Escaping malnutrition by shifting habitats: A driver of three-spined stickleback invasion in Lake Constance

Fatty acids, and especially long-chain polyunsaturated fatty acids, are biologically important components in the metabolism of vertebrates, including fish. Essential fatty acids (EFA) are those that in a given animal cannot be synthesized or modified from precursors and must therefore be acquired via the diet. Because EFAs are often unevenly distributed in nature, this requirement may drive species to make behavioral or ecological adaptations to avoid malnutrition. This is especially true for fish like the three-spined stickleback (Gasterosteus aculeatus L.) of Upper Lake Constance (ULC), whose recent marine ancestors evolved with access to EFA-rich prey, but which found themselves in an EFA-deficient habitat. An unexpected and unprecedented ecological shift in the ULC stickleback population from the littoral to pelagic zones in 2012 might be linked to EFA availability, triggering ecological release and enabling them to build a hyperabundant population while displacing the former keystone species, the pelagic whitefish Coregonus wartmanni. To test this hypothesis, sticklebacks from the littoral and pelagic zones of ULC were sampled seasonally in two consecutive years, and their stomach contents and fatty acid profiles were analysed. Pelagic sticklebacks were found to possess significantly higher values of an important EFA, docosahexaenoic acid (DHA), especially during autumn. Evaluation of the DHA supply suggests that sticklebacks feeding in the littoral zone during autumn could not meet their DHA requirement, whereas DHA availability in the pelagic zone was surplus to demand. During autumn, pelagic sticklebacks consumed large amounts of DHA-rich prey, that is, copepods, whereas littoral sticklebacks relied mainly mostly on cladocerans, which provide much lower quantities of DHA. Access to pelagic zooplankton in 2012 was possibly facilitated by low densities of previously dominant zooplanktivorous whitefish. The present study offers a convincing physiological explanation for the observed expansion of invasive sticklebacks from the littoral to the pelagic zones of Lake Constance, contributing to a phase shift with severe consequences for fisheries.

Epigenetic and Genetic Differentiation Between Coregonus Species Pairs

Phenotypic diversification is classically associated with genetic differentiation and gene expression variation. However, increasing evidence suggests that DNA methylation is involved in evolutionary processes due to its phenotypic and transcriptional effects. Methylation can increase mutagenesis and could lead to increased genetic divergence between populations experiencing different environmental conditions for many generations, though there has been minimal empirical research on epigenetically induced mutagenesis in diversification and speciation. Whitefish, freshwater members of the salmonid family, are excellent systems to study phenotypic diversification and speciation due to the repeated divergence of benthic-limnetic species pairs serving as natural replicates. Here we investigate whole genome genetic and epigenetic differentiation between sympatric benthic-limnetic species pairs in lake and European whitefish (Coregonus clupeaformis and Coregonus lavaretus) from four lakes (N = 64). We found considerable, albeit variable, genetic and epigenetic differences between species pairs. All SNP types were enriched at CpG sites supporting the mutagenic nature of DNA methylation, though C>T SNPs were most common. We also found an enrichment of overlaps between outlier SNPs with the 5% highest FST between species and differentially methylated loci. This could possibly represent differentially methylated sites that have caused divergent genetic mutations between species, or divergent selection leading to both genetic and epigenetic variation at these sites. Our results support the hypothesis that DNA methylation contributes to phenotypic divergence and mutagenesis during whitefish speciation.

The Effects of Enzymes, Species, and Storage of Raw Material on Physicochemical Properties of Protein Hydrolysates from Whitefish Heads

The rest raw materials of whitefish have great potential for increased utilisation and value creation. Whitefish heads have a high protein content and should be considered a healthy protein source for the growing population's demands for sustainable protein. In this study, the heads of four different species of whitefish were processed via enzymatic hydrolysis, namely cod (Gadus morhua), cusk (Brosme bromse), haddock (Melanogrammus aeglefinus), and saithe (Pollachius virens), using three commercially available enzymes. Trials were conducted after 0, 3, and 6 months of the frozen storage of heads. A proximate analysis, molecular weight distribution, and protein solubility were evaluated for each of the products. The results show that, although the enzymatic hydrolysis of rest raw materials from different species of whitefish yielded products of slightly different characteristics, this process is viable for the production of high-quality protein from cod, cusk, haddock, and saithe heads. Six months of frozen storage of heads had a minimal effect on the yield and proximate composition of hydrolysates.

Thermal Preconditioning Alters the Stability of Hump-Snout Whitefish (Coregonus fluviatilis) and Its Hybrid Form, Showing Potential for Aquaculture

One of the little-studied ways that climate warming or temperature increases in aquaculture could affect aquatic animals is through accelerated aging. This study is dedicated to understanding the principles of molecular and cellular aging in the target tissues of juvenile whitefishes (Yenisei hump-snout whitefish and its hybrid) under the influence of acute heat stress (up to 26 °C), and the effects of thermal preconditioning as pre-adaptation. Non-adapted stressed hump-snout whitefish showed a higher induction threshold for functionally active mitochondria in the blood and a decrease in telomerase activity in the liver after heat shock exposure as a long-term compensatory response to prevent telomere shortening. However, we observed heat-induced telomere shortening in non-adapted hybrids, which can be explained by a decrease in mitochondrial membrane stability and a gradual increase in energy demand, leading to a decrease in protective telomerase activity. The pre-adapted groups of hump-snout whitefish and hybrids showed a long-term or delayed response of telomerase activity to heat shock, which served as a therapeutic mechanism against telomere shortening. We concluded that the telomerase and telomere responses to thermal stress demonstrate plasticity of tolerance limits and greater stability in hump-snout whitefish compared with hybrids.

Genomic selection for survival under naturally occurring Saprolegnia oomycete infection in farmed European whitefish Coregonus lavaretus

Saprolegnia oomycete infection causes serious economic losses and reduces fish health in aquaculture. Genomic selection based on thousands of DNA markers is a powerful tool to improve fish traits in selective breeding programs. Our goal was to develop a single nucleotide polymorphism (SNP) marker panel and to test its use in genomic selection for improved survival against Saprolegnia infection in European whitefish Coregonus lavaretus, the second most important farmed fish species in Finland. We used a double digest restriction site associated DNA (ddRAD) genotyping by sequencing method to produce a SNP panel, and we tested it analyzing data from a cohort of 1,335 fish, which were measured at different times for mortality to Saprolegnia oomycete infection and weight traits. We calculated the genetic relationship matrix (GRM) from the genome-wide genetic data, integrating it in multivariate mixed models used for the estimation of variance components and genomic breeding values (GEBVs), and to carry out Genome-Wide Association Studies for the presence of quantitative trait loci (QTL) affecting the phenotypes in analysis. We identified one major QTL on chromosome 6 affecting mortality to Saprolegnia infection, explaining 7.7% to 51.3% of genetic variance, and a QTL for weight on chromosome 4, explaining 1.8% to 5.4% of genetic variance. Heritability for mortality was 0.20 to 0.43 on the liability scale, and heritability for weight was 0.44 to 0.53. The QTL for mortality showed an additive allelic effect. We tested whether integrating the QTL for mortality as a fixed factor, together with a new GRM calculated excluding the QTL from the genetic data, would improve the accuracy estimation of GEBVs. This test was done through a cross-validation approach, which indicated that the inclusion of the QTL increased the mean accuracy of the GEBVs by 0.28 points, from 0.33 to 0.61, relative to the use of full GRM only. The area under the curve of the receiver-operator curve for mortality increased from 0.58 to 0.67 when the QTL was included in the model. The inclusion of the QTL as a fixed effect in the model increased the correlation between the GEBVs of early mortality with the late mortality, compared to a model that did not include the QTL. These results validate the usability of the produced SNP panel for genomic selection in European whitefish and highlight the opportunity for modeling QTLs in genomic evaluation of mortality due to Saprolegnia infection.

Allopatric origin of sympatric whitefish morphs with insights on the genetic basis of their reproductive isolation

The European whitefish (Coregonus lavaretus) species complex is a classic example of recent adaptive radiation. Here, we examine a whitefish population introduced to northern Finnish Lake Tsahkal in the late 1960s, where three divergent morphs (viz. littoral, pelagic, and profundal feeders) were found 10 generations after. Using demographic modeling based on genomic data, we show that whitefish morphs evolved during a phase of strict isolation, refuting a rapid sympatric divergence scenario. The lake is now an artificial hybrid zone between morphs originated in allopatry. Despite their current syntopy, clear genetic differentiation remains between two of the three morphs. Using admixture mapping, we identify five SNPs associated with gonad weight variation, a proxy for sexual maturity and spawning time. We suggest that ecological adaptations in spawning time evolved in allopatry are currently maintaining partial reproductive isolation in the absence of other barriers to gene flow.

Can young-of-the-year invasive fish keep up with young-of-the-year native fish? A comparison of feeding rates between invasive sticklebacks and whitefish

Invasion of non-native species might alter food web structure and the strength of top-down control within lake ecosystems. As top-down control exerted by fish populations is often dominated by young of the year fish, the impact of new fish species might depend on the feeding rates of the juvenile fish. Here we provide comparative analyses of feeding rates of juvenile whitefish (Coregonus wartmanni) - a native and specialised planktivore and an invasive generalist (sticklebacks, Gasterosteus aculeatus). We studied feedings rates of whitefish and sticklebacks in aquaria experiments using 2 cm to 8 cm fish feeding on seven zooplankton species common to Lake Constance. As whitefish hatch several months earlier than sticklebacks, 0+ whitefish are larger than 0+ sticklebacks throughout the year and hence are predicted to have higher feeding rates on especially large zooplankton species. We show that sticklebacks as small as 2 cm were able to feed on the largest zooplankton species of Lake Constance. Further, stickleback feeding rates were similar to both the same size 0+ whitefish and the larger 0+ whitefish co-occurring with smaller 0+ sticklebacks. Hence, 0+ sticklebacks will compete with 0+ whitefish for the same zooplankton species, therefore the invasion of sticklebacks is unlikely to change the relative feeding pressure by individual 0+ fish on zooplankton species.

Freeze-Chilling of Whitefish: Effects of Capture, On-Board Processing, Freezing, Frozen Storage, Thawing, and Subsequent Chilled Storage-A Review

The current review investigates how whitefish quality is affected by capture at sea, on board handling, freezing, double freezing, frozen storage, thawing, and chilled storage. Packaging of fillets in MAP and vacuum are also covered. The main goal was to evaluate the freeze-chilling concept as a possible method for the fishing industry for all-year-round marketing of fish captured during the relatively short fishing period. The review covers both the effect of each processing step in the supply chain as well as the combined effect of all steps in the chain from sea to consumer, including post-thawing chilled storage, defined as the freeze-chilling method.

Ultra-acute exposure to cadmium does not impair whitefish sperm motility

Cadmium (Cd) exposure can impair the traits of aquatic animals associated with reproduction. In natural lakes Cd is typically detected at concentrations below 0.001 mg l^-1 . The authors investigated the impact of ultra-acute Cd exposure on sperm motility in European whitefish (Coregonus lavaretus). They activated sperm with water containing various nominal concentrations of Cd and recorded sperm motility parameters. Only the highest Cd concentration (500 mg l^-1 ) was associated with decreased sperm swimming velocity and increases in both the percentage of static cells and curvature of the sperm swimming trajectory. The results indicate that environmentally realistic concentrations of Cd during the sperm motility activation are not critically harmful to male C. lavaretus fertilization potential.

A taxonomic revision of the whitefish of lakes Brienz and Thun, Switzerland, with descriptions of four new species (Teleostei, Coregonidae)

The alpha taxonomy of the endemic whitefish of lakes Brienz and Thun, Switzerland, is revised. We evaluate the status of seven known species: Coregonus steinmanni sp. nov., Coregonus profundus sp. nov. and Coregonus acrinasus sp. nov. are endemic to Lake Thun; Coregonus Brienzii sp. nov. is endemic to Lake Brienz; and C. alpinus, C. albellus, and C. fatioi from lakes Brienz and Thun are redescribed. One of these species, C. alpinus, is revised, since the lectotype for this species is incongruent with the species description given by Kottelat (1997) and Kottelat and Freyhof (2007). The name C. alpinus is thus retained for the lectotype designated by Kottelat (1997) and a new description of this taxon provided. For the species otherwise described by Kottelat (1997) and Kottelat and Freyhof (2007) as C. alpinus the new name C. profundus is designated. Coregonus acrinasus is genetically partially of allochthonous origin, closely related to the radiation of Lake Constance, and we therefore compare it to all recognized species of Lake Constance, C. wartmanni, C. macrophthalmus, C. arenicolus, and C. gutturosus.

"Balchen": One representative of the Swiss Alpine whitefish radiation

Salmonids are of particular interest to evolutionary biologists due to their incredible diversity of life-history strategies and the speed at which many salmonid species have diversified. In Switzerland alone, over 30 species of Alpine whitefish from the subfamily Coregoninae have evolved since the last glacial maximum, with species exhibiting a diverse range of morphological and behavioural phenotypes. This, combined with the whole genome duplication which occurred in the ancestor of all salmonids, makes the Alpine whitefish radiation a particularly interesting system in which to study the genetic basis of adaptation and speciation and the impacts of ploidy changes and subsequent rediploidization on genome evolution. Although well-curated genome assemblies exist for many species within Salmonidae, genomic resources for the subfamily Coregoninae are lacking. To assemble a whitefish reference genome, we carried out PacBio sequencing from one wild-caught Coregonus sp. "Balchen" from Lake Thun to ~90× coverage. PacBio reads were assembled independently using three different assemblers, falcon, canu and wtdbg2 and subsequently scaffolded with additional Hi-C data. All three assemblies were highly contiguous, had strong synteny to a previously published Coregonus linkage map, and when mapping additional short-read data to each of the assemblies, coverage was fairly even across most chromosome-scale scaffolds. Here, we present the first de novo genome assembly for the Salmonid subfamily Coregoninae. The final 2.2-Gb wtdbg2 assembly included 40 scaffolds, an N50 of 51.9 Mb and was 93.3% complete for BUSCOs. The assembly consisted of ~52% transposable elements and contained 44,525 genes.

A Comparison of Pneumatic and Hand Stripping of Whitefish (Coregonus lavaretus) Eggs for Artificial Reproduction

Simple Summary

This paper describes a technique of pneumatic stripping of whitefish (Coregonus lavaretus) eggs with the use of oxygen, nitrogen, and air. This study demonstrates that pneumatic stripping allows the collection of high-quality whitefish eggs. Moreover, we found that gas flow rates should not exceed 0.5 L∙min⁻¹ to minimize post-spawning mortality in whitefish. The eggs obtained by pneumatic stripping using oxygen, nitrogen, or air had high hatching rates. We assumed that air stripping is a promising approach for improvement of the whitefish stripping procedure.

Abstract

We describe the technique of pneumatic stripping of whitefish (Coregonus lavaretus) eggs with the use of oxygen, nitrogen, and air. Eggs obtained via the traditional method (by pressing the abdominal surfaces) served as a control group. It was established that the gas flow rate during pneumatic stripping should not exceed 0.5 L∙min⁻¹, since higher air flow resulted in increased post-spawning mortality. The pneumatic stripping method of egg collection was no faster than hand stripping; however, the time required per female was more consistent. It was found that the pH of the ovarian fluid obtained during hand and pneumatic stripping was not related to the success rate of fertilization. Pneumatic stripping resulted in a higher quality of collected eggs and a higher and more consistent hatching rate as compared with the hand-stripped samples, regardless of the gas used. The results presented here lead us to recommend the pneumatic method for obtaining eggs from whitefish, since it is a simple, reproducible method and improves the reproductive performance and developmental success of the fish eggs.

A comparative study of quality and safety of Atlantic cod (Gadus morhua) fillets during cold storage, as affected by different thawing methods of pre-rigor frozen headed and gutted fish

BACKGROUND

The catch of marine whitefish is typically seasonal, whereas the land-based processing industry has a need for all-year stable supply of raw materials. This challenge can be met by applying fish frozen at sea. When using frozen fish, the methods employed for thawing may influence the safety and quality of the final product. This study aimed to investigate the applicability of novel thawing strategies in order to provide an all-year supply of high-quality and safe cod products.

RESULTS

Comparative investigations of quality and safety factors after thawing in water, with and without air circulation, and contact thawing were performed. The parameters included water-holding capacity, thawing loss, drip loss, cooking yield, sensory evaluation and microbiological analyses (including total volatile bases nitrogen). Water thawing with air circulation provided faster thawing than water thawing without air circulation and contact thawing. For all three methods, the quality of the thawed fish was acceptable and the shelf life of the fillets during chilled storage was between 10 and 14 days post-filleting.

CONCLUSION

The results show that controlled freezing of cod, followed by appropriate thawing, may provide the processing industry with an all-year delivery of raw materials, without compromising quality and safety of the final product. © 2017 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Does eutrophication-driven evolution change aquatic ecosystems?

Eutrophication increases primary production and changes the relative abundance, taxonomic composition and spatial distribution of primary producers within an aquatic ecosystem. The changes in composition and location of resources alter the distribution and flow of energy and biomass throughout the food web. Changes in productivity also alter the physico-chemical environment, which has further effects on the biota. Such ecological changes influence the direction and strength of natural and sexual selection experienced by populations. Besides altering selection, they can also erode the habitat gradients and/or behavioural mechanisms that maintain ecological separation and reproductive isolation among species. Consequently, eutrophication of lakes commonly results in reduced ecological specialization as well as genetic and phenotypic homogenization among lakes and among niches within lakes. We argue that the associated loss in functional diversity and niche differentiation may lead to decreased carrying capacity and lower resource-use efficiency by consumers. We show that in central European whitefish species radiations, the functional diversity affected by eutrophication-induced speciation reversal correlates with community-wide trophic transfer efficiency (fisheries yield per unit phosphorus). We take this as an example of how evolutionary dynamics driven by anthropogenic environmental change can have lasting effects on biodiversity and ecosystem functioning.This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'.

Mitochondrial DNA phylogeography of least cisco Coregonus sardinella in Alaska

This study presents the first detailed analysis of the mitochondrial DNA diversity of least cisco Coregonus sardinella in Alaska using a 678 bp segment of the control region (D-loop) of the mitochondrial genome. Findings suggest that the history of C. sardinella in Alaska differs from that of other species of Coregonus present in the state and surrounding regions. The examined populations of C. sardinella are genetically diverse across Alaska. Sixty-eight distinct mitochondrial haplotypes were identified among 305 individuals sampled from nine locations. The haplotype minimum spanning network and phylogeny showed a modest level of geographic segregation among haplotypes, suggesting high levels of on-going or recent connectivity among distant populations. Observed Φ_ST values and the results of homogeneity and AMOVAs indicate incipient genetic differentiation between aggregations in three broad regional groups. Sites north of the Brooks Range formed one group, sites in the Yukon and Selawik Rivers formed a second group and sites south of the Yukon drainage formed the third group. Overall, the sequence data showed that a large proportion of mtDNA genetic variation in C. sardinella is shared across Alaska, but this variation is not homogeneously distributed across all regions and for all haplotype groups.

The Resistome of Farmed Fish Feces Contributes to the Enrichment of Antibiotic Resistance Genes in Sediments below Baltic Sea Fish Farms

Our previous studies showed that particular antibiotic resistance genes (ARGs) were enriched locally in sediments below fish farms in the Northern Baltic Sea, Finland, even when the selection pressure from antibiotics was negligible. We assumed that a constant influx of farmed fish feces could be the plausible source of the ARGs enriched in the farm sediments. In the present study, we analyzed the composition of the antibiotic resistome from the intestinal contents of 20 fish from the Baltic Sea farms. We used a high-throughput method, WaferGen qPCR array with 364 primer sets to detect and quantify ARGs, mobile genetic elements (MGE), and the 16S rRNA gene. Despite a considerably wide selection of qPCR primer sets, only 28 genes were detected in the intestinal contents. The detected genes were ARGs encoding resistance to sulfonamide (sul1), trimethoprim (dfrA1), tetracycline [tet(32), tetM, tetO, tetW], aminoglycoside (aadA1, aadA2), chloramphenicol (catA1), and efflux-pumps resistance genes (emrB, matA, mefA, msrA). The detected genes also included class 1 integron-associated genes (intI1, qacEΔ1) and transposases (tnpA). Importantly, most of the detected genes were the same genes enriched in the farm sediments. This preliminary study suggests that feces from farmed fish contribute to the ARG enrichment in farm sediments despite the lack of contemporaneous antibiotic treatments at the farms. We observed that the intestinal contents of individual farmed fish had their own resistome compositions. Our result also showed that the total relative abundances of transposases and tet genes were significantly correlated (p = 0.001, R² = 0.71). In addition, we analyzed the mucosal skin and gill filament resistomes of the farmed fish but only one multidrug-efflux resistance gene (emrB) was detected. To our knowledge, this is the first study reporting the resistome of farmed fish using a culture-independent method. Determining the possible sources of ARGs, especially mobilized ARGs, is essential for controlling the occurrence and spread of ARGs at fish farming facilities and for lowering the risk of ARG spread from the farms to surrounding environments.

Predation by signal crayfish Pacifastacus leniusculus on fish eggs and its consequences for coregonid recruitment

The character and magnitude of predation by the invasive, ectothermic Pacifastacus leniusculus, a crayfish widely introduced to Europe and Japan from North America, on the eggs of coregonid fishes, vendace Coregonus albula and whitefish Coregonus lavaretus were examined by experimentation, modelling and field data. The present results showed that P. leniusculus has the potential to be very efficient predator of fish eggs under winter conditions, but the predation by P. leniusculus did not significantly decrease production of coregonid larvae during the years with a high P. leniusculus population in the study lake. Hence, the mortality caused by the novel invertebrate predator appeared to compensate for other yet unexplored mortality factors instead of having an additive effect on the present salmonids.

Eco-genetic model to explore fishing-induced ecological and evolutionary effects on growth and maturation schedules

Eco-genetic individual-based models involve tracking the ecological dynamics of simulated individual organisms that are in part characterized by heritable parameters. We developed an eco-genetic individual-based model to explore ecological and evolutionary interactions of fish growth and maturation schedules. Our model is flexible and allows for exploration of the effects of heritable growth rates (based on von Bertalanffy and biphasic growth patterns), heritable maturation schedules (based on maturation reaction norm concepts), or both on individual- and population-level traits. In baseline simulations with rather simple ecological trade-offs and over a relatively short time period (<200 simulation years), simulated male and female fish evolve differential genetic growth and maturation. Further, resulting patterns of genetically determined growth and maturation are influenced by mortality rate and density-dependent processes, and maturation and growth parameters interact to mediate the evolution of one another. Subsequent to baseline simulations, we conducted experimental simulations to mimic fisheries harvest with two size-limits (targeting large or small fish), an array of fishing mortality rates, and assuming a deterministic or stochastic environment. Our results suggest that fishing with either size-limit may induce considerable changes in life-history trait expression (maturation schedules and growth rates), recruitment, and population abundance and structure. However, targeting large fish would cause more adverse genetic effects and may lead to a population less resilient to environmental stochasticity.