediterranean). The sagittae were removed from hakes ≤20 cm total length. Left otoliths were ground and polished to obtain thin frontal sections. Otolith microstructure was analysed under a compound green light-polarising microscope. A power curve with intercept was fitted to the length-age data to describe the growth of M. merluccius. According to the growth curve, a mean length of 18 cm was reached at the end of the first year of life. The validation of the otolith increment periodicity was performed by means of two indirect methods.     

Variability in the composition of lupin (Lupinus angustifolius) meals influences their digestible nutrient and energy value when fed to rainbow trout (Oncorhynchus mykiss)

Over a series of seven separate experiments 76 different lupin (Lupinus angustifolius) meals were assessed for their digestible dry matter, protein, amino acid and energy characteristics when fed to rainbow trout. Two reference diets (a common basal diet and a reference lupin meal) were also included in each experiment. Minimal variance in the digestibility parameters of both reference diets was observed among the experiments ensuring that there was a high degree of robustness in the across-experiment evaluations. Using simple and multiple-regression techniques, principal diet and ingredient composition factors affecting diet and ingredient digestibilities and ingredient digestible values were explored within the dataset. Using simple linear regression, it was shown that nitrogen digestibility of the lupin meals was negatively influenced by ingredient lignin content, but positively affected ingredient protein (N × 6.25) content. The energy digestibility of the lupin meals was positively affected by a range of compositional features including protein, sum of amino acids and negatively affected by carbohydrate content. The digestible nutrient and energy content of the meals reflected the combined effects of both ingredient digestibilities and ingredient composition. The digestible nitrogen content of the lupin meals was positively affected by protein (N × 6.25), sum of amino acids and energy content, but was negatively affected by lignin and carbohydrate content. The digestible sum of amino acids was also positively affected by protein, sum of amino acids, but only negatively affected by carbohydrate content, not lignin content. The digestible energy content of the lupin meals was also positively affected by protein, sum of amino acids and their own energy density, but only negatively affected by carbohydrate content. Multiple linear regression modelling supported that together ingredient protein and lignin content were the strongest predictors of digestible protein value, explaining close to 60% of the variability in this parameter. Discrete reassessment of these relationships using non-linear analysis methods provided a stronger interpretation of the ingredient composition effects. In recognition of this, a functional model including terms for ingredient protein and lignin content on the digestible protein value was defined. This study demonstrates that within one raw material type that not only does significant variability in the digestible value of the raw materials exist, but that it is possible to identify compositional features of that raw material that are intrinsically influencing their own digestible value.     

Spatial and temporal mitochondrial DNA genetic homogeneity of dolphinfish populations (Coryphaena hippurus) in the eastern central Pacific

Dolphinfish (Coryphaena hippurus) samples were collected over four consecutive years from four locations in the eastern central Pacific to evaluate the genetic variation in a 751 bp segment of the mitochondrial NADH subunit 1 (ND1) to test for the presence of genetic population structure. Sequence analyses revealed no significant differences among collections from the same location in the different years sampled nor between locations. Mismatch distributions, estimations of population expansion parameters, and neutrality tests revealed significant fluctuations in population size in coincidence with past glacial and interglacial periods during the late Pleistocene. The low levels of nucleotide diversities and shallow coalescence of mtDNA genealogies observed were coincident with the estimated demographic parameters and neutrality tests, in suggesting the presence of important past population size fluctuations or range expansion. The prevention of the accumulation of deep lineages independently on how it was originated, probably delayed the emergence of a population divergence process which might account for the lack of genetic differences detected.     

Assessing the green sea urchin (Strongylocentrotus drobachiensis) stock in Maine, USA

The green sea urchin (Strongylocentrotus drobachiensis) fishery is of great importance to Maine’s economy. The fishery took off in the late 1980s as a result of expanding export markets, but has experienced substantial decline in landings since 1992 because of large decreases in urchin stock abundance. Fishery-independent surveys have not been conducted, and no formal stock assessment has been done prior to this study. Using the data collected from the fishery and urchin life history parameters derived from scientific studies, we conducted a formal stock assessment for the urchin stock. A stochastic observation-error length-structured model is used to describe the dynamics of the sea urchin population. A robust Bayesian approach is used for estimating fishery parameters because of concerns of possible outliers in fisheries data and mis-specification of priors. This study shows that the current stock is only 10% of the virgin stock biomass and that the exploitation rate is close to 40% suggesting that a large reduction in exploitation rate is necessary.     

Population age and sex structure of Aphanius fasciatus Nardo, 1827 (Pisces: Cyprinodontidae) in the Mesolongi and Etolikon lagoons (W. Greece)

The population structure of Aphanius fasciatus in the Mesolongi and Etolikon lagoonal system was studied, using 5794 fish. Significant differences were observed in the number of individuals of each sex, the age and size composition and survival. The overall males to females sex ratio was 1:2.44, although there was seasonal variation. During the reproductive period the percentage of males in the population decreased significantly, while after reproduction and during recruitment they increased. The females in each age class were larger than the males (40.33 mm and 36.72 mean total length for females and males, respectively). The survival rate of females was greater than males (0.73 for females and 0.60 for males). The strategy of this species is to invest in female individuals.     

栉孔扇贝、虾夷扇贝及其杂交子代的MSAP分析

运用甲基化敏感扩增多态性(methylation-sensitive amplification polymorphism,MSAP)技术对栉孔扇贝(♀)、虾夷扇贝(♂)及其杂交子一代、子二代基因组DNA胞嘧啶甲基化水平进行了研究,并分析了DNA甲基化与各性状的相关性及其与杂种优势的关系。结果表明,(1)DNA甲基化率与壳宽、总重等表型值呈正相关的关系,而与壳长、壳高、软体重和闭壳肌重4个性状表型值呈负相关的关系,其中闭壳肌重与甲基化率的相关性达到极显著水平(P<0.01);(2)虾夷扇贝、栉孔扇贝、F1代、F2代的总甲基化率分别为32.79%、24.13%、19.98%、20.18%,杂交种F1代的甲基化水平低于双亲,是两种扇贝杂交的结果;F1代的甲基化模式经过了重新调整,其变化相对其亲本主要有4种类型:甲基化水平相同、去甲基化、超甲基化、次甲基化,且去甲基化位点多于超甲基化位点。结果证实杂种优势的产生与杂交种F1代基因组DNA甲基化模式的改变和重新调整有关,丰富了杂种优势机理研究内容。     

三疣梭子蟹EcR基因的克隆及表达分析

为研究蜕皮激素受体(EcR)在甲壳动物生长和生殖过程中的作用,采用反转录PCR(RT-PCR)和cDNA 末端快速扩增(RACE)技术,克隆了三疣梭子蟹蜕皮激素受体 (PtEcR)基因全长cDNA序列(GenBank登录号:KC354381),运用实时荧光定量PCR(qRT-PCR)方法,分析该基因在不同组织、蜕皮时期和二次卵巢发育阶段的表达特 征。结果表明,PtEcR cDNA全长2 231 bp,包含1 269 bp ORF,编码422个氨基酸;推导的PtEcR氨基酸序列与已公布的其他甲壳动物EcR进行比对,发现一致性 达67%～97%;系统进化树分析PtEcR与其它甲壳动物EcR聚为一支,而昆虫EcR聚为另一支。PtEcR在检测的三疣梭子蟹10个组织中均有表达,其中在Y-器(YO)表达量最高。在蜕皮周期中,自蜕皮后期至蜕皮前期D2亚期PtEcR在YO中的表达量一直较低;至D3亚期和D4亚期,PtEcR表达量显著升高,这与血 淋巴中20-羟基蜕皮酮(20E)浓度在D3/D4亚期显著升高相协同,表明PtEcR在三疣梭子蟹蜕皮过程中起着重要的作用。二次卵巢发育阶段,PtEcR在YO和肝胰 腺(Hp)中的表达量自Ⅱ期逐渐升高至Ⅳ期达到最高;卵巢(Ov)中,则在Ⅰ、Ⅲ期较低,Ⅱ、Ⅳ期较高,表明PtEcR可能参与卵巢发育和卵黄发生。     

尼罗罗非鱼微卫星标记与主要生长性状的相关性分析

为了筛选到与尼罗罗非鱼生长相关的分子标记,并对这些标记进行准确性鉴定,运用65个微卫星标记对鹭业和番禺2个尼罗罗非鱼群体进行了PCR扩增,再利用SPSS软件一般线性模型(GLM)对这些微卫星位点与尼罗罗非鱼体重等主要生长性状进行了标记性状连锁关联分析。结果表明,鹭业群体中有8个微卫星标记(UNH130,UNH183,UNH911,GM558,UNH211,UNH176,UNH914和UNH974)与主要生长性状显著或极显著相关(P<0.05或P<0.01),其中有2个微卫星标记(UNH914和UNH974)与番禺群体的主要生长性状显著或极显著相关(P<0.05或P<0.01),1个微卫星标记(UNH176)只与体重显著相关(P<0.05)。通过对与生长性状相关标记的基因型和表型值进行多重比较,得到了对体重、体长和体高3种性状有利的基因型或等位基因。发现了对罗非鱼生长性状有显著效应的微卫星位点,为开展罗非鱼的分子标记辅助育种提供了有价值的遗传标记。     

日本沼虾五群体形态性状对体质量的通径分析

为筛选出影响日本沼虾体质量的主要形态性状,以便确定人工选育的理想测定指标,以太湖、鄱阳湖、白洋淀、微山湖及淀山湖的野生日本沼虾为研究对象,随机选取各群体90尾虾测定19个形态指标,采用简单相关分析和通径分析等多元回归分析方法分析各群体对体质量作用较为突出的形态性状,并进行聚类分析。通径分析结果显示,太湖群体体长、头胸甲宽、第二步足长、头胸甲高、尾扇长对体质量的通径系数达到极显著,逐步回归建立其对体质量的回归方程、回归截距及相应的回归系数分别为–9.878、0.075、0.314、0.011、0.320、0.222;鄱阳湖群体头胸甲长、尾扇长、尾节宽、头胸甲宽、头胸甲高、尾节高、体长性状对体质量的通径系数达到极显著,回归截距和相应的回归系数分别为–1.618、0.392、–0.280、0.703、0.524、–0.359、0.688、–0.061;白洋淀群体体长、头胸甲宽、第二步足长和尾扇长对体质量的通径系数达到极显著,其回归截距和相应的回归系数分别为–4.796、0.082、0.222、0.007、0.136;微山湖群体头胸甲长、腹节高、第二步足长、腹节宽对体质量的通径系数达到极显著,其回归截距和相应的回归系数分别为–7.644、0.248、0.329、0.025、0.301;淀山湖群体体长、第二步足长、头胸甲宽、尾节宽、腹节宽对体质量的通径系数达到极显著,其回归截距和相应的回归系数为–6.257、0.019、0.018、0.164、0.264、0.162。体长与头胸甲性状在不同群体中都对体质量的作用十分明显。聚类结果显示,地理位置越接近,形态上越相似。研究表明,各个地区被保留的性状与体质量的复相关系数为0.965、0.904、0.902、0.971、0.955,为影响各自群体体质量的主要自变量。     

Catch per unit effort standardization of the eastern Bering Sea walleye pollock (Theragra chalcogramma) fleet

A general linear model (GLM) was used to standardize catch per unit effort (CPUE) data for Alaska walleye pollock (Theragra chalcogramma) from the Bering Sea fleet for the years 1995–1999. Data were stratified temporally by year and season and spatially by area using either Alaska Department of Fish and Game (ADF&G) or National Marine Fisheries Service (NMFS) reporting areas. Four factors were used: vessel identification (ID) number, vessel speed, percentage of pollock by weight in the haul (a measure of targeting), and whether most of the haul took place before or after sunset. At least 29 combinations of main effects, quadratic covariates, and interactions were tested for each year/area/season stratum. GLM models explained from 31 to 48% of the total sums of squares. Vessel identification number was included in all models and explained the most variability. Of the remaining factors, the square of the percentage of pollock in the haul was included in most models, following an F-test to determine parsimony. Analysis of the vessel identification number coefficients indicated that larger vessels tended to have higher CPUEs; and that this relationship differed between dedicated catcher vessels and offshore catcher processors. Coefficient estimates and response surfaces generally indicated increased CPUEs with the percentage of pollock in the haul and showed mixed results with vessel speed. The vessel identification number incorporated most vessel characteristics, leaving vessel speed primarily as a fitting variable with less biological meaning. The year/area/season stratification procedure was found to be necessary due to the unbalanced design, which otherwise would have factor levels with no data in a large combined model. In addition, the stratification procedure reduced the variability in CPUE substantially.