Salmon Escapement Research Articles

Transcriptomic comparison of communally reared wild, domesticated and hybrid Atlantic salmon fry under stress and control conditions

BackgroundDomestication is the process by which organisms become adapted to the human-controlled environment. Since the selection pressures that act upon cultured and natural populations differ, adaptations that favour life in the domesticated environment are unlikely to be advantageous in the wild. Elucidation of the differences between wild and domesticated Atlantic salmon may provide insights into some of the genomic changes occurring during domestication, and, help to predict the evolutionary consequences of farmed salmon escapees interbreeding with wild conspecifics. In this study the transcriptome of the offspring of wild and domesticated Atlantic salmon were compared using a common-garden experiment under standard hatchery conditions and in response to an applied crowding stressor.ResultsTranscriptomic differences between wild and domesticated crosses were largely consistent between the control and stress conditions, and included down-regulation of environmental information processing, immune and nervous system pathways and up-regulation of genetic information processing, carbohydrate metabolism, lipid metabolism and digestive and endocrine system pathways in the domesticated fish relative to their wild counterparts, likely reflective of different selection pressures acting in wild and cultured populations. Many stress responsive functions were also shared between crosses and included down-regulation of cellular processes and genetic information processing and up-regulation of some metabolic pathways, lipid and energy in particular. The latter may be indicative of mobilization and reallocation of energy resources in response to stress. However, functional analysis indicated that a number of pathways behave differently between domesticated and wild salmon in response to stress. Reciprocal F1 hybrids permitted investigation of inheritance patterns that govern transcriptomic differences between these genetically divergent crosses. Additivity and maternal dominance accounted for approximately 42 and 25% of all differences under control conditions for both hybrids respectively. However, the inheritance of genes differentially expressed between crosses under stress was less consistent between reciprocal hybrids, potentially reflecting maternal environmental effects.ConclusionWe conclude that there are transcriptomic differences between the domesticated and wild salmon strains studied here, reflecting the different selection pressures operating on them. Our results indicate that stress may affect certain biological functions differently in wild, domesticated and hybrid crosses and these should be further investigated.

Population Trends for Chinook and Summer Chum Salmon in Two Yukon River Tributaries in Alaska

AbstractAn essential management objective of the Yukon Delta and Koyukuk National Wildlife Refuges in Alaska is to conserve fish and wildlife populations and habitats in their natural diversity. In keeping with this objective, the U.S. Fish and Wildlife Service installed weirs in two tributaries of the Yukon River, the East Fork Andreafsky and Gisasa rivers, in 1994 to collect information on salmon populations that used them. The weirs have been in operation for >23 y. Chinook Oncorhynchus tshawytscha and summer Chum Salmon O. keta were counted and sampled for various demographic data each year as they migrated through the weirs to upstream spawning areas. Here we examine this record of population data to describe and compare long-term variation in run abundance, run timing, length and age structure, sex composition, and production for these salmon populations. Fishery managers often look to multiple monitoring projects in-season seeking corroboration of observed run qualities; therefore, we also considered whether Yukon River main-stem indicators of abundance were correlated with these tributary escapements. Our analyses suggest long-term stability of these populations despite large annual variations in most metrics we examined. Annual escapements have varied by factors of 3–5 for Chinook Salmon and >23 for summer Chum Salmon, yet only the Chinook Salmon population in the Gisasa River appears to be declining. Main-stem abundance indicators were not correlated with Chinook Salmon escapements but were strongly correlated with summer Chum Salmon escapements. Run timing has varied annually by as much as a week earlier or later than average for all four populations with no trend over time. Mean age of the Chinook Salmon populations declined over time but remained stable for the summer Chum Salmon populations. Chinook Salmon populations in the East Fork Andreafsky and Gisasa rivers averaged 35% and 28% female, respectively. Both summer Chum Salmon populations averaged close to 50% female. Length at age has been stable or slightly declining for all four populations. Production over time was strongly correlated within species for populations in the two rivers, and averaged >1 recruit/spawner for all populations except Chinook Salmon from the Gisasa River. We discuss these findings in the context of major changes in the fishery and the environments these populations experience.

BASIS FOR SELECTION OF RIVERS FOR MONITORING ON THE STOCKS OF CHUM AND PINK SALMON IN THE AMUR RIVER

The monitoring of chum and pink salmon escapement to spawning grounds in the Amur River basin was stopped in 2009. To start it again, a proved choice of the rivers is necessary for adequate controlling of these species number, by the spawning habitats of their population groups within the basin. For this purpose, results of the monitoring in 1949–2000 and the data on human settlements in the medieval times are analyzed. The lower reaches of the Amur were anciently inhabited by the paleoasiatic Nivkh people and the upper reaches where the fall chum spawned in spring waters were inhabited by the people of Pokrovskaya archeological culture — their burial grounds coincided with the spawning area of fall chum salmon. To reach these spawning grounds, fall chum salmon migrated up to the distance of 3427 km from the Amur mouth, but since the 20th century they occur rarely in the upper reaches of the Amur, in particular within Chinese territory where they are not observed in more than 50 years; recently they spawn in spring waters at the distance 500–1200 km from the Amur mouth, mainly in its right tributaries. The reproduction centers of other two populations of chum salmon, as the summer chum and fall chum breeding in hyporheic waters, are located in the Amgun River basin (the lower left tributary of the Amur). The fourth population is the lake chum salmon breeding in spring waters of Lake Chlya located on the left bank in the lower reaches of the Amur River. Centers of reproduction for both pink salmon populations, differentiated by even and odd years of spawning, are located in the Amgun River. Several test rivers are selected within all mentioned centers of reproduction, they are: Kerbi, Duki, Im, Somnya, Aksha, Khilka, Beshenaya, Gur, Anui, Khor, Kur, and Bira. This list is similar to the list of the rivers where chum and pink salmons were monitored in the 20th century

Swimming with the fishes: validating drift diving to identify farmed Atlantic salmon escapees in the wild

AEI Aquaculture Environment Interactions Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections AEI 11:417-427 (2019) - DOI: https://doi.org/10.3354/aei00326 Swimming with the fishes: validating drift diving to identify farmed Atlantic salmon escapees in the wild S. Mahlum1,2,*, H. Skoglund1, T. Wiers1, E. S. Norman1, B. T. Barlaup1, V. Wennevik3, K. A. Glover2,3, K. Urdal4, G. Bakke3, K. W. Vollset1 1NORCE Norwegian Research Centre, LFI, Nygårdsgt. 112, 5008 Bergen, Norway 2Department of Biology, University of Bergen, Thormøhlensgate 53 A & B, 5006 Bergen, Norway 3Institute of Marine Research, PO Box 1870, Nordnes, 5817 Bergen, Norway 4Rådgivende Biologer AS, Edvard Griegs vei 3, 5059 Bergen, Norway ABSTRACT: Escaped farmed Atlantic salmon Salmo salar interbreeding with wild conspecifics represents a threat to the genetic integrity and viability of wild populations. Therefore, it is necessary to accurately quantify escapees in riverine systems to monitor and mitigate interactions with wild conspecifics. Drift diving surveys are presently used in Norway to quantify the number of wild and escaped farmed salmon in rivers. However, limited information is available on the validity of the method for distinguishing escapees from wild conspecifics. Comparing the proportion of escapees calculated from drift diving (mean = 8.5%) and net captures (mean = 8.6%), we found that drift diving was well correlated with net captures (adj. r2 = 0.79). Furthermore, scale analysis from an independent data set demonstrated a 98% true positive rate when identifying and capturing farmed escapees during drift diving. The results of this study indicate that drift diving is an accurate and robust method for quantifying escaped farmed salmon, at least in rivers where observation conditions are adequate for snorkeling. In general, drift diving can be a valuable tool for stakeholders to quickly assess broad spatial extents with limited time and resources. KEY WORDS: Snorkeling · Domesticated salmon · Aquaculture · Bayesian · Method comparison · Escaped farmed salmon · Mitigation Full text in pdf format PreviousNextCite this article as: Mahlum S, Skoglund H, Wiers T, Norman ES and others (2019) Swimming with the fishes: validating drift diving to identify farmed Atlantic salmon escapees in the wild. Aquacult Environ Interact 11:417-427. https://doi.org/10.3354/aei00326Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in AEI Vol. 11. Online publication date: August 22, 2019 Print ISSN: 1869-215X; Online ISSN: 1869-7534 Copyright © 2019 Inter-Research.

COMPLEX MONITORING OF SALMON SPAWNERS ESCAPEMENT TO THE KAMCHATKA RIVER IN REAL TIME REGIME

Complex method of quick quantitative evaluation of the spawners escapement to the Kamchatka River is developed for pacific salmons on the base of analysis of their passing dynamics through certain parts of the river (main stream, tributaries, spawning grounds). The runs of different temporal forms of anadromous salmons were separated taking into account their biological parameters using the data of biological analysis of commercial catches in Ust-Kamchatsky district. The spawners abundance was evaluated from CPUE value for the main stream where control catches of spawners were made in the periods predetermined for escapement, and directly using two duplicate hydroacoustic complexes for the tributary important for salmons reproduction or visually from ashore, boats, or flying vehicles for other tributaries. These data were coupled with general assessments of the escapement values in the river basin from helicopters. Numeral model was developed to evaluate the salmons escapement to the spawning grounds. The escapement dynamics was simulated retrospectively for sockeye, chum and coho salmon in 2016 and 2017. The method was successfully used for fishery management in the fishery campaign of 2018. Efficiency of the fishery regime was estimated using this approach. The value of sockeye salmon escapement was determined as enough for medium reproduction, and the values of chum and coho salmons escapement — as enough for medium or high reproduction. For chinook salmon, the model was not tested, but the method of control catches was developed and applied as a part of integrated methodology for quantitative operational assessment of escapement.

Studying Kenai River Fisheries’ Social-Ecological Drivers Using a Holistic Fisheries Agent-Based Model: Implications for Policy and Adaptive Capacity

Alaska’s salmon fisheries are one of the more intensely managed natural resources in the world. The state’s salmon fisheries support recreational, subsistence, and commercial harvest with multiple billions of dollars flowing into the economy, and define the cultural identity of many Alaskans. Fishery management practices rely on historic records to set policies with two goals: to meet salmon escapement quota and to maximize salmon harvest. At the same time, rapid social and ecological changes to the sub-Arctic are already impacting salmon runs and fisheries management. Combined with the inability of fishery managers to test the outcome of proposed policy changes, an understanding of the role social and ecological drivers play in harvest and effort is required. To address the two-forked problem of understanding socio-ecological dynamics and potential policy responses to ecological and social changes, we (1) conducted stakeholder workshops to solicit key system drivers, (2) built an integrated agent based model (ABM) of the system’s socio-ecological dynamics, and (3) tested the impacts of alternative future scenarios of ecological, social, and policy changes on the system’s outcomes. We previously constructed and validated a high-fidelity, data-driven, agent-based model of the Kenai River, Alaska that simulates seasonal harvest of sockeye and Chinook salmon, the fishing activities of the personal use fishery, commercial drift, and set gillnet agents. We study the role of key stakeholder and ecological drivers, using the ABM decision support tool, and their implications for fisheries management policies. Analysis of the scenario based studies found resilience in management of commercial fisheries to changing salmon migration dynamics, a lack of adaptive capacity in recreational (personal use) dipnet users to altered sockeye salmon runs, and the possible utility of introducing management measures in the dipnet fishery to manipulate sockeye escapement levels. These findings represent the usefulness of this type of ABM in assisting fishery managers everywhere in investigating possible future outcomes of different management or ecological scenarios.

The effect of artificial illumination on Chinook salmon behavior and their escapement out of a midwater trawl bycatch reduction device

The Pacific hake (Merluccius productus) midwater trawl fishery is the largest groundfish fishery off the U.S. West Coast by volume. Catches comprise mainly Pacific hake, however, bycatch of Chinook salmon (Oncorhynchus tshawytscha) can be an issue affecting the fishery as Endangered Species Act (ESA) listed Evolutionarily Significant Units represent a portion of the total Chinook salmon bycatch. We conducted two separate experiments evaluating the influence of artificial illumination on Chinook salmon behavior and their escapement out a bycatch reduction device (BRD) in a Pacific hake midwater trawl. In Experiment 1, we tested whether Chinook salmon could be attracted out specific escape windows of a BRD equipped with multiple escape windows using artificial illumination. In Experiment 2, we compared Chinook salmon escapement rates out of the BRD between tows conducted with and without artificial illumination to determine if illumination can enhance their escapement. Our results show that artificial illumination can influence where Chinook salmon exit out of the BRD, but also demonstrate that illumination can be used to enhance their escapement overall. As conservation of ESA-listed Chinook salmon is an ongoing management priority, our research contributes new information on how artificial illumination can minimize adverse interactions between the Pacific hake fishery and Chinook salmon.

Development and evaluation of SNP panels for the detection of hybridization between wild and escaped Atlantic salmon (Salmo salar) in the western Atlantic

Hybridization between wild and escaped cultured Atlantic salmon (Salmo salar) can threaten the stability and persistence of locally adapted wild populations. Here we describe the development and validation of a genomic-based approach to quantify recent hybridization between escapee and wild salmon in the western Atlantic. Based on genome-wide single nucleotide polymorphism (SNP) scans of wild and cultured salmon, collectively diagnostic panels were created for Newfoundland and the Canadian Maritimes. These panels were capable of both discriminating hybrids from nonhybrids and of correctly assigning individuals to hybrid class (i.e., pure wild, pure farm, F1, F2, and backcrosses) with a high degree of accuracy (Newfoundland 96 SNPs > 90%, Maritimes 720 SNPs > 80%). These genomic panels permit the assessment of the impacts of past and future farmed salmon escape events on wild populations and can inform the protection and conservation of wild Atlantic salmon genetic integrity in the western Atlantic.

Estimating the relative fitness of escaped farmed salmon offspring in the wild and modelling the consequences of invasion for wild populations.

Throughout their native range, wild Atlantic salmon populations are threatened by hybridization and introgression with escapees from net‐pen salmon aquaculture. Although domestic–wild hybrid offspring have shown reduced fitness in laboratory and field experiments, consequential impacts on population abundance and genetic integrity remain difficult to predict in the field, in part because the strength of selection against domestic offspring is often unknown and context‐dependent. Here, we follow a single large escape event of farmed Atlantic salmon in southern Newfoundland and monitor changes in the in‐river proportions of hybrids and feral individuals over time using genetically based hybrid identification. Over a three‐year period following the escape, the overall proportion of wild parr increased consistently (total wild proportion of 71.6%, 75.1% and 87.5% each year, respectively), with subsequent declines in feral (genetically pure farmed individuals originating from escaped, farmed adults) and hybrid parr. We quantify the strength of selection against parr of aquaculture ancestry and explore the genetic and demographic consequences for populations in the region. Within‐cohort changes in the relative proportions of feral and F1 parr suggest reduced relative survival compared to wild individuals over the first (0.15 and 0.81 for feral and F1, respectively) and second years of life (0.26, 0.83). These relative survivorship estimates were used to inform an individual‐based salmon eco‐genetic model to project changes in adult abundance and overall allele frequency across three invasion scenarios ranging from short‐term to long‐term invasion and three relative survival scenarios. Modelling results indicate that total population abundance and time to recovery were greatly affected by relative survivorship and predict significant declines in wild population abundance under continued large escape events and calculated survivorship. Overall, this work demonstrates the importance of estimating the strength of selection against domestic offspring in the wild to predict the long‐term impact of farmed salmon escape events on wild populations.

A genetic tool for evaluating male‐mediated stock introgression in Atlantic salmon

Abstract The Atlantic salmon shows strong population structure with reduced gene flow, owing to homing behaviour. Supportive breeding with allochtonous parr or fish‐farm escapees could affect native population genetic structure by the introgression of foreign genes. Mature male parr are potentially powerful vehicles for promoting introgression: they can fertilize eggs in competition with anadromous males. As a consequence, foreign males contribute more to introgression than foreign females. This effect must be taken into account for the correct development of conservation programmes. Foreign males constitute an inadvertent way to disrupt the genetic structure, as the allochtonous parr or fish‐farm escapees can survive in the river during the parr stage. A short polymorphic fragment of the sex‐determining gene (sdY) was used as a marker to assess introgression via males into south European salmon populations. In order to find haplotype variants for the intronic sequence of sdY, samples were investigated from 16 different rivers across the distribution range of the salmon, together with historical samples (1950–1960) from three Spanish rivers. Two novel haplotypes, in addition to the three already described in Atlantic salmon, were found for this locus. Most samples, including historical ones, displayed the common haplotype (D) previously found in salmon all over Europe; however, north European haplotype variants were also detected in salmon inhabiting the southern European rivers that were systematically supplemented with foreign stocks between 1981 and 1994. Analysis of haplotype variation in the sdY intron constitutes a powerful and inexpensive tool, not only to specifically assess male‐mediated introgression into natural populations of Atlantic salmon, but also for monitoring salmon escapees.

River ecosystem resilience to extreme flood events.

Floods have a major influence in structuring river ecosystems. Considering projected increases in high‐magnitude rainfall events with climate change, major flooding events are expected to increase in many regions of the world. However, there is uncertainty about the effect of different flooding regimes and the importance of flood timing in structuring riverine habitats and their associated biotic communities. In addition, our understanding of community response is hindered by a lack of long‐term datasets to evaluate river ecosystem resilience to flooding. Here we show that in a river ecosystem studied for 30 years, a major winter flood reset the invertebrate community to a community similar to one that existed 15 years earlier. The community had not recovered to the preflood state when recurrent summer flooding 9 years later reset the ecosystem back to an even earlier community. Total macroinvertebrate density was reduced in the winter flood by an order of magnitude more than the summer flood. Meiofaunal invertebrates were more resilient to the flooding than macroinvertebrates, possibly due to their smaller body size facilitating greater access to in‐stream refugia. Pacific pink salmon escapement was markedly affected by the winter flood when eggs were developing in redds, compared to summer flooding, which occurred before the majority of eggs were laid. Our findings inform a proposed conceptual model of three possible responses to flooding by the invertebrate community in terms of switching to different states and effects on resilience to future flooding events. In a changing climate, understanding these responses is important for river managers to mitigate the biological impacts of extreme flooding effects.

Counting of salmon escapements from aerial video images captured using a drone

Counting of salmon escapements from aerial video images captured using a drone

Predicting the impacts of escaped farmed Atlantic salmon on wild salmon populations

The escape of Atlantic salmon (Salmo salar) from aquaculture facilities can result in both negative genetic and ecological interactions with wild populations, yet the ability to predict the associated risk to wild populations has remained elusive. Here we assess the potential of a spatiotemporal database of aquaculture facility locations, production estimates, and escape events to predict the distribution of escaped farmed salmon and genetic impacts on wild populations in the Northwest Atlantic. Industry production data, reported escape events, and in-river detections of escaped farmed salmon were collected from across the Northwest Atlantic. Genetic estimates of impact were obtained using single nucleotide polymorphisms (95 loci) representing aquaculture and wild salmon throughout the region (30 populations, 3048 individuals). Both the number of escaped farmed salmon detected at counting facilities and the magnitude of genetic impacts were positively correlated with a cumulative spatial measure of aquaculture production. Our results suggest that the risk of escapees and genetic introgression from wild–farmed salmon interactions can be assessed using information on farm production characteristics. This represents a first step in predicting the impact of existing cage-based farms on wild Atlantic salmon.

Current status of natural spawning of chum salmon Oncorhynchus keta in rivers with or without hatchery stocking on the Japan Sea side of northern Honshu, Japan

Information on the status of natural spawning is needed on the Japan Sea side of northern Honshu, Japan for ecosystem-based sustainable management of chum salmon resources. We conducted on-site visual surveys in October–December of 2015 and 2016 that targeted spawning chum salmon redds in all rivers > 5 km long (total 94 rivers) in Akita, Yamagata, Niigata (including Sado Island), and Toyama prefectures. The ratio of rivers found to host natural reproduction to the total number of surveyed rivers was 93.6% (44/47) in stocked rivers and 74.5% (35/47) in non-stocked rivers. These results show that there is a wide occurrence of natural reproduction of chum salmon in these rivers, regardless of the history of hatchery stocking. The density of spawning redds (number of redds/1000 m2) as an indicator of chum salmon escapements did not differ (P = 0.54) between stocked rivers (mean 3.5, N = 49) and non-stocked rivers (mean 2.4, N = 36),when rivers where no redds were observed were excluded from the analysis. These results suggest that chum salmon escapements into non-stocked rivers may not be negligible. Conservation measures for wild fish are needed in stocked and non-stocked rivers to promote enhancement programs based on natural reproduction.

Ispol'zovanie foto- i videofiksatsii dlya otsenki kolichestva proizvoditelej tikhookeanskikh lososej na nerestilishchakh i putyakh ikh migratsij: nekotorye metodicheskie podkhody

Ispol'zovanie foto- i videofiksatsii dlya otsenki kolichestva proizvoditelej tikhookeanskikh lososej na nerestilishchakh i putyakh ikh migratsij: nekotorye metodicheskie podkhody

Constrained by markets: processing costs limit potential for managing predator–prey interactions in a commercial fishery

Summary Selective fisheries may impact non‐target species as well as limit the productivity of target species if their predators are not harvested. The outcomes of multi‐species harvest strategies that include targeting predators depend on ecological and economic constraints, although the development of ecosystem‐based management plans has typically focused on ecological constraints. In Chignik, Alaska, sockeye salmon support a valuable commercial fishery and, as juveniles, are preyed upon by coho salmon, a species not subject to a targeted harvest. Whether exploitation of coho salmon would enhance overall fishery value by releasing sockeye salmon from predation constraints is not understood. We employ simulation models to examine the ecological and economic conditions necessary for directly targeting coho salmon to benefit fishers and seafood processors, two distinct but inter‐dependent stakeholders in this ecosystem. Model results indicate fishers are likely to experience increased value regardless of economic constraints, as long as coho salmon predation negatively affects sockeye salmon productivity. However, seafood processors are much more limited in the conditions which produce increased economic value, constrained by greater operation costs required to process harvested coho salmon. Synthesis and applications. The unique economic constraints and opportunities of different stakeholders can present contrasting outlooks on the potential benefits of alternative harvest strategies, even if the alternative strategies are predicted to increase yield. The findings herein demonstrate the importance of considering multiple stakeholders when considering alternative management strategies. Depending on the level of risk stakeholders are willing to accept, an active adaptive management strategy reducing coho salmon escapement to low levels could provide valuable information about ecosystem structure as well as potentially providing the greatest economic benefit to the fishery.

The ecological profile of Atlantic salmon escapees entering a river throughout an entire season: diverse in escape history and genetic background, but frequently virus-infected

In 2014, 129 farmed salmon escapees captured in an upstream-migration trap located in the river Etne, western Norway, were investigated for viral infections, age at escape, size, and genetic composition. The frequency of escapees positive for salmonid alphavirus (SAV), piscine orthoreovirus (PRV), and infectious salmon anaemia virus (ISAV) was 12, 79, and <1%, respectively. Fatty acid analysis demonstrated that the individuals had escaped from farms at different stages of the production cycle, although the majority had probably escaped from farms in the same year as their capture in the river. Genetic analyses demonstrated that the escapees originated from multiple farms. This was also supported by the distribution of fish size and timing of entry into the river. A combination of genetic, fatty acid and viral infection analyses showed that in the river Etne in 2014: (i) most of the fish entering the river were infected with one or more viruses, (ii) the majority of them had escaped in the same year that they entered the river, (ii) they originated from multiple farm sources, and (iv) two of the identified genetic groups likely originated from two recent and distinct escape events. This is the first study to integrate results from multiple analytical methods in order to reveal the ecological and genetic diversity of escaped farmed fish entering a river with native salmon population throughout an entire season.

Siblingship tests connect two seemingly independent farmed Atlantic salmon escape events

AEI Aquaculture Environment Interactions Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections AEI 8:497-509 (2016) - DOI: https://doi.org/10.3354/aei00194 Siblingship tests connect two seemingly independent farmed Atlantic salmon escape events María Quintela1,*, Vidar Wennevik1, Anne G. E. Sørvik1, Øystein Skaala1, Ove T. Skilbrei1,†, Kurt Urdal2, Bjørn Torgeir Barlaup3, Kevin A. Glover1,4 1Institute of Marine Research, Post Box 1870, Nordnes, 5817 Bergen, Norway 2Rådgivende Biologer AS, Bredsgården, 5003 Bergen, Norway 3Uni Research Environment, PO Box 7810, 5020 Bergen, Norway 4Department of Biology, University of Bergen, 5020 Bergen, Norway *Corresponding author: maria.quintela.sanchez@imr.no †Deceased ABSTRACT: Aquaculture escapees represent a threat to the genetic integrity of native populations, may spread infectious agents and display ecological interactions with wild fish. DNA-based identification methods are well established for tracing Atlantic salmon escapees back to their farms of origin. However, traditional genetic assignment approaches are not always able to single out the farm of origin in cases where several potential farm sources rear fish from the same genetic line, and display strongly overlapping allele frequencies. We investigated whether an alternative statistical approach, which involves ad hoc identification of sibling relationships, circumvents the challenge of overlapping allele frequencies. We analysed the following samples collected in 2013: (1) 221 farmed escapees captured in several rivers in the Ryfylke region of Norway, (2) 139 farmed escapees captured some 150 km away in an upstream fish migration trap in the River Etne, and (3) 779 farmed salmon sampled from 17 cages on 10 farms in Ryfylke. Siblingship tests increased the precision of identification of escapees back to their farm of origin over genetic assignment and population statistic approaches. Together with other non-genetic data, siblingship tests were also able to connect 2 seemingly independent escape events, demonstrating that some of the salmon escaping from 1 or 2 farms in Ryfylke took approximately 1 mo to migrate 150 km northwards before entering the River Etne. Finally, we demonstrated that the genetic background of the escapees captured in the River Etne during the course of an entire season was represented by the 3 major breeding programs in Norway. KEY WORDS: Salmon farming · Aquaculture · Farmed escapees · Microsatellites · Assignment analyses · COLONY · Trap Full text in pdf format PreviousCite this article as: Quintela M, Wennevik V, Sørvik AGE, Skaala Ø and others (2016) Siblingship tests connect two seemingly independent farmed Atlantic salmon escape events. Aquacult Environ Interact 8:497-509. https://doi.org/10.3354/aei00194 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in AEI Vol. 8. Online publication date: September 01, 2016 Print ISSN: 1869-215X; Online ISSN: 1869-7534 Copyright © 2016 Inter-Research.

Widespread genetic introgression of escaped farmed Atlantic salmon in wild salmon populations

AbstractFarmed Atlantic salmon (Salmo salar) escape from net pens and enter rivers to spawn, potentially resulting in genetic introgression and reduced fitness of wild salmon. Here, we quantify genetic introgression of farmed to wild salmon, using molecular genetic markers, in populations from 147 salmon rivers, representing three-quarters of the total wild salmon spawning population in Norway. For 109 rivers with adult modern samples and sample sizes of 20 or more, the average level of farmed genetic introgression was 6.4% (median = 2.3%), with a range between 0.0% and 42.2%. Fifty-one of these rivers showed significant farmed genetic introgression when compared with historical reference samples. We observed a highly significant correlation between estimated farmed introgression and average proportion of escaped farmed salmon. We quantify levels of introgression as unweighted averages or weighted by population sizes, to compare geographical regions and to compare levels of introgression in rivers and fjords designated as locations deserving a high level of protection. We found a generally lower level of introgression in National Salmon Rivers and National Salmon Fjords subjected to formal protection by parliament. We conclude that farmed to wild genetic introgression is high in a large proportion of Norwegian salmon rivers, with the highest levels found in the most intensive areas of salmon farming. The extensive genetic introgression documented here poses a serious challenge to the management of farmed and wild Atlantic salmon in Norway and, in all likelihood, in other regions where farmed-salmon escape events occur with regularity

Overdispersion in the Estimation of Salmon Escapements by Mark–Recapture Surveys and Its Related Factors

AbstractThe Petersen method, a well-known mark–recapture method, is frequently used in the estimation of escapement of Pacific salmon Oncorhynchus spp. Robust estimates and associated variances can be obtained when the underlying assumptions of this method are met. However, in field surveys, it is often difficult to meet these assumptions because wild animals are often not randomly distributed. When the sampling variance of the estimator exceeds its binomial variance (resulting in overdispersion), the Petersen model underestimates variance. We assessed the occurrence of overdispersion in the mark–recapture data collected to estimate the escapements of Masu Salmon Oncorhynchus masou in a river in northern Japan in 1998 and 1999. The dispersion parameters estimated from 2-year data were 2.89 and 2.51 for males and 1.45 and 1.52 for females, indicating that overdispersion occurred in all cases. The magnitude of overdispersion for males exceeded that for females, probably related to differences in the postspa...