The appeal of genetic inference methods to assess population genetic structure and guide management efforts is grounded in the correlation between the genetic similarity and gene flow among populations. Effects of such gene flow are typically genomewide; however, some loci may appear as outliers, displaying above or below average genetic divergence relative to the genomewide level. Above average population, genetic divergence may be due to divergent selection as a result of local adaptation. Consequently, substantial efforts have been directed toward such outlying loci in order to identify traits subject to local adaptation. Here, we report the results of an investigation into the molecular basis of the substantial degree of genetic divergence previously reported at allozyme loci among North Atlantic fin whale (Balaenoptera physalus) populations. We sequenced the exons encoding for the two most divergent allozyme loci (MDH-1 and MPI) and failed to detect any nonsynonymous substitutions. Following extensive error checking and analysis of additional bioinformatic and morphological data, we hypothesize that the observed allozyme polymorphisms may reflect phenotypic plasticity at the cellular level, perhaps as a response to nutritional stress. While such plasticity is intriguing in itself, and of fundamental evolutionary interest, our key finding is that the observed allozyme variation does not appear to be a result of genetic drift, migration, or selection on the MDH-1 and MPI exons themselves, stressing the importance of interpreting allozyme data with caution. As for North Atlantic fin whale population structure, our findings support the low levels of differentiation found in previous analyzes of DNA nucleotide loci.
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Due to an improved understanding of past climatological conditions, it has now become possible to study the potential concordance between former climatological models and present-day genetic structure. Genetic variability was assessed in 26 samples from different rivers of Atlantic salmon in Iceland (total of 2,352 individuals), using 15 microsatellite loci. F-statistics revealed significant differences between the majority of the populations that were sampled. Bayesian cluster analyzes using both prior information and no prior information on sampling location revealed the presence of two distinguishable genetic pools - namely, the Northern (Group 1) and Southern (Group 2) regions of Iceland. Furthermore, the random permutation of different allele sizes among allelic states revealed a significant mutational component to the genetic differentiation at four microsatellite loci (SsaD144, Ssa171, SSsp2201 and SsaF3), and supported the proposition of a historical origin behind the observed variation. The estimated time of divergence, using two different ABC methods, suggested that the observed genetic pattern originated from between the Last Glacial Maximum to the Younger Dryas, which serves as additional evidence of the relative immaturity of Icelandic fish populations, on account of the re- colonization of this young environment following the Last Glacial Maximum. Additional analyzes suggested the presence of several genetic entities which were likely to originate from the original groups detected.
Shallow population structure is generally reported for most marine fish and explained as a consequence of high dispersal, connectivity and large population size. Targeted gene analyzes and more recent genome-wide studies have challenged such view, suggesting that adaptive divergence might occur even when neutral markers provide genetic homogeneity across populations. Here, 381 SNPs located in transcribed regions were used to assess large- and fine-scale population structure in the European hake (Merluccius merluccius), a widely distributed demersal species of high priority for the European fishery. Analysis of 850 individuals from 19 locations across the entire distribution range showed evidence for several outlier loci, with significantly higher resolving power. While 299 putatively neutral SNPs confirmed the genetic break between basins (FCT = 0.016) and weak differentiation within basins, outlier loci revealed a dramatic divergence between Atlantic and Mediterranean populations (FCT range 0.275–0.705) and fine-scale significant population structure. Outlier loci separated North Sea and Northern Portugal populations from all other Atlantic samples and revealed a strong differentiation among Western, Central and Eastern Mediterranean geographical samples. Significant correlation of allele frequencies at outlier loci with seawater surface temperature and salinity supported the hypothesis that populations might be adapted to local conditions. Such evidence highlights the importance of integrating information from neutral and adaptive evolutionary patterns towards a better assessment of genetic diversity. Accordingly, the generated outlier SNP data could be used for tackling illegal practices in hake fishing and commercialization as well as to develop explicit spatial models for defining management units and stock boundaries.
Perfluorinatedalkyl acids (PFAAs) are of growing concern due to possible health effects on humans. Exposure assessments indicate that fish consumption is one of the major sources of perfluorooctane sulfonate (PFOS) exposure to humans, one of the major PFASs, whereas concerns of overestimation of this exposure source have been raised. Therefore, PFAAs concentrations in fish from the North Atlantic (Icelandic fishing grounds) in the flesh of different fish species were investigated along with more detailed analyzes of tissue concentrations in cod (Gadus morhua) and lumpfish (Cyclopterus lumpus). Further, fish feed was investigated as a possible source of PFAAs in aquaculture by examining fish meal as feed ingredient. No PFAAs were detected in the edible part of all fish samples, except for PFOS in pollock (Pollachius virens, 0.05 ng / g wet weight). PFOS was the only PFAA detected in the fish meal samples with the exception of PFOSA in blue whiting (Micromesistius poutassou) meal (0,45 ng / g dry weight (dw)), where the PFOS concentration was 1,3–13 ng / g dw in the capelin (Mallotus villosus) and mackerel (Scomber scombrus) meal samples. The conclusions of the study are that fish commonly consumed from the Icelandic fishing grounds are unlikely to be an important source of PFAAs exposure.
The stock structure of turbot was investigated between samples from S-Norway, the Irish Sea and the Kattegat, using 12 microsatellite loci and compared to the turbot caught in Icelandic waters. Highly significant genetic differentiation was observed between samples from Kattegat and other areas. Significant genetic differentiation was also observed between the Irish Sea sample on one hand and Iceland and S-Norway on the other hand. No significant genetic differentiation was observed between Iceland and S-Norway. Otoliths of 25 turbot, age ranging from 3 to 19 years, were subjected to nearly 300 mass spectrometry determinations of stable oxygen and carbon isotopes. Oxygen isotope composition (δ18O) in the otolith samples was used to estimate ambient temperature at time of otolith accretion, and yielded estimated temperatures experienced by the turbot ranging from 3 to 15 ° C. Overall, the genetic analysis indicates panmixia between turbot in Icelandic and Norwegian waters. While the extensive migration of larvae between Norway and Iceland is unlikely, passive drift of turbot larva from other areas (eg Ireland) cannot be ruled out.
Several bacteriophages that infect different strains of the thermophilic bacterium Rhodothermus marinus were isolated and their infection pattern was studied. One phage, named RM378 was cultivated and characterized. The RM378 genome was also sequenced and analyzed. The phage was grouped as a member of the Myoviridae family with A2 morphology. It had a moderately elongated head, with dimensions of 85 and 95 nm between opposite apices and a 150 nm long tail, attached with a connector to the head. RM378 showed a virulent behavior that followed a lytic cycle of infection. It routinely gave lysates with 1011 pfu / ml, and sometimes reached titers as high as 1013 pfu / ml. The titer remained stable up to 65 ° C but the phage lost viability when incubated at higher temperatures. Heating for 30 min at 96 ° C lowered the titer by 104. The RM378 genome consisted of ds DNA of 129,908 bp with a GC ratio of 42.0 % and contained about 120 ORFs. A few structural proteins, such as the major head protein corresponding to the gp23 in T4, could be identified. Only 29 gene products as probable homologs to other proteins of known function could be predicted, with most showing only low similarity to known proteins in other bacteriophages. These and other studies based on sequence analysis of a large number of phage genomes showed RM378 to be distantly related to all other known T4-like phages.
A novel and non-ubiquitous thermostable DNA polymerase in Thermus antranikianii was expressed in E. coli, isolated and biochemically characterized. The enzyme here referred to as Thermophi, has a C-terminal polymerase domain and a proofreading 3 ′ → 5 ′ exonuclease domain, but lacks the 5 ′ → 3 ′ exonuclease domain. The corresponding gene is apparently only found in some but not all Thermus strains. The initial rate of specific activity of this polymerase on nicked DNA was about 360,000 U / mg protein. The optimum activity was found at 55 ° C, pH 8.5 and 1.5 mM Mg+2. The polymerase was stable at 70 ° C and lost 50% of its activity after 5 min at 85 ° C, but could be stabilized above 80 ° C by the addition of 0.5 M L-proline. A pronounced strand-displacement activity was indicated by the large amount of DNA produced by the enzyme after an overnight, isothermal incubation in the presence of hexamer primers. Both single and double stranded DNA was isothermally amplified by the enzyme. The amplified DNA was large and apparently highly branched material and composed of both single and double stranded DNA. The produced material could be partly digested by T7 enonuclease I but it was difficult to cut with common restriction enzymes. Amplification of selected genes from dilute samples was successfully demonstrated with the human β-actin gene. Good amplification was also found with 5 microsatellite markers from salmon DNA. Thermophi amplifies DNA by orders of magnitude but upon extended reaction time the DNA becomes very large and highly branched. It is composed of both single and double strands and then correctly amplified sequences only represent about 10-20% of the total DNA, and long stretches of TATATA repeats frequently occur in the amplified DNA.
Increasing consumer demand for seafood, combined with concern over the health of our oceans, has led to many initiatives aimed at tackling destructive fishing practices and promoting the sustainability of fisheries. An important global threat to sustainable fisheries is Illegal, Unreported and Unregulated (IUU) fishing, and there is now an increased emphasis on the use of trade measures to prevent IUU-sourced fish and fish products from entering the international market. Initiatives encompass new legislation in the European Union requiring the inclusion of species names on catch labels throughout the distribution chain. Such certification measures do not, however, guarantee accuracy of species designation. Using two DNA-based methods to compare species descriptions with molecular ID, we examined 386 samples of white fish, or products labeled as primarily containing white fish, from major UK supermarket chains. Species specific real-time PCR probes were used for cod (Gadus morhua) and haddock (Melanogrammus aeglefinus) to provide a highly sensitive and species-specific test for the major species of white fish sold in the UK. Additionally, fish-specific primers were used to sequence the forensically validated barcoding gene, mitochondrial cytochrome oxidase I (COI). Overall levels of congruence between product label and genetic species identification were high, with 94.34% of samples correctly labeled, though a significant proportion in terms of potential volume, were mislabelled. Substitution was usually for a cheaper alternative and, in one case, extended to a tropical species. To our knowledge, this is the first published study encompassing a large-scale assessment of UK retailers, and if representative, indicates a potentially significant incidence of incorrect product designation.
Value added products such as fish protein hydrolysates (FPH) can be produced from fish by-products. Lipid oxidation and bad taste are the major challenge in the commercialization of bioactive FPH. The aim of this research was to study the production of high quality FPH from fish by-products prepared by enzymatic hydrolysis using a natural antioxidant extracted from the Icelandic brown algae Fucus vesiculosus (Fv). FPH were produced from cod waste material; ie cod bone mince, in the absence and presence of an Fv extract (Fv-e). Oxidation during FPH production was evaluated (lipid hydroperoxides and thiobarbituric acid reactive substances). The FPH were sensory analyzed (generic descriptive analysis) and in vitro antioxidant activity was evaluated. Results show that Fv–e contributed to better tasting FPH with regard to bitter, soap, fish oil and rancidity taste. Results from the oxidation and antioxidant activity assays indicated a protecting effect of Fv-e during processing.
Fish protein hydrolysates (FPH) have many desirable properties, however heating and shifts in pH can cause oxidation during enzymatic hydrolysis. The objective was to investigate oxidative processes during enzymatic hydrolysis of fish protein and the impact of oxidation on the antioxidant and immunomodulating ability of FPH. Protease P “Amano” 6 was used to hydrolyze cod protein in the presence and absence of pro-oxidants at pH 8 and 36 ° C to achieve 20% degree of hydrolysis. Results from thiobarbituric acid reactive substances (TBARS) and sensory analysis indicate that oxidation can develop rapidly during hydrolysis. A cellular antioxidant assay using a HepG2 cell model indicated a negative impact of oxidation products on antioxidant properties of the FPH while results obtained in chemical assays showed a negligible impact. Results from a dendritic cell model indicating that oxidation products may affect anti-inflammatory activity in the body. This study provides important information regarding bioactive FPH.