Browsing by Subject "SALMON SALMO-SALAR"

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  • Lemopoulos, Alexandre; Prokkola, Jenni M.; Uusi-Heikkilä, Silva; Vasemägi, Anti; Huusko, Ari; Hyvarinen, Pekka; Koljonen, Marja-Liisa; Koskiniemi, Jarmo; Vainikka, Anssi (2019)
    The conservation and management of endangered species requires information on their genetic diversity, relatedness and population structure. The main genetic markers applied for these questions are microsatellites and single nucleotide polymorphisms (SNPs), the latter of which remain the more resource demanding approach in most cases. Here, we compare the performance of two approaches, SNPs obtained by restriction-site-associated DNA sequencing (RADseq) and 16 DNA microsatellite loci, for estimating genetic diversity, relatedness and genetic differentiation of three, small, geographically close wild brown trout (Salmo trutta) populations and a regionally used hatchery strain. The genetic differentiation, quantified as F-ST, was similar when measured using 16 microsatellites and 4,876 SNPs. Based on both marker types, each brown trout population represented a distinct gene pool with a low level of interbreeding. Analysis of SNPs identified half- and full-siblings with a higher probability than the analysis based on microsatellites, and SNPs outperformed microsatellites in estimating individual-level multilocus heterozygosity. Overall, the results indicated that moderately polymorphic microsatellites and SNPs from RADseq agreed on estimates of population genetic structure in moderately diverged, small populations, but RADseq outperformed microsatellites for applications that required individual-level genotype information, such as quantifying relatedness and individual-level heterozygosity. The results can be applied to other small populations with low or moderate levels of genetic diversity.
  • O'Sullivan, Ronan James; Aykanat, Tutku; Johnston, Susan E.; Kane, Adam; Poole, Russell; Rogan, Ger; Prodöhl, Paulo A.; Primmer, Craig R.; McGinnity, Philip; Reed, Thomas Eric (2019)
    Comparing observed versus theoretically expected evolutionary responses is important for our understanding of the evolutionary process, and for assessing how species may cope with anthropogenic change. Here, we document directional selection for larger female size in Atlantic salmon, using pedigree-derived estimates of lifetime reproductive success as a fitness measure. We show the trait is heritable and, thus, capable of responding to selection. The Breeder's Equation, which predicts microevolution as the product of phenotypic selection and heritability, predicted evolution of larger size. This was at odds, however, with the observed lack of either phenotypic or genetic temporal trends in body size, a so-called "paradox of stasis." To investigate this paradox, we estimated the additive genetic covariance between trait and fitness, which provides a prediction of evolutionary change according to Robertson's secondary theorem of selection (STS) that is unbiased by missing variables. The STS prediction was consistent with the observed stasis. Decomposition of phenotypic selection gradients into genetic and environmental components revealed a potential upward bias, implying unmeasured factors that covary with trait and fitness. These results showcase the power of pedigreed, wild population studies-which have largely been limited to birds and mammals-to study evolutionary processes on contemporary timescales.
  • Shikano, Takahito; Järvinen, Antero; Marjamaki, Paula; Kahilainen, Kimmo K.; Merilä, Juha (2015)
    Variation in presumably neutral genetic markers can inform us about evolvability, historical effective population sizes and phylogeographic history of contemporary populations. We studied genetic variability in 15 microsatellite loci in six native landlocked Arctic charr (Salvelinus alpinus) populations in northern Fennoscandia, where this species is considered near threatened. We discovered that all populations were genetically highly (mean F-ST approximate to 0.26) differentiated and isolated from each other. Evidence was found for historical, but not for recent population size bottlenecks. Estimates of contemporary effective population size (N-e) ranged from seven to 228 and were significantly correlated with those of historical N-e but not with lake size. A census size (N-C) was estimated to be approximately 300 individuals in a pond (0.14 ha), which exhibited the smallest N-e (i.e. N-e/N-C = 0.02). Genetic variability in this pond and a connected lake is severely reduced, and both genetic and empirical estimates of migration rates indicate a lack of gene flow between them. Hence, albeit currently thriving, some northern Fennoscandian populations appear to be vulnerable to further loss of genetic variability and are likely to have limited capacity to adapt if selection pressures change.
  • Reed, Thomas E.; Prodohl, Paulo; Bradley, Caroline; Gilbey, John; McGinnity, Philip; Primmer, Craig R.; Bacon, Philip J. (2019)
    While evolutionary responses require heritable variation, estimates of heritability (h(2)) from wild fish populations remain rare. A 20-year molecular pedigree for a wild Scottish population of Atlantic salmon (Salmo salar) was used to investigate genetic contributions to (co) variation in two important, correlated, phenotypic traits: "sea age" (number of winters spent at sea prior to spawning) and size-at-maturity (body length just prior to spawning). Sea age was strongly heritable (h(2) = 0.51) and size exhibited moderate heritability (h(2) = 0.27). A very strong genetic correlation (r(G) = 0.96) between these traits implied the same functional loci must underpin variation in each. Indeed, body size within sea ages had much lower heritability that did not differ significantly from zero. Thus, within wild S. salar populations, temporal changes in sea age composition could reflect evolutionary responses, whereas rapid changes of body size within sea ages are more likely due to phenotypic plasticity. These inheritance patterns will influence the scope of evolutionary responses to factors such as harvest or climate change and, hence, have management implications for salmonid populations comprising a mix of sea ages.
  • Tossavainen, Marika; Lahti, Katariina; Edelmann, Minnamari; Eskola, Reetta; Lampi, Anna-Maija; Piironen, Vieno; Korvonen, Pasi; Ojala, Anne; Romantschuk, Martin (2019)
    Microalgal cultivation in aquaculture wastewater (AWW) from recirculating aquaculture systems (RAS) is an approach for combined production of valuable algal biomass and AWW treatment. The growth, nutrient uptake, fatty acid (FA) profile, and tocopherol content of mixed algal cultures of Euglena gracilis with Selenastrum grown in AWWs from pikeperch (Sander lucioperca) and catfish (Clarias anguillaris) RAS were studied. The highest algal biomass (1.5gL(-1)), lipid (84.9mgL(-1)), and tocopherol (877.2gL(-1)) yields were achieved in sludge-amended pike perch AWW. Nutrient removal rates in experiments were 98.9-99.5 and 98.4-99.8% for NH4-N and PO4-P, and 75.4-89.2% and 84.3-95.7% for TN and TP, respectively, whereas the COD was reduced by 45.8-67.6%. Biomass EPA and DHA content met, while ARA and tocopherol content exceeded the requirements for fish feed. Algal cultivation in AWWs is a promising alternative for AWW treatment while providing a replacement for fish oil in feed.
  • Whitlock, Rebecca; Mäntyniemi, Samu; Palm, Stefan; Koljonen, Marja-Liisa; Dannewitz, Johan; Östergren, Johan (2018)
    1. 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. 2. 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. 3. 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. 4. 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.
  • Teacher, Amber G. F.; Shikano, Takahito; Karjalainen, Marika E.; Merila, Juha (2011)
  • Alioravainen, Nico; Prokkola, Jenni M.; Lemopoulos, Alexandre; Härkönen, Laura; Hyvärinen, Pekka; Vainikka, Anssi (2020)
    Behaviour that is adaptive in captivity may be maladaptive in the wild and compromise postrelease survival of hatchery fish. The understanding of behavioural variation displayed immediately after release could help to improve hatchery protocols and development of behavioural tests for assessing the fitness of fish reared for releases. We characterized the postrelease behaviour of common-garden-raised offspring of wild resident, captive-bred migratory, and hybrid brown trout (Salmo trutta) in two experiments: in small artificial channels and in high and low densities in seminatural streams. The results from seminatural streams showed that hatchery fish were more likely to disperse downstream from the initial stocking site compared with hybrid and wild strain fish. The small-scale experiment did not reveal this ecologically pivotal difference in postrelease performance among strains, and individual responses were inconsistent between the experiments. Circadian activity patterns did not differ among strains. These detailed observations of postrelease behaviour reveal important intrinsic differences in dispersal traits among brown trout strains and suggest that selective breeding and crossbreeding can substantially affect these traits.
  • EFSA Panel Contaminants Food Chain; Knutsen, Helle; Alexander, Jan; Barregård, Lars; Bignami; Bruschweiler; Ceccatelli; Cottrill; Dinovi; Edler; Grasl-Kraupp; Hogstrand; Nebbia; Oswald; Petersen; Rose; Roudot; Schwerdtle; Vleminckx; Vollmer; Wallace; Furst; Håkansson, Helen; Halldorsson; Lundebye; Pohjanvirta, Raimo Kalevi; Rylander; Smith; van Loveren; Waalkens-Berendsen; Zeilmaker; Binaglia; Gomez Ruiz; Horvath; Christoph; Ciccolallo; Ramos Bordajandi; Steinkellner; Hoogenboom, Ron (2018)
    The European Commission asked EFSA for a scientific opinion on the risks for animal and human health related to the presence of dioxins (PCDD/Fs) and DL-PCBs in feed and food. The data from experimental animal and epidemiological studies were reviewed and it was decided to base the human risk assessment on effects observed in humans and to use animal data as supportive evidence. The critical effect was on semen quality, following pre- and postnatal exposure. The critical study showed a NOAEL of 7.0 pg WHO2005-TEQ/g fat in blood sampled at age 9 years based on PCDD/F-TEQs. No association was observed when including DL-PCB-TEQs. Using toxicokinetic modelling and taking into account the exposure from breastfeeding and a twofold higher intake during childhood, it was estimated that daily exposure in adolescents and adults should be below 0.25 pg TEQ/kg bw/day. The CONTAM Panel established a TWI of 2 pg TEQ/kg bw/week. With occurrence and consumption data from European countries, the mean and P95 intake of total TEQ by Adolescents, Adults, Elderly and Very Elderly varied between, respectively, 2.1 to 10.5, and 5.3 to 30.4 pg TEQ/kg bw/week, implying a considerable exceedance of the TWI. Toddlers and Other Children showed a higher exposure than older age groups, but this was accounted for when deriving the TWI. Exposure to PCDD/F-TEQ only was on average 2.4- and 2.7-fold lower for mean and P95 exposure than for total TEQ. PCDD/Fs and DL-PCBs are transferred to milk and eggs, and accumulate in fatty tissues and liver. Transfer rates and bioconcentration factors were identified for various species. The CONTAM Panel was not able to identify reference values in most farm and companion animals with the exception of NOAELs for mink, chicken and some fish species. The estimated exposure from feed for these species does not imply a risk.