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The increase in abundance of great cormorants (Phalacrocorax carbo sinensis) over the last decades has caused concern for the sustainability of fish populations. Cormorants are opportunistic piscivorous birds that eat fish from a wide range of species and sizes, in marine, lacustrine and riverine habitats. It has been documented that juvenile salmonids are under significant predation pressure by great cormorants, although knowledge on the predation of adult salmonids by cormorants is limited. In this study, adult anadromous brown trout (Salmo trutta) were tagged over multiple years with PIT tags during their spawning migration in a Danish lowland river. Two nearby cormorant colonies were subsequently scanned for PIT tags to estimate predation rate. It was estimated that by minimum 15.4% of tagged adult sea trout were predated by cormorants. The majority of the individuals were predated in the river, and females were more likely to be predated than males. Moreover, length had a significant effect on predation probability: individuals between 35 and 43 cm had the highest likelihood to be predated, while smaller and larger individuals were less likely to be predated. Our findings challenge the assumption that cormorants do not prey on reproductively mature salmonids. Furthermore, predation of mature individuals may have implications for the recruitment and sustainability of the population.

Reproduction represents the most energetically demanding period of life for many organisms. Capital breeders, such as anadromous sea trout (Salmo trutta), provide a particularly interesting group of organisms to study within the context of reproduction because they rely on energy stores accrued before breeding to reproduce and sustain all phenotypic and behavioral changes related to reproduction. Energy allocation into current reproduction therefore cannot be mitigated via food intake, resulting in an important life history trade-off. For this reason, exploring indexes related to energetics in salmonids can provide powerful insights into the physiological costs of reproduction. In this study, we sampled blood from and PIT tagged 232 fish captured in the wild before the spawning season. We recaptured and resampled 74 individuals (53 females and 21 males) at the end of the spawning season. Females were further divided into spawning phases (nonspawned, partially spawned, and spawned individuals), though males could not be classified as such. We compared nutritional correlates (triglycerides, cholesterol, calcium, inorganic phosphorus, and total protein), stress correlates (cortisol, sodium, potassium, chloride, and glucose), and indexes of tissue damage (aspartate aminotransferase) between initial capture and recapture as well as among spawning phases in females. We found that nutritional status decreased in all fish throughout the spawning season but that it was substantially lower in females that had spawned. We further found that spawning itself appears stressful, with elevated glucose in partially spawned females and elevated cortisol in male sea trout at recapture. Our findings thus support the idea that the cost of reproduction is energetically high and that incurred stress and a decrease in nutritional status are important physiological costs.

Salmo trutta Linnaeus, 1758 [I]—Brown trout Taxonomy. Original description: Salmo trutta Linnaeus, 1758: 308 (European rivers; no types known).— Afghanistan synonyms: None.—Revisions: Berg (1948: 235); Scĥffmann (2021: 35); Segherloo et al. (2021: 10).—Illustration: Berg (1948: 238, figs. 143–144). Status in Afghanistan. First record from Afghanistan by Coad (1981: 8); confirmed by Coad (2014: 318 as exotic species).—Afghanistan materials: None. Distribution and habitat. Distribution in Afghanistan: Amu Darya drainage.—General distribution: Northeastern Atlantic: Norway south to Iberian Peninsula; Baltic Sea; North Sea; Mediterranean Sea; Europe: northeastern Atlantic watersheds and upper Danube basin, south to Sicily; introduced widely elsewhere.—Habitat: This species lives in cold streams, rivers, and lakes. Spawns in rivers and streams with swift water. Lacustrine populations migrate to tributaries and lake outlets, rarely spawning on stone or wave-washed lake shores. Spawning sites are usually characterized by the downward movement of water into gravel. Freshwater. Economic importance. Commercially important. Reasons of introduction. Aquaculture/research. Conservation. Not relevant (introduced species). Remarks. Salmo trutta was described originally from European rivers. This name was applied from the British Isles to Afghanistan but many subspecies have been recognised as distinct species. Additionally, it introduced many countries all over the world.Afghanstan is not include natural distribution range of the species. Therefore, current status of the species should be clarifying in the country., Published as part of Çiçek, Erdoğan, Fricke, Ronald, Eagderi, Soheil, Sungur, Sevil, Coad, Brian W & Hamdard, Mohammad Hamid, 2023, Fishes of Afghanistan; a revised and updated annotated checklist, pp. 1-69 in Zootaxa 5305 (1) on page 43, DOI: 10.11646/zootaxa.5305.1.1, http://zenodo.org/record/8048564, {"references":["Linnaeus, C. (1758) Systema Naturae. Vol. 1. Ed. X. [Systema naturae per regna tria naturae, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Tomus I. Editio decima, reformata]. Impensis Direct. Laurentii Salvii, Holmiae, ii + 824 pp.","Berg, L. S. (1948) s. n. In: Ryby presnych vod SSSR i sopredelnych stan. [Freshwater fishes of the U. S. S. R. and adjacent countries]. Vol. 1. 4 th Edition. Opredeliteli po faune SSSR. [Guide to the fauna of the U. S. S. R.], Moskva. Freshwater fishes of the U. S. S. R. and adjacent countries No. 27. Russian Academy of Sciences, USSR, Moskva, 466 pp. [in Russian. English translation available, Israel Prog. Sci. Transl., Jerusalem, 1962, 504 pp.]","Segherloo, I. H., Freyhof, J., Berrebi, P., Ferchaud, A. - L., Geiger, M., Laroche, J., Levin, B. A., Normandeau, E. & Bernatchez, L. (2021) A genomic perspective on an old question: Salmo trouts or Salmo trutta (Teleostei: Salmonidae)? Molecular Phylogenetics and Evolution, 162 (107204), 1 - 16. https: // doi. org / 10.1016 / j. ympev. 2021.107204","Coad, B. W. (1981) Fishes of Afghanistan, an annoted checklist. National Museum of Canada Publications in Zoology, 14, i - v + 1 - 26.","Coad, B. W. (2014) Fishes of Afghanistan. Pensoft Publishers, Sofia-Moscow. 393 pp."]}

International audience; On one hand, studies on Salmo biological variations during the last centuries have led to the morphological description of several Salmo species (>50). On the other hand, Salmo trutta is seen as a polymorphic species, i.e. including populations with different morphotypes and ecotypes, subdivided into nine genetically divergent evolutionary lineages. For 30 years, phylogeographic and phylogenetic investigations tried to solve the Salmo systematic problem using the mitochondrial control region, sometimes combined with other mitochondrial (e.g. protein coding region or rRNA genes) or nuclear (e.g. allozymes or microsatellites) markers. With the advent of high throughput next-generation sequencing, complete mitogenomes were made available for Salmo phylogenetic studies. Even better, complete genome or chromosomes with annotations as well as genes of interest can now be loaded from public database. However, in the genomic era, some challenges still need to be addressed such as an appropriate taxon sampling or the identification of orthologous genes before having an accurate phylogeny. In the present review, I examine how traditional molecular markers contributed to our knowledge of trout systematics, and what we can expect from the genomics revolution.

Three fish species (Schizothorax richardsonii, Salmo trutta and Neolissochilus hexagonolepis) were collected from Punatsang Chhu river and sample tissues of muscles and gills were analyzed for Al, As, Ba, Cd, Co, Cr, Cu, Fe, K, Mn, Mo, Ni, Pb, Se, Sr and Zn using Inductively Coupled Plasma Optical Emission Spectrometry (ICP-OES). Principal Component Analysis (PCA) for each species grouped elements with higher concentration in gills compared to muscle tissues. The Man-Whitney test revealed significant difference between tissues sources and concentrations of Al, Ba, Cd, Co, Fe, K, Mn, Mo, Ni, Sr and Zn in S. richardsonii, Al, Ba, Co, Fe, K, Mn, Ni, Sr and Zn in S. trutta and Al, Ba, Co, Cr, Fe, K, Mn, Sr and Zn in N. hexagonolepis. The Kruskal-Wallis test for inter-species variation revealed significant difference in concentration of As, Cr, Cu, Fe, Mn, Ni and Zn in muscle tissues and Ba, Cr, Cu, Mn, Sr and Zn concentrations in gills of three species. Spearman correlation between levels of elements and fish size (weight and length) revealed positive and negative relationships for concentrations of As, Ba, Cd, Co, Cr, Cu, Fe, K, Mn, Ni, Pb, Sr, and Zn and concentrations of Al, Ba, Cd, Co, Fe, K, Mn, Mo, Ni, Sr and Zn respectively, both at p < 0.001 and p < 0.005.

Genomic studies have largely been accelerated by the advances of next generation sequencing technologies since the beginning of the millennium. This, in turn, has motivated the generation of more reference genome assemblies not only in model organisms but also in species of scientific interest. In the present study, we employed a comparison study between the two different reference genome assemblies available for the same species, Salmo trutta, in GenBank. The results indicated an overall 90% similarity index between the two assemblies. Furthermore, the inversion regions of which assembly needs corrections were detected. Taking into account the whole genome duplication origin of the Salmonidae family, both assemblies were of good quality. However, the updated version of the Wellcome Sanger Institute assembly (fSalTru_1.2) outperformed the Norwegian assembly and was detected as the best available reference genome assembly in Salmo trutta.

Producción Científica, River fragmentation and alterations in flow and thermal regimes are the main stressors affecting migrating fish, which could be aggravated by climate change and increasing water demand. To assess these impacts and define mitigation measures, it is vital to understand fish movement patterns and the environmental variables affecting them. This study presents a long-term (1995–2019) analysis of upstream migration patterns of anadromous and potamodromous brown trout in the lower River Bidasoa (Spain). For this, captures in a monitoring station were analyzed using Survival Analysis and Random Forest techniques. Results showed that most upstream movements of potamodromous trout occurred in October–December, whereas in June–July for anadromous trout, although with differences regarding sex and size. Both, fish numbers and dates varied over time and were related to the environmental conditions, with different influence on each ecotype. The information provided from comparative studies can be used as a basis to develop adaptive management strategies to ensure freshwater species conservation. Moreover, studies in the southern distribution range can be crucial under climate warming scenarios, where species are expected to shift coldwards., Proyecto de innovación docente de la Universidad de Valladolid (PIF-UVa 2017), Ministerio de Ciencia, Innovación y Universidades (grant PTQ2018-010162), Publicación en abierto financiada por el Consorcio de Bibliotecas Universitarias de Castilla y León (BUCLE), con cargo al Programa Operativo 2014ES16RFOP009 FEDER 2014-2020 DE CASTILLA Y LEÓN, Actuación:20007-CL - Apoyo Consorcio BUCLE

1. Repeatable individual variation in behaviour has been demonstrated in all taxa, though few studies have explored the broader ecological consequences of such consistent behaviour.2. We tagged and tracked 401 individual sea trout (Salmo trutta) with passive integrated transponder telemetry over two to four spawning seasons as they migrated between freshwater and marine environments to spawn and feed, respectively.3. We found the timing (time of river entry) and duration of migration (time spent in freshwater and time spent at sea) to be repeatable within individuals across years. In addition, we identified two peaks in return migration timing; a group of summer-migrating fish, and a group of fall-migrating fish. At the time of first spawning, sea trout differed in size depending on how long the first marine phase was, but summer-migrating fish were smaller in all subsequent spawnings. Furthermore, summer-migrating fish had significantly better marine survival than fall-migrating fish.4. Our study suggests that the timing of arrival in freshwater is an important fitness-relevant trait, such that summer-migrating fish have decreased fitness but remain in somewhat safer conditions, while fall-migrating fish have increased fitness but are exposed to more risky conditions. Taken together, our findings suggest that migration timing and duration is determined via a trade-off between size and survival, which resulted in two evolutionary stable strategies.

Brown trout (Salmo trutta) is an important aquaculture species in Germany, but its production faces challenges due to global warming and a high embryo mortality. Climate factors might influence the fish’s bacterial community (BC) and thus increase embryo mortality. Yet, knowledge of the physiological BC during ontogeny in general is scarce. In this project, the BC of brown trout has been investigated in a period from unfertilized egg to 95 days post fertilization (dpf) using 16S rRNA gene amplicon sequencing. Developmental changes differed between early and late ontogeny and major differences in BC occurred especially during early developmental stages. Thus, analysis was conducted separately for 0 to 67 dpf and from 67 to 95 dpf. All analyzed stages were sampled in toto to avoid bias due to different sampling methods in different developmental stages. The most abundant phylum in the BC of all developmental stages was Pseudomonadota, while only two families (Comamonadaceae and Moraxellaceae) occurred in all developmental stages. The early developmental stages until 67 dpf displayed greater shifts in their BC regarding bacterial richness, microbial diversity, and taxonomic composition. Thereafter, in the fry stages, the BC seemed to stabilize and changes were moderate. In future studies, a reduction in the sampling time frames during early development, an increase in sampling numbers, and an attempt for biological reproduction in order to characterize the causes of these variations is recommended.

Partial migration is common in a variety of taxa and has important ecological and evolutionary implications, yet the underlying factors that lead to different migratory strategies are not clearly understood. Given the importance of temperature in serving as a cue for migration, along with its role in regulating metabolism, growth, reproduction, and survival, we examined how intraspecific variation in critical thermal maximum (CTmax) values influenced migratory strategy (residency vs. migration), timing of migration, growth, and predation vulnerability in a wild population of partially anadromous juvenile brown trout (Salmo trutta). Using passive integrated transponder telemetry and mark-recapture techniques, we identified individuals that out-migrated to sea, assumed residency, and were predated by cormorants several months later. Acute thermal stress induced by conducting CTmax trials did not affect the final fate of assayed fish compared with controls. We found that mass and body condition predicted CTmax and migration timing, but CTmax failed to predict migratory strategy or timing, growth (of resident fish), or predation vulnerability. Although there may be links between mass, thermal tolerance, and migration strategy, the relationship between CTmax and migration remains unclear. The role of upper thermal tolerance in influencing life-history strategies should not be neglected, however, as alternative indicators of thermal tolerance could be further explored. The high degree of variation in CTmax estimates warrants additional investigation of how increasingly prevalent high-temperature events might drive selection toward thermally tolerant extremes, which is particularly relevant in a rapidly warming world.

In recent years, the numbers of native brown trout caught by anglers has declined throughout the Czech Republic. In this study, we focus on individual factors potentially related to this negative trend, based primarily on long-term angling catch data (2000-2020) for twenty fishing grounds of the Czech and Moravian angling unions covering twelve upland trout streams. The results indicate that angling pressure, expressed as annual number of attendances, is the most important factor in the decline of trout populations, with drought caused by climate change as a secondary factor. There is a clear need for changes in current fisheries management practice, using new sustainable development scenarios, in order to protect and improve unfavourable conditions for natural brown trout populations.

A survey of trout species was carried out to assess the trout stocks' quality inhabiting the Palena River Basin, one of the most important rivers for recreational angling in Chilean Patagonia. Six sampling campaigns were carried out over 16 selected stretches of the river between February 2012 and June 2013. A total of 912 trout were collected, 57% rainbow trout ( Oncorhynchus mykiss ), 33.3% brown trout ( Salmo trutta ), and 9.6% brook trout ( Salvelinus fontinalis ). Also, one tiger trout ( Salmo trutta × Salvelinus fontinalis ) (a hybrid between brown and brook trout) was recorded. Results showed that both rainbow trout and brown trout shared the same reaches of the river, with very similar feeding habits, while brook trout inhabited smaller and more enclosed streams. Maturity stages (V-VI) were recorded from the fish sampled over the period spring-summer-autumn in the case of rainbow trout; autumn-winter for brook trout, and summer-autumn for brook trout. One of the study's most notable features was the small size of the mature brook trout, reaching 17.5 cm in length for gravid females and 12.4 cm for mature males at age 2 + . The maximum age recorded for rainbow and brown trout was 6 + , with a maximum length of 69.8 and 58.5cm, respectively, while for brook trout, the maximum age recorded was 3 + for a female with a length of 29.9 cm length and 2 + for a male of 16.6 cm.

Our understanding of how microbiome signatures are modulated in wild fish populations remains poorly developed and has, until now, mostly been inferred from studies in commercial and farmed fish populations. Here, for the first time, we have studied changes in the skin and blood microbiomes of the Salmo trutta population of the volcanic Kerguelen archipelago located at the northern limit of the Antarctic Ocean. The Kerguelen Islands present a natural framework of population expansion and reveal a likely situation representing further climate change in distribution areas. Our results showed that S. trutta of the Kerguelen Islands has a microbiome signature distinct from those of salmonids of the Northern Hemisphere. Our study also revealed that the skin and blood microbiomes differ between sedentary and migratory S. trutta. While 18 phyla were shared between both groups of trout, independent of the compartment, 6 phyla were unique to migratory trout. Further analyses showed that microbiome signatures undergo significant site-specific variations that correlate, in some cases, with the peculiarity of specific ecosystems. Our study also revealed the presence of potential pathogens at particular sites and the impact of abiotic factors on the microbiome, most notably due to the volcanic nature of the environment. This study contributes to a better understanding of the factors that modulate the microbiome signatures of migratory and sedentary fish populations. It will also help to better monitor the impacts of climate change on the colonization process in the sub-Antarctic region.

For successful evaluation of the overall effects of salmon louse infestation on brown trout population dynamics, it is crucial to have a realistic understanding of how lice infestation distributions are generated and how they should be interpreted. Here, we simulated the potential effects of spatio-temporal variance in lice larvae densities, temporal variance in sea trout marine migration timing and spatial variance in marine habitat use on lice infestation distributions. We show that, when sampling populations with individual variation in marine behaviour, e.g. from post-smolts to veteran migrants, we must expect multi-modal mixture lice infestation distributions. Applying standard statistical distributions, such as the Poisson, negative binomial or zeroinflated distributions, can be too simplistic and give biased results. Temporary increases in salmon lice load in a given area may have inconsistent effects among individuals of a population and may be critical for vulnerable groups such as post-smolts, dependent on timing. For many analyses, it will be necessary to resolve the contributions from groups of fish with different lice infestation expectations due to spatio-temporal differences in habitat use within the overall mixture distribution. Another consequence is that different data sources, obtained by different methods or sampled at different locations and periods, must be expected to give different lice infestation distributions, even when sampling the same population. We also discuss additional factors that may complicate the interpretation of salmon lice infestation distributions on sea trout, such as lice-induced mortality, and behavioural changes, such as premature return to less saline water for delousing. Salmo trutta · Lepeophtheirus salmonis · Anadromy · Marine migration · Aquaculture · Negative binomial distribution · Zero-inflated models © The authors 2020. Open Access under Creative Commons by Attribution Licence. Use, distribution and reproduction are un - restricted. Authors and original publication must be credited.

11 Pág. Centro de Investigación en Sanidad Animal (CISA), Proliferative kidney disease (PKD), caused by the myxozoan parasite Tetracapsuloides bryosalmonae, is suspected to contribute to the decline of wild brown trout Salmo trutta populations. Different factors need to be taken into consideration for PKD outbreaks. Among them, water temperature appears as a main driver of the disease. To understand the epidemiology and impact of the disease on wild fish populations, reliable sampling approaches to detect the presence of T. bryosalmonae-infected fish are needed. This study aimed to characterize the seasonal variation of the prevalence of T. bryosalmonae-infected fish in brown trout populations in two small streams with differing temperature regimes between upstream and downstream sites. As water temperature is known to influence PKD manifestation in brown trout, we hypothesized that the number of T. bryosalmonae-positive fish, as well as their seasonal distribution, will vary between upper and downstream parts of the two streams. Since, in field studies, results can strongly vary across years, we extended the study over a 3-year-period. The number of infected fish and the intensity of infection were assessed by histology. The results confirmed the hypothesis of pronounced temporal- and site-related differences in the percentage of PKD-positive fish and the intensity of the infection. Comparison of water temperatures (total degree days as well as the number of days with a daily mean temperature ≥15 °C) with PKD data indicated that temperature was the driving factor for the temporal development and the intensity of the infection. A mean of 1500 degree days or 30 days with a daily mean temperature ≥15 °C was required before the infection could be detected histologically. From our findings, recommendations are derived for a water temperature-driven sampling strategy campaigns that enables the detection of PKD infection and prevalence in wild brown trout populations., This research was partly funded by the SWISS federal food safety and veterinary office through the pilot program “Adaptation to climate change”, partly by the SWISS national science foundation Sinergia grant number CRSII3_147649_1, and partly by the general directorate of the environment of the canton of Vaud. CB was funded by SNF Post Doc Mobility Fellowship number P400PB_183824

Hormones have been used to change phenotypic sex in many fish species. However, information specific to changing sex in brown trout Salmo trutta is lacking. This study compared the effectiveness of two different 17β-estradiol (estradiol) concentrations (20 mg/kg and 30 mg/kg) fed to brown trout for 60 days, beginning at initial feeding. At 456 days post-initial feeding, the 20 mg/kg and 30 mg/kg treatment groups were 84% and 86% female, respectively. These values were significantly higher than the 47% females observed in the control group which did not receive dietary estradiol. At the end of the 60-day estradiol treatment period, weight gain, percent weight gain, and feed conversion ratio were all significantly lower in the tanks of fish receiving estradiol than in the control tanks. Individual fish fed estradiol also weighed significantly less and were significantly shorter than the fish not receiving estradiol-coated feed. Mortality ranged from 1.0 to 2.4% among the treatments and was not significantly different. After 105 days post-initial feeding, weight gain, percent weight gain, and feed conversion ratio were not significantly different among the treatments. At 456 days post-initial feeding, individual fish were significantly longer and heavier in the 20 mg/kg estradiol treatment compared to the fish in the control treatment, and the fish in the 30 mg/kg estradiol treatment were similar to the other two treatments. This study is the first to document the successful sex reversal of brown trout using estradiol. While the estradiol treatments used in this study did not lead to complete feminization, the observed 85-to-15% female-to-male phenotypic ratio indicates the successful feminization of genetic males. The levels of feminization observed in this study are suitable for this initial step to potentially develop a YY male broodstock to control invasive brown trout populations.

Atlantic trout (Salmo trutta) are native in the northern perialpine lakes and probably also in Lake Sils in the alpine section of the Inn-Danube catchment. Atlantic trout were recorded in all lakes in the Rhine catchment except Upper Zurich, Biel and Rousses. In the Rhone catchment, Atlantic S. trutta have been widely introduced, any may be native only in Lake Geneva. In the Rhone lakes this species was missing from Projet Lac catches of only the smallest lakes: Remoray, Bonlieu and Bret. It is not known which of these lakes may have hosted the native Rhone or zebra tout Salmo rhodanensis in the past, and what happened to these populations. Atlantic trout S. trutta has also been introduced into all surveyed southern perialpine lakes, as well as Lake Poschiavo. Indeed, S. trutta were recorded in every lake of the Po catchment, except Varese (which did not have any trout). Salmo trutta is known to hybridize with southern Salmo species in some water bodies where they have been introduced, and remain distinct in others. The massive stocking of S. trutta into southern drainages is thought to have led to nearly complete displacement of the native species in some drainages [164]. This makes the proper assessment of trout diversity in southern drainage systems very important, but also complicated. Projet Lac recorded Atlantic trout Salmo trutta and three Adriatic-endemic Salmo species in the southern lakes: Salmo marmoratus (marbled trout) in lakes Maggiore, Lugano and Poschiavo, Salmo cenerinus (northern Italian brook trout) only in Lake Poschiavo, and three individuals resembling Salmo carpio (carpione) in Lake Garda. “Engadiner trout” were also identified in Lake Sils, characterized by very few large black spots and genetically belonging to the Danubian Salmo labrax. This taxon coexists with Salmo trutta in Lake Sils as two genomically distinct species (Figure 46). Finally, a local lake trout type was documented in Lake Poschiavo, with an unusual pattern of very dense large black spots. This taxa genetically resembled S. marmorata in the mitochondrial barcode, but Salmo cenerinus at microsatellite markers, with considerable introgression from Salmo trutta (Figure 47). This likely native form of lake trout in Poschiavo and is referred to in this report as Salmo sp. “Blackspot”. Based on information from local fisheries authorities, this trout form spawns in the lake, where an annual spawn fishery takes place.This makes it ecologically unique in Switzerland.The only other known lake-spawning trout in the perialpine region is S. carpio of Lake Garda, which is interestingly of similar hybrid origins (mitochondrially S. marmoratus, otherwise mostly S. cenerinus). [165] It is noteworthy that Projet Lac recorded lake trout forms of S. marmorata in Lake Maggiore.The highest abundance and diversity of trout was recorded in the alpine lakes Sils (Danube catchment) with two native species, and Poschiavo (Po catchment) with three native and two non-native species. The Salmo labrax (Danube trout) phenotype was recorded in both lakes.This lineage is native to the Danube catchment, and has been introduced into Lake Poschiavo. Salmo sp. “Blackspot” was recorded also in Lake Sils where it was possibly introduced from Lake Poschiavo. In Poschiavo, the two species native to the Po river catchment, Salmo cenerinus and Salmo marmoratus were confirmed as genetically distinct from one another and from S. trutta, but with strong signs of hybridization (Figure 47), possibly associated with the arrival of S. trutta and S. labrax in the lake. Some genetic differences remain that correspond to the different phenotypes (Figure 47)., Published as part of Alexander, Timothy & Seehausen, Ole, 2021, Diversity, distribution and community composition of fish in perialpine lakes – " Projet Lac " synthesis report, Eawag: Swiss Federal Institute of Aquatic Science and Technology on page 135, DOI: 10.5281/zenodo.5779569

Metabolism defines the energetic cost of life, yet we still know relatively little about why intraspecific variation in metabolic rate arises and persists. Spatio-temporal variation in selection potentially maintains differences, but relationships between metabolic traits (standard metabolic rate (SMR), maximum metabolic rate (MMR), and aerobic scope) and fitness across contexts are unresolved. We show that associations between SMR, MMR, and growth rate (a key fitness-related trait) vary depending on the thermal regime (a potential selective agent) in offspring of wild-sampled brown trout from two populations reared for approximately 15 months in either a cool or warm (+1.8°C) regime. SMR was positively related to growth in the cool, but negatively related in the warm regime. The opposite patterns were found for MMR and growth associations (positive in warm, negative in the cool regime). Mean SMR, but not MMR, was lower in warm regimes within both populations (i.e. basal metabolic costs were reduced at higher temperatures), consistent with an adaptive acclimation response that optimizes growth. Metabolic phenotypes thus exhibited a thermally sensitive metabolic ‘floor’ and a less flexible metabolic ‘ceiling’. Our findings suggest a role for growth-related fluctuating selection in shaping patterns of metabolic variation that is likely important in adapting to climate change.

A new record of a marble trout mtDNA haplotype known to be restricted to Adriatic basin (called marmoratus lineage within Salmo trutta complex) has been reported from Eşen Stream in the Aegean Sea basin of southeastern Turkey, based on sequence data of the mitochondrial DNA control region. The results of this study showed a single unique haplotype from this population, called MATR1. Phylogenetic analyses of this haplotype along with other haplotypes belonging to different mitochondrial DNA lineages of the S. trutta complex confirmed the existence of the marmoratus lineage in Turkey, suggesting a possible river capture between the Adriatic and Aegean Sea basins until the last (Würmian) marine regression.

Early-life experiences can shape life histories and population dynamics of wild animals. To examine whether stressful stimuli experienced in early life resulted in carryover effects in later life stages, we conducted several experimental manipulations and then monitored wild fish with passive integrated transponder tags during juvenile out-migration and adult return migration. In total, 3,217 juvenile brown trout (Salmo trutta) were subjected to one of six manipulations: chase to exhaustion, thermal challenge, food deprivation, low-concentration cortisol injection, high-concentration cortisol injection, and sham injection, plus a control group. Cortisol and food deprivation treatments were previously shown to have short-term effects on juveniles, such as lower survival to out-migration and changes in migration timing. However, it remained unknown whether any of the six manipulations had effects that carried over into the adult phase. We therefore investigated whether these extrinsic manipulations, as well as intrinsic factors (size and condition), affected probability of return as adults and time spent at sea. Of the 1,273 fish that out-migrated, 146 returned as adults. We failed to detect any effect of treatments on return rates, while high-concentration cortisol weakly affected time spent at sea in one tagging event. We also found that juvenile condition was positively correlated to likelihood of adult return in only one tagging event. Overall, our findings did not identify either intrinsic factors or extrinsic stressful early-life experiences that have strong effects on fish that survive to adulthood. This suggests that some species may be more resilient than others to stressful stimuli encountered early in life.

This paper reports heavy metal and metalloid accumulation in wild brown trout (Salmo trutta L., 1758 complex) raised in freshwater and uncontaminated Sardinia system (Italy). Metals are widespread pollutants of aquatic systems, and their contamination can originate from anthropogenic activities such as industrial waste, agricultural and domestic environments, and geochemical release. Fish has a relevant position within the human diet; moreover, fishes can accumulate metals, making them a valuable tool as biomarkers for risk assessment studies. The concentration of 22 metals and metalloids after chemical digestion was assessed by inductively coupled plasma-optic emission spectroscopy (ICP-OES) in both the guts and the edible part (EP, muscle + skin) of brown trout. The results, expressed as μg g−1, showed different levels of accumulation in the EP and guts, following the series Cu > Zn > Ba > Al > Sr > Fe > Pb and Fe > Al > Hg > As > Mn > Cu > Ba > B > Zn > Pb, respectively. PCA analysis showed a fairly good correlation between the total lipid and SAFA content and Cd, Hg, and Pb accumulation in the gut. Non-carcinogenic risk assessment, expressed as THQ (target hazard quotient), showed values far below 1 for all metals in muscles, while high As and Hg contamination of the gut draws attention to possible health risks which should be discarded from the fish before consumption. TR (target cancer risk) values showed alarmingly high values for As and Cd when the fish were consumed entirely (gut + EP), while Pb levels were far below the safety levels.

Species–environment relationships were studied between the occurrence of 13 fish and lamprey species and 9 mainly map‐based environmental variables of Finnish boreal small streams. A self‐organizing map (SOM) analysis showed strong relationships between the fish species and environmental variables in a single model (explained variance 55.9%). Besides basic environmental variables such as altitude, catchment size, and mean temperature, land cover variables were also explored. A logistic regression analysis indicated that the occurrence probability of brown trout, Salmo trutta L., decreased with an increasing percentage of peatland ditch drainage in the upper catchment. Ninespine stickleback, Pungitius pungitius (L.), and three‐spined stickleback, Gasterosteus aculeatus L., seemed to benefit from urban areas in the upper catchment. Discovered relationships between fish species occurrence and land‐use attributes are encouraging for the development of fish‐based bioassessment for small streams. The presented ordination of the fish species in the mean temperature gradient will help in predicting fish community responses to climate change., Species–environment relationships were studied between the occurrence of 13 fish and lamprey species and 9 mainly map‐based environmental variables of Finnish boreal small streams. Modelling fish species occurrence in streams with a logistic regression and self‐organizing map indicated clear species–environment relationships. The results support the development of fish‐based bioassessment for small streams and help in predicting fish assemblage changes in a warming climate.

Nodular Gill Disease (NGD) in highly intensive farming systems plays a major role in production losses and its outbreaks can result in cumulative mortality exceeding 60%, especially during the winter months and early spring. NGD was described in rainbow trout farms of North America and Europe and appears to be caused by different species of amoebae, for example both testate (Roghostoma minus) and naked amoebae belonging to five genera. In the last few years, NGD is widespread in rainbow trout farms of northern and central Italy. In March 2017, during the epidemiological investigations into NGD in salmonid farms of northern Italy, the first cases of branchitis referable to amoebic infection in juvenile brown trout (Salmo trutta L.) were observed. Twenty‐five live and moribund brown trout from each tank were collected at monthly intervals from March to May 2017 for a total of 150 fish. The samples were subjected to necropsy, parasitological analysis, histology and bacteriological and virological examinations for diagnostic purposes. Histological examination of gills from diseased and moribund brown trout showed characteristic pathological signs of NGD infection. The most significant change was the development of heavy gill lesions with variable degrees of lamellar fusion, especially in the distal part of filaments (clubbing), with obliteration of interlamellar spaces. A limited number of amoebae were detected along the surface of the gills. The lesions observed in fresh mounts and in histological sections obtained from the gills of the infected brown trout confirmed to be less serious than those detected in affected rainbow trout of the same farm. Therefore, this investigation, which reports for the first time NGD in brown trout, has shown that S. trutta would be less susceptible to this pathology than rainbow trout.

We present a genome assembly from an individual female Salmo trutta (the brown trout; Chordata; Actinopteri; Salmoniformes; Salmonidae). The genome sequence is 2.37 gigabases in span. The majority of the assembly is scaffolded into 40 chromosomal pseudomolecules. Gene annotation of this assembly on Ensembl has identified 43,935 protein coding genes.

We present a genome assembly from an individual female Salmo trutta (the brown trout; Chordata; Actinopteri; Salmoniformes; Salmonidae). The genome sequence is 2.37 gigabases in span. The majority of the assembly is scaffolded into 40 chromosomal pseudomolecules. Gene annotation of this assembly on Ensembl has identified 43,935 protein coding genes.

Tras la recogida de información de reos en 9 ríos gallegos, a partir de la pesquería oficial y del trabajo realizado en 5 estaciones de captura de peces en 4 cuencas hidrográficas, gracias a la aplicación de métodos como la determinación de la edad mediante la lectura de escamas, el retrocálculo y el marcado/recaptura, se realizó el análisis de ésta información al objeto de caracterizar estas poblaciones. Se describe el ciclo vital de la forma anadroma de la trucha común, por primera vez en la península Ibérica, analizando las diferencias encontradas entre las pobaciones estudiadas. Se hallaron diferencias entre las poblaciones estudiadas. Las poblaciones de reos que habitan en los ríos del norte de Galicia (Rías Altas) crecen menos, tanto en el río como en el mar, se repoducen más tarde y más veces que las poblaciones de los ríos del sur (Rías Baixas), mientras que las poblaciones de las Rías Centrales tienen caracteristicas intermedias. Estas diferencias son debidas al menos parcialmente concluyendo que son compatibles con la existencia de adaptaciones locales en estas poblaciones. 2022-03-23

Freshwater acidification is characterised by elevated concentrations of aqueous aluminium. Global emissions of acidifying agents are reduced due to international agreements, and freshwater acidification has shifted from chronic to a more episodic character. The recovery of fish populations in acidified areas is likely to depend on the individual’s ability to recover from short-time aluminium exposures. We exposed brown trout (Salmo trutta) to an Al-rich medium, nominal concentration 600 µg L–1, for 0.5, 2, 6, 8 and 11 hours, before transfer to circumneutral Al-poor water for recovery. As controls, fish were either exposed for 11 hours to an acidified Al-poor medium or to untreated water. Some mortality during the first 24 hours of the recovery period occurred in fish exposed for 11, 8 and 6 hours to aluminium. No mortality during recovery was observed in the remaining groups. Aluminium exposure led to increased haematocrit and plasma lactate concentration, decreased plasma chloride concentration, deposition of aluminium on gill surfaces, and morphological alteration of the gill structures. The responses depended on exposure time. Aluminium deposited on the gill disappeared and plasma lactate levels were at control levels after 1 day in the recovery water, while haematocrit and plasma chloride levels were at control levels after 14 days of recovery. Gills in fish exposed to aluminium for 11 hours were almost fully recovered after 14 days. We conclude that the toxic response in brown trout exposed to an acutely toxic aluminium challenge is reversible. Moreover, the first 24 hours after aluminium exposures is the most critical period for the fish recovery. Further, it takes no more than 14 days for brown trout to fully recover from an acute toxic aluminium exposure, and only 1 day if the aluminium challenge is moderate.

Long-term data from marked animals provide a wealth of opportunities for studies with high relevance to both basic ecological understanding and successful management in a changing world. The key strength of such data is that they allow us to quantify individual variation in vital rates (e.g. survival, growth, reproduction) and then link it mechanistically to dynamics at the population level. However, maintaining the collection of individual-based data over long time periods comes with large logistic efforts and costs and studies spanning over decades are therefore rare. This is the case particularly for migratory aquatic species, many of which are in decline despite their high ecological, cultural and economical value. This paper describes two unique publicly available time series of individual-based data originating from a 51-year mark-recapture study of a land-locked population of large-sized migratory brown trout (Salmo trutta) in Norway: the Hunder trout. In the period 1966-2015, nearly 14,000 adult Hunder trout have been captured and individually marked during their spawning migration from Lake Mjøsa to the river Gubrandsdalslågen. Almost a third of those individuals were later recaptured alive during a later spawning run and/or captured by fishermen and reported dead or alive. This has resulted in the first data series: a mark-recapture-recovery dataset spanning half a century and more than 18,000 capture records. The second data series consists of additional data on juvenile and adult growth and life-history schedules from half of the marked individuals, obtained by means of scale-sample analysis. The two datasets offer a rare long-term perspective on individuals and population dynamics and provide unique opportunities to gain insights into questions surrounding management, conservation and restoration of migratory salmonid populations and freshwater ecosystems.

Background Long-term data from marked animals provide a wealth of opportunities for studies with high relevance to both basic ecological understanding and successful management in a changing world. The key strength of such data is that they allow us to quantify individual variation in vital rates (e.g. survival, growth, reproduction) and then link it mechanistically to dynamics at the population level. However, maintaining the collection of individual-based data over long time periods comes with large logistic efforts and costs and studies spanning over decades are therefore rare. This is the case particularly for migratory aquatic species, many of which are in decline despite their high ecological, cultural and economical value. New information This paper describes two unique publicly available time series of individual-based data originating from a 51-year mark-recapture study of a land-locked population of large-sized migratory brown trout (Salmo trutta) in Norway: the Hunder trout. In the period 1966-2015, nearly 14,000 adult Hunder trout have been captured and individually marked during their spawning migration from Lake Mjøsa to the river Gubrandsdalslågen. Almost a third of those individuals were later recaptured alive during a later spawning run and/or captured by fishermen and reported dead or alive. This has resulted in the first data series: a mark-recapture-recovery dataset spanning half a century and more than 18,000 capture records. The second data series consists of additional data on juvenile and adult growth and life-history schedules from half of the marked individuals, obtained by means of scale-sample analysis. The two datasets offer a rare long-term perspective on individuals and population dynamics and provide unique opportunities to gain insights into questions surrounding management, conservation and restoration of migratory salmonid populations and freshwater ecosystems.

With rapid global change, organisms in natural systems are exposed to a multitude of stressors that likely co‐occur, with uncertain impacts. We explored individual and cumulative effects of co‐occurring environmental stressors on the striking, yet poorly understood, phenomenon of facultative migration. We reared offspring of a brown trout population that naturally demonstrates facultative anadromy (sea migration), under different environmental stressor treatments and measured life history responses in terms of migratory tactics and freshwater maturation rates. Juvenile fish were exposed to reduced food availability, temperatures elevated to 1.8°C above natural conditions or both treatments in combination over 18 months of experimental tank rearing. When considered in isolation, reduced food had negative effects on the size, mass and condition of fish across the experiment. We detected variable effects of warm temperatures (negative effects on size and mass, but positive effect on lipids). When combined with food restriction, temperature effects on these traits were less pronounced, implying antagonistic stressor effects on morphological traits. Stressors combined additively, but had opposing effects on life history tactics: migration increased and maturation rates decreased under low food conditions, whereas the opposite occurred in the warm temperature treatment. Not all fish had expressed maturation or migration tactics by the end of the study, and the frequency of these ‘unassigned’ fish was higher in food deprivation treatments, but lower in warm treatments. Fish showing migration tactics were smaller and in poorer condition than fish showing maturation tactics, but were similar in size to unassigned fish. We further detected effects of food restriction on hypo‐osmoregulatory function of migrants that may influence the fitness benefits of the migratory tactic at sea. We also highlight that responses to multiple stressors may vary depending on the response considered. Collectively, our results indicate contrasting effects of environmental stressors on life history trajectories in a facultatively migratory species.

Today's river systems have been extensively modified, requiring us to rethink how we approach the management of these important ecosystems. We evaluated the effects of removing 6 weirs in River Villestrup (Jutland, Denmark) on the smolt run of brown trout (Salmo trutta) over the course of 12 years. During 5 of these years, we evaluated the number, size, and timing of smolts during their downstream migration. We found an increase in smolt output following the weir removals, along with a decrease in average length and indications of an earlier peak migration. Our results suggest that barrier removal has led to an increase in spawning success by adults, fry survival, recruitment, and smolt migration success. Weir removal is therefore a viable management approach to restore connectivity in freshwater streams and rivers, which promotes the passage of smolts as they migrate to marine environment

Individual fish identification and recognition is an important step in the conservation and management of fisheries. One of most frequently used methods involves capturing and tagging fish. However, these processes have been reported to cause tissue damage, premature tag loss, and decreased swimming capacity. More recently, marine video recordings have been extensively used for monitoring fish populations. However, these require visual inspection to identify individual fish. In this work, we proposed an automatic method for the identification of individual brown trouts, Salmo trutta. We developed a deep convolutional architecture for this purpose. Specifically, given two fish images, multi-scale convolutional features were extracted to capture low-level features and high-level semantic components for embedding space representation. The extracted features were compared at each scale for capturing representation for individual fish identification. The method was evaluated on a dataset called NINA204 based on 204 videos of brown trout and on a dataset TROUT39 containing 39 brown trouts in 288 frames. The identification method distinguished individual fish with 94.6% precision and 74.3% recall on a NINA204 video sequence with significant appearance and shape variation. The identification method takes individual fish and is able to distinguish them with precision and recall percentages of 94.6% and 74.3% on NINA204 for a video sequence with significant appearance and shape variation.

Saprolegnia infections are among the main parasitic diseases affecting farmed salmonids. The distribution and potential transfer of Saprolegnia spp. between farms and the natural environment has been scarcely investigated. Therefore, this work aimed to study the diversity and abundance of oomycete species in salmonid farms, tributary water, and effluent water systems. Four trout farms in Italy and two Atlantic salmon farms in Scotland were considered. In Italian farms, 532 isolates of oomycetes were obtained from fish and water, at upstream, inside, and downstream the farms. In Scottish farms, 201 oomycetes isolates were obtained from water outside the farm and from fish and water inside the farming units. Isolates were identified to the species level through amplification and sequencing of the ITS rDNA region. In Italy, S. parasitica was significantly more present in farmed than in wild fish, while in water it was more frequently isolated from the wild, particularly in effluent systems, not associated with more frequent isolation of S. parasitica in wild fish downstream the farm. In Scotland, S. parasitica was the most prevalent species isolated from fish, while isolates from water were mostly Pythium spp. with few S. parasitica isolates from upstream and downstream the farms., European Union’s Horizon 2020 research and innovation programme under grant agreement No. 634429

Phenotypic plasticity can be viewed as the first level of defense of organism homeostasis against environmental stress and therefore represents the potential to deal with rapid environmental changes. Transitions between low complexity, artificial environments and complex, natural habitats can promote phenotypic plasticity. Here, we conducted an experimental introduction with juvenile brown trout to evaluate the plasticity of shape in response to a transition between contrasting environments. We released 202 juvenile trout reared under hatchery conditions in a natural stream and analyzed changes in shape and morphological variability after 5 months. A geometric morphometrics approach based on 14 landmarks was used to compare changes in body shape for 37 fish recaptured at the end of the experiment. A similar number of hatchery and wild fish caught at the receptor stream were used as controls for shape in the two environments. After 5‐months, fish showed significant change in shape, shifting from elongated to robust shapes, and affecting to the relative position of the caudal peduncle. These new shapes were closer to wild than to the hatchery shapes, suggesting a process of rapid phenotype change. Moreover, these changes were concomitant with a marked increase in morphological variability. Our results support the hypothesis that phenotypic plasticity is a major potential for adjustment to environmental change but not the idea that shape can be constrained by initial shapes. We confirmed the “increased” variance hypothesis and phenotype convergence with wild morphs. This has important implications because stresses the role of phenotypic plasticity as a buffer that allows organisms to cope with important environmental discontinuities at time scales that preclude the onset of adaptive adjustments. We suggest that environmental conditioning and shape plasticity can overcome both reduced morphological diversity and phenotype uncoupling with habitat characteristics resulting from initial rearing in low complexity artificial environments.

International audience; Gathering information on both individual movement and gene flow is rarely possible when studying dispersal among populations in fish species. It is, however, possible to assess both at a reasonable cost in Salmo trutta L. on the Atlantic coast of Europe where the facultative anadromous species is composed of discrete populations of brown trout residents occupying distinct river systems, but exchanging phenotypically distinguishable sea trout migrants. We performed two kinds of genetic analyses using individual microsatellite genotypes: the stock identification of sea trout entering each corridor and the estimates of effective dispersal through each corridor. We observed that individual movement (nonlocal individuals of each source population ranging from 4% to 35% of the sea trout run) never translates into effective dispersal except in one of four migratory corridors examined. The likely origin of this uniquely detected gene flow event is discussed in the light of well-documented migratory fish management actions undertaken in the past in the studied area.

Purpose. To study food resources, feeding conditions and trophic relationships of the brown trout (Salmo trutta morpha fario), rainbow trout (Oncorhynchus mykiss), and European grayling (Thymallus thymallus) in a Transcarpatioan river. Methodology. The material on the food resources and feeding of the brown trout, rainbow trout, and European grayling was collected in summer period of 2012 on the Shypit river. The study was performed on two different sites of the river: the first one was located on the middle pre-mountain reach of the river (upstream of the Hydroelectric power plant), the second one – on the mountain reach of the river (near tourist base) on typical biotopes: I – with boulders and riffles with fast current; II – with medium size stones and low riffles with moderate current; III – with small stones, sand and slow current. The material was collected and processed according to standard and unified hydrological, ichthyological, and trophological methods. Findings. We studied the level of macrozoobenthos development and obtained data on feeding and trophic relationships among brown trout, rainbow trout, and European grayling on different biotopes on pre-mountain and mountain reaches of the Shypit river. The number of “soft” macrozoobenthos on different biotopes varied from 972 to 2576 ind./m2 with biomasses from 6.3 to 121.8 g/m2. Total diet overlap index (DOI) between brown trout and rainbow trout on the biotope with boulders and fast current in the pre-mountain reach was 32.4% by number and 20.3% by biomass, while that on the mountain reach was 49.6% and 52.9%, respectively. On the biotope with medium size stones and moderate current, the diet overlap index between rainbow trout and European grayling in the pre-mountain reach was 19.0% by number and 27.9% by biomass. Originality. First study of the diet and tropic relationships of the brown trout, rainbow trout, and еuropean grayling on different reached of the Shypit river. Practical value. The results of this work can be used when calculating the amounts of brown trout, rainbow trout, and European grayling to be stocked into rivers of the Transcarpathian region.

402 p. La cuenca carbonífera El Bierzo es una zona importante de minería donde esta actividad y su legado dejado durante décadas, han alterado los ecosistemas acuáticos de la comarca. El río Boeza, principal cauce fluvial de estudio que acaba desembocando en el río Miño, recibe aguas contaminadas de su tributario el río Tremor. En el presente trabajo se ha estudiado tanto la calidad del agua como del sedimento, a través de su análisis físico-químico y del contenido metálico. Los resultados muestran que las zonas cercanas a los focos de contaminación tienen una concentración mayor de metales que el tramo fluvial tomado como control o punto limpio. Paralelamente se ha medido la concentración de metales en las comunidades de macroinvertebrados y de trucha común (Salmo trutta). Por último, la zona ofrece un escenario especial para estudiar la recolonización por parte de la fauna macroinvertebrada de un cauce fluvial, del arroyo Rodrigatos, en cuya cuenca se han llevado a cabo varias labores de restauración, entre las que destaca la construcción de un tratamiento pasivo para decantar los metales de un drenaje de mina que vertía en el arroyo. Con el paso del tiempo, en que la presión minera ha ido disminuyendo, el arroyo Rodrigatos ha sido capaz de recuperar parte de la fauna macrobentónica más tolerante a la polución metálica. Además, el sistema de tratamiento pasivo ha sido satisfactorio en la retención de varios metales importantes como el Al y el Fe

Despite that the study of individual repeatability is a common topic in behavioral ecology, virtually nothing is known about inter-annual variability in the marine migratory behavior of iteroparous salmonids that can complete multiple feeding migrations in their lifespan. Behavioral data from 38 anadromous brown trout (Salmo trutta), tracked by acoustic telemetry in 2–3 consecutive marine feeding migrations in two Norwegian fjord systems, were analyzed for intra-individual repeatability in key aspects of their marine migration. Individual brown trout displayed significant inter-annual consistency in marine area use and in the timing of marine exit (i.e. when they returned to spawning rivers), but not in the timing of marine entry or the time spent in the marine environment each year. Our study raises new questions about how anadromous brown trout respond to changing conditions and anthropogenic factors in the marine environment. Intra-individual repeatability of brown trout linked to changing environmental conditions should therefore be a focus for future studies. Copyright © 2019 Eldøy, Bordeleau, Crossin and Davidsen. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY)

Many species are capable of facultative migration, but the relative roles of extrinsic versus intrinsic factors in generating diverse migratory tactics remain unclear. Here we explore the proximate drivers of facultative migration in brown trout in an experimental laboratory setting. The effects of reduced food, as a putative environmental cue, were examined in two populations: one that exhibits high rates of anadromy (sea-migration) in nature, and one that does not exhibit anadromy in nature. Juveniles derived from wild-caught parents were reared for two years under four environmental treatments: low food in years 1 and 2 (Low-Low); high food in years 1 and 2 (High-High), low food in year 1 and high in year 2 (Low-High), and vice versa (High-Low). Food restriction had a significant effect on migratory tactics, with the frequency of smolts (juveniles choosing migration) highest in the Low-Low treatment in both populations. No individuals became smolts in the High-High treatment, and intermediate smolting rates were observed in the Low-High and High-Low treatments. Higher overall smolting rates in the naturally anadromous population suggested an inherited component to anadromy/migration decisions, but both populations showed variability in migratory tactics. Importantly, some fish from the naturally non-anadromous population became smolts in the experiment, implying the capacity for migration was lying ‘dormant’, but they exhibited lower hypo-osmoregulatory function than smolts from the naturally anadromous population. Tactic frequencies in the naturally anadromous population were more affected by food in the 2nd year, while food in the 1st year appeared more important for the naturally non-anadromous population. Migratory tactics were also related to sex, but underpinned in both sexes by growth in key periods, size and energetic state. Collectively these results reveal how migration decisions are shaped by a complex interplay between extrinsic and intrinsic factors, informing our ability to predict how facultatively migratory populations will respond to environmental change.

Developing genomic insights is challenging in nonmodel species for which resources are often scarce and prohibitively costly. Here, we explore the potential of a recently established approach using Pool‐seq data to generate a de novo genome assembly for mining exons, upon which Pool‐seq data are used to estimate population divergence and diversity. We do this for two pairs of sympatric populations of brown trout (Salmo trutta): one naturally sympatric set of populations and another pair of populations introduced to a common environment. We validate our approach by comparing the results to those from markers previously used to describe the populations (allozymes and individual‐based single nucleotide polymorphisms [SNPs]) and from mapping the Pool‐seq data to a reference genome of the closely related Atlantic salmon (Salmo salar). We find that genomic differentiation (F ST) between the two introduced populations exceeds that of the naturally sympatric populations (F ST = 0.13 and 0.03 between the introduced and the naturally sympatric populations, respectively), in concordance with estimates from the previously used SNPs. The same level of population divergence is found for the two genome assemblies, but estimates of average nucleotide diversity differ (π¯ ≈ 0.002 and π¯ ≈ 0.001 when mapping to S. trutta and S. salar, respectively), although the relationships between population values are largely consistent. This discrepancy might be attributed to biases when mapping to a haploid condensed assembly made of highly fragmented read data compared to using a high‐quality reference assembly from a divergent species. We conclude that the Pool‐seq‐only approach can be suitable for detecting and quantifying genome‐wide population differentiation, and for comparing genomic diversity in populations of nonmodel species where reference genomes are lacking., We explore the potential of a newly established approach that relies on Pool‐seq data to generate de novo genome assemblies in nonmodel species upon which Pool‐seq data are used to estimate population divergence and diversity. Estimates of population differentiation between sympatric brown trout (Salmo trutta) populations are qualitatively similar to those found from a previously used SNP panel and highly concordant to estimates from mapping our data to the publicly available Atlantic salmon (Salmo salar) reference genome. The Pool‐seq only approach is deemed suitable for detecting population differentiation in nonmodel species for which reference genomes are lacking.

Background Enormous variability in skin colour and patterning is a characteristic of teleost fish, including Salmonidae fishes, which present themselves as a suitable model for studying mechanisms of pigment patterning. In order to screen for candidate genes potentially involved in the specific skin pigment pattern in marble trout (labyrinthine skin pattern) and brown trout (spotted skin pattern), we conducted comparative transcriptome analysis between differently pigmented dermis sections of the adult skin of the two species. Results Differentially expressed genes (DEGs) possibly associated with skin pigment pattern were identified. The expression profile of 27 DEGs was further tested with quantitative real-time PCR on a larger number of samples. Expression of a subset of ten of these genes was analysed in hybrid (marble x brown) trout individuals and compared with the complexity of their skin pigment pattern. A correlation between the phenotype and the expression profile assessed for hybrid individuals was detected for four (gja5, clcn2, cdkn1a and tjp1) of the ten candidate genes tested. The potential role of these genes in skin pigment pattern maintenance is discussed. Conclusions Our results indicate that the maintenance of different pigment patterns in trout is dependent upon specific communication—involving gap junctions, tight junctions and ion channels—between chromatophores present in differentially pigmented skin regions. Electronic supplementary material The online version of this article (10.1186/s12864-019-5714-1) contains supplementary material, which is available to authorized users.

Due to the ecological concerns and preservation of genetic resources, the characterization of genetic structure of the brown trout (Salmo trutta) was carried out on the "Braduljica" fish farm. DNA was isolated from fin clips of 10 individuals, and after that molecular PCR-RFLP methods were used for distinguishing between Atlantic and Danubian lineages based on control region of the mitochondrial DNA (CR mtDNA) and lactate dehydrogenase gene of the nuclear DNA (LDH nDNA). Based on phenotypic characteristics it was estimated that out of 10 individuals included in this study five belonged to the allochtonous Atlantic lineage and remaining five belonged to the native Danubian lineage of brown trout. However, results of molecular analyses showed a high percentage of allochthonous genes among the individuals, which confirms the hybridization between these two lineages. Also, the results showed that the selection based on the phenotype is not adequate. In order to continue with proper broodstock management, it is necessary to eliminate allochtonous individuals of the Atlantic lineage from the broodstock. U cilju zaštite ţivotne sredine i genetiĉkih resursa potoĉne pastrmke (Salmo trutta) u radu je ispitivana genetiĉka struktura ove vrste na ribnjaku ―Braduljica‖ u blizini Ivanjice. DNK je izolovana iz odseĉaka peraja 10 jedinki, a nakon toga molekularne PCR-RFLP metode su korišćene za razlikovanje izmeĊu atlantske i dunavske linije na bazi kontrolnog regiona mitohondrijalne DNK (KR mtDNK) i jedarnog gena za laktat dehidrogenazu (LDH nDNK). Na osnovu fenotipskih karakteristika procenjeno je da je pet jedinki pripadalo alohtonoj atlantskoj liniji, a preostalih pet autohtonoj dunavskoj liniji potoĉne pastrmke. MeĊutim, rezultati molekularnih analiza pokazali su prisustvo visokog procenta alohtonih gena u analiziranom uzorku, što potvrĊuje hibridizaciju izmeĊu ove dve linije. TakoĊe, rezultati ukazuju na to da selekcija na osnovu fenotipa nije adekvatna. Kako bi ribnjak nastavio da se bavi gajenjem potoĉne pastrmke za potrebe poribljavanja okolnih reka, neophodno je da se eliminišu jedinke atlantske linije iz matiĉnog fonda.

Cytogenetic analysis of brown trout, Salmo trutta, have been described for different populations and morphs; however, cytogenetic analysis of interspecific brown trout hybrids is unknown. Cultured kidney cells from four brown trout subspecies (Salmo trutta abanticus, S.t. caspius, S.t. fario and S.t. labrax) and their reciprocal hybrids were karyotyped using conventional staining, C-banding and Ag-NOR staining techniques. Chromosome number (2N) and chromosome arm number (NF) ranged from76 to 80 and 98 to 102, respectively. Silver staining revealed the presence of NOR sites on the short arm of the submetacentric chromosome. The size and number of NOR sites showed uniformity. The presence of heterochromatin on different chromosome arms was confirmed by C-banding. The presence and position of constitutive heterochromatin showed variability among individuals. Chromosome structures of purebred brown trout subspecies belonging to the Danubian linage and their hybrids were similar, and no distinctive characteristics were observed in any of the species. The results of this study are applicable to the development of improved conservation and management strategies for brown trout., Caryologia. International Journal of Cytology, Cytosystematics and Cytogenetics, V. 72 N. 4 (2019)

International audience; Individual interactions are crucial to many ecological processes but are difficult to quantify for long periods in aquatic animals. In this study, we applied a digital proximity logging device recently developed for terrestrial animals to a freshwater fish, the brown trout (Salmo trutta L.). After preliminary calibration and quantification of detection errors, we recorded the interactions occurring between five male and four female brown trout in an artificial channel during one week of the spawning season. The 55,637 logs recorded allowed us to describe the encounter network and its fine scale evolution. In particular, the time spent with females varied a lot across males, from two to 24 h in a five-day period, and the males, which spent the most time with females tended to mate more. At the individual level, the temporal distribution of encounters reflected shifts in dominance status, with males sequentially taking over exclusive proximity with females before spawning. Beyond sexual encounters, the method presented here could be applied to many processes interesting to fish ecologists, such as predator-prey interactions, intra and interspecific competition or disease transmission

Accepted manuscript version. Published version available in Effects of fish species composition on Diphyllobothrium spp. infections in subarctic brown trout - is three-spined stickleback a key species? (2016) 39(11), s.1313-1323. . Subarctic populations of brown trout (Salmo trutta) are often heavily infected with cestodes of the genus Diphyllobothrium, assumedly because of their piscivorous behavior. This study explores possible associations between availability of fish prey and Diphyllobothrium spp. infections in lacustrine trout populations. Trout in i) allopatry (group T); ii) sympatry with Arctic charr (Salvelinus alpinus) (group TC); and iii) sympatry with charr and three-spined stickleback (Gasterosteus aculeatus) (group TCS) were contrasted. Mean abundance and intensity of Diphyllobothrium spp. were higher in group TCS compared to group TC and group T. Prevalence however was similarly higher in group TCS and group TC compared to group T. Zero-altered negative binomial modelling identified lowest probability of infection in group T and similar probabilities of infection in group TC and group TCS, whereas the highest intensity was predicted in group TCS. Evidently, the most infected trout were from the group co-occurring with stickleback (TCS), assumedly due to a high availability of suitable prey fishes. In conclusion, our study demonstrates elevated Diphyllobothrium spp. infections in lacustrine trout populations where fish prey are available, and suggests that highly available and easily caught stickleback prey may play a key role in the transmission of Diphyllobothrium spp. parasite larvae.

Body composition (total crude protein, lipid, ash, dry matter and moisture) and fatty acid profiles were compared between wild and farmed brown trout and between farmed rainbow trout. Farmed brown trout contained the highest amount of crude protein (18.39%), whereas farmed rainbow trout contained higher levels of crude lipid (2.35%). Thirty six fatty acids were found, including sixteen saturated fatty acids (SFA), nine monounsaturated fatty acids (MUFA) and eleven polyunsaturated fatty acids (PUFA). The most abundant SFA in all fish were palmitic acid and stearic acid. However, the most abundant fatty acids in all trout samples were MUFA and PUFA. MUFA were the most abundant fatty acid in farmed brown trout because of high abundance of oleic acid in this samples (35.46g / 100g fatty acids). PUFA were predominating in the samples of wild brown trout and of rainbow trout 56.16 and 56.29g/100g fatty acids, respectively). Linoleic acid was the most abundant fatty acid reported in the rainbow trout (47.17g/100g fatty acids). Significantly higher amounts of docosahexaenoic acid, α-linolenic acid, arachidonic acid and eicosapentaenoic acid were observed in the wild trout samples. Wild brown trout contained significantly more docosahexaenoic acid, α-linolenic acid, Eicosapentaenoic acidArachidonic acid. Sensory quality evaluation, by a consumers’ panel, revealed all samples were equally well accepted. A composição corporal (teores de proteína, gordura total, cinzas, matéria seca e humidade) e os perfis de ácidos gordos da trutafário (selvagem e proveniente de aquacultura) e da truta-arco-íris (cultivada) foram comparados. A truta-fário cultivada continha a maior quantidade de proteína bruta (18,39%), enquanto a truta arco-íris possuía teores mais elevados de lípidos (2,35%). Foram detectados 36 ácidos graxos, incluindo 16 ácidos graxos saturados (SFA), nove ácidos graxos monoinsaturados (MUFA) e 11 ácidos graxos poliinsaturados (PUFA). Os SFA mais abundantes foram o ácido palmítico e o ácido esteárico. No entanto, os ácidos graxos mais abundantes em todas as amostras de truta foram os MUFA e os PUFA. A grande abundância de ácido oleico existente nas amostras de truta-fário cultivada (35,46g/100g de ácidos graxos) faz com que os MUFA sejam os ácidos graxos mais abundantes nesta variedade de truta (42,43g/100g de ácidos graxos) Nas amostras de truta-fário selvagem e nas de truta arco-íris predominaram os PUFA (56,16 e 56,29g/100g de ácidos graxos, respetivamente), sendo o ácido linoleico o mais abundante na truta-arco-íris (47,17g/100g de ácidos graxos). Nas amostras trutafário selvagem foram observadas quantidades significativamente mais elevadas de ácido docosahexaenóico, ácido α-linolênico, ácido acidoaraquidônico e ácido eicosapentaenóico. Todas as amostras foram igualmente bem aceitas por um painel de consumidores. info:eu-repo/semantics/publishedVersion

Juvenile salmonids experience high mortality when negotiating lentic waters during their downstream migration to the sea. The development of artificial lakes and wetlands in streams has become a widely used management tool to reduce nutrient load to coastal areas. Such wetlands may threaten anadromous populations. In this study we quantify net ground speed of downstream migrating brown trout Salmo trutta smolts in equally long stream and lake sections in a Danish lowland stream and artificial lake. This was done by passive integrated transponder telemetry in 2016 and 2017. Mean net ground speed in the stream section was 36.58 km day-1 and 0.8 km day-1 in the lake section. This decrease of net ground speed through the lake may lead to prolonged exposure to predators and probably contributes to high mortalities threatening anadromous populations.

Lipid metabolism involves complex pathways, which are regulated in a similar way across vertebrates. Hormonal and hypolipidemic deregulations cause lipid imbalance from fish to humans, but the underlying mechanisms are far from understood. This study explores the potential of using juvenile brown trout to evaluate the in vivo interferences caused by estrogenic (17α-ethinylestradiol – EE2), androgenic (testosterone – T), and hypolipidemic (clofibrate – CLF) compounds in lipidic and/or peroxisomal pathways. Studied endpoints were from blood/plasma biochemistry, plasma fatty acid profile, ultrastructure of hepatocytes and abundance of their peroxisomes to mRNA expression in the liver. Both T and CLF caused minimal effects when compared to EE2. Estrogenized fish had significantly higher hepatosomatic indexes, increased triglycerides and very-low density lipoproteins (VLDL) in plasma, compared with solvent control. Morphologically, EE2 fish showed increased lipid droplets in hepatocytes, and EE2 and T reduced volume density of peroxisomes in relation to the hepatic parenchyma. Polyunsaturated fatty acids (PUFA) in plasma, namely n−3 PUFA, increased with EE2. EE2 animals had increased mRNA levels of vitellogenin A (VtgA), estrogen receptor alpha (ERα), peroxisome proliferator-activated receptor alpha (PPARα), PPARαBa and acyl-CoA long chain synthetase 1 (Acsl1), while ERβ-1, acyl-CoA oxidase 1–3I (Acox1–3I), Acox3, PPARγ, catalase (Cat), urate oxidase (Uox), fatty acid binding protein 1 (Fabp1) and apolipoprotein AI (ApoAI) were down-regulated. In summary, in vivo EE2 exposure altered lipid metabolism and peroxisome dynamics in brown trout, namely by changing the mRNA levels of several genes. Our model can be used to study possible organism-level impacts, viz. in gonadogenesis. © 2018 Elsevier This study was primarily funded by FCT - Foundation for Science and Technology , through the project PTDC/CVT/115618/2009 and grants given to Tânia V. Madureira ( SFRH/BPD/97139/2013 ) and Tiago Simões ( SFRH/BD/98266/2013 ). It was also partially supported by the Strategic Funding UID/Multi/04423/2013 and UID/MAR/04292/2013 granted to CIMAR and MARE, respectively, through national funds provided by FCT and European Regional Development Fund (ERDF), in the framework of the program PT2020 . The work was implemented in the Framework of the Structured Program of R&D&I INNOVMAR - Innovation and Sustainability in the Management and Exploitation of Marine Resources (NORTE-01-0145-FEDER-000035), namely within the Research Line ECOSERVICES, supported by the Northern Regional Operational Programme ( NORTE2020 ), through ERFD. This study is also included in the Integrated Program of SR&TD "SmartBioR" (reference Center-01-0145-FEDER-000018), cofunded by Centro 2020 program, by PT2020, through the ERDF.

International audience; Salmonid females invest heavily in reproduction, through gamete production, habitat selection and maternal care. Habitat selection and maternal care are expected to provide shelter for eggs against scouring and predators. However, females also tend to produce variable egg sizes, and this trait may interact with habitat quality to influence the survival of offspring. In this study, we aimed at evaluating the role of female habitat selection on egg survival conditional on individual egg size and female body size. We monitored female reproductive activity in two natural rivers for 3 years, in order to relate nest characteristics to female body size. Bigger females dug deeper nests at lower shear stress force. Right after the end of nest construction, we sampled a part of the eggs laid by each female, measured them individually, and placed them back using capsules within their original position in the nest. At time of hatching, the capsules within the nest were collected and individual egg mortality was assessed. Our results indicate that scouring was the main driver for mortality (75%) and that nest burial depth and shear stress force above the nest both influenced scouring. However, subsequent survival was influenced by neither nest characteristics, individual egg size, nor the interaction between both. It is therefore expected that traits or tactics that reduce nest scouring probability should be under strong selection

The biological and anthropogenic (management) factors that may contribute to the expansion of non-native lineages in managed fish have been studied in this work taking brown trout (Salmo trutta) as a model species. The changes of users’ opinion about stocking was studied employing social science methodology (surveys). The evolution of hatchery stocks together with the outcome of stocking were analysed with two genetic tools: the LDH-C1* locus (marker of non-native stocks) and six microsatellite loci (for assignment of wild trout to the natural population or putative hatchery stocks). Consulted stakeholders were convinced of the correctness of releasing only native stocks, although in practice the hatcheries managed by them contained important proportions of non-native gene carriers. Our results suggest that allochthonous individuals perform better and grow faster in hatchery conditions than the native ones. We also find a dilution of the impact of this kind of suplementation in wild conditions. The use of only native individuals as hatchery breeders tested for the presence of non-native alleles previously to the artificial crosses must be a priority. Surveys can help steer policy making toward decisions that will be followed by the public, but they should not be used to justify science.