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In this article, we present the first use of genetic assignment to determine the origins of farmed Atlantic salmon (Salmo salar L.) escaping directly into freshwater. Juvenile fish (n = 220) sampled from rotary screw traps operating on tributaries of Loch Shin in Scotland had characteristics suggesting they were of farm origin (scale losses, fin damage, and vaccination marks). To investigate their origins, baseline samples (n = 1200) were collected from the two freshwater smolt rearing facilities on the Loch. Baseline analysis with 186 single-nucleotide polymorphic (SNP) markers identified three assignment units associated with the aquaculture strains in production, Mowi and Aquagen at Site A and Fanad at Site B. Exclusion analysis identified at least 37% of the suspected escapees as being of farmed origin, 95% from Site A and 5% from B. The non-random nature of fish collection and trapping locations prevented determination of either absolute proportions of escapees in the entire Shin system or escape proportions from each site. However, it was clear that fish from both sources had escaped. The study demonstrates that genetic assignment to farm origin is possible in a novel situation in which fish have escaped at the smolt stage directly into freshwater. [ABSTRACT FROM AUTHOR]

The South African (SAF) yellowfin tuna (Thunnus albacares) fishery represents a potential example of misalignment between management units and biological processes. The SAF fishery spans an operational stock with a boundary at 20°E, either side of which fish are considered part of Atlantic or Indian Ocean regional stocks. However, the actual recruitment of fish from Atlantic and Indian Ocean spawning populations into SAF waters is unknown. To address this knowledge gap, genomic analysis (11 101 SNPs) was performed on samples from Atlantic and Indian Ocean spawning sites, including SAF sites spanning the current stock boundary. Outlier loci conferred high discriminatory power to assignment tests and revealed that all SAF fish were assigned to the Indian Ocean population and that no Atlantic Ocean fish appeared in the SAF samples. Additionally, several Indian Ocean migrants were detected at the Atlantic spawning site demonstrating asymmetric dispersal and the occurrence of a mixed-stock fishery in Atlantic waters. This study highlights both the spatial inaccuracy of current stock designations and a misunderstanding of interactions between the underlying biological units, which must be addressed in light of local and global declines of the species. Specifically, the entire SAF fishery must be managed as part of the Indian Ocean stock. [ABSTRACT FROM AUTHOR]

Atlantic cod (Gadus morhua) in Skagerrak are structured into distinct ecotypes or stock components that have been severely depleted over the past decades. To improve our understanding of how local commercial and recreational fisheries influence cod stocks, we investigated whether these user groups target different stock components of cod. Cod were sampled from the recreational rod and line fishery and from commercial shrimp trawlers catching cod as by-catch. Based on a large set of single nucleotide polymorphisms (SNPs), we defined a subset of 27 semi-diagnostic SNPs designed to discriminate between two cod stock components: "inner fjord" cod and "North Sea" cod, designated by their dominant habitat preferences. Genetic assignments of fishery-caught cod indicated that 4% of individuals caught by shrimp trawlers belonged to the inner fjord cod component and 96% to the North Sea, whereas among cod caught by recreational fishers, the estimated percentages were 11.8 and 88.2%, respectively. Our findings confirm the existence of two sympatric cod stock components in coastal Skagerrak, indicating that existing management units are biologically inappropriate and should be reconsidered. Furthermore, more attention should be given to recreational angling to reduce fishing mortality on the depleted inner fjord cod component. [ABSTRACT FROM AUTHOR]

This study initially aimed to investigate the genetic population/stock structuring of Lethrinus nebulosus in the Southwest Indian Ocean (SWIO) to inform management practices in light of emerging evidence of overharvesting of this species throughout its distribution. Adult samples were genotyped for 14 nuclear microsatellites and by sequencing fragments of the mtDNA control region and COI gene. A salient feature of the data was the congruent cyto-nuclear partitioning of samples into two high divergent, reciprocally monophyletic groups. This indicates that despite no a priori evidence, hitherto described L. nebulosus in the SWIO comprises two cryptic species that co-occur among southern samples. This intermingling indicates that, at least in southern samples, both species are being indiscriminately harvested, which may severely compromise sustainability. Limited microsatellite differentiation was detected within both species, though there was some evidence of isolation in the Mauritian population. In contrast, mtDNA revealed a pattern consistent with chaotic genetic patchiness, likely promoted by stochastic recruitment, which may necessitate a spatial bet-hedging approach to management to satisfy fishery management and conservation goals. [ABSTRACT FROM AUTHOR]

The rivers in northernmost Europe support many of the largest wild Atlantic salmon stocks supplying up to 60% of the total annual catch in the world, but very little is known about their relative contributions to coastal fisheries. We generated a comprehensive Atlantic salmon genetic baseline consisting of 185 populations along the Norwegian, Barents and White Sea coasts, genotyped for a high number of genetic markers, which has a dense geographical coverage and includes all notable stocks in the region. The hierarchical genetic structure observed was the basis for defining 7 regional and 26 local re3porting groups (RGs) enabling practical implementation of genetic stock identification (GSI). The GSI accuracy varied across populations and the study area, depending on the level of genetic structuring, but a high level of accuracy was achieved when individuals were classified to regional (97%) or to local (90%) RGs. Simulations showed that salmon from the majority of the largest populations in northernmost Europe can be reliably identified in Norwegian and Russian coastal mixed-stock fisheries. The baseline will be an invaluable resource for development of future adaptive management regimes for Atlantic salmon in northern Europe. [ABSTRACT FROM AUTHOR]

Identification of cryptic species can have profound implications in fishery management, conservation and biodiversity contexts. In the North Atlantic, the genus Sebastes is currently represented by four species, although additional cryptic species have been assumed. The connectivity of the gene-pools within the genus in Greenland waters, in particular, remains largely unexplored. Using a panel of 13 microsatellite markers for 720 fish, we explored the species complex of Sebastes norvegicus in Greenland waters. Genetic analyses provided evidence for three cryptic species in samples that were morphologically identified as S. norvegicus. They were termed S. norvegicus -A, S. norvegicus -B, and S. norvegicus- giants. A few phenotypic features exist to identify adult S. norvegicus giants, but no characteristics have been identified for the two other cryptic species. The proposed cryptic species should be recognized in the management regime to ensure sustainable exploitation and conservation of Sebastes species in Greenland waters. [ABSTRACT FROM AUTHOR]