Genetic differentiation among Atlantic salmon reared in sea‐cages reveals a non‐random distribution of genetic material from a breeding programme to commercial production

Seven samples, each consisting of approximately 50 Atlantic salmon, were collected from five marine farms in Norway. These farms reported to rear fish originating from the same commercial breed; however, all samples followed a unique route of production from breeder to marine farm via egg, fry and smolt producers. A group of farmed escapees (n=50) were also captured. Following genotyping with 18 microsatellite loci, the global F_ST was 0.083, and pair‐wise values were as high as 0.158. Four clusters, with varying degrees of genetic differentiation, were identified among samples from the farms, and the source of the escapees was identified successfully. It is suggested that the genetic differences observed among samples from the farms were created through the process of genetic drift, facilitated by parallel sub‐strains, extensive within‐strain selection and low to moderate numbers of adults contributing to batches of eggs. In conclusion, this study has demonstrated that genetic identification of escaped Atlantic salmon, back to the farm of origin, may be possible even when farms rear fish reported to originate from a single breeder.     

Dispersal of large farmed Atlantic salmon, Salmo salar, from simulated escapes at fish farms in Norway and Scotland

Abstract  Individually tagged farmed Atlantic salmon, Salmo salar L., were released from fish farms in simulated escapes in Scotland ( n  =   678) and Norway ( n  =   597) to compare migratory behaviour and dispersal. Large fish (510–870 mm fork length) were released to simulate the escape of aquaculture growers. Fish were released in spring and all recaptures of tagged fish were reported during summer and autumn of the year of release. Recapture rates were respectively 7.0 and 0.6% of the salmon released in Norway and Scotland, indicating a higher mortality or a lower exploitation or reporting rate for Scottish fish. Recaptures of Norwegian fish were all from Norway and mostly within 150 km of the release site; 64% were taken by anglers in fresh water. By contrast, the three salmon recaptured from the release in Scotland were reported from Norway (Hardangerfjord and Lofoten) and western Sweden (River Göta); two detached tags were found on beaches in Scotland north of the release site. These findings establish the capacity for long distance dispersal among escapees from aquaculture facilities and suggest a net easterly bias in long distance dispersal of salmon escaping from Scottish fish farms.     

Incidence and timing of wild and escaped farmed Atlantic salmon (Salmo salar) in Norwegian rivers inferred from video surveillance monitoring

Run timing of escaped farmed Atlantic salmon Salmo salar vs. wild fish was compared by the use of video camera surveillance in 15 rivers over several years, covering 1600 km of the Norwegian coastline (from 58°N to 69°N). Annual runs of wild salmon varied among rivers from <200 fish to more than 10 000. During the surveillance period that for most rivers extended from late May to early October, larger‐sized salmon (fish ≥ 65 cm) generally entered the rivers earlier than small fish. The percentage of salmon identified as escaped farmed fish ranged from 0.1% to 17% across rivers with an average of 4.3%. Estimates of escapees are, however, assumed to represent minimum values because an unknown number of farmed fish passing the video cameras may have been misclassified as wild fish. By the use of a linear mixed model and generalised additive mixed models, it was found that the relationship between run timing and fish length differed significantly between farmed and wild salmon. While small‐sized farmed and wild fish (<65 cm) entered the river at about the same time, wild large salmon returned on average 1–2 weeks earlier than similarly sized escapees. The proportion of large‐sized farmed escapees also increased until late August and decreased thereafter. In contrast, there was a relatively constant and lower proportion of small‐sized escapees throughout the season. Within the surveillance period, there was no evidence of any exceptionally late runs of fish classified as escaped farmed salmon.     

Survival of Atlantic salmon captured in and released from a commercial trap-net: Potential for selective harvesting of stocked salmon

The major wild Atlantic salmon stocks in the Baltic Sea began to recover in the late 1990s. This recovery has been partly due to strict regulations in the Gulf of Bothnia that effectively prevent salmon fisheries during the peak migration. About half of the migrating salmon, however, are reared fish that could be harvested. We simulated a limited trap-net fishery that selectively harvested reared salmon and released wild fish, and studied the survival and migration of the released salmon. We tagged and released 1970 salmon caught in the trap-nets along the coast in 2001 and 2002. The mean maximum capture and release induced mortality of salmon was 11%, ranging between 4% and 21% in different release groups by year, sea age and number of releases. The cumulative mortality for the total salmon population on their spawning migration in the Gulf of Bothnia was below 5%, and it would not increase considerably after the first capture and release events, provided fishing effort is not excessive and fish are handled properly. Survival of trap-net captured and released Baltic salmon appears high and their migration behavior is not altered due to this handling. Several preconditions, however, should be considered before selective fishing is introduced in the Gulf of Bothnia salmon fishery.     

Population genetic structure of Atlantic salmon,Salmo salar L., in the River Tamar,southwest England

Abstract Population genetic studies can be useful for informing conservation and management. In Atlantic salmon, Salmo salar L., population structuring frequently occurs between river systems, but contrasting patterns occur within rivers, highlighting the need for catchment‐specific studies to inform management. Here, population structure of Atlantic salmon was examined in the River Tamar, United Kingdom, using 12 microsatellite loci. Gene diversity and allelic richness ranged from 0.80 to 0.84 and from 8.96 to 10.24, respectively. Some evidence of genetic structure was found, including significant genetic differentiation between samples in different subcatchments (pairwise θ and tests of genic differentiation), results from assignment tests and a pattern of isolation by distance. Conversely, structure revealed only one population cluster, and an analysis of molecular variance showed no significant variation between subcatchments. Evidence of population bottlenecks depended on the mutation model assumed and is discussed with reference to catchment‐specific studies of stock abundance. Implications for implementing management actions are considered.     

南海北部陆架水域多齿蛇鲻与花斑蛇鲻的年龄与生长

文章利用线粒体细胞色素b (cytochrome b, cytb)基因全序列作为分子标记,分析了中国近海和陆架的花斑蛇鲻(Saurida undosquamis)的遗传结构特征。从8个采样点266尾样本中共检测到142种单倍型,各采样点均表现出很高的单倍型多样性(0.925 1~0.992 9)和较低的核苷酸多样性(0.003 145~0.003 852)。单倍型的中间连接网络图呈现以4个优势共享单倍型为中心的星状发散结构,未发现与地理群体对应的谱系结构。分子方差分析表明花斑蛇鲻的遗传变异绝大部分(99.79%)来自种群内的个体之间,而群体之间几乎没有贡献遗传变异。成对遗传分化系数(F_ST)显示花斑蛇鲻群体间基因交流频繁,不存在明显的遗传差异,是一个随机交配群。中性检验表明种群历史动态显著偏离稳定种群模型,核苷酸错配分布表明花斑蛇鲻历史上曾经历过种群的快速扩张,扩张时间推算约在距今4万~10万年之前。研究结果表明,中国近海和陆架的花斑蛇鲻遗传分化不显著,在渔业上可以作为一个单元来管理。

     

Return migration of adult Atlantic salmon, Salmo salar, in relation to water diverted through a power station

Abstract  The migration of Atlantic salmon, Salmo salar L., returning to the River Suldalslågen, Norway, was studied in relation to redirection of freshwater flow through a power station. The outlet of the power station is situated in the Hylsfjord, a fjord adjacent to the river mouth. Seventy-two salmon were tagged with acoustic transmitters, released in the outer part of the fjord system and automatically recorded when entering the Hylsfjord or the river. Data were collected during one period when the power station was running and two periods when the power station was closed. The release of water from the power station did not greatly attract the salmon during their return migration. Proportions of salmon entering the river or time from release to entering the river did not differ among salmon tagged in the different periods. The salmon were recorded in the Hylsfjord both when the power station was running and closed and there were no differences in number of times, number of days or hours recorded in the Hylsfjord among salmon tagged in the three periods. The only significant difference found among periods was duration of continuous stays in the inner part of the Hylsfjord. This may indicate a slight attraction to the freshwater release, but the difference seems small (1.8 vs. 0.7 h) compared with the time the fish stayed in the fjord system before entering the river (16–85 days).     

剑尾鱼RW-H近交系20个微卫星位点的遗传结构

为了对水生实验动物剑尾鱼(Xiphophorus helleri)RW-H系近交15代的遗传结构进行研究,寻找该近交系的标志基因位点,选择20个在野生剑尾鱼群体具多态性的微卫星位点,对剑尾鱼RW-H系(红眼白体)30尾个体进行分析。结果表明,其中有17个位点为单态,有可能作为该近交系的标志基因位点;另外3个位点Msa012、Msa033和Msc036具有多态性,多态信息含量值分别为0.3047、0.3457和0.3648。通过Pop-gene 3.2软件分析得知全部基因位点的纯合率达到了95.83%,个体间平均遗传距离为0.0482(0.000 0~0.1625),遗传相似系数为0.9518(0.8500~1.0000),说明剑尾鱼RW-H系已经具有很高的近交程度。几个多态性位点的发现,可以指导近交选育,加快选育进度。本研究方法不仅检测出剑尾鱼RW-H系具较低的遗传多样性,而且可为中国建立分子水平的实验动物监测标准提供基础数据。     

Behaviour and mortality of downstream migrating Atlantic salmon smolts at a small power station with multiple migration routes

Salmon smolts were released upstream of a run‐of‐river hydropower site and recaptured downstream for inspection. Descending fish behaviour through three possible migration routes (turbines, fishway, spillway) was analysed using telemetry, fyke nets and diving. Tagged smolts did not follow the main water flow; over 70% used the fishway, which received only about 10% of the flow. The turbines received about 80% of the water, but <25% of the smolts. Smolts were not fully stopped from entering the turbines by the 25‐mm bar racks. Mortality of smolts passing through the Kaplan turbines was at minimum 36%. No mortality was found in fish moving through the fishway or spillway. This shows that small and fast‐rotating Kaplan turbines can cause relatively high mortality. No mortality in alternative migration routes resulted in a total mortality for descending smolts at the hydropower station of 8.5%, emphasising the importance of providing functional alternative migration routes.     

Micro-particles in recirculating aquaculture systems: particle size analysis of culture water from a commercial Atlantic salmon site

As part of a larger study of micro-particles in a recirculating, cold water aquaculture system for juvenile Atlantic salmon (Salmo salar), particle size analyses were carried out on the culture and makeup waters over several months followed by samples of feed stirred in water. The particle size distributions followed the power law described in [Aquacult. Eng. 19 (1999): 259] but with a superimposed spike at around 4 μm in the culture water, which was not present in make-up waters. A similar spike appeared in the feed samples indicating that the spike had a feed origin. While the absolute value of the power law exponent (designated β, or the Beta value) was in the range of 2.6–3.6, consistent with aquacultural waters, the build-up of fine particles, expected in a recirculating system with time and which would have been indicated by an increase in Beta value to above 4, did not occur due to a system high water turn-over rate flushing much of the finer particles. There is a particle counts increase occurring across the degasser/oxygenator that needs further investigation.     

Genetic connectivity and phylogeography of the night shark (Carcharhinus signatus) in the western Atlantic Ocean: Implications for conservation management

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Population genetic divergence of bonnethead sharks Sphyrna tiburo in the western North Atlantic: Implications for conservation

1. Sharks are a priority for conservation because numerous species, including small-sized coastal species, are being heavily exploited by commercial and recreational fisheries. Understanding the genetic population structure of sharks is key to effective management, maximizing their evolutionary potential in a rapidly changing environment and preventing population declines.
2. Limited dispersal is an important factor promoting population divergence for several coastal shark species. The genetic variation in 14 microsatellite loci and 21,006 single nucleotide polymorphisms genotyped using restriction-site-associated DNA sequencing was analysed to assess the genetic structure of the bonnethead shark, Sphyrna tiburo, in the western North Atlantic.
3. Genetic differences were identified among three well-defined regions: the western Florida coast, the south-eastern US Atlantic coast, and the southern Gulf of Mexico. Results support previous studies based on mitochondrial DNA sequences in defining differences among these regions and suggest limitations of bonnethead sharks in routinely performing long-distance migrations.
4. The limited connectivity among regions explains the pattern of genetic divergence but also reported divergence at the species/subspecies level. These genetically discrete bonnethead populations have independent evolutionary histories that may include local adaptations to specific areas.
5. Bonnethead sharks are currently managed as two stocks in the USA owing to recent genetic, tagging, and life history studies; however, no stock assessments or management plans exist for Mexico. These results not only serve to reinforce US management strategies and provide critical data about the extent of gene flow and sex dispersal among populations, but also begin the process of effective management in the waters of Mexico to ensure the long-term productivity and resilience of this species. With an absence of gene flow between populations from US waters and the southern Gulf of Mexico, there is a need for management plans based upon independent biological and population dynamics data since limited or no opportunities for populations to interchange individuals may occur to re-establish population viability.

     

The risk of individual fish being captured multiple times in a catch and release fishery

The proportion of angled Atlantic salmon Salmo salar L. being caught and released has increased. If individuals are repeatedly captured, this may have fish welfare consequences. Of 995 Atlantic salmon tagged during catch and release in eight Norwegian rivers, 10% were captured twice, while 3% were captured three times within the same fishing season. The probability that released salmon were captured again decreased with decreasing time left of the fishing season, decreased for larger‐sized fish and varied among rivers/years. Increased exploitation rates within the river, indicating an increased fishing pressure, strongly increased the probability that fish would be recaptured. However, the proportion of salmon caught a second time was much lower than the total exploitation rates in the same rivers (which was on average 46%). For fish tagged in the sea, the likelihood of being angled decreased with time since entering the river, which may explain why the recapture rates of caught and released fish were lower than the total exploitation rates.     

Distribution of infectious pancreatic necrosis virus (IPNV) in wild marine fish from Scottish waters with respect to clinically infected aquaculture sites producing Atlantic salmon, Salmo salar L

This study represents the first large-scale investigation of IPNV in Scottish wild marine fish. Kidney samples were taken from 30 627 fish comprising 37 species and 45 isolations were made from nine different species, illustrating these as reservoirs of IPNV in Scottish waters. The estimated prevalence of IPNV in the Scottish marine environment was low at 0.15% (90% confidence intervals, (CI) of 0.11-0.19%). This was significantly greater in fish caught less than 5.0 km from IPN-positive fish farms in Shetland, at 0.58% (90% CI of 0.45-0.77%). This prevalence persisted and did not significantly decrease over the 16-month period of study. The estimated prevalence of IPNV for each positive species was less than 1% with the statistically non-significant exceptions of flounder, Platichthys flesus (L.), at 12.5% (90% CI of 0.64-47.06%) and saithe, Pollachius virens (L.), at 1.11% (90% CI of 0.49-2.19%). The 45 isolates were titrated and all but two were below the detection limit of the test (<55 PFU g(-1)). Titres of 3.8 x 10(2) PFU g(-1) and 2.8 x 10(1) PFU g(-1) were calculated from common dab, Limanda limanda (L.), and saithe, respectively. This study provides evidence that clinical outbreaks of IPN in farmed Atlantic salmon may cause a localized small increase in the prevalence of IPNV in wild marine fish.     

Long‐term epidemiological survey of Kudoa thyrsites (Myxozoa) in Atlantic salmon (Salmo salar L.) from commercial aquaculture farms

Kudoa thyrsites (Myxozoa) encysts within myocytes of a variety of fishes. While infected fish appear unharmed, parasite‐derived enzymes degrade the flesh post‐mortem. In regions of British Columbia (BC), Canada, up to 4–7% of fillets can be affected, thus having economic consequences and impacting the competitiveness of BC's farms. K. thyrsites was monitored in two farms having high (HP) or low (LP) historical infection prevalence. At each farm, 30 fish were sampled monthly for blood and muscle during the first year followed by nine samplings during year two. Prevalence and intensity were measured by PCR and histology of muscle samples. In parallel, fillet tests were used to quantify myoliquefaction. Infections were detected by PCR after 355 and 509 degree days at LP and HP farms, respectively. Prevalence reached 100% at the HP farm by 2265 degree days and declined during the second year, whereas it plateaued near 50% at the LP farm. Infection intensities decreased after 1 year at both farms. Blood was PCR‐positive at both farms between 778 and 1113 degree days and again after 2000 degree days. This is the first monitoring project in a production environment and compares data between farms with different prevalence.     

The use of spearfishing competition data in fisheries management: evidence for a hidden near collapse of a coastal fish community of Galicia (NE Atlantic Ocean)

The use of commercial catch statistics to estimate overfishing consequences has been criticised, but alternative long‐term data sets are rare. Long time‐series data sets from recreational fisheries competitions have been used to infer trends in coastal fish communities. Here an historic archive (1953–2007) of recreational spear fisheries in Galicia (NW Spain) was employed to estimate long‐term changes in coastal ecosystems. Using generalised additive regression models, decreases in the abundances of coastal rocky reef fishes of up to 76% over the last 50 years were found. In the same period, the mean body weight also decreased by 76%. In addition, relative catch frequency has decreased for the most valuable commercial species. Overfishing, amongst other human impacts, has brought these ecosystems so close to collapse that it is urgent to implement measures to ensure their recovery.     

Changes in angler participation and demographics: analysis of a 17‐year licence stub return system for Atlantic salmon

Abstract Patterns of change in angler participation and demographics were examined for the recreational Atlantic salmon, Salmo salar L., fishery in Newfoundland and Labrador, Canada. An analysis of a licence stub return system, 1994–2010, showed a significant decline in resident angler participation, but this was not consistent across all regions of the Province. Mean age of anglers increased significantly, varying from 39.0 years in 1994 to 46.5 years by 2010. In some regions, mean age rose by over 12 years since the mid‐1990s, reflecting a decline in the recruitment of younger anglers. The return rate of angler logs also declined over time and was found to vary by age, sex and area of angler residence. Women and older anglers, and those living in specific rural areas had a greater tendency to return a record of their catch history than men and younger anglers. Identified changes in participation and demographics, which can affect exploitation and ultimately abundance, could be used to develop management measures that would maximise both harvest and socio‐economic benefits to the varied users of the resource.     

Genetic diversity in a Tasmanian hatchery population of Atlantic salmon (Salmo salar L.) compared with its Canadian progenitor population

The level of genetic diversity in a cultured Atlantic salmon (Salmo salar) population from Tasmania, Australia was examined at 11 microsatellite loci and compared with that in its progenitor population from the River Philip in Nova Scotia, Canada. The reference progenitor population consisted of archived scales collected from wild River Philip salmon in 1971 and 1972, not long after salmon from this river were imported into Australia in the mid‐1960s. The Tasmanian hatchery stock had a significant reduction in the mean number of alleles (31–43%) and mean allelic richness (28–39%) across all microsatellite loci compared with the wild Canadian population. Mean heterozygosity levels remained unchanged. Estimates of per‐generation effective population sizes for the Tasmanian population, based on allele frequency temporal variance with the wild progenitor population, ranged from 102–207 individuals and reflected hatchery records.