Genetic drift in a hatchery and the maintenance of genetic diversity in hatchery-wild systems

ABSTRACT:   Loss of within-population genetic diversity by genetic drift is related to stocking. In order to reduce it, selective use of wild-born individuals for hatchery broodstock is proposed. Its effectiveness is evaluated by the analytical method and numerical simulation. Results indicated that it is effective, especially when the ratio of released hatchery-produced individuals is high in the natural population. Loss of within-population genetic diversity by a few other strategies of broodstock preparation is also analyzed by numerical simulation and the effectiveness of these is also discussed.     

Economic,ecological and genetic impacts of marine stock enhancement and sea ranching: A systematic review

Hatchery release is one of the most popular management tools in fisheries, forestry and wild life management, while its negative impacts on wild populations are a global concern. Research and monitoring of its impacts are generally lacking, and the usefulness of hatchery release for fisheries and conservation objectives is unclear. Here, I evaluated positive and negative impacts of worldwide marine stock enhancement and sea ranching programmes in a systematic review associated with meta‐analyses with the goal of reducing bias of the review. Vast numbers of individuals of more than 180 species are released into the wild each year, but most studies are at experimental stages to assess its potential, and empirical studies are sparse for evaluating the impact on fishery production. Most cases are economically unprofitable except for a few successful cases or unevaluated. The effects of releasing juveniles can be dwarfed by the magnitude of natural recruitment when the spawning stock produces much larger recruitment than released juveniles. Density‐dependent growth caused by competition of food can be substantial, and growth rates of hatchery and wild fish and other competitive species can simultaneously be reduced when stocking exceeded the carrying capacity. Relative reproductive success can vary depending on the species, seed quality and environmental factors. Empirical studies show evidence of substantial gene flow from hatcheries, but fitness reduction in stocked populations has not been reported. The results represent the current state of worldwide marine stock enhancement and sea ranching activity and provide key information for growing fields of artificial propagation and conservation.     

Genetic diversity of red sea bream Pagrus major in western Japan in relation to stock enhancement

SUMMARY: Stock enhancement is used in Japan as a tool to help the replenishment of wild populations of red sea bream Pagrus major . In this study, we analyzed the genetic diversity and composition of wild red sea bream at seven locations around Shikoku Island, South-west Japan, using three microsatellite loci. This analysis was done to test the hypothesis that: (i) red sea bream comprises a single Mendelian population along Japan; and (ii) stock enhancement programs around Shikoku Island are causing genetic differentiation among wild stocks. The results indicated that some locations from the Shikoku area were not significantly different from the rest of Japan, supporting the hypothesis of a single Mendelian population. Significant departures from Hardy–Weinberg equilibrium and significant pairwise F_ST among locations indicated genetic instability within this region. We suggest that the stock enhancement programs made in the region are the possible cause of this genetic instability. A management scheme for the hatcheries involved in the stock enhancement of red sea bream is presented.     

Validity of fluctuating asymmetry as a gauge of genetic stress in ayu stocks

An increasing demand for stocking of hatchery-reared ayu, Plecoglossus altivelis, has aroused concerns about their genetic status which has an effect on their post-stocking performance and the conservation of native biodiversity. Instead of costly analysis, fluctuating asymmetry (FA) was examined to test its suitability as an indirect measure of genetic diversity. Two bilateral traits, pectoral and pelvic fin rays, were targeted, and two wild and four hatchery populations of ayu were sampled for comparison. Frequency of FA in soft-rays was not similar between specimens in both pelvic and pectoral fins. The wild populations did not show FA incidences lower than the hatchery populations, suggesting a considerable degree of environmental stress operating in the wild populations. Comparison between the hatchery populations showed overall increasing FA incidence with the decrease in genetic diversity, although the correlation was not complete in detail. In conclusion, FA can be used as a convenient tool to compare genetic status, but quantified evaluation is rather limited to monitoring changes in the genetic variation within a hatchery population.     

中国明对虾第一代和第六代人工选育群体的遗传结构分析

采用RAPD技术对中国明对虾(Fenneropenaeus chinensis)第一代和第六代人工选育群体的遗传结构及其分化进行了分析。在20个10bp随机引物中筛选出16个引物,共扩增出89条DNA片段,其中多态性片段分别为34和30条,多态位点比例分别为38．2％5和33．71％。对2群体的遗传学参数计算结果表明：2群体间遗传分化指数为0．1408,属中等程度分化;群体间的遗传变异平均为0．197,由此可见,80％的遗传变异来自于群体内,而近20％的变异则是来自于群体间;第六代群体的多态位点比例和遗传多态度均低于第一代群体,这可能与人工定向选育过程中注重经济性状有关。     

The development of size variation in Dover sole,Solea solea and turbot,Scophthalmus maximus: genetic variability between different geographical and among year class farmed strains

Growth and variation in size of turbot and sole larvae originating from different genetic sources were compared at different stocking densities, including genetically based information that might lead to a better knowledge of heterogeneity in cultivated populations. There was no effect of density on growth rate in either species. However, between the two sole batches there was an earlier metamorphosis of faster growing fish from Norway. In sole groups after metamorphosis, variation was stable and therefore no development of size variation was observed. There was no density effect on size variation within turbot batches before, or after metamorphosis. Spreading rate and growth rate were positively correlated in sole larvae indicating that growth of the smaller fish was not equal to the larger ones, but size variation followed a different pattern in turbot. No evidence for either overall significant heterozygosity excess, or deficiency was evidenced in the farmed strains of either species . However, significant differences between farmed populations in terms of genetic variability (θ) were reported, which was rather attributed to within differentiation than between strains. One could safely argue that different strains of Dover sole originated from different genetic sources (factorial analysis). Moreover, when the analysis was extended to individual loci to assess whether specific loci had any consistently larger, or smaller effect on heterozygosity, locus specific significant trends were discerned in turbot. A positive Heterozygosity Fitness (growth rate) Correlation (HFC) suggests that heterozygotes reported enhanced growth rates compared with homozygous ones in flatfish larvae, thus special precautions should be taken into account whenever different genetic structure patterns emerge, because of various flatfish broodstock geographical origin and year class samples.     

Evaluation of the effect of stock enhancement in the coastal waters of Guangdong,China

A total of 14.573 million fish fry and 96.32 million shrimp larvae were released across 31 locations into the coastal waters off Guangdong, China, in 2010. The released fish and shrimp were sampled through a combination of market and fishing log‐book surveys. The combined fishery production reached 362 868 kg. The input–output ratio was 1:5.99 for released fish (over 3 years) and 1:11.01 for released shrimp (over 2 years). The average increase in income was 721 RMB per capita. Approximately 240 thousand fish (after 3 years) and 1.2 million shrimp (after 2 years) survived to sexual maturity and could contribute to the spawning stock. The stockings were approximately one‐seventh of the fish and one‐half of the shrimp stocking carrying capacities, respectively. Based on these results, the intensity of stocking could be increased. Stocking and recapture strategies should be adjusted to align with the optimal stocking carrying capacity determined from this study.     

基于线粒体控制区序列的南海圆舵鲣种群遗传结构分析

利用线粒体控制区(D-loop) 高变区序列作为遗传标记, 分析了中国南海5N～21N 之间7 个圆舵鲣( Auxis rochei) 地理群体的遗传结构特征。201尾样本的D-loop 区序列共检测到185 种单倍型。各个采样点均呈现出很高的单倍型多样性(0.958 2～1.000 0)和较高的核苷酸多样性(0.034 327～0.041 235) 的特征。单倍型邻接关系树未呈现与地理群体对应的谱系结构。分子方差分析和成对遗传分化系数(FST) 显示南海海域圆舵鲣的遗传变异主要来自群体内(98.33%) , 群体间基因交流频繁, 是一个随机交配群。核苷酸不配对分布和中性检验表明南海圆舵鲣在更新世晚期曾经历过种群的快速扩张。结果表明, 南海圆舵鲣具有丰富的遗传多样性水平, 遗传分化不显著, 在渔业上可以作为一个单元来管理。     

象山缢蛏养殖群体和野生群体遗传多样性的比较

于2001年4月，在浙江象山港虾塘和象山外海滩涂分别采集100个缢蛏(Sinonovacula constricta Lamarck)样品，采用聚丙烯酰胺凝胶电泳技术，分析了2个群体各38个样本的EST、ADH、MDH、IDH、ME、LDH、GDH、SOD、SDH、ATP等10种同工酶，分别记录了30、29个基因位点。其中s-MDH-1、SDH、s—ME、ATP-1、ATP-2等5个位点为多态位点。象山野生缢蛏群体的多态位点比例(17．24％)和群体平均杂合度观察值(0．0377)都明显高于养殖群体(16．67％，0．0314)。结果表明，与其他贝类比较缢蛏象山养殖和象山野生群体拥有较低的遗传变异水平，其中象山野生群体比养殖群体遗传变异水平高。     

Pedigree analysis of recaptured fish in the stock enhancement program of spotted halibut Verasper variegatus

ABSTRACT:   Spotted halibut Verasper variegatus hatchery juveniles produced in 2002 were genotyped using three microsatellite DNA markers (msDNA) and then released into natural waters. Subsequently, recaptured individuals were examined using msDNA. In order to evaluate the effectiveness of the stock enhancement program, from the genetic point of view, a pairwise F _ST test was implemented to estimate the genetic divergence between the wild captive broodstock, the hatchery offspring and the recaptured samples. The analysis showed significant differentiation between the broodstock and recaptured samples. Pedigree determination using msDNA was used to calculate the effective population size of the recaptured stock, which was found to be very low ( N _e ≈ 8). Equal family survivability was observed between the two recaptured stocks, but not between the released and recaptured stock. The number of identified families was higher and more equalized in the hatchery offspring compared to the recaptured samples, where the number of families declined. This fact was caused by an unequal family survivability just before or just after release. Separately, the number of contributing parents to the hatchery offspring was lower than the broodstock census number. Consequently, these two facts caused the genetic divergence of the recaptured stock from the broodstock.     

基于线粒体控制区的中国南海海域卵形鲳鲹遗传多样性

为探讨中国南海重要经济鱼类卵形鲳鲹(Trachinotus ovatus)的遗传多样性,测定了广东闸坡、乌石、安铺和广西东兴以及海南新盈等5个地理群体97 ind样品的线粒体控制区5'端359 bp序列,发现47个变异位点,32个单倍型,总体呈现高单倍型多样性(h=0.951)和高核苷酸(π=0.020 9)多样性的特点。在邻接树和单倍型网络图中出现2个分化显著但不存在明显地理聚群的分支,推测二者的分化时间约为60~18万年前(中更新世),可能是中更新世冰期海平面下降形成边缘海而导致隔离,间冰期海平面上升后出现二次接触。不同地理群体间的遗传分化不显著(Fst=-0.022 4~0.045 3),AMOVA分析也显示97%以上的遗传变异来源于群体内个体间。卵形鲳鲹2个谱系及总体的核苷酸错配图呈现多峰,中性检验均为负值不显著(P0.05),表明都未经历过大规模的种群扩张,处于相对稳定的状态。     

中国南海斑节对虾5个地理群体线粒体18S rRNA基因序列比较分析

摘要：本文对中国南海海域5个斑节对虾野生群体（三亚群体（SY）、深圳群体（SZ）、阳江群体（YJ）、湛江群体（ZJ）、北海群体（BH））100个样品的 16SrRNA 序列进行PCR扩增,并对扩增产物进行了测序。用Clustal_X排序软件对测序所得的100个16S rRNA序列进行比对。通过ARLEQUIN软件对所得100个mtDNA16S rRNA序列进行比较分析,共检测出28个变异位点,19种单倍型。三亚、深圳、阳江、湛江以及北海等5个野生群体的核苷酸多样性（π）依次分别为0.00435,0.00586,0.01050,0.01081,0.01168。三亚、深圳、阳江、湛江以及北海等5个野生群体的单倍型多样性（H）依次分别为0.6895, 0.5211, 0.5737, 0.6000, 0.7211。对5个野生群体的16S rRNA序列进行FST分析,结果表明湛江、北海群体分别与三亚、深圳两个群体有显著的遗传差异,其余群体之间的遗传差异不显著。对5个群体进行AMOVA分析,结果表明5个群体间存在显著性遗传差异。对5个群体构建分子系统树,结果表明：三亚和深圳群体之间的亲缘关系最近;北海、湛江群体与三亚、深圳群体的亲缘关系很远。以上结果表明,中国南海海域5个斑节对虾野生群体可以为斑节对虾的选择育种提供两个基础群体：一个是三亚、深圳野生原种基础群体;另一个是湛江和北海野生原种基础群体。     

大泷六线鱼放流群体与野生群体遗传多样性比较

基于线粒体DNA控制区高变区部分序列和4对微卫星标记,对大泷六线鱼放流群体及自然海域群体的遗传多样性与遗传差异进行了比较分析。线粒体DNA控制区序列分析的结果显示,413尾个体共检测到单倍型117种,其中仅Hap₃、 Hap₇和Hap₁7为共享单倍型,占总单倍型数目的 2.5%;放流、野生群体特有单倍型分别为20种和66种,分别占总单倍型数的17.09%和56.41%,放流群体特有单倍型数明显低于野生群体;放流群体和野生群体核苷酸多样性分别为0.005 1～0.006 7和0.005 8～0.007 5,单倍型多样性分别为0.856 7～0.949 9和0.883 1～0.954 9,遗传多样性均较高。微卫星标记分析结果显示,放流、野生群体平均等位基因数(Na)分别为13～44和13～27,平均多态信息含量为0.885 6和0.874 0,均具较高的遗传多态性;群体遗传结构分析结果表明,放流、野生群体间遗传分化水平较低。研究表明,山东近海大泷六线鱼放流群体与野生群体均具有较丰富的遗传多样性,且遗传结构未存在显著的群体分化...     

中国南海康氏马鲛线粒体COI序列遗传变异分析

在测定的采自广东饶平、阳江和广西东兴海域的62尾康氏马鲛( Scomberomorus commerson) 线粒体COI基因711 bp序列中,共检测到26个变异位点,18个单倍型,总体呈现出高单倍型多样性( Hd=0.8080.040)和低核苷酸多样性(=0.004 00.000 6)的特点。邻接树上出现了3个分支, 分支间Fst为0.811～0.833且P0.001,Nm为0.1～0.117;AMOVA分析显示分支间遗传变异占82.61%。表明3个分支间分化程度高,推测分歧时间为(89～22.67)万年前中更新世时期,可能原因是受到更新世冰期和间冰期交替的影响。但分支内与分支间都有不同地理来源的个体,没有出现明显的地理聚群;不同地理群体间Fst为-0.027～0.066,Nm均大于4或小于0;群体内个体间变异为96.34%。均表明群体间基因交流频繁,遗传分化程度并不高。3个分支中Clade A分支经历过种群快速扩张事件,可能是末次冰期期间康氏马鲛进入外海并受洋流及生存空间改变的影响。     

Monitoring of the genetic variability of the hatchery and recaptured fish in the stock enhancement program of the rare species barfin flounder <Emphasis Type="Italic">Verasper moseri</Emphasis>

ABSTRACT:   In relation to the stock enhancement program for barfin flounder, hatchery juveniles produced in 2001 were genotyped using microsatellite DNA markers (msDNA) and then released to natural waters. Subsequently, recaptured individuals, designated as 'tentative recaptured', were examined using msDNA. In order to evaluate the effectiveness of the stock enhancement program, pairwise F _ST and genic differentiation tests were used to estimate the genetic divergence between the wild samples, the hatchery broodstock, and the tentative recaptured samples. Analysis showed significant differentiation among these three groups. Pedigree determination by msDNA was used to establish the origin of the tentative recaptured individuals, in order to elucidate whether they were hatchery produced, 'real recaptured', or wild specimens. Wild individuals were not found. The effective population size of the real recaptured stock was very low ( N _e = 16.6). Equal family survivability was observed between the released and real recaptured stocks, indicating that the genetic variability of the released stock was maintained in the natural environment. Future broodstock management, breeding designs, and family contribution equalization of the offspring to be released will be required in this rare species to avoid unintended genetic differentiation between the wild population and the hatchery broodstock.     

基于线粒体控制区序列的三疣梭子蟹增殖放流亲蟹遗传多样性研究

为研究山东沿海三疣梭子蟹增殖放流亲蟹群体的遗传多样性状况,实验采用536 bp的线粒体DNA控制区片段作为分子标记,对4个亲蟹群体的遗传多样性和遗传结构进行了分析。结果显示,301个三疣梭子蟹个体共检测到155个单倍型,4个群体的单倍型多样度为0.972 3~0.993 0,核苷酸多样度为0.021 2~0.023 6,表现出丰富的遗传多样性。AMOVA分析和Fst分析结果均显示,4个三疣梭子蟹亲蟹群体间遗传分化微弱,未形成明显的遗传结构,NJ系统树中未出现与各群体相对应的的谱系分支。研究表明,4个增殖放流亲蟹群体的遗传多样性丰富,且其遗传结构与放流海域的野生群体间没有明显分化,种质资源质量较好。此外,群体历史动态分析显示,渤海南部和黄海北部的三疣梭子蟹历史上曾经历过群体扩张事件。     

Interannual differences in larval haddock survival: hypothesis testing with a 3D biophysical model of Georges Bank

The ultimate goal of early life studies of fish over the past century has been to better understand recruitment variability. As evident in the Georges Bank haddock (Melanogrammus aeglefinus) population, there is a strong relationship between recruitment success and processes occurring during the planktonic larval stage. This research sought new insights into the mechanisms controlling the recruitment process in fish populations using biological–physical modeling methods together with laboratory and field data sets. We created the first three‐dimensional model of larval haddock on Georges Bank by coupling models of hydrodynamics, lower trophic levels, a single copepod species, and larval haddock. Interactions between feeding, metabolism, growth, vertical behavior, advection, predation, and the physical environment of larval haddock were quantitatively investigated using the coupled models. Particularly, the model was used to compare survival over the larval period and the sources of mortality in 1995 and 1998, 2 years of disparate haddock recruitment. The results of model simulations suggest that the increased egg hatching rates and higher food availability, which reduced starvation and predation, in 1998 contributed to its larger year‐class. Additionally, the inclusion of temperature‐dependent predation rates produced model results that better agreed with observations of the mean hatch date of survivors. The results from this biophysical model imply that food limitation and its related losses to starvation and predation, especially from hatch to 7 mm, may be responsible for interannual variability in recruitment and larval survival outside of the years studied.     

Early detection of reproduction deficits and the compensatory potential of enhancement stocking for vendace,Coregonus albula,fisheries in German lakes

Enhancement stocking is a widespread but rarely evaluated practice in German vendace, Coregonus albula L. fisheries, which is precautionarily carried out to buffer yield fluctuations. However, it is assumed that stocking of larval vendace can elevate year‐class strength only in the presence of substantial reproductive deficits, which so far cannot be detected prior to the spring time period when stocking is conducted by fisheries managers. Simple measures for the early quantification of natural reproduction were tested, and the efficiency of larval enhancement stocking in a lake with strong reproduction deficits was analysed. Analysis in four lakes over 3 years revealed a significant positive correlation between standardised catches of vendace larvae caught with pump‐driven illuminated traps in spring and the abundance of young‐of‐year (YoY) vendace in the following autumn, whereas standardised catches of spawners were insufficient to forecast YoY recruitment. In a lake with low natural vendace reproduction, stocked vendace contributed 73–100% of year‐class strength and fisheries yield. Accordingly, enhancement stocking can efficiently compensate for reproduction deficits, and the simple larvae sampling method may facilitate early detection of these deficits, which would allow fisheries managers to respond accordingly through larvae stocking.     

Microsatellite genetic variation in wild and hatchery populations of the sea cucumber (Apostichopus japonicus Selenka) from northern China

Farming of the sea cucumber Apostichopus japonicus (Selenka) started 20 years ago and is still in rapid expansion in China. In order to assess the genetic status of both wild and cultivated stocks of this species, we used eight microsatellite markers to estimate the level of genetic diversity within five hatchery stocks and two wild populations of A. japonicus, and compared the degree of genetic differentiation between them. High levels of polymorphism were observed over all loci. The mean alleles and expected heterozygosities over the seven stocks were 10.4–12.3 and 0.735–0.783 respectively. The results of the microsatellite survey provide no evidence to show that hatchery practice of the sea cucumber in China to date has significantly affected the genetic variability of the cultured stocks. Significant differentiation was found between most pairs of the hatchery stocks and wild populations (F_st range: 0.008–0.036), and no obvious difference was detected between the wild populations (F_st=0.008). The information on the genetic variation and differentiation obtained in this study can be applied for future genetic monitoring of A. japonicus aquaculture stocks and will be useful for future genetic improvement by selective breeding, and for designing suitable management guidelines for these genetic materials.     

Erosion of the native genetic resources of brown trout in Spain

Abstract– We analyzed the introduction of hatchery-reared trout in the Riutort Creek, a small stream in the eastern Spanish Pyrennees. We used gene correlation matrices between individuals to analyze the fish coancestry in the Riutort Creek samples and in the hatchery stock. Hatchery fish disturbed the single ancestry in the native population of the creek, and were clearly detected with principal coordinate analysis of the gene correlation matrix. The amount of introgression produced by successful introductions was estimated from the principal coordinate analysis projections of the matrix of F_ST values between the putative native Riutort Creek population, the hatchery stock and the introgressed population. In only two years the amount of introgression rose to 10%, indicating that 5% of the native ancestry is lost each year as a result of the stocking program. Based on these results, we review the present understandings on the genetic impact of hatchery fish on indigenous Spanish brown trout populations. The stocking of these populations involves a non-native broodstock widespread through the Spanish hatcheries, but successful stockings appear to be limited to wild populations subjected to occasional releases in protected or unfished areas. Surprisingly, extensive stocking in fished areas result in a more limited genetic impact on the recipient native population.