Genetic identification of native populations of fluvial white-spotted charr <Emphasis Type="Italic">Salvelinus leucomaenis</Emphasis> in the upper Tone River drainage

ABSTRACT:   Stocking of exogenous, hatchery-reared white-spotted charr Salvelinus leucomaenis has been conducted throughout much of their range in Honshu Island, Japan, to increase angling opportunities. Although the native charr populations are thought to have declined because of hybridization with introduced fish, their distribution and genetic status have been uncertain. Fine population structures of charr in the upper Tone River drainage were examined using mitochondrial DNA and microsatellite analyses so as to clarify the presence of native populations. One common mtDNA haplotype was detected in all populations in the Ohashi River and Watarase River, and four and one tributary populations were monomorphic for such haplotypes, respectively. However, several haplotypes, considered to have originated from stocked hatchery fish, were observed in the stocked and the remaining populations. Judging from the genetic integrity over a fine geographic scale, the former were considered as indicative of native populations and the latter as admixtures with hatchery fish. Comparisons of genetic diversity, deviations from the Hardy–Weinberg equilibrium, principal component analysis, and relatedness estimations based on microsatellite DNA can also provide evidence for distinguishing native populations from those influenced by hatchery fish.     

Assessing the long-term genetic impact of historical stocking events on contemporary populations of Atlantic salmon, Salmo salar

Abstract  Supplementation of wild fish with non-native or domesticated fish is common practice. However, these stocked and native fish differ both ecologically and genetically and, in the wild, they interact in a multitude of ways, often with negative repercussions for the native population. This study assessed the long-term genetic impact of historical stocking activities on a contemporary population of Atlantic salmon, Salmo salar L. During the 1960s salmon from hatcheries in Scotland and Iceland were transplanted to the River Dart, England. Microsatellite loci were used to assess the current level of population admixture between samples taken from the source location of the stocked fish during the 1960s and contemporary Dart populations. After allowances were made for natural genetic relationships between donor and recipient populations, the long-term impact of the historical stocking events on a catchment scale appears minimal. However, one tributary consistently reflected closer genetic relationships with the donor populations, indicating a possible long-term impact on a localised scale.     

Impacts of hatchery release on genetic structure of rock carp <Emphasis Type="Italic">Procypris rabaudi</Emphasis> in the upper Yangtze River,China

Rock carp Procypris rabaudi is a vulnerable endemic fish in the upper Yangtze River. Hatchery release has been carried out as a major stock enhancement strategy for this species. Ten microsatellite loci were chosen to compare genetic variation between one wild population and two hatchery groups to evaluate the potential impacts of hatchery release on the genetic structure of the wild population. Two different models indicated strong evidence of recent bottlenecks in all groups. The hatchery groups were lower in the mean number of alleles per locus, allelic richness, and allelic diversity compared with the wild population. The 80% membership coefficient indicated that 14% of the wild fish could be assigned as hybrids of wild and hatchery fish. Our results suggested that hatchery release will further reduce the natural genetic diversity in the wild population, change the genetic structure of the rock carp population, and may not benefit restoration of this vulnerable fish species.     

Forecasting the genetic influences of red drum stock enhancement in South Carolina

The South Carolina Department of Natural Resources (SCDNR) began stocking red drum, Sciaenops ocellatus (Linnaeus), in 1989 to augment the abundance of juveniles available for recreational harvest in South Carolina estuaries. While stock enhancement can help supplement wild populations under high fishing pressure, releasing hatchery‐raised fish into the wild also presents the risk of decreased genetic diversity. An individual‐based model (IBM) was developed to forecast the genetic influences of stocking on the wild spawning population to inform responsible stocking strategies. Model results indicated the SCDNR red drum stock enhancement programme should maintain mean contributions of stocked fish no greater than 30% per year class over a 45‐year stocking period, coupled with at least 10 effective breeders in the hatchery replaced annually, to maintain current levels of genetic diversity estimated in the wild population. The IBM is a useful tool for hatchery managers to guide responsible stock enhancement.     

Estimating the origins of adult chum salmon <Emphasis Type="Italic">Oncorhynchus keta</Emphasis> in the Okhotsk and Sea of Japan regions using discriminant analysis of scale characteristics

Linear discriminant analysis (LDA) based on scale patterns was used to develop a methodology of estimating regional origins of chum salmon. Age-4 fish were sampled in 2004–2006 from 12 river stocks of the Okhotsk and Sea of Japan (SJ) regions from Hokkaido to Honshu. The scale radius at the first annulus of each fish was separated into i intervals and the radius of each interval was divided by the number of scale circuli within the interval to quantify scale patterns. The i variables and five other morphometric measurements were used in a stepwise LDA to classify the following regional groups: Hokkaido and Honshu (I), Okhotsk and SJ (II), Okhotsk, Hokkaido SJ and Honshu SJ (III). Percentages of correctly classified fish (hit rates) improved with increased i but tended to be close to asymptotic values in all cases. Hit rates for each river stock in case (I) ranged from 74.3% to 100% (mean 97.2%), estimated by direct maximum likelihood methods using predictor variable sets from the best models for LDAs. Hit rates were lower in cases (II) and (III). This study demonstrated that scale patterns are useful for classifying the origins of chum salmon, at least between Hokkaido and Honshu.     

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.     

Genetic effects of introduced hatchery stocks on indigenous brown trout (Salmo trutta L.) populations in Spain

Abstract– To assess the levels of gene introgression from cultured to wild brown trout populations, four officially stocked locations and four nonstocked locations were sampled for one to three consecutive years and compared to the hatchery strain used for stocking. Allozyme analysis for 25 loci included those previously described as providing allelic markers distinguishing hatchery stocks and native populations. Different levels of hybridization and introgression with hatchery índividuals were detected in stocked drainages as well as in protected locations. These findings indicate that new policies for stocking and monitoring hatchery fish are needed if gene pools of wild Spanish brown trout populations are to be preserved.     

Genetic diversity and divergence among clam <Emphasis Type="Italic">Cyclina sinensis</Emphasis> populations assessed using amplified fragment length polymorphism

ABSTRACT:   The genetic diversity and population structure of Cyclina sinensis were assessed using amplified fragment length polymorphism (AFLP). Three hundred and fifty-four AFLP loci were analyzed in 160 individuals collected from Lvshun, Lianyungang, Yueqing and Dongxing of coastal China. High levels of genetic diversity were detected, where the percentage of polymorphic loci and average expected heterozygosity ranged 88.4–98.9% and 0.304–0.365, respectively. Analysis of molecular variance showed that variation among populations (24.4%) was highly significant ( P  < 0.001). Accordingly, the global fixation index ( θ _B) averaged over loci was high (0.205). The large genetic differences among populations indicate restricted gene flow, congruent with limited dispersal capability of C. sinensis . The unweighted pair group method with arithmetic mean (UPGMA) tree topology constructed on the basis of Nei's genetic distances between populations showed a clear separation of the northern two populations from the southern two populations, suggesting that gene flow between the northern and southern regions is extremely low. This finding is additionally supported by the separate clustering of the four populations in the results of principal coordinate analysis. The useful information obtained in this study will offer insights to fine-tune conservation and fishery management measures in the future.     

Genetic and morphological divergences between wild and captive‐bred populations of Salmo trutta abanticus

Salmo trutta abanticus is a non‐anadromous trout species native to Lake Abant and Seven Lakes in Turkey. A restocking programme by captive breeding was initiated in 1999 to support S. trutta abanticus population. Reared 2‐year‐old juveniles from randomly caught wild parental individuals in Maçka breeding farm were introduced into Lake Abant. We aimed to compare genetic and morphological divergences between wild‐ and captive‐bred populations using seven microsatellite loci and geometric morphometric measurements. A significant genetic and morphological divergences were detected between all population in F_st and canonical variate analysis based on geometric morphometric with 10 homolog landmark. Eighty‐six microsatellites alleles were recorded across loci. Number of private alleles, observed alleles and observed heterozygosity are statistically significant higher in Maçka captive‐bred population than Lake Abant and Seven Lakes populations. Of 42 tests, three departures from Hardy–Weinberg equilibrium were detected in all populations after Bonferroni correction. Two pairs of loci (Ssa85 – Str73 and Str73‐Str543) in Maçka, one pairs of loci (Ssa85‐Str73) in Abant and two pairs of loci (Ssa85‐Str60 and Str73‐Str543) in Seven Lakes populations show linkage disequilibrium. Population structure analysed with Structure software showed three genetic groups (?K = 3) in our studied populations. Relatedness estimates show higher mean relatedness values (r = 0.220 ± 0.230) for Maçka captive‐breed population than wild populations of Abant Lake and Seven Lakes (r = 0.140 ± 0.210 and r = 0.170 ± 0.200 respectively).     

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.     

Current status of the brown trout (Salmo trutta) populations within eastern Pyrenees genetic refuges

Since the end of the 20th century, some headwaters of rivers in the eastern Pyrenees have been designated as genetic refuges to protect remaining native brown trout (Salmo trutta) diversity. The declaration was based on limited or no evidence of genetic impact from released non‐native Atlantic hatchery fish. Hatchery releases were completely banned into the genetic refuges, but pre‐existing fishing activities were maintained. Specific locations in each refuge have been monitored every 2–3 trout generations to update genetic information to accurately assess the contribution of these reservoirs to the preservation of native brown trout gene pools. This work updates genetic information to year 2014 in three of these locations (in Ter, Freser and Flamisell rivers). Previous studies identified hatchery introgressed populations within refuges and suggested discrepancies between the underlying intention of the genetic refuges and the gene pools detected. Therefore, we also examined genetic divergences among locations inside refuge river segments. Combined information at five microsatellite and the lactate dehydrogenase C (LDH‐C*) loci showed reduced but significant temporal native allele frequency fluctuations in some of the above specific locations that did not modify overall levels of local diversity and river divergences. Bayesian clustering analyses confirmed the presence of differentiated native units within each genetic refuge. Some locations of the Freser River within the genetic refuge area showed high hatchery impact of non‐native fish (over 20%). We discuss additional local actions (releases of native fish, selective removals and fishery reinforcement with sterile individuals) to improve the conservation objective of genetic refuges.     

漠斑牙鲆微卫星标记筛选及美国群体遗传结构分析

采用磁珠富集法筛选适合漠斑牙鲆遗传多样性分析的微卫星分子标记。筛选共获得43条序列,其中完美型26个,占60.5%;非完美型14个,占32.6%;复合型3个,占6.9%。选取其中14对特异性好且扩增效率高的微卫星引物,对采自美国北卡罗来纳州沿海的漠斑牙鲆野生群体和养殖群体进行遗传多样性及遗传结构比较分析。研究结果表明,12对引物的扩增产物具有多态性,其中7个位点为高度多态(PIC>0.5)。两个群体中共检测到90个等位基因。12个多态性微卫星位点在两个群体中的平均观察杂合度(Ho)和期望杂合度(He)分别为0.36和0.57。9个位点在整个群体中呈现出不同程度的偏离遗传平衡(P<0.05),且偏离平衡的位点均表现为杂合子缺失(Fis>0)。野生群体和养殖群体间的遗传距离为0.1115,群体间的遗传分化微弱(Fst=0.0438)。     

A Genetic Assessment of a Red Drum,Sciaenops ocellatus,Stock Enhancement Program

The South Carolina Department of Natural Resources began a stock enhancement research program for red drum, Sciaenops ocellatus, as a possible management strategy for augmenting the availability of juveniles for recreational harvest in South Carolina estuaries. Between 1999 and 2011, approximately 6 million juveniles and 260 million larvae were stocked into the Charleston Harbor (CH) estuary, and proportions of stocked fish were found through standardized sampling as high as 49.6% within a subadult year‐class and up to 12% within the spatially separate spawning population. This study evaluated the genetic influences of stocking on the spawning population, using microsatellite loci, and examined any changes in genetic diversity metrics over the course of the stock enhancement program. Percent contribution of stocked fish among subadult and adult collections was compared against measures of genetic diversity. No statistically significant correlations were found among genetic diversity metrics, suggesting that responsible stocking of red drum as small juveniles has not altered the genetic diversity of adults spawning offshore the CH. Life‐history characteristics likely play a large role in mitigating changes in genetic diversity, despite high contributions of stocked fish in some years, because red drum exhibit a long adult life span and benefit from overlapping generations.     

Population structure and stock identification of chum salmon Oncorhynchus keta from Japan determined by microsatellite DNA variation

Variation at 14 microsatellite loci was surveyed in 26 chum salmon Oncorhynchus keta populations from Japan, one population from West Kamchatka and three populations from North America to determine population structure. Microsatellites were then applied to estimate stock composition of chum salmon in mixed-stock fisheries. The genetic differentiation index (F _st) over all populations and loci was 0.031, with individual locus values ranging from 0.010 to 0.081. Seven regional populations were observed in Japanese chum salmon, with late-run populations from the Pacific Coast of Honshu the most distinct. Japanese populations displayed greater genetic diversity than did those in North America. Transplantation history in some Japanese river populations influenced their present genetic characteristics. Analysis of simulated mixtures from fishery sampling suggested that accurate and precise regional estimates of stock composition should be produced when the microsatellites were used to estimate stock compositions. Stock compositions for a 2005 sample of maturing, migrating chum salmon off the north-west coast of Hokkaido near the border of the Sea of Japan and the Sea of Okhotsk indicated that this region may be a migration corridor for Hokkaido populations from the Sea of Japan coast. Microsatellites have the ability to provide fine-scale resolution of stock composition in Japanese coastal fisheries.     

草鱼野生与选育群体遗传变异微卫星分析

为探究经过2个选育世代后选育群体遗传多样性和遗传结构的变化,实验采用多重PCR技术对4个野生草鱼群体(邗江、九江、石首、吴江)和2个选育群体(F1和F2)进行了微卫星序列遗传变异分析。结果显示,6个草鱼群体遗传多样性水平较高,2个选育群体除了平均等位基因数外,其他遗传多样性参数均小于4个野生群体。哈迪—温伯格平衡(Hardy-Weinberg equilibrium)检测显示,在120个群体—位点组合中有62个位点显著偏离哈迪—温伯格平衡,62个群体—位点组合中只有11个组合其近交系数值为负值,其余的51个组合的Fis均为正值。6个草鱼群体AMOVA分析结果显示,3.75%的变异来自于群体间,96.25%的变异来自于群体内,整体的遗传分化指数值为0.038。进一步分析各个群体间Fst,只有石首群体与F1、F2群体之间的Fst大于0.05,处于中等分化,其余群体间分化程度较低,且F2群体与4个野生群体之间Fst比F1群体与4个野生群体之间的Fst大。奈氏标准遗传距离分析结果显示,2个选育群体与野生群体之间的遗传距离大于野生群体之间的遗传距离。基于Dn建立的UPGMA系统发育树得出了相同的结果,即2个选育群体与野生群体之间的亲缘关系比4个野生群体之间的亲缘关系要远。研究表明,经过2个世代选育后,相比4个野生群体,2个选育群体遗传多样性虽有部分下降,但仍处于较高的水平,2个选育群体的遗传结构已发生变化,但其遗传分化程度尚不明显。本研究结果为制定出更加完善有效的选育方案提供了重要参考。     

Weight-based virtual population analysis of Pacific cod Gadus macrocephalus off the Pacific coast of southern Hokkaido, Japan

ABSTRACT:   Age-based population assessment is widely used, but there are cases where information on age or even body length of landed fish is difficult to collect. In the present study, the biomass and fishing mortality of the southern Hokkaido stock of Pacific cod Gadus macrocephalus was estimated directly from body weight composition, using weight-based virtual population analysis, from 1994 to 2000. The estimated biomass over 1 kg body weight was 5607 t in 1994 and increased to 7908 t in 2000. The increase was explained by an increase in recruitment.     

三疣梭子蟹莱州湾、舟山野生个体定向交配产生F2代家系的AFLP分析

以三疣梭子蟹莱州湾、舟山野生群体杂交（莱州湾♀×舟山♂）产生F2代家系63个个体及F1代亲本为实验群体,采用AFLP分子标记对其进行遗传分析。35对选择性引物共扩增出1742个位点,其中分离位点为417个,不分离位点为1325个,多态位点比例为23．9％。在分离位点中,符合1：1孟德尔分离比例的位点为226个,占总分离位点数的54．2％;偏离1：1孟德尔分离比例的位点为31个,占总分离位点数7．4％。符合3：1孟德尔分离比例的位点为128个,占总分离位点数的30．7％;偏离3：1孟德尔分离比例的位点为32个,占总分离位点数的7．7％。家系内基因多样性指数为0．130,Shannon指数为0．193。遗传距离分析显示,子代个体与母本Nei’s遗传距离介于0．064～0．111之间,与父本Nei’s遗传距离介于0．065～0．107之间。其中,63号个体与48号个体分别与父、母本亲缘关系最远。本实验中,偏分离位点比例属正常范围,杂交F2代家系遗传多样性偏低。本研究结果为三疣梭子蟹野生群体及家系遗传多样性分析,遗传连锁图谱构建等方面提供一定的技术支持。     

Comprehensive assessment of the genetic diversity and population structure of cultured populations of golden pompano, <Emphasis Type="Italic">Trachinotus ovatus</Emphasis> (Linnaeus, 1758), by microsatellites

Golden pompano, Trachinotus ovatus, belongs to the family Carangidae. Within one decade, this species has rapidly become one of the most important cultured marine fish species in South China. However, the lack of a comprehensive genetic diversity assessment hinders the conservation of natural resources and management of cultured populations. Thus, we sampled one wild population and six cultured populations of golden pompano, which represented the whole cultured population, to assess the genetic diversity and population structure. The level of genetic diversity was low compared with those of other cultured fish, as the values of allelic richness, number of effective alleles and expected heterozygosity in the combined whole sample were 3.709, 2.592, and 0.591, respectively. These populations were little differentiated (Fst?=?0.02091, p value?=?0.00), and the whole sample did not show an explicit population structure at the individual level. The effective population size in each cultured population was small and in the whole sample was acceptable for a closed selection system. The pedigree reconstruction showed no evidence of artificial disturbance in mating. This general survey of cultured golden pompano populations showed the common characteristics of domestication with wild inputs. However, the low level of and potential decrease in genetic diversity should receive close attention in future breeding programs. In addition, we recommend wide surveys of natural resources and the establishment of closed breeding systems to increase genetic gain.     

Benefits of repeated stocking with adult,hatchery‐reared brown trout,Salmo trutta,to recreational fisheries?

Abstract  Recaptures of adult, hatchery-reared, brown trout, Salmo trutta L., and fishing time from anglers were used to evaluate the benefits of stocking programmes with repeated releases of adult brown trout. The recapture rate varied between 17% and 29%. The time between stocking and capture (referred to as residence time) varied between 1 and 160 days (median 3–49 days). Between 67% and 84% of trout caught in the river were recently released fish. Fishing effort increased after stocking, thereby increasing the impact of angling on wild stocks. Stocking with adult brown trout decreases the impact of angling on wild trout only if the time spent fishing by all anglers is kept stable. Furthermore, because of the short residence time of stocked trout, long-term impacts through competition for space and food, or genetic impact through introgression, are limited.     

Estimates of Linkage Disequilibrium and Effective Population Size in Wild and Selected Populations of the Pacific Oyster Using Single‐nucleotide Polymorphism Markers

The level and extent of linkage disequilibrium (LD) and effective population size (Ne) were studied in three selected lines and a wild population of Pacific oyster, Crassostrea gigas, using 61 single‐nucleotide polymorphisms. Significant differences were detected in the average r² between the selected lines and wild population for both syntenic and nonsyntenic loci with LD beyond population‐specific critical values (P<0.05). Moreover, the proportions of syntenic and nonsyntenic loci with the expected LD level in the wild population were lower than that in the selected lines. Taken together, the LD level of the selected lines was higher than that of the wild population. The extent of LD analysis showed that a short range of LD (0–0.23 cM) was detected in the four populations, and the decay distance was lower in the wild population than in the selected lines. Ne values ranged from 47.6 to 58.5 in the selected lines and ranged from 527.9 to 709.6 with infinite upper limits in the wild population. Further variance analysis of LD demonstrated that genetic drift and epistatic selection might account for the increased LD levels in selected lines. The LD information will be valuable for further association study and marker‐assisted selection in oysters.