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  • 1
    In: Methods in Ecology and Evolution, Wiley, Vol. 9, No. 4 ( 2018-04), p. 1017-1035
    Abstract: Inferring the dynamics of populations in time and space is a central challenge in ecology. Intra‐specific structure (for example genetically distinct sub‐populations or meta‐populations) may require methods that can jointly infer the dynamics of multiple populations. This is of particular importance for harvested species, for which management must balance utilization of productive populations with protection of weak ones. Here we present a novel method for simultaneous learning about the spatio‐temporal dynamics of multiple populations that combines genetic data with prior information about abundance and movement, akin to an integrated population modelling approach. We apply the Bayesian genetic mixed stock analysis to 17 wild and 10 hatchery‐reared Baltic salmon ( S. salar ) stocks, quantifying uncertainty in stock composition in time and space, and in population dynamics parameters such as migration timing and speed. The genetic data were informative about stock‐specific movement patterns, updating priors for migration path, timing and speed. Use of a population dynamics model allowed robust interpolation of expected catch composition at areas and times with no genetic observations. Our results indicate that the commonly used “equal prior probabilities” assumption may not be appropriate for all mixed stock analyses: incorporation of prior information about stock abundance and movement resulted in more plausible and precise estimates of mixture compositions in time and space. The model we present here forms the basis for optimizing the spatial and temporal allocation of harvest to support the management of mixed populations of migratory species.
    Type of Medium: Online Resource
    ISSN: 2041-210X , 2041-210X
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2018
    detail.hit.zdb_id: 2528492-7
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  • 2
    Online Resource
    Online Resource
    Wiley ; 2020
    In:  Molecular Ecology Resources Vol. 20, No. 2 ( 2020-03), p. 498-510
    In: Molecular Ecology Resources, Wiley, Vol. 20, No. 2 ( 2020-03), p. 498-510
    Abstract: Determining the origin of individuals in mixed population samples is key in many ecological, conservation and management contexts. Genetic data can be analyzed using genetic stock identification (GSI), where the origin of single individuals is determined using Individual Assignment (IA) and population proportions are estimated with Mixed Stock Analysis (MSA). In such analyses, allele frequencies in a reference baseline are required. Unknown individuals or mixture proportions are assigned to source populations based on the likelihood that their multilocus genotypes occur in a particular baseline sample. Representative sampling of populations included in a baseline is important when designing and performing GSI. Here, we investigate the effects of family sampling on GSI, using both simulated and empirical genotypes for Atlantic salmon ( Salmo salar ). We show that nonrepresentative sampling leading to inclusion of close relatives in a reference baseline may introduce bias in estimated proportions of contributing populations in a mixed sample, and increases the amount of incorrectly assigned individual fish. Simulated data further show that the induced bias increases with increasing family structure, but that it can be partly mitigated by increased baseline population sample sizes. Results from standard accuracy tests of GSI (using only a reference baseline and/or self‐assignment) gave a false and elevated indication of the baseline power and accuracy to identify stock proportions and individuals. These findings suggest that family structure in baseline population samples should be quantified and its consequences evaluated, before carrying out GSI.
    Type of Medium: Online Resource
    ISSN: 1755-098X , 1755-0998
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2020
    detail.hit.zdb_id: 2406833-0
    SSG: 12
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  • 3
    In: Evolutionary Applications, Wiley, Vol. 17, No. 4 ( 2024-04)
    Abstract: Fishing has the potential to influence the life‐history traits of exploited populations. However, our understanding of how fisheries can induce evolutionary genetic changes remains incomplete. The discovery of large‐effect loci linked with ecologically important life‐history traits, such as age at maturity in Atlantic salmon ( Salmo salar ), provides an opportunity to study the impacts of temporally varying fishing pressures on these traits. A 93‐year archive of fish scales from wild Atlantic salmon catches from the northern Baltic Sea region allowed us to monitor variation in adaptive genetic diversity linked with age at maturity of wild Atlantic salmon populations. The dataset consisted of samples from both commercial and recreational fisheries that target salmon on their spawning migration. Using a genotyping‐by‐sequencing approach (GT‐seq), we discovered strong within‐season allele frequency changes at the vgll3 locus linked with Atlantic salmon age at maturity: fishing in the early season preferentially targeted the vgll3 variant linked with older maturation. We also found within‐season temporal variation in catch proportions of different wild Atlantic salmon subpopulations. Therefore, selective pressures of harvesting may vary depending on the seasonal timing of fishing, which has the potential to cause evolutionary changes in key life‐history traits and their diversity. This knowledge can be used to guide fisheries management to reduce the effects of fishing practices on salmon life‐history diversity. Thus, this study provides a tangible example of using genomic approaches to infer, monitor and help mitigate human impacts on adaptively important genetic variation in nature.
    Type of Medium: Online Resource
    ISSN: 1752-4571 , 1752-4571
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2024
    detail.hit.zdb_id: 2405496-3
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  • 4
    In: Conservation Genetics, Springer Science and Business Media LLC, Vol. 22, No. 1 ( 2021-02), p. 35-51
    Abstract: Anadromous salmonid fishes frequently exhibit strong geographic population structuring. However, population genetic differentiation of Atlantic salmon ( Salmo salar ) at fine geographic scales differs across equivalent spatial extents in different regions. So far, fine-scale genetic differentiation has not been assessed in rivers of the Baltic Sea, a region that contains an evolutionarily distinct Atlantic salmon lineage. Thus, Baltic salmon are currently managed on the river level, without focus on potential genetic structure and diversity within rivers. Here, we used microsatellites to characterize the genetic structure of wild juvenile salmon sampled throughout the interconnected, northern Baltic Tornio and Kalix Rivers. We found genetic differentiation within the two rivers, but not between them: salmon in the upper reaches differed from individuals in the lower reaches, regardless of river system. Further, examining smolts migrating from the river to the sea and adults returning from the sea to spawn, we found an association between the genetic structure and seasonal migration timing. Out-migrating smolts genetically assigned to upper river reaches were older and tended to reach the sea later in the season than smolts from the lower reaches. In contrast, mature adults originating from the upper reaches returned to the river early in the season. Our observation of genetic population structuring between downstream and upstream reaches of the large Tornio and Kalix rivers, and its association with migration timing, implies that careful temporal management of the northern Baltic fisheries would help to preserve the diversity and sustainability of the wild salmon stocks of these rivers.
    Type of Medium: Online Resource
    ISSN: 1566-0621 , 1572-9737
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 2015081-7
    SSG: 12
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  • 5
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2016
    In:  Conservation Genetics Vol. 17, No. 1 ( 2016-2), p. 177-191
    In: Conservation Genetics, Springer Science and Business Media LLC, Vol. 17, No. 1 ( 2016-2), p. 177-191
    Type of Medium: Online Resource
    ISSN: 1566-0621 , 1572-9737
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2016
    detail.hit.zdb_id: 2015081-7
    SSG: 12
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  • 6
    Online Resource
    Online Resource
    The Royal Society ; 2021
    In:  Proceedings of the Royal Society B: Biological Sciences Vol. 288, No. 1949 ( 2021-04-28)
    In: Proceedings of the Royal Society B: Biological Sciences, The Royal Society, Vol. 288, No. 1949 ( 2021-04-28)
    Abstract: Intra-species genetic homogenization arising from anthropogenic impacts is a major threat to biodiversity. However, few taxa have sufficient historical material to systematically quantify long-term genetic changes. Using archival DNA collected over approximately 100 years, we assessed spatio-temporal genetic change in Atlantic salmon populations across the Baltic Sea, an area heavily impacted by hydropower exploitation and associated with large-scale mitigation stocking. Analysis was carried out by screening 82 SNPs in 1680 individuals from 13 Swedish rivers. We found an overall decrease in genetic divergence and diminished isolation by distance among populations, strongly indicating genetic homogenization over the past century. We further observed an increase in genetic diversity within populations consistent with increased gene flow. The temporal genetic change was lower in larger wild populations than in smaller wild and hatchery-reared ones, indicating that larger populations have been able to support a high number of native spawners in relation to immigrants. Our results demonstrate that stocking practices of salmon in the Baltic Sea have led to the homogenization of populations over the last century, potentially compromising their ability to adapt to environmental change. Stocking of reared fish is common worldwide, and our study is a cautionary example of the potentially long-term negative effects of such activities.
    Type of Medium: Online Resource
    ISSN: 0962-8452 , 1471-2954
    Language: English
    Publisher: The Royal Society
    Publication Date: 2021
    detail.hit.zdb_id: 1460975-7
    SSG: 12
    SSG: 25
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  • 7
    Online Resource
    Online Resource
    Canadian Science Publishing ; 2004
    In:  Canadian Journal of Zoology Vol. 82, No. 12 ( 2004-12-01), p. 1864-1870
    In: Canadian Journal of Zoology, Canadian Science Publishing, Vol. 82, No. 12 ( 2004-12-01), p. 1864-1870
    Abstract: During 1960–2002, the arrival times of all spawning male and female Atlantic salmon (Salmo salar L., 1758) and brown trout (Salmo trutta L., 1758) entering Dalälven River were recorded. To study the role of environmental variation in spawning migration timing, we used long-term temperature (river and sea) and river discharge data. For salmon, the spawning migration peak was strongly correlated with mean monthly sea and river temperatures during spring: salmon arrived earlier when temperatures were higher and later when temperatures were lower. River discharge explained little of the variation in migration timing. Female salmon migration showed a stronger correlation with temperature than male salmon migration, and female salmon arrived ≈18 days earlier than males. Trout showed a larger variation in their spawning migration, but river and sea temperatures and river discharge explained little of the variation. Trout females arrived ≈7 days earlier than males. The sea and river temperatures were highly correlated during the spawning migration, indicating that large climate processes determine the temperature regimes in the Baltic Sea and its tributaries. Time of arrival at the river was not correlated with ovulation date; a female salmon or brown trout arriving late could ovulate almost immediately, whereas a female arriving early could wait to ovulate.
    Type of Medium: Online Resource
    ISSN: 0008-4301 , 1480-3283
    RVK:
    Language: English
    Publisher: Canadian Science Publishing
    Publication Date: 2004
    detail.hit.zdb_id: 1490831-1
    SSG: 12
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  • 8
    In: Aquatic Conservation: Marine and Freshwater Ecosystems, Wiley, Vol. 31, No. 8 ( 2021-08), p. 1970-1982
    Abstract: The noble crayfish ( Astacus astacus ) is an endangered freshwater species in Europe. The main threat is from lethal crayfish plague, caused by the oomycete Aphanomyces astaci that has been spread over Europe by introduced North American crayfish species, acting as chronic carriers of the disease. Most of the remaining noble crayfish populations are found in the Baltic Sea area, and there is an urgent need to implement conservation actions to slow down or halt the extinction rate in this region. However, limited knowledge about the genetic structure of populations in this area has so far precluded the development of conservation strategies that take genetic aspects into consideration. Key objectives of this large‐scale genetic study, covering 77 locations mainly from northern Europe, were to describe the contemporary population genetic structure of the noble crayfish in the Fennoscandian peninsula (Sweden, Norway, and Finland), taking postglacial colonization history into account, and to evaluate how human activities such as stocking have affected the genetic structure of the populations. Analyses of 15 microsatellite markers revealed three main genetic clusters corresponding to populations in northern, middle, and southern Fennoscandia, with measures of genetic diversity being markedly higher within populations in the southern cluster. The observed genetic structure probably mirrors two main colonizations of the Baltic Sea basin after the last glaciation period. At the same time, several deviations from this pattern were observed, reflecting past human translocations of noble crayfish. The results are discussed in relation to the conservation and management of this critically endangered species. In particular, we recommend increased efforts to protect the few remaining noble crayfish populations in southern Fennoscandia and the use of genetic information when planning stocking activities, such as reintroductions following local extinctions.
    Type of Medium: Online Resource
    ISSN: 1052-7613 , 1099-0755
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2021
    detail.hit.zdb_id: 1146285-1
    detail.hit.zdb_id: 1496050-3
    SSG: 12
    SSG: 14
    SSG: 21
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  • 9
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2004
    In:  Hereditas Vol. 122, No. 3 ( 2004-05-28), p. 293-294
    In: Hereditas, Springer Science and Business Media LLC, Vol. 122, No. 3 ( 2004-05-28), p. 293-294
    Type of Medium: Online Resource
    ISSN: 0018-0661
    RVK:
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2004
    detail.hit.zdb_id: 2092962-6
    SSG: 12
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  • 10
    Online Resource
    Online Resource
    Canadian Science Publishing ; 2008
    In:  Canadian Journal of Fisheries and Aquatic Sciences Vol. 65, No. 8 ( 2008-08), p. 1738-1748
    In: Canadian Journal of Fisheries and Aquatic Sciences, Canadian Science Publishing, Vol. 65, No. 8 ( 2008-08), p. 1738-1748
    Abstract: Several studies have shown that fish shoals may consist of closely related individuals. It has been found, for example, that released out-migrating salmon smolts tend to aggregate with kin, including when sibling groups have been reared separately. We used genetic microsatellite markers to test whether “shoals” of adult Atlantic salmon ( Salmo salar ) during the marine phase (i.e., aggregations of fish caught in drift nets at offshore feeding areas in the Baltic Sea) consisted of closely related individuals (full-siblings, half-siblings). We found no evidence of kin cohesiveness related to shoals, however. Despite a weak overall tendency for individuals assigned to the same population (river or stock) to occur together, estimates of genetic relatedness in combination with consistent heterozygote deficiencies, and results from mixed-stock analyses and assignment tests collectively indicated that shoals consisted of unrelated fish from multiple populations.
    Type of Medium: Online Resource
    ISSN: 0706-652X , 1205-7533
    Language: English
    Publisher: Canadian Science Publishing
    Publication Date: 2008
    detail.hit.zdb_id: 7966-2
    detail.hit.zdb_id: 1473089-3
    SSG: 21,3
    SSG: 12
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