Salmonid Species Research Articles

Genetic diversity insights from population genomics and machine learning tools for Nordic Arctic charr (Salvelinus alpinus) populations

Arctic charr (Salvelinus alpinus) is a salmonid species of high ecological and commercial value in the Holarctic region. Nevertheless, more information is needed about its underlying genetic diversity and population structure in the Nordics, especially regarding farmed populations. High-throughput sequencing was applied in three Arctic charr populations of anadromous or landlocked origin from Finland, Norway and Sweden. More specifically, the animals from the Swedish and Norwegian populations originated from a major egg supplier and producer, respectively. Furthermore, in the case of the Finnish population, the sampled animals originated from the only active conservation program for Arctic charr in the country with a potential interest in farming. Using double-digest restriction site-associated DNA sequencing (ddRAD-seq) on more than 500 fish, over 2000 single nucleotide polymorphisms (SNPs), both in the form of individual SNPs and as read haplotypes, were used to study the genetic diversity and structure of those populations. Genetic diversity metrics were similar between the Norwegian and the Swedish populations. However, substantially lower (40–50 %) genetic diversity was found in the Finnish population. Moreover, considerable genetic differentiation was implied between the studied populations as the mean fixation index (FST) was above 0.1 in all pairwise comparisons. All populations were easily discernible through either principal component analysis (PCA) or discriminant analysis of principal components (DAPC). In addition, unsupervised machine learning models such as K-means, Gaussian and Bayesian Gaussian mixtures were assessed for their ability to detect genetic clusters. A preceding dimensionality reduction step by PCA resulted in all three models, suggesting that the most probable number of clusters was three. Overall, our study affirmed the utility of the developed ddRAD-seq genotyping method and unveiled the genetic structure of the studied populations, both of which could contribute to their more efficient management by captive breeding.

Matings Between Individuals with Similar Major Histocompatibility Complex (MHC) Improve Offspring Survival in the Rainbow Trout (Oncorhynchus mykiss)

The major histocompatibility complex (MHC) consists of genes involved in immune response and molecular discrimination between self and non-self. MHC genes are the most polymorphic in vertebrates. The origin and maintenance of polymorphism in MHC genes in populations is still unresolved. Mechanisms such as sexual selection and heterozygote advantage have been suggested as explanations for this high variability. In this study, a farmed population of rainbow trout (Oncorhynchus mykiss) characterized by the presence of specific MHC class IIB gene haplotypes at a frequency higher (30%) than that expected from random matings was investigated. Therefore, it was hypothesized that disassortative matings occur with an adaptive advantage for females, resulting in improved reproductive performance when mated with individuals with similar MHC haplotypes. Genetic analyses of the breeders were performed to define the MHC haplotypes and to perform specific matings. The effect of mating was evaluated by analyzing the survival rate of the offspring at various stages of incubation until swim-up. The reproductive performance of the offspring derived from specimens with similar haplotypes showed a better survival trend during the first life stages and reduced malformations. The results obtained are in contrast with the heterozygous advantage theory, therefore it was hypothesized, as for other salmonid species, the presence of a positive selection towards locally adapted MHC genes that promotes reproduction between genetically similar individuals.

The possibilities of using of captive and domestic broodstocks for saving of natural populations. 2. Salmonidae. Atlantic salmon (Part 1)

In first review we considered the problems of creation of sturgeon broodstocks in freshwater with full exclusion of marine phase. Several species of salmonids (trouts) which easily change their life stategy (sea trout/brown trout Salmo trutta, steelhead/rainbow trout, brook trout Salvelinus fontinalis and other chars) also could be grown in fresh water up to definitive sizes and maturation. Atlantic salmon differs from above species. In present article the intraspecific structure of Atlantic salmon and its life strategies (anadromous, potamodromos and riverine/residential), development of methods of artificial propagation of salmonids and possibilities of Atlantic salmon growing in conditions of freshwater farm are considered. Three types of broodstocks could be created — sea-run (wild), captive (grown from wild smolts) and domestic (grown from eggs) ones. The creation of domestic freshwater broodstock of Atlantic salmon is more complicated in comparison with trouts because of precocious maturation of great percent of males and low quality of mature germinal cells in males and females. The other negative features of domestic breeders are decreased genetic variability, increased straying and reduced reproductive success. So commercial aquaculture uses traditional scheme of transfer of large smolts (near 100 g) to sea cages. Conservation aquaculture prefers wild non-resident breeders. Atlantic salmon is characterized by riverspecific broodstocks, so each river should have its own broodstock. As a result domestic broodstock of Atlantic salmon in conservation aquaculture could be used only as last measure when all other possibilities are already exhausted.

Temporal and spatial use of a freshwater lake by upstream and downstream migrating adult Atlantic salmon Salmo salar.

Atlantic salmon Salmo salar typically enter fresh water several months prior to spawning and just as pools can provide areas of refuge in river systems, lakes may also provide important refuge habitat during the spawning migration. Using acoustic telemetry we examined the spatial and temporal movements of wild and a ranched strain of Atlantic salmon in a freshwater lake where the main spawning areas were located upstream of the lake. Over the study period (2011-2014), returning adult wild salmon spent an average of 228 days in fresh water and 90% of that time in the lake. On entering the lake, most wild salmon moved quickly to the northern part of the lake, close to the main inflow, spending an average 76% of the time in this location. The average number of days wild fish were absent from the lake during the main spawning period varied between years, ranging from 10 to 26 days for females and 32 to 35 days for males. Seventy four per cent (17/23) of salmon spawners returned to the lake and two salmon subsequently died in the lake post-spawning. Atypically, two salmon were resident in the lake for the whole period in 2013/14. During the study, wild salmon were detected at depths within the top 5 m for 73% of the time. Median depths post-spawning were greater than in the pre-spawning period, when salmon were found to spend extensive periods at depths in excess of 10 m. In July 2013, when the lake was stratified, thermal regulation behaviour was observed in wild salmon, whereby salmon moved to cooler deeper water when water temperatures at 1 m exceeded 20°C. In contrast to wild salmon, the majority of ranch salmon returned to the traps downstream of the lake prior to the spawning period, which would be expected as they were released as smolts below the freshwater lake. Ranch fish spent an average 80% of the time in the vicinity of receivers in the south of the lake and an average 98% of the time within the top 5 m. However, two ranch females were resident in the lake until the following spring and one ranch female moved upstream into the river during the spawning period. Clearly, in this catchment the lake provides an important habitat for migrating adult salmon. In the context of climate change, where thermal and hydrological regimes in rivers are expected to change in response to changes in air temperature and precipitation patterns, the availability of deep lakes that stratify in the summer and cool water refuges in river systems is likely to play a key role in the sustenance and conservation of salmonid species. Information about the migration patterns of Atlantic salmon in undisturbed freshwater systems may also assist in resolving issues associated with fish passage in impacted rivers and inform management decisions.

Temporal Patterns of Fish Occurrence in the Colorado River, Grand Canyon in Response to Temperature, Largescale Drought, and Newly Exposed Habitat

ABSTRACTTwo large dams on the Colorado River, Glen Canyon and Hoover Dam, have profoundly altered the river within Grand Canyon. Owing to widespread drought and increased water usage throughout the Southwest, water levels in Lake Mead declined by over 40 m since 2000, exposing over 80 km of newly emerged riverine habitat in the western Grand Canyon that experiences higher water temperatures and increased turbidity relative to upstream portions of the Colorado River within the Grand Canyon. Our objective was to investigate how the probability of fish occurrence has changed within the Colorado River in Grand Canyon as abiotic conditions have shifted in relation to these altered environmental conditions. We used 22 years of long‐term fish monitoring data, from 2000 to 2022, on the mainstem of the Colorado River in the Grand Canyon to map the probability of occurrence based upon modeled water temperature for native and common nonnative salmonid species through space (river kilometer) and time in relation to declining water levels in Lake Mead. Our results suggest that native fish occurrence is strongly correlated with longitudinally increasing water temperature, while nonnative trout species were negatively correlated with increased water temperature downstream from the dam. Further, we found that nonnative trout species have experienced decreases in their probability of occurrence through time, while natives have experienced an increase in probability of occurrence. Information on distribution of fish prior to reservoir declines, and how the fish assemblage has shifted coincident with environmental changes, can help inform future management of native and nonnative fish in highly regulated river systems.

Using Genetic Data to Determine Origin for Out-Migrating Smolt and Returning Adult Steelhead Trout (Oncorhynchus mykiss) in a Southeast Alaska Drainage.

Oncorhynchus mykiss is a partially migratory salmonid species, and many migratory populations (known as steelhead) have declined in recent decades in the western United States and Canada. Closely related resident populations (known as rainbow trout) may be an effective resource in the recovery of these declining migratory populations. However, the extent to which different populations of resident rainbow trout produce migratory individuals and how likely these individuals are to return as adults to spawn remains unknown. One limitation to answering these questions is the identification of loci that accurately segregate between migratory and resident populations. To address this limitation, we used existing genomic data from a well-studied population of O. mykiss from Southeastern Alaska (Sashin Creek) to identify loci that segregate between phenotypes. We then utilized Double Mismatch Allele-Specific qPCR (DMAS-qPCR) to genotype 233 smolts out-migrating from Sashin Creek and 99 returning adult steelhead trout across a five-year period to determine (a) the origin of out-migrating smolts and returning adults and (b) to quantify the extent to which the resident population contributes to the migratory population. Our results show that 37.3% of out-migrating smolts were produced from resident parents, whereas 19.3% of returning adults had resident parents. Ultimately, these results demonstrate that resident populations of rainbow trout produce migrant offspring that successfully complete their migration and return to spawn, increasing population sizes and likely improving genetic diversity. Therefore, conservation efforts should consider landlocked resident populations for producing smolts when developing recovery plans for migratory steelhead populations.

Distinct food-web transfers of 137Cs to fish in river and lake ecosystems: A case study focusing on masu salmon in the Fukushima evacuation zone

This study was conducted to elucidate the spatial and size variations, and food-web transfer of 137Cs in freshwater fish in the upper reaches of the Ukedo River system, a highly contaminated river system flowing through the Fukushima evacuation zone. Fish collection and environmental surveys were conducted in the summer of 2020 at five forest rivers and at the Ogaki Dam reservoir (an artificial lake) with different air dose rates (mean 0.20–3.32 μSv/h). From the river sites, two salmonid species (masu salmon and white-spotted charr) were sampled, with masu salmon generally exhibiting higher 137Cs concentrations, ranging widely (10.6 Bq/kg-wet to 13.0 kBq/kg-wet) depending on the fish size (size effect) and site. The 137Cs concentrations in masu salmon were explained by the air dose rates, 137Cs concentrations in water, sediments (excluding the lake site), and primary producers, with site-specific variations. In the rivers, masu salmon (fluvial type with parr marks) mainly fed on terrestrial insects with higher 137Cs concentrations compared with those of aquatic insects, indicating that 137Cs was transferred mainly to fish through the allochthonous forest food-web during summer. In the lake, masu salmon (lake-run type with larger size and silvery body coloration) mainly preyed on smaller fish with lower 137Cs concentrations, demonstrating that 137Cs is transferred to fish through the autochthonous lake food-web with biomagnification. Differences in 137Cs concentrations among masu salmon (mean 441 Bq/kg-wet) and other fish species (mean 74.8 Bq/kg-wet to 2.35 kBq/kg-wet) were also found in the lake. The distinct 137Cs transfers to river and lake fish were supported by stable isotope analysis: δ15N and δ13C values enriched stepwisely through the food-webs were, respectively, higher and lower in the lake. Our results obtained using multiple approaches clearly revealed the distinct food-web transfer of 137Cs in river and lake ecosystems. These findings can contribute to prediction of radioactive contamination in freshwater fish in the Fukushima evacuation zone.

Survey of the invasive alien pink salmon (Oncorhynchus gorbuscha) for infective agents in the Fennoscandian Rivers Tana and Neiden

Pink salmon (Oncorhynchus gorbuscha, Walbaum 1792) is an invasive alien species in the Fennoscandian rivers, and its growing populations cause concern for their impact on the native salmonids and river ecosystems. One of the major concerns is fish diseases and the potential ability of pink salmon to transmit pathogens to the native salmonid species. In this study, pink salmon were sampled during their spawning migration in the Rivers Tana and Neiden in northern Norway and Finland in 2021. The fish were surveyed for viral hemorrhagic septicemia virus (VHSV), infectious pancreatic necrosis virus (IPNV), infectious salmon anemia virus (ISAV), salmonid alphavirus (SAV), piscine orthoreovirus (PRV), Renibacterium salmoninarum, and Gyrodactylus salaris. No viral diseases or infections with R. salmoninarum or G. salaris were detected. However, 23 % of the fish were found infected with a parasitic roundworm, Hysterothylacium aduncum. Additionally, external anomalies, such as hemorrhages or lesions in the skin, were observed in 35 % of the fish studied, and some of the fish exhibited degenerative myopathy. Based on this study, pink salmon appears not to pose a high infection risk to the native salmonid fish populations in the Rivers Tana and Neiden. Nevertheless, the results demonstrate that pink salmon have the potential to carry salmonid pathogens. More information on the susceptibility of pink salmon to different pathogens and on the overall effect this invasive species has on native fish species is needed. As the number of migrating pink salmon in the Fennoscandian rivers appears to increase, the potential risk of parasites and other pathogens spreading between fish species will also rise.

Genetic diversity of salmonid fishes in the eastern part of the Onega Peninsula, Northern European Russia

The Onega Peninsula in the White Sea, north-western Russia, is a habitat for ecologically and economically significant salmonid species, i.e. Atlantic salmon Salmo salar Linnaeus, 1758 and brown trout S. trutta Linnaeus, 1758 (Salmoninae). However, these populations are currently understudied in terms of molecular approach. In this work, we assessed the genetic diversity and differentiation of S. salar and S. trutta from the eastern part of the Onega Peninsula based on mitochondrial (COI and cytb) and nuclear (RAG1) markers. We also traced a phylogeographic pattern of these species. Populations of brown trout in the studied watercourses mainly share low haplotype and nucleotide diversity, with the exception of the moderate values in the Gosdarea River. In turn, Atlantic salmon in the Ust’-Yaren’ga River has higher genetic diversity than brown trout. Our study reveals great importance of conservation measures and monitoring, as well as parasite pressure control, especially for brown trout, in the eastern part of the Onega Peninsula.

A study investigating heavy metals in salmonids products marketed in Spain

Spain is the second European country that consumes the most fish, with salmon being the second most consumed. Therefore, the safety of salmonids for human health is a hot topic that requires more research. In this study we measured arsenic, cadmium, mercury and lead (As, Cd, Hg and Pb respectively) in 54 samples of four salmonid species (Oncorhynchus gorbuscha, O. keta, O. mykiss and S. salar) acquired in Asturias (North Spain) supermarkets, imported from other regions. O. mykiss samples (N = 30) from local farms located on two nearby rivers in the same region were also analyzed as well as river water. Marketed samples were authenticated through DNA barcoding. No species substitution was found, while five samples from O. keta exhibited contradictory information about the geographical origin in the label. The label indicated that they were from “Northwest Pacific” and “FAO area 67”. The Northwest Pacific catch zone corresponds to FAO 61, while FAO 67 is located in Northeast Pacific. Only one market sample exceeded the legal limit of Pb and none for other metals. Five S. salar samples from Denmark surpassed the safety limits marked for As, and other five samples from different species for Hg, but correcting for the expected proportion of the toxic form of these elements only three exceeded the safety limits for Hg and none for As. The importance of local contamination was emphasized for different metal profiles according to different content in water. Overall, health risk assessment indicate that salmonids sold in Spain can be considered safe for human consumption.

Dietary starch, non-starch polysaccharides and their interactions affect nutrient digestibility, faecal waste production and characteristics differentially in three salmonids: Rainbow trout, Atlantic salmon and Arctic charr

Waste management has emerged as a critical issue in aquaculture. In this study, we examined the impact of dietary starch and non-starch polysaccharides (NSP) content on nutrient digestibility, faecal waste production, faecal removal efficiency and the faecal characteristics in three salmonid species, namely rainbow trout (Oncorhynchus mykiss), Atlantic salmon (Salmo salar) and Arctic charr (Salvelinus alpinus). Four diets were formulated according to a 2 × 2 factorial design. The first factor, starch, was tested by including 0% gelatinised wheat flour (low starch) or 20% gelatinised wheat flour (high starch) in a plant-based basal diet. The second factor, NSP, was tested by adding 0% NSP source (low NSP) or 10% NSP source (high NSP). High NSP level was achieved by adding an equal mixture of soya hull (5%) and wheat bran (5%). Diets were tested in triplicates for each species and feeding was done restrictively. Experimental duration was 42 days for rainbow trout and Atlantic salmon and 49 days for Arctic charr. Among the three species investigated, Arctic charr had the lowest digestibility values for most nutrients, whereas rainbow trout and Atlantic salmon values were comparable. High starch level in the diet reduced the macronutrient (protein, fat and ash) digestibility in all three species. High starch and high NSP levels in the diet increased faecal waste production, with the effect being more pronounced for the NSP content of the diet. High dietary starch levels increased the proportion of smaller-sized particles, while high NSP content increased the ability of faecal particles to withstand mechanical stress. The high starch level in the diet lowered faecal removal efficiency but increased by high NSP content. The highest and lowest faecal removal efficiency was recorded for Atlantic salmon and Arctic charr, respectively. The amount of non-removed faeces accumulating in the system was increased by the high starch levels in rainbow trout and Atlantic salmon but remained unaffected by the NSP content of the diet across the species. No interaction effect between starch and NSP content of diets was observed for faecal removal efficiency and non-removed faeces. Among the three species investigated, Arctic charr had the maximum amount of non-removed faeces per kilogram of dry matter feed.

First case of ichthyophonosis in farmed rainbow trout Oncorhynchus mykiss in Serbia.

Ichthyophonosis is a disease caused by the mesomycetozoean parasite Ichthyophonus hoferi that affects a variety of fish species, including rainbow trout Oncorhynchus mykiss Walbaum. This disease is characterized by granulomatous lesions and necrosis in various organs, which can have severe impacts on the health and welfare of the fish. Ichthyophonosis has been found in several parts of the world, including Europe, and is a significant concern in the aquaculture industry and for populations of wild marine fishes. The rainbow trout is a widely cultured salmonid species in many countries, including Serbia. Although the presence of I. hoferi in rainbow trout has been reported in several countries, it has never been documented in Serbia. In this article, we report the first case of ichthyophonosis in rainbow trout in Serbia.

Activin Signaling Pathway Specialization During Embryonic and Skeletal Muscle Development in Rainbow Trout (Oncorhynchus mykiss).

Activin signaling is essential for proper embryonic, skeletal muscle, and reproductive development. Duplication of the pathway in teleost fish has enabled diversification of gene function across the pathway but how gene duplication influences the function of activin signaling in non-mammalian species is poorly understood. Full characterization of activin receptor signaling pathway expression was performed across embryonic development and during early skeletal muscle growth in rainbow trout (RBT, Oncorhynchus mykiss). Rainbow trout are a model salmonid species that have undergone two additional rounds of whole genome duplication. A small number of genes were expressed early in development and most genes increased expression throughout development. There was limited expression of activin Ab in RBT embryos despite these genes exhibiting significantly elevated expression in post-hatch skeletal muscle. CRISPR editing of the activin Aa1 ohnolog and subsequent production of meiotic gynogenetic offspring revealed that biallelic disruption of activin Aa1 did not result in developmental defects, as occurs with knockout of activin A in mammals. The majority of gynogenetic offspring exhibited homozygous activin Aa1 genotypes (wild type, in-frame, or frameshift) derived from the mosaic founder female. The research identifies mechanisms of specialization among the duplicated activin ohnologs across embryonic development and during periods of high muscle growth in larval and juvenile fish. The knowledge gained provides insights into potential viable gene-targeting approaches for engineering the activin receptor signaling pathway and establishes the feasibility of employing meiotic gynogenesis as a tool for producing homozygous F1 genome-edited fish for species with long-generation times, such as salmonids.

A new method for regionalization of the vertebral column in salmonids based on radiographic hallmarks.

Current procedures to establish vertebral column regionalization (e.g., histology) in fish are time consuming and difficult to apply. The aim of this study was to develop a more rapid and accurate radiology-based method for Atlantic salmon (Salmo salar). A detailed analysis of 90 animals (4 kg) led to the establishment of region-specific radiographic hallmarks. To elucidate its transferability to other salmonid species, radiography was carried out in brown trout (Salmo trutta), Arctic char (Salvelinus alpinus), rainbow trout (Oncorhynchus mykiss), pink salmon (Oncorhynchus gorbuscha), and Chinook salmon (Oncorhynchus tshawytscha). This method was also evaluated for whole ungutted fish. The vertebral column of Atlantic salmon can be subdivided into five regions (R1-R5) based on anatomy: postcranial (R1, V1, and V2), abdominal (R2, V3-V26), transitional (R3, V27-V36), caudal (R4, V37-V53), and ural (R5, V54-V59). The following specific radiographic hallmarks allow the identification of regions: (i) lack of ribs in R1, (ii) modified parapophysis of the first vertebra of R3, (iii) prominent hemal spine of the first vertebra of R4, and (iv) the separated hemal spine of the most cranial pre-ural vertebra of R5. These hallmarks were all transferable to the other salmonid species assessed. The results include a further description of various region-specific characteristics in Atlantic salmon. The method was found applicable for sedated/whole ungutted fish, verifying it as quick and easy compared to other regionalization methods. The regions defined by radiology in this study agree with the vertebral column regions recently defined for Chinook salmon (O. tshawytscha). Thus, and considering the results of this study on various salmonid species, the currently developed regionalization protocol can be generally used for salmonids.

Tire-derived contaminants 6PPD and 6PPD-Q: Analysis, sample handling, and reconnaissance of United States stream exposures

The environmental ubiquity of tire and road wear particles (TRWP) underscores the need to understand the occurrence, persistence, and environmental effects of tire-related chemicals in aquatic ecosystems. One such chemical is 6PPD-quinone (6PPD-Q), a transformation product of the tire antioxidant 6PPD. In urban stormwater runoff 6PPD-Q can exceed acute toxicity thresholds for several salmonid species and is being implicated in significant coho salmon losses in the Pacific Northwest. There is a critical need to understand the prevalence of 6PPD-Q across watersheds to identify habitats heavily affected by TRWPs. We conducted a reconnaissance of 6PPD and 6PPD-Q in surface waters across the United States from sites (N = 94) with varying land use (urban, agricultural, and forested) and streamflow to better understand stream exposures. A rapid, low-volume direct-inject, liquid chromatography mass spectrometry method was developed for the quantitation of 6PPD-Q and screening for 6PPD. Laboratory holding times, bottle material, headspace, and filter materials were investigated to inform best practices for 6PPD-Q sampling and analysis. Glass bottles with PTFE-lined caps minimized sorption and borosilicate glass fiber filters provided the highest recovery. 6PPD-Q was stable for at least 5 months in pure laboratory solutions and for 75 days at 5 °C with minimal headspace in the investigated surface water and stormwaters. Results also indicated samples can be frozen to extend holding times. 6PPD was not detected in any of the 526 analyzed samples and there were no detections of 6PPD-Q at agricultural or forested sites. 6PPD-Q was frequently detected in stormwater (57%, N = 90) and from urban impacted sites (45%, N = 276) with concentrations ranging from 0.002 to 0.29 μg/L. The highest concentrations, above the lethal level for coho salmon, occurred during stormwater runoff events. This highlights the importance of capturing episodic runoff events in urban areas near ecologically relevant habitat or nursery grounds for sensitive species.

Transcriptomic and Epigenomic Responses to Cortisol-Mediated Stress in Rainbow Trout (Oncorhynchus mykiss) Skeletal Muscle.

The production and release of cortisol during stress responses are key regulators of growth in teleosts. Understanding the molecular responses to cortisol is crucial for the sustainable farming of rainbow trout (Oncorhynchus mykiss) and other salmonid species. While several studies have explored the genomic and non-genomic impacts of cortisol on fish growth and skeletal muscle development, the long-term effects driven by epigenetic mechanisms, such as cortisol-induced DNA methylation, remain unexplored. In this study, we analyzed the transcriptome and genome-wide DNA methylation in the skeletal muscle of rainbow trout seven days after cortisol administration. We identified 550 differentially expressed genes (DEGs) by RNA-seq and 9059 differentially methylated genes (DMGs) via whole-genome bisulfite sequencing (WGBS) analysis. KEGG enrichment analysis showed that cortisol modulates the differential expression of genes associated with nucleotide metabolism, ECM-receptor interaction, and the regulation of actin cytoskeleton pathways. Similarly, cortisol induced the differential methylation of genes associated with focal adhesion, adrenergic signaling in cardiomyocytes, and Wnt signaling. Through integrative analyses, we determined that 126 genes showed a negative correlation between up-regulated expression and down-regulated methylation. KEGG enrichment analysis of these genes indicated participation in ECM-receptor interaction, regulation of actin cytoskeleton, and focal adhesion. Using RT-qPCR, we confirmed the differential expression of lamb3, itga6, limk2, itgb4, capn2, and thbs1. This study revealed for the first time the molecular responses of skeletal muscle to cortisol at the transcriptomic and whole-genome DNA methylation levels in rainbow trout.

Bias and variation in salmonid redd counting using remotely piloted vehicles

AbstractRedd surveys estimate spawning population size for many salmonid species. Studies of field‐based redd counting methods highlight observer bias caused by redd density, observer experience, and environmental factors. Researchers have begun using remotely piloted vehicles (RPVs, drones) to count redds; yet, no studies have quantified bias and variability in counts. This study aimed to quantify the influence of redd density, observer experience, and environmental factors (namely, water clarity) on redd counting bias and variability when using RPVs. We found that technological and procedural improvements from our previous study increased precision and reduced variability among observers (coefficient of variation, сυ = 11% compared to сυ = 42%). Redd density was the leading covariate causing differences between RPV and both “best counts” (p < 0.05) and field counts (p < 0.05). We found a reduction in variability with experience level (no experience сυ = 78%; semi‐experienced сυ = 33%; experienced сυ = 20%), with no directional bias in counting. Our paper is the first to quantify observer bias in RPV‐based redd counts. This study describes RPV methods and can help agencies decide how to use RPVs in redd counting and incorporate RPV methods into long‐term datasets.

Ecological evolution of salmonids

For the first time, ecological evolution of salmonid fishes is analyzed using the method of historical biogeography, considering formation of ecology and reproductive biology for these species under planetary climatic and geological changes. Climate cooling in the Cenozoic and associated reconstruction of the food base for salmonids had a major impact on evolution of their ecology. This process began at the Asian coast of the North Pacific much earlier than at the American coast and was much more intense there. The salmonids developed marine and oceanic feeding that led to their stocks increasing and a subsequent imbalance with freshwater prey. Adapting to this imbalance, the species of gen. Oncorhynchus came to irreversible reduction of organs and functions in the fresh water and absolute mortality of producers. Egg development lengthened in cold environments, and anadromous and semi-anadromous salmonid species were forced to spawn earlier, so that the larvae would hatch during the spring bloom of their prey. Gradually, the timing of their spawning shifted from early spring to winter and then to fall; accordingly, the spawning run to the rivers began earlier, in particular in the northern areas. The spawning season of atlantic salmon Salmo salar and brown trout Salmo trutta shifted to a fall and spring-summer spawning run in the north of their range and to a winter-spring and fall spawning run in the south of their range, but there is currently no reason to consider these runs as seasonal races, given that both cases evolved from a single run in the process of evolutionary changes when the spawning season was interrupted by either winter cooling or summer warming in the lower river reaches and at the coast. The northern and southern populations of salmonid fishes in the Pacific separated, too, because of these ecological changes in the late Pliocene, in conditions of cold climate. Being in isolation, they diverged enough to be considered as separate taxa rather than seasonal races.

Optimizing placement of bioretention systems in the US Puget Sound region

AbstractThe Puget Sound Basin, US Pacific Northwest, is experiencing rapid population and urban growth. This growth adversely impacts local ecosystems, especially the spawning and rearing habitat for several salmonid species. Sustainable urban design strategies such as green stormwater infrastructure (GSI) are required in the region to manage stormwater onsite when new development occurs. However, the effectiveness of any GSI depends on its location relative to where stormwater is produced. This study aimed to develop a Geographic Information System (GIS)‐based framework for the optimal placement of GSI, specifically bioretention systems. We computed the Hydrologic Sensitivity Index (λHSI, indicating runoff generation potential at a landscape location) for the lower Puyallup River Watershed study area. The index and federal and state feasibility criteria were used to identify suitable sites for bioretention systems. The suitability of identified sites was verified through ground‐truthing, including soil sampling and infiltration testing. We found that 2.5% of the watershed area was suitable for bioretention, concentrated in the center and north of the study watershed. The method described in this study can be readily applied to watersheds for which spatial data (topography, soil, and land use) are available. We recommend choosing locations with high λHSI when resources are limited since these locations contribute most to runoff generation and urban flooding.

Advances in salmonid genetics-Insights from Coastwide and beyond.

This article summarizes the Special Issue of Evolutionary Applications focused on "Advances in Salmonid Genetics." Contributions to this Special Issue were primarily presented at the Coastwide Salmonid Genetics Meeting, held in Boise, ID in June 2023, with a focus on Pacific salmonids of the west coast region of North America. Contributions from other regions of the globe are also included and further convey the importance of various salmonid species across the world. This Special Issue is comprised of 22 articles that together illustrate major advances in genetic and genomic tools to address fundamental and applied questions for natural populations of salmonids, ranging from mixed-stock analyses, to conservation of genetic diversity, to adaptation to local environments. These studies provide valuable insight for molecular ecologists since salmonid systems offer a window into evolutionary applications that parallel conservation efforts relevant and applicable beyond salmonid species. Here, we provide an introduction and a synopsis of articles in this Special Issue, along with future directions in this field. We present this Special Issue in honor of Fred Utter, a founder and leader in the field of salmonid genetics, who passed away in 2023.