Single generation epigenetic change in captivity and reinforcement in subsequent generations in a delta smelt (Hypomesus transpacificus) conservation hatchery.

A refugial population of the endangered delta smelt (Hypomesus transpacificus) has been maintained at the Fish Conservation and Culture Laboratory (FCCL) at UC Davis since 2008. Despite intense genetic management, fitness differences between wild and cultured fish have been observed at the FCCL. To investigate the molecular underpinnings of hatchery domestication, we used whole-genome bisulfite sequencing to quantify epigenetic differences between wild and hatchery-origin delta smelt. Differentially methylated regions (DMRs) were identified from 104 individuals by comparing the methylation patterns in different generations of hatchery fish (G1, G2, G3) with their wild parents (G0). We discovered a total of 132 significant DMRs (p < .05) between G0 and G1, 132 significant DMRs between G0 and G2, and 201 significant DMRs between G0 and G3. Our results demonstrate substantial differences in methylation patterns emerged between the wild and hatchery-reared fish in the early generations in the hatchery, with a higher proportion of hypermethylated DMRs in hatchery-reared fish. The rearing environment was found to be a stronger predictor of individual clustering based on methylation patterns than family, sex or generation. Our study indicates a reinforcement of the epigenetic status with successive generations in the hatchery environment, as evidenced by an increase in methylation in hypermethylated DMRs and a decrease in methylation in hypomethylated DMRs over time. Lastly, our results demonstrated heterogeneity in inherited methylation pattern in families across generations. These insights highlight the long-term consequences of hatchery practices on the epigenetic landscape, potentially impacting wild fish populations.

Host specificity and virulence of Flavobacterium psychrophilum: a comparative study in ayu (Plecoglossus altivelis) and rainbow trout (Oncorhynchus mykiss) hosts.

Flavobacterium psychrophilum, the causative agent of bacterial cold-water disease, is a devastating, worldwide distributed, fish pathogen causing significant economic loss in inland fish farms. Previous epidemiological studies showed that prevalent clonal complexes (CC) differ in fish species affected with disease such as rainbow trout, coho salmon and ayu, indicating significant associations between particular F. psychrophilum genotypes and host species. Yet, whether the population structure is driven by the trade of fish and eggs or by host-specific pathogenicity is uncertain. Notably, all F. psychrophilum isolates retrieved from ayu belong to Type-3 O antigen (O-Ag) whereas only very few strains retrieved from other fish species possess this O-Ag, suggesting a role in outbreaks affecting ayu. Thus, we investigated the links between genotype and pathogenicity by conducting comparative bath infection challenges in two fish hosts, ayu and rainbow trout, for a collection of isolates representing different MLST genotypes and O-Ag. Highly virulent strains in one host species exhibited low to no virulence in the other. F. psychrophilum strains associated with ayu and possessing Type-3 O-Ag demonstrated significant variability in pathogenicity in ayu, ranging from avirulent to highly virulent. Strikingly, F. psychrophilum strains retrieved from rainbow trout and possessing the Type-3 O-Ag were virulent for rainbow trout but not for ayu, indicating that Type-3 O-Ag alone is not sufficient for pathogenicity in ayu, nor does it prevent pathogenicity in rainbow trout. This study revealed that the association between a particular CC and host species partly depends on the pathogen's adaptation to specific host species.

Evolution of the ecological niche behind the largest disjunct freshwater fish distribution in the world.

Ecological processes that are behind distributions of species that inhabit isolated localities, complex disjunct distributions, remain poorly understood. Traditionally, vicariance and dispersion have been proposed as explanatory mechanisms that drive such distributions. However, to date, our understanding of the ecological processes driving evolution of ecological niches associated with disjunct distributions remains rudimentary. Here, we propose a framework to deconstruct drivers of such distribution using World's most widespread freshwater fish Galaxias maculatus as a model and integrating marine and freshwater environments where its life cycle may occur. Specifically, we assessed ecological and historical factors (Gondwanan vicariance, marine dispersion) and potential dispersion (niche-tracking) that explain its distribution in the Southern Hemisphere. Estimated distribution was consistent with previously reported distribution and mainly driven by temperature and topography in freshwater environments and by primary productivity and nitrate in marine environments. Niche dynamics of G. maculatus provided evidence of synergy between vicariance and marine dispersion as explanatory mechanisms of its disjunct distribution, suggesting that its ecological niche was conserved since approximately 30 Ma ago. This integrated assessment of ecological niche in marine and freshwater environments serves as a generic framework that may be applied to understand processes underpinning complex distributions of diadromous species.

Los procesos ecológicos que subyacen a las distribuciones de especies que habitan en localidades aisladas, distribuciones disjuntas complejas, siguen siendo poco conocidos. Tradicionalmente, se han propuesto la dispersión y la vicarianza como mecanismos explicativos de tales distribuciones. Sin embargo, hasta la fecha, nuestra comprensión de los procesos ecológicos que impulsan la evolución de los nichos ecológicos de distribuciones disjuntas sigue siendo rudimentaria. Aquí proponemos un marco para de­construir los factores que impulsan dicha distribución, utilizando como modelo el pez de agua dulce con distribución más extendida del mundo, Galaxias maculatus, e integrando los entornos marinos y dulceacuícolas en los que se desarrolla su ciclo vital. En concreto, evaluamos los factores ecológicos e históricos (vicarianza gondwánica, dispersión marina) que explican su distribución en el hemisferio sur. La distribución estimada coincide con la descrita anteriormente para la especie y está determinada principalmente por la temperatura y la topografía en ambientes dulceacuícolas, y la productividad primaria y el nitrato en ambientes marinos. La dinámica de nicho de G. maculatus aportó pruebas de la sinergia entre vicarianza y dispersión marina como mecanismos explicativos de su distribución disjunta, lo que sugiere que su nicho ecológico se conservó desde hace aproximadamente 30 Ma. Esta evaluación integrada del nicho ecológico en ambientes marinos y dulceacuícolas puede aplicarse para comprender los procesos que subyacen a las distribuciones complejas de especies diádromas.

A Y-linked anti-Müllerian hormone type-II receptor is the sex-determining gene in ayu, Plecoglossus altivelis.

Whole-genome duplication and genome compaction are thought to have played important roles in teleost fish evolution. Ayu (or sweetfish), Plecoglossus altivelis, belongs to the superorder Stomiati, order Osmeriformes. Stomiati is phylogenetically classified as sister taxa of Neoteleostei. Thus, ayu holds an important position in the fish tree of life. Although ayu is economically important for the food industry and recreational fishing in Japan, few genomic resources are available for this species. To address this problem, we produced a draft genome sequence of ayu by whole-genome shotgun sequencing and constructed linkage maps using a genotyping-by-sequencing approach. Syntenic analyses of ayu and other teleost fish provided information about chromosomal rearrangements during the divergence of Stomiati, Protacanthopterygii and Neoteleostei. The size of the ayu genome indicates that genome compaction occurred after the divergence of the family Osmeridae. Ayu has an XX/XY sex-determination system for which we identified sex-associated loci by a genome-wide association study by genotyping-by-sequencing and whole-genome resequencing using wild populations. Genome-wide association mapping using wild ayu populations revealed three sex-linked scaffolds (total, 2.03 Mb). Comparison of whole-genome resequencing mapping coverage between males and females identified male-specific regions in sex-linked scaffolds. A duplicate copy of the anti-Müllerian hormone type-II receptor gene (amhr2bY) was found within these male-specific regions, distinct from the autosomal copy of amhr2. Expression of the Y-linked amhr2 gene was male-specific in sox9b-positive somatic cells surrounding germ cells in undifferentiated gonads, whereas autosomal amhr2 transcripts were detected in somatic cells in sexually undifferentiated gonads of both genetic males and females. Loss-of-function mutation for amhr2bY induced male to female sex reversal. Taken together with the known role of Amh and Amhr2 in sex differentiation, these results indicate that the paralog of amhr2 on the ayu Y chromosome determines genetic sex, and the male-specific amh-amhr2 pathway is critical for testicular differentiation in ayu.

Parasite and genetic diversity of big-scale sand smelt (Atherina boyeri Risso, 1810) populations in their natural and expansion ranges in Ukraine.

The big-scale sand smelt (Atherina boyeri) is an Atlanto-Mediterranean amphidromous fish species found within the Black Sea. Here, we assess differences in the parasite fauna of big-scale sand smelt populations from their natural range in the northwestern Black Sea and from their expansion range in the Lower and Middle River Dnipro. In addition, we undertook a microsatellite analysis to assess the genetic similarity of fish from the different locations. We found that the parasite community of fish in their natural range was wider than that from their expansion range. While the Gulf of Odesa was most distant from all other localities by parasite community composition and the Dnipro Reservoir was characterised by an absence of parasites (newest and most distant expansion locality), only fish from the Danube Delta showed a significant genetic difference. Our results suggest that the parasite community of big-scale sand smelt is primarily influenced by environmental factors, such as habitat type, water salinity and/or prey composition. Both microsatellite analysis and parasite community species composition (e.g. the presence of the marine Telosentis exiguus in the Kakhovka Reservoir and freshwater Raphidascaris sp. in the Gulf of Odesa) confirmed that populations in the River Dnipro reservoirs had, at some time, been connected with native marine populations, thus also confirming the species' amphidromous nature.

Linkage between spatiotemporal distribution of environmental DNA and phenological activity in an amphidromous fish, ayu Plecoglossus altivelis altivelis, in a river located in its northernmost distributional area.

Environmental DNA (eDNA) is a promising tool for the continuous monitoring of fish ecology and diversity. However, its potential for describing the phenological activity of fish has rarely been examined. This study aimed to elucidate a linkage between the spatiotemporal distribution of eDNA and the phenology of an amphidromous fish, ayu Plecoglossus altivelis altivelis, in a river in Hokkaido, Japan, which is its northernmost distributional area. A significant positive correlation between eDNA concentration and catch per unit effort of P. a. altivelis in the river confirmed the use of eDNA as a surrogate for the abundance of P. a. altivelis. eDNA of P. a. altivelis was first detected in late April on a sandy beach adjacent to the river mouth. Subsequent to its first detection at the lowest site in the river in early May, eDNA spread throughout the river, indicating the upstream migration of P. a. altivelis. Spawning activity was also represented by a rapid increase in eDNA concentration and its surge at night in the lowest reaches of the river during September and October. These results suggest that upstream migration and spawning primarily commenced when the water temperature reached 10°C and decreased below 20°C, respectively. This observation is consistent with the behavioral responses observed in P. a. altivelis populations from other regions of Japan. Consequently, this study demonstrated that eDNA distribution was closely linked to the phenological activity of P. a. altivelis and that eDNA is a powerful tool for studying the phenology of migratory fishes.

Analysis of the genetic structure of the introduced clearhead icefish (Protosalanx chinensis) populations in northern China.

When species are introduced to a new environment, they can quickly adapt to the environment and may differ from the indigenous species. The indigenous population of Protosalanx chinensis has a high level of genetic diversity, but it is unclear on the genetic diversity of the introduced populations in northeast China, which supports the major production of P. chinensis in the world. A total of 556 individuals of P. chinensis were collected during 2016-2021, from Lianhuan Lake (LHL), Xingkai Lake (XK), and Shuifeng Reservoir (SF), and one population was collected from the indigenous Taihu Lake (TH). Overall, 36 haplotypes were detected, and the genetic differences in P. chinensis populations within and between river basins were investigated. The nucleotide diversity (π) of the populations ranged from 0.0005 to 0.0032, and the haplotype diversity (Hd) ranged from 0.455 to 0.890, with the highest genetic diversity in the TH population, followed by the SF population, and lower genetic diversity in the XK and LHL populations. The analysis of the genetic differentiation index (Fst) and the genetic distance between populations showed that there was significant genetic differentiation between the TH population and the other populations. More sampling points have been set up in LHL for further analysis; the Dalong Lake (DL) and the Xiaolong Lake (XL) populations were far from the other populations within the LHL population. In this study, we didn't find a correlation between population size, stability, and genetic diversity, and the ecological measures of management should be decisive to the population dynamics. These results provide a basis for the rational utilization and effective management of P. chinensis.

Gorges partition diversity within New Zealand flathead Galaxias populations.

Understanding the landscape factors governing population connectivity in riverine ecosystems represents an ongoing challenge for freshwater biologists. We used DNA sequence analysis to test the hypothesis that major geomorphological features underpin freshwater-limited fish diversity in a tectonically dynamic region of New Zealand. Phylogeographic analysis of 101 Galaxias depressiceps cytochrome b sequences, incorporating 55 localities from southern New Zealand, revealed 26 haplotypes, with only one shared among rivers. We detect strong hierarchical genetic differentiation both among and within river systems. Genetic structuring is particularly pronounced across the Taieri River system (63 individuals from 35 sites, 18 haplotypes), with 92% of variation partitioned among locations. Distinctive within-river genetic clusters are invariably associated with major subcatchment units, typically isolated by substantial gorges. The anomalous distribution of a single lineage across a major drainage divide is consistent with local, tectonically driven headwater capture. We conclude that major landscape features such as gorges can strongly partition riverine fish diversity and constrain freshwater biodiversity.

Ecological variation in invasive brown trout (Salmo trutta) within a remote coastal river catchment in northern Patagonia complicates estimates of invasion impact.

Salmonids were first introduced into the Chilean fresh waters in the 1880s, and c. 140 years later, they are ubiquitous across Chilean rivers, especially in the southern pristine fresh waters. This study examined the brown trout (Salmo trutta) and native taxa ecology in two adjacent but contrasting rivers of Chilean Patagonia. During spring 2016 and spring-fall 2017 we examined the variation in benthic macroinvertebrate and fish community composition and characterized fish size structure, stomach contents, and stable isotopes (δ13 C and δ15 N) to understand population structure, fish diet, and trophic interactions between S. trutta and native taxa. The native Galaxias maculatus (puye) dominated the fish community (74% of abundance). S. trutta was less abundant (16% of survey catch) but dominated the fish community (over 53%) in terms of biomass. S. trutta showed distinct diets (stomach content analysis) in the two rivers, and individuals from the larger river were notably more piscivorous, consuming native fish with a relatively small body size (<100-mm total length). Native fishes were isotopically distinct from S. trutta, which showed a wider isotopic niche in the smaller river, indicating that their trophic role was more variable than in the larger river (piscivorous). This study provides data from the unstudied pristine coastal rivers in Patagonia and reveals that interactions between native and introduced species can vary at very local spatial scales.

Comparative evaluation for the performance of environmental DNA and RNA analyses targeting mitochondrial and nuclear genes from ayu (Plecoglossus altivelis).

Environmental DNA and RNA (eDNA and eRNA; collectively eNA) analyses have the potential for non-invasive and cost-efficient biomonitoring compared with traditional capture-based surveys. Although various types of eNA particles, including not only mitochondrial eDNA but also nuclear eDNA and their transcripts, are present in the water, performances of eNA detection and quantification have not yet been evaluated sufficiently across multiple mitochondrial and nuclear genes. We conducted a tank experiment with ayu (Plecoglossus altivelis) to compare the detection sensitivity, yields per water sample, and quantification variability between replicates of each type of eNAs. The assay targeting the multi-copy nuclear gene exhibited a higher sensitivity than the assay targeting the mitochondrial gene, and both the target eDNA and eRNA concentrations per water sample were higher for the nuclear gene. On the contrary, variation in eRNA quantifications per sample does not necessarily correspond to that in eDNA, and the intra-sample quantification variability (represented as the CVs between PCR replicates) tended to be larger for eRNA than eDNA. Our results suggested that, even if suitable to the sensitive detection of species occurrence, the use of eRNA particularly derived from multi-copy nuclear gene may not be necessarily appropriate for the reliable assessment of species abundance. The findings in this study would help optimize eNA analyses for making biomonitoring and stock assessment in aquatic environments more efficient and reliable.

Does the loss of diadromy imply the loss of salinity tolerance? A gene expression study with replicate nondiadromous populations of Galaxias maculatus.

The recurrent colonization of freshwater habitats and subsequent loss of diadromy is a major ecological transition that has been reported in many ancestrally diadromous fishes. Such residency is often accompanied by a loss of tolerance to seawater. The amphidromous Galaxias maculatus has repeatedly colonized freshwater streams with evidence that freshwater-resident populations exhibit stark differences in their tolerance to higher salinities. Here, we used transcriptomics to gain insight into the mechanisms contributing to reduced tolerance to higher salinities in freshwater resident populations. We conducted an acute salinity challenge (0 ppt to 23-25 ppt) and measured osmoregulatory ability (muscle water content) over 48 h in three populations: diadromous, saltwater intolerant resident (Toltén), and saltwater tolerant resident (Valdivia). RNA sequencing of the gills identified genes that were differentially expressed in association with the salinity change and associated with the loss of saltwater tolerance in the Toltén population. Key genes associated with saltwater acclimation were characterized in diadromous G. maculatus individuals, some of which were also expressed in the saltwater tolerant resident population (Valdivia). We found that some of these "saltwater acclimation" genes, including the cystic fibrosis transmembrane conductance regulator gene (CFTR), were not significantly upregulated in the saltwater intolerant resident population (Toltén), suggesting a potential mechanism for the loss of tolerance to higher salinities. As the suite of differentially expressed genes in the diadromous-resident comparison differed between freshwater populations, we hypothesize that diadromy loss results in unique evolutionary trajectories due to drift, so the loss of diadromy does not necessarily lead to a loss in upper salinity tolerance.

La colonización recurrente de hábitats de agua dulce y la subsecuente pérdida de diadromía es una transición ecológica importante que ha sido reportada en varias especies de peces con ancestros diádromos. Esta residencia está acompañada frecuentemente por la pérdida de tolerancia a ambientes de agua salada. Galaxias maculatus, especie anfídroma, ha colonizado ríos repetidamente y existe evidencia que las poblaciones residentes presentan diferencias respecto a la tolerancia al agua salada. En este estudio, usamos transcriptómica para dilucidar los mecanismos que contribuyen a la reducida tolerancia a altas salinidades en las poblaciones residentes de agua dulce. Realizamos un desafío agudo de salinidad (0 ppt a 23-2 ppt) y medimos la habilidad osmoreguladora (contenido de agua en músculo) por 48 horas en individuos de tres poblaciones: una diádroma, una intolerante a agua salada (Toltén) y una tolerante a agua salada (Valdivia). Con el secuenciamiento de ARN de las branquias identificamos los genes expresados diferencialmente al cambio de salinidad y cuales están asociados a la pérdida de tolerancia a agua salada en la población de Toltén. Genes claves asociados a la aclimatación al agua salada fueron caracterizados en individuos diádromos, algunos de ellos también se expresaron en la población residente tolerante al agua salada (Valdivia). Sin embargo, algunos genes involucrados en la aclimatación al agua salada, incluyendo el gen regulador de la conductancia transmembrana de la fibrosis quística (CFTR), no se diferenciaron significativamente en la población residente intolerante al agua salada (Toltén), sugiriendo un mecanismo potencial de la pérdida de tolerancia a ambientes con salinidad elevada. Como el conjunto de genes expresados difiere entre las dos poblaciones residentes al compararse con la población diádroma, hipotetizamos que la pérdida de diadromía resulta en trayectorias evolutivas únicas debido a deriva génica, por lo que la pérdida de la diadromía no necesariamente conlleva a la pérdida de la tolerancia a aguas saladas.

Bifenthrin, a Ubiquitous Contaminant, Impairs the Development and Behavior of the Threatened Longfin Smelt during Early Life Stages.

The Longfin Smelt (Spirinchus thaleichthys) population in the San Franscisco Bay/Sacramento-San Joaquin Delta (Bay-Delta) has declined to ∼1% of its pre-1980s abundance and, as a result, is listed as threatened under the California Endangered Species Act. The reasons for this decline are multiple and complex, including the impacts of contaminants. Because the spawning and rearing seasons of Longfin Smelt coincide with the rainy season, during which concentrations of contaminants increase due to runoff, we hypothesized that early life stages may be particularly affected by those contaminants. Bifenthrin, a pyrethroid insecticide commonly used in agricultural and urban sectors, is of concern. Concentrations measured in the Bay-Delta have been shown to disrupt the behavior, development, and endocrine system of other fish species. The objective of the present work was to assess the impact of bifenthrin on the early developmental stages of Longfin Smelt. For this, embryos were exposed to 2, 10, 100, and 500 ng/L bifenthrin from fertilization to hatch, and larvae were exposed to 2, 10, and 100 ng/L bifenthrin from one day before to 3 days post-hatch. We assessed effects on size at hatch, yolk sac volume, locomotory behavior, and upper thermal susceptibility (via cardiac endpoints). Exposure to these environmentally relevant concentrations of bifenthrin did not significantly affect the cardiac function of larval Longfin Smelt; however, exposures altered their behavior and resulted in smaller hatchlings with reduced yolk sac volumes. This study shows that bifenthrin affects the fitness-determinant traits of Longfin Smelt early life stages and could contribute to the observed population decline.

Isolation and characterization of 17 polymorphic microsatellite loci with tri- and tetra-nucleotide repeat motifs for Ayu (Plecoglossus altivelis) using next-generation sequencing.

BACKGROUND: Ayu or sweetfish, Plecoglossus altivelis, an amphidromous fish ranging in the northwestern Pacific, is economically important inland fisheries and aquaculture resources. Genetic characterization of wild Ayu and derived culture seeds with competent molecular genetic markers is still insufficient for their sustainable use. Microsatellite DNA markers with larger repeat motifs (e.g. tri- and tetra-nucleotide motifs) are convenient and accurate compared with those having mono- and di-nucleotide motifs, but the latter motifs characterized most Ayu microsatellite markers developed previously. METHODS AND RESULTS: Here, we isolated and characterized 17 polymorphic microsatellite DNA markers with tri- and tetra-nucleotide repeat motif using next-generation sequencing. Alleles per locus varied from 6 to 23. The observed and expected heterozygosities ranged from 0.542 to 1.000 and 0.709 to 0.951, respectively. Polymorphic information content (PIC) of 15 out of the 17 loci were high (≧ 0.700), suggesting them to be highly informative. Twelve of the 17 loci were used for preliminary assignment test among three collections, and successfully allocated the examined fish to the original populations. CONCLUSION: The novel polymorphic microsatellite markers developed herein will be useful to examine the genetic diversity and population structure of wild Ayu and the effect of seed transplantation on native populations, providing a tool for conservation and sustainable adaptive management of this species.

No observed developmental effects in early life stages of capelin (Mallotus villosus) exposed to a water-soluble fraction of crude oil during embryonic development.

The rise in offshore oil and gas operations, maritime shipping, and tourism in northern latitudes enhances the risk of oil spills to sub-Arctic and Arctic coastal environments. Therefore, there is a need to understand the potential adverse effects of petroleum on key species in these areas. Here, we investigated the effects of oil exposure on the early life stages of capelin (Mallotus villosus), an ecologically and commercially important Barents Sea forage fish species that spawns along the coast of Northern Norway. Capelin embryos were exposed to five different concentrations (corresponding to 0.5-19 µg/L total PAHs) of water-soluble fraction (WSF) of crude oil from 6 days post fertilization (dpf) until hatch (25 dpf), and development of larvae in clean seawater was monitored until 52 dpf. None of the investigated endpoints (embryo development, larval length, heart rate, arrhythmia, and larval mortality) showed any effects. Our results suggest that the early life stages of capelin may be more robust to crude oil exposure than similar life stages of other fish species.

No difference between critical and sprint swimming speeds for two galaxiid species.

Researchers have used laboratory experiments to examine how fish might be affected by anthropogenic alterations and conclude how best to adjust fish passage and culvert remediation designs in response. A common way to document swimming performance for this purpose is measuring fish critical swimming speed (Ucrit ). Nonetheless, the Ucrit protocol as defined by Brett [(1964) Journal of the Fisheries Research Board of Canada, 21, 1183-1226] may be inappropriate for studying swimming performance and determining how it relates to upstream migration in benthic fish, as they may not actively swim throughout the entire Ucrit test. An alternative method to estimate swimming performance is sprint swimming speed (Usprint ), which is suggested to be a measure of the burst speed of fish rather than maximum sustained swimming speed. The authors conducted comparative swimming performance experiments to evaluate whether Usprint can be used to compare swimming performance of benthic species to that of pelagic, actively swimming species. They measured individual swimming speeds of inanga (Galaxias maculatus), an actively swimming pelagic species, and banded kokopu (Galaxias fasciatus), a fish that exhibits benthic station-holding behaviour, using both the Usprint and Ucrit test. Experiments revealed that no significant statistical difference between swimming speeds was estimated using the Ucrit and Usprint test protocols for both G. maculatus and G. fasciatus. The result of this study suggests that fish swimming speeds obtained using these two methods are comparable for the species used in this study. By using Usprint for benthic-associated fish and Ucrit for pelagic fish, we may be able to compare a broader range of species' swimming abilities for use in a fish passage context.

Rainbow smelt (Osmerus mordax) influence on walleye (Sander vitreus) recruitment decline: mtDNA evidence supporting the predation hypothesis.

Rainbow smelt (Osmerus mordax) have been introduced widely but are associated with declines in walleye (Sander vitreus) recruitment. A primary hypothesis for these declines is that O. mordax consume larval S. vitreus. We confirmed overlapping spatial-temporal distributions of larval S. vitreus and O. mordax in our study system and used mtDNA analyses to determine if O. mordax stomach contents contained S. vitreus. Approximately 20% of O. mordax composite stomach samples were considered positive for S. vitreus consumption. These findings support the predation hypothesis and have S. vitreus management/stocking implications.

Expanding non-invasive approaches for fish-health monitoring: A survey of the epidermal mucous metabolomes of phylogenetically diverse freshwater fish species.

There is a pressing need for more-holistic approaches to fisheries assessments along with growing demand to reduce the health impacts of sample collections. Metabolomic tools enable the use of sample matrices that can be collected with minimal impact on the organism (e.g., blood, urine, and mucus) and provide high-throughput, untargeted biochemical information without the requirement of a sequenced genome. These qualities make metabolomics ideal for monitoring a wide range of fish species, particularly those under protected status. In the current study, we surveyed the relative abundances of 120 endogenous metabolites in epidermal mucus across eight freshwater fish species belonging to seven phylogenetic orders. Principal component analysis was used to provide an overview of the data set, revealing strong interspecies relationships in the epidermal mucous metabolome. Normalized relative abundances of individual endogenous metabolites were then used to identify commonalities across multiple species, as well as those metabolites that showed notable species specificity. For example, taurine was measured in high relative abundance in the epidermal mucus of common carp (Cyprinus carpio), northern pike (Esox lucius), golden shiner (Notemigonus crysoleucas), rainbow trout (Oncorhynchus mykiss), and rainbow smelt (Osmerus mordax), whereas γ-amino butyric acid (GABA) exhibited a uniquely high relative abundance in flathead catfish (Pylodictis olivaris). Finally, hierarchical cluster analysis was used to evaluate species relatedness as characterized by both the epidermal mucous metabolome (phenotype) and genetic phylogeny (genotype). This comparison revealed species for which relatedness in the epidermal mucous metabolome composition closely aligns with phylogenetic relatedness (e.g., N. crysoleucas and C. carpio), as well as species for which these two measures are not well aligned (e.g., P. olivaris and Polyodon spathula). These, and other findings reported here, highlight novel areas for future research with fish, including development of epidermal mucous-based markers for non-invasive health monitoring, sex determination, and hypoxia tolerance.

Machine learning based assessment of small-bodied fish tracking to evaluate spoiler baffle fish passage design.

Fish passage research is important to mitigate the adverse effects of fragmented river habitats caused by waterway structures. The scale at which this research is undertaken varies from small-scale laboratory prototype studies to in-situ observations at various fish passage structures and bottlenecks. Using DeepLabCut, we introduce and evaluate a machine learning based workflow to track small-bodied fish in order to facilitate improved fish passage management. We specifically studied the behaviour and kinematics of Galaxias maculatus, a widespread diadromous Southern Hemisphere fish species. Upstream fish passage was studied in the presence of three different patches of spoiler baffles at an average water velocity of 0.4 m/s. In semi-supervised mode, the fish locations were extracted, and fish behaviour, such as swimming pathways and resting locations, was analysed based on extracted positions and recorded kinematic parameters. Individual fish behaviour and kinematic parameters were then used to assess the suitability of the three different spoiler baffle designs for enhancing fish passage. Using this technique, we were able to demonstrate where different spoiler baffle configurations resulted in significant differences in fish passage success and behaviour. For example, medium-spaced smaller baffles provided more accessible and uniform resting locations, which were required for efficient upstream passage. Results are discussed in relation to fish passage management at small instream structures.

Empirical evidence of nonlinearity in bottom up effect in a marine predator-prey system.

The strength of species interactions may have profound effects on population dynamics. Empirical estimates of interaction strength are often based on the assumption that the interaction strengths are constant. Barents Sea (BS) cod and capelin are two fish populations for which such an interaction has been acknowledged and used, under the assumption of constant interaction strength, when studying their population dynamics. However, species interactions can often be nonlinear in marine ecosystems and might profoundly change our understanding of food chains. Analysing long-term time series data comprising a survey over 37 years in the Arcto-boreal BS, using a state-space modelling framework, we demonstrate that the effect of capelin on cod is not linear but shifts depending on capelin abundance: while capelin is beneficial for cod populations at high abundance; below the threshold, it becomes less important for cod. Our analysis therefore shows the importance of investigating nonlinearity in species interactions and may contribute to an improved understanding on species assemblages.

Molecular and functional characterization of a ladderlectin-like molecule from ayu (Plecoglossus altivelis).

Ladderlectin is a member of C-type lectins (CTLs) in teleost fish and involved in innate immune defense. In this study, ayu (Plecoglossus altivelis) ladderlecin-like (PaLL-like) sequence was cloned, which encodes a polypeptide of 172 amino acids that includes a signal peptide and characteristic C-type lectin-like domains (CTLDs). Phylogenetically, PaLL-like was most closely related to its teleost counterpart from shishamo smelt (Spirinchus lanceolatus). Expression analysis revealed a ubiquitous expression profile, with highest expression detected in liver and its expression was up-regulated following Vibiro anguillarum infection. Similar to canonical CTLs, PaLL-like exhibited carbohydrate-binidng capacities to a wide range of well-defined mono-/di-saccharides and likely confer PaLL-like the ability to agglutinate all tested bacterial, including three Gram-positive species (i.e., Listeria monocytogenes, Staphylococcus aureus and Streptococcus iniae) and eight Gram-negative species (i.e., Edwardsiella tarda, Aeromonas (A.) hydrophila, Escherichia coli, Vibrio (V.) harveyi, V. anguillarum, V. parahemolyticus, A. versoni and V. vulnificus), in a calcium-dependent manner. Further functional studies revealed that PaLL-like displayed immunomodulatory activities leading to enhanced bactericidal activity of serum, pathogen opsonization and macrophage activation with increased expression of pro-inflammatory cytokines (i.e., PaIL-1ß and PaTNF-α). Collectively, these immunomodulatory activities of PaLL-like suppressed proliferations of V. anguillarum in targeted tissued in vivo and likely contributed to the increased survival rate of infected-fish. Overall, our results demonstrated PaLL-like is a critical component of innate immunity and provides protective effects against bacterial infection.