Anguilla Rostrata Research Articles

Effects of Dietary Inclusion of Enzymatically Hydrolyzed Compound Soy Protein on the Growth Performance and Intestinal Health of Juvenile American Eels (Anguilla rostrata).

The enzymatic hydrolysis of soybeans could enhance their application as an ingredient and alternative to fishmeal in aquafeeds. Here, a 10-week feeding trial was conducted to evaluate the impacts of different dietary inclusion levels of enzymatically hydrolyzed compound soy protein (EHCS) on the growth performance and intestinal health of juvenile American eels (Anguilla rostrata). Five experimental diets were formulated with graded EHCS inclusion levels at 0% (EHCS0), 8% (EHCS8), 16% (EHCS16), 24% (EHCS24), and 32% (EHCS32). Each diet was randomly assigned to four replicate tanks. The results showed that eels fed the EHCS8 diet exhibited superior growth performance, decreased serum lipid content, and increased immunity compared to those fed the EHCS0 diet. Eels fed the EHCS8 diet also displayed improved intestinal histology, enhanced antioxidant capacity and balance of intestinal microbiota as well as an enhanced proliferation of probiotics compared to those receiving the EHCS0 diet. Compared with eels fed the EHCS0 diet, those fed the EHCS16 diet exhibited comparable growth performance and values for the aforementioned markers. The quadratic regression analysis of weight gain rate and feed efficiency against the dietary EHCS inclusion levels determined the maximum levels of dietary EHCS inclusion for American eels range from 17.59% to 17.77%.

Mislabeled and ambiguous market names in invertebrate and finfish seafood conceal species of conservation concern in Calgary, Alberta, Canada.

The mislabeling of seafood, wherein a food product's marketed name does not match its contents, has the potential to mask species of conservation concern. Less discussed is the role of legally ambiguous market names, wherein a single name could be used to sell multiple species. Here we report the first study in Canada to examine mislabeling and ambiguous market names in both invertebrate (e.g., bivalve, cephalopod, shrimp) and finfish products. A total of 109 invertebrate and 347 finfish products were sampled in Calgary between 2014 and 2020. Market names were documented from the label or equivalent and determined to be precise (the name could apply to only one species) or ambiguous (multiple species could be sold under that name). A region of the cytochrome c oxidase I gene was sequenced and compared to reference sequences from boldsystems.org. Samples were considered mislabeled if the species identified through DNA barcoding did not correspond to the market name, as determined through the Canadian Food Inspection Agency Fish List. Mislabeling was further differentiated between semantic mislabeling, wherein the market name was not found on the Fish List but the barcode identity was in line with what a consumer could reasonably have expected to have purchased; invalid market names, wherein the market name was so unusual that no legitimate inferences as to the product's identity could be made; and product substitution, wherein the DNA barcode identified the product as a species distinct from that associated with the market name. Invalid market names and product substitutions were used to provide conservative estimates of mislabeling. The global conservation status of the DNA-identified invertebrate or finfish was determined through the International Union for the Conservation of Nature Red List. A logistic regression was used to determine the relationship between precision and accuracy in predicting conservation status of the sampled species. There was no significant difference in mislabeling occurrence between invertebrates (33.9% total mislabeling occurrence, 20.2% product substitution) and finfish (32.3% total mislabeling occurrence, 21.3% product substitution/invalid market names). Product substitutions sometimes involved species of conservation concern, such as foods marketed as freshwater eel (Anguilla rostrata) that were determined through DNA barcoding to be European eel (Anguilla anguilla), or cuttlefish balls putatively identified as the Endangered threadfin porgy (Evynnis cardinalis). Product substitutions and ambiguous market names were significantly associated with the sale of species of conservation concern, but ambiguity was a more important predictor. Although preventing the mislabeling of seafoods can and must remain a priority in Canada, our work suggests that moving towards precise names for all seafood products will better support sustainable fisheries goals.

Environmental cues for downstream‐migrating American Eel at a hydroelectric facility

AbstractObjectiveThe purpose of study was to identify environmental factors that influence downstream migration and passage of American Eels Anguilla rostrata in Roanoke Rapids Lake, a reservoir on the Roanoke River formed by the Roanoke Rapids Dam and Power Station.MethodsYellow‐ and silver‐phase American Eels were outfitted with acoustic transmitters and monitored during four out‐migration periods from October 2019 through March 2023 using acoustic telemetry receivers placed in Roanoke Rapids Lake and the Roanoke River downstream of the power station. The timing of downstream passage through the power station was determined using acoustic detection data. Poisson regression models were used to analyze American Eel detections in the context of environmental variables that were hypothesized to cue out‐migration.ResultOut‐migration probability of American Eels from Roanoke Rapids Lake was influenced by time of day, rainfall, and change in lake level attributable to hydropower operations. Predictive models of out‐migration probability demonstrated that the number of migrating American Eels was widely variable across environmental conditions and was particularly sensitive to changes in lake level.ConclusionThe results of this study suggest that management actions, such as scheduled water releases from a dam and the consequent change in lake level (or correlated factors), can influence the onset and timing of American Eel out‐migration.

The effects of coated inorganic trace minerals on the growth performance, mineral retention, and intestinal health comparing with inorganic and organic trace minerals for juvenile American eels (Anguilla rostrata)

This study was conducted to compare the effects of coated inorganic trace minerals (CITM) with those of inorganic and organic trace minerals on the growth performance, mineral retention in the whole-body, and intestinal health of juvenile American eels (Anguilla rostrata). Eels were randomly divided into the inorganic trace minerals (ITM) group, organic trace minerals (OTM) group, coated inorganic trace minerals I (CITM I) group, and coated inorganic trace minerals II (CITM II) group, respectively. The supplementation level of trace minerals in the CITM II group was 50 % of those in the CITM I group. Eels were fed experimental diets for ten weeks. Compared with the ITM group, weight gain rate, specific growth rate, protein efficiency, and feed efficiency of those in the CITM I and CITM II groups were increased. Eels in the CITM I group exhibited higher retention rates of calcium, phosphorus, and zinc in whole body than those in the ITM and OTM groups. CITM I group displayed the increased levels of high-density lipoprotein cholesterol, immunoglobulin M, and D-lactic acid compared to the ITE group. Compared with the ITM and OTM groups, CITM I and CITM II groups showed enhanced intestinal histology and activities of intestinal amylase, lipase, and glutathione peroxidase (GSH-Px), coupled with an increase of GSH content. Proteome analysis demonstrated that, compared to the ITE group, CITM I group displayed enhanced intestinal protein abundance associated with vitamin digestion and absorption, fat digestion and absorption, cysteine and methionine metabolism, and amino acid biosynthesis. In conclusion, CITM is more beneficial for the growth performance, mineral retention in the whole-body, and intestinal health of juvenile American eels compared to ITM and OTM sources. Our findings provide valuable insights into the application of the coated trace minerals sources in the diets for American eels and potentially for other fish species.

Public preferences for policies promoting the conservation of a universally threatened species (Anguilla spp.): Insights from a choice experiment in Japan

The population of the Northern temperate eel species (Anguilla spp.) has undergone a significant decline, resulting in their classification as Endangered (American eel Anguilla rostrata and Japanese eel Anguilla japonica) or Critically Endangered (European eel Anguilla anguilla) by the IUCN. The growing global demand for Japanese cuisine and processed eel products could potentially exacerbate the vulnerability of these species. This research examines the acceptability of conservation policies among Japanese consumers. A discrete choice experiment was employed to investigate the social acceptance of target levels for national eel consumption reduction and to examine the trade-offs made by individuals between various policy instruments (e.g., combat against illegal trade, research on artificial reproduction, shift to substitute species, public awareness campaigns, eco-labelling) and the costs that they may be willing to incur. The econometric analysis identified two distinct groups with contrasting preferences. The first group exhibited strong support for the current situation. Conversely, the second group expressed preferences for expanding public intervention. We further explored the sources of heterogeneity. Paradoxically, we found that education attainment and environmental knowledge in relation to consumption motivations influenced individual preferences for the status quo. However, individuals with higher pro-environmental attitudes are more likely to accept a national target of consumption reduction. They are willing to pay for demand-oriented policy instruments to complement existing supply-side measures.

Short‐term survival and growth of American Eel elvers marked with visible implant elastomer tags

AbstractObjectiveVisible implant elastomer (VIE) tags are commonly used as a cost‐effective tool for marking small fish, making them valuable in mark–recapture studies. It is crucial to quantify the impact of tagging procedures on fish survival to address inferential bias in mark–recapture studies. We assessed marking‐related mortality and growth in American Eel Anguilla rostrata elvers in a 40‐day laboratory experiment, following VIE tag application.MethodsThere were 500 elvers (80–149 mm) that were divided into four treatment groups and one control group. Treatment groups were tagged with two tags in three body locations (anterior, central, posterior on left bilateral side) or with two tags in all three locations, while the control group remained untagged. Eels were retained in experimental tanks, and mortality rates were compared.ResultThe VIE tagging did not significantly affect survival, which was 90.9% across all treatment groups and 92% for the untagged control group; nor did it affect growth.ConclusionThe application of VIE tags on various body parts should be a safe and effective method for marking American Eel elvers.

The antimicrobial peptide Sparamosin26–54 exhibits antiviral activity against three aquatic enveloped viruses through lipid-binding-mediated virus lysis

The aquaculture industry is faced with huge economic losses caused by various enveloped virus infections, such as white spot syndrome virus (WSSV), Rana grylio virus (RGV), and Anguillid Herpesvirus 1 (AngHV). The urgent need for readily available broad-spectrum antiviral agents has led to the exploration of antiviral peptides (AVPs), among which antimicrobial peptides (AMPs) with antiviral activity have attracted increasing attention. Sparamosin26–54 (derived from Scylla paramamosain) is a promising antimicrobial agent. In this study, we found that Sparamosin26–54 significantly inhibited WSSV transcription and replication (as indicated by VP28 gene and protein levels), irreversibly inactivated virions, and impeded viral entry before binding to the cell. Transmission electron microscopy observations showed that Sparamosin26–54 had a direct destructive effect on WSSV virions. Lipidomic analysis and ELISA assay highlighted that Sparamosin26–54 had a potent affinity for phosphatidic acid (PA) and phosphatidylserine (PS) of WSSV. Liposome leakage assays further revealed a pronounced effect of Sparamosin26–54 on membrane lipid compositions, emphasizing its efficacy against the other two enveloped viruses (RGV and AngHV), but not against the non-enveloped virus, American eel adomavirus (AEAdov). Notably, in three animal models of viral infection, Sparamosin26–54 reduced viral loads in tissues, increased survival, or decreased infection rates in a concentration-dependent manner. Importantly, Sparamosin26–54 showed no animal toxicity under different modes of administration and could maintain antiviral activity in the complex aquatic environment. Taken together, Sparamosin26–54 was proved to be effective against three enveloped viruses, possibly inducing viral lysis via lipid-binding, providing an alternative approach for combating enveloped virus infections.

An experimental study of benthic habitat selection in yellow-phase American eels (Anguilla rostrata)

An experimental study of benthic habitat selection in yellow-phase American eels (Anguilla rostrata)

Preparation of valine-curcumin conjugate and its in vitro antibacterial and antitumor activity and in vivo biological effects on American eels (Anguilla rostrata)

Curcumin (Cur) exhibits diverse natural pharmacological activities, despite its limited water solubility (hydrophobicity) and low bioavailability. In this investigation, a valine-curcumin conjugate (Val-Cur) was synthesized through amino acid side chain modification, and its solubility increased to 1.78 mg/mL. In vitro experimental findings demonstrated that the antibacterial activity of Val-Cur against Escherichia coli, Staphylococcus aureus, Aeromonas hydrophila, and Vibrio parahaemolyticus was significantly superior to that of Cur. The inhibition rate of Val-Cur against HepG2 (human hepatocellular carcinoma) cells was higher than that of Cur at low concentrations (below 25 μmol/L), although the IC50 value of Val-Cur did not differ significantly from that of Cur. In vivo biological effects of Val-Cur were assessed by adding it into the feed (150 mg/kg) of American eels (Anguilla rostrata). Val-Cur significantly improved the growth performance (↑weight gain rate, ↑specific growth rate, and ↓feed conversion rate) and activities of intestinal digestive enzymes (amylase and lipase) and antioxidant enzymes (superoxide dismutase) in American eels. Additionally, Val-Cur significantly improved serum biochemical indices (↑high-density lipoprotein cholesterol, ↓low-density lipoprotein cholesterol, ↓aspartate and alanine aminotransferases). Furthermore, Val-Cur increased intestinal microbial diversity, reduced the abundance of potentially pathogenic bacteria (Spiroplasma, Clostridium, and Pseudomonas), and elevated the abundance of beneficial digestion-promoting bacteria (Romboutsia, Phyllobacterium, Romboutsia sedimentorum, and Clostridium butyricum) conducive to glucose metabolism (P < 0.05). To the best of our knowledge, this study is the first to explore water-soluble curcumin in aquaculture, and the findings will lay the groundwork for the potential application of water-soluble curcumin in the field of aquaculture.

Transcriptome analysis of host anti-Aeromonas hydrophila infection revealed the pathogenicity of A. hydrophila to American eels (Anguilla rostrata)

Aeromonas hydrophila is a commonly pathogenic bacterium in cultivated eels, but its pathogenicity to American eel (Anguilla rostrata) and the molecular mechanism of host anti-A. hydrophila infection remains uncertain. In this study, LD50 of A. hydrophila to American eels was determined and bacterial load in the liver and kidney of eels was assessed post 2.56 doses of LD50 of A. hydrophila infection. The results showed that the LD50 of A. hydrophila to American eels was determined to be 3.9 × 105 cfu/g body weight (7.8 × 106 cfu/fish), and the bacterial load peaked at 36 h post the infection (hpi) in the liver. Then, the histopathology was highlighted by congestion in splenic blood vessels, atrophied glomeruli, and necrotic hepatocytes. Additionally, the results of qRT-PCR revealed that 18 host immune-related genes showed significantly up or downregulated post-infection compare to that of pre-infection. Finally, results of the RNA-seq revealed 10 hub DEGs and 7 encoded proteins play essential role to the anti-A. hydrophila infection in American eels. Pathogenicity of A. hydrophila to American eels and RNA-seq of host anti-A. hydrophila infection were firstly reported in this study, shedding new light on our understanding of the A. hydrophila pathogenesis and the host immune response to the A. hydrophila infection strategies in gene transcript.

Discontinuous, biphasic, ontogenetic shifts in the metabolic allometry of aquatic animals?

Several investigations in recent years have reported patterns of discontinuous, biphasic, loglinear variation in the metabolic allometry of aquatic animals. These putative shifts in pattern of allometry have been attributed to changes in the primary site for gas exchange from cutaneous to branchial as animals undergo ontogenetic changes in size, shape, and surface area. Because of the important implications of the earlier research with regard to both physiology and evolution, I re-examined data that purportedly support claims of discontinuous, biphasic allometry in oxygen consumption versus body size of American eels (Anguilla rostrata) and spiny lobsters (Sagmariasus verreauxi). I used ANCOVA to fit three different statistical models to each set of logarithmic transformations and then assessed the fits by Akaike's Information Criterion. The observations for both species were described better by a single straight line fitted to the full distribution than by a biphasic model. Eels, lobsters, and other aquatic animals undergo changes in shape and surface area as they grow, but such changes are not necessarily accompanied by changes in the pattern of metabolic allometry.

Pre‐impoundment fish migrations in the Mobile Basin, Alabama

AbstractAssessing the status of several migratory fishes in the Mobile River Basin, Alabama, has been complicated due to a general lack of historical data on their life history, habitat requirements, and distributions. Whether distributions were restricted by natural or man‐made barriers to migration is difficult to answer because few scientific collections were made before dams were built, and the earliest dams were built at the largest biogeographic barrier in the basin: the geological fall line. Therefore, we used what information was available, including anecdotal information, primarily records from archived newspapers and government reports, to describe the ranges of six migratory species prior to the construction of dams in the Mobile Basin. We describe the complicated history of Alabama Shad Alosa alabamae and show that range declines may have been masked by the stocking of American Shad Alosa sapidissima in the late 19th century. We show that Gulf Sturgeon Acipenser oxyrinchus desotoi probably migrated well above the fall line in the Coosa River, and may have been sympatric with Lake Sturgeon Acipenser fulvescens. We found no records of Alabama Sturgeon Scaphirhynchus suttkusi above the fall line. American Eel Anguilla rostrata migrated above the fall line in every Mobile Basin river before dams were built. Finally, Paddlefish Polyodon spathula may have once occurred above the fall line in at least two rivers, but they persist today in impounded reaches in the coastal plain, unlike some other species. We hope that future work will continue to consider archival sources of information to re‐trace the histories of imperilled species.

Δfur mutant as a potential live attenuated vaccine (LAV) candidate protects American eels (Anguilla rostrata) from Vibrio harveyi infection

The eel farming industry is highly susceptible to Vibriosis. Although various types of vaccines against Vibriosis have been investigated, there is limited research on decreasing the virulence of Vibrions through gene knockout and utilizing it as live attenuated vaccines (LAV). In this study, we aim to develop a LAV candidate against Vibrio harveyi infection in American eels (Anguilla rostrata) using a ferric uptake regulator (fur) gene mutant strain of V. harveyi (Δfur mutant). After the eels were administrated with the Δfur mutant at the dose of 4 × 102 cfu/g body weight, the phagocytic activity of the leucocytes, plasma IgM antibody titers, activity of lysozyme and Superoxide Dismutase (SOD) enzyme, and gene expression levels of 18 immune related proteins were detected to evaluate the protection effect of the LAV. Preliminary findings suggest that the LAV achieved over 60% relative percent survival (RPS) after the American eels were challenged by a wild-type strain of V. harveyi infection on 28 and 42 days post the immunization (dpi). The protection was mainly attributed to increased plasma IgM antibody titers, higher levels of lysozyme, enhanced activity of SOD and some regulated genes encoded immune related proteins. Together, the Δfur mutant strain of V. harveyi, as a novel LAV vaccine, demonstrates promising protective effects against V. harveyi infection in American eels, thus presenting a potential candidate vaccine for fish farming.

Comparative phenotype and transcriptome analysis revealed the role of ferric uptake regulator (Fur) in the virulence of Vibrio harveyi isolated from diseased American eel (Anguilla rostrata).

Vibrio harveyi is commonly found in salt and brackish water and is recognized as a serious bacterial pathogen in aquaculture worldwide. In this study, we cloned the ferric uptake regulator (fur) gene from V. harveyi wild-type strain HA_1, which was isolated from diseased American eels (Anguilla rostrata) and has a length of 450 bp, encoding 149 amino acids. Then, a mutant strain, HA_1-Δfur, was constructed through homologous recombination of a suicide plasmid (pCVD442). The HA_1-Δfur mutant exhibited weaker biofilm formation and swarming motility, and 18-fold decrease (5.5%) in virulence to the American eels; compared to the wild-type strain, the mutant strain showed time and diameter differences in growth and haemolysis, respectively. Additionally, the adhesion ability of the mutant strain was significantly decreased. Moreover, there were 15 different biochemical indicators observed between the two strains. Transcriptome analysis revealed that 875 genes were differentially expressed in the Δfur mutant, with 385 up-regulated and 490 down-regulated DEGs. GO and KEGG enrichment analysis revealed that, compared to the wild-type strain, the type II and type VI secretion systems (T2SS and T6SS), amino acid synthesis and transport and energy metabolism pathways were significantly down-regulated, but the ABC transporters and biosynthesis of siderophore group non-ribosomal peptides pathways were up-regulated in the Δfur strain. The qRT-PCR results further confirmed that DEGs responsible for amino acid transport and energy metabolism were positively regulated, but DEGs involved in iron acquisition were negatively regulated in the Δfur strain. These findings suggest that the virulence of the Δfur strain was significantly decreased, which is closely related to phenotype changing and gene transcript regulation.

Transcriptome Analysis of Host Anti-Vibrio harveyi Infection Revealed the Pathogenicity of V. harveyi to American Eel (Anguilla rostrata).

Vibrio harveyi, a recently discovered pathogenic bacterium isolated from American eels (Anguilla rostrata), poses uncertainties regarding its pathogenesis in American eel and the molecular mechanisms underlying host defense against V. harveyi infection. This study aimed to determine the LD50 of V. harveyi in American eel and assess the bacterial load in the liver, spleen, and kidney post-infection with the LD50 dose. The results showed that the LD50 of V. harveyi via intraperitoneal injection in American eels over a 14d period was determined to be 1.24 × 103cfu/g body weight (6.2 × 104cfu/fish). The peak bacterial load occurred at 36h post-infection (hpi) in all three organs examined. Histopathology analysis revealed hepatic vein congestion and thrombi, tubular vacuolar degeneration, and splenic bleeding. Moreover, quantitative reverse transcription polymerase chain reaction (qRT-PCR) results indicated significant up or downregulation of 18 host immune- or anti-infection-related genes post 12 to 60 hpi following the infection. Additionally, RNA sequencing (RNA-seq) unveiled 7 hub differentially expressed genes (DEGs) and 11 encoded proteins play crucial roles in the anti-V. harveyi response in American eels. This study firstly represents the comprehensive report on the pathogenicity of V. harveyi to American eels and RNA-seq of host's response to V. harveyi infection. These findings provide valuable insights into V. harveyi pathogenesis and the strategies employed by the host's immune system at the transcriptomic level to combat V. harveyi infection.

An Anguillid lens: how Eels reconnect people and waterways

The population decline of American Eels (Anguilla rostrata) in North America represents multiple crises: ecosystem destruction, industrial impact, forced relocation, cultural disenfranchisement, water degradation, and biodiversity loss. Once a key component of Indigenous societies, trade routes, economies, and ceremonial cycles, today Eels experience migration barriers and habitat degradation stemming from waterway abuse and land use alteration. The development of agricultural and industrial social norms has led to dramatic reductions in Eel populations across North America. Fishery agencies familiar with Eel life cycles often list species as depleted, and disappearance of Eels is well-accepted in all sectors. Related species of Anguillid Eels are in decline globally. Yet, in some areas, American Eels continue to migrate, grow, and even thrive. This article proposes Eel continuity as powerful survivorship in troubled times, a counter-narrative to overwhelming stories of environmental pessimism. Although Eels are often discredited, reviled, and disrespected by Americans and Canadians alike, their contributions to marine and aquatic zones are underestimated and poorly understood. This article employs a reflexive method of dialogue and commentary from two Eel advocates with interdisciplinary training and backgrounds, who envision relational, wisdom-based practices that meaningfully integrate Indigenous, community, academic, and other forms of knowledge about Eels and about water.

Characterizing Sex Ratios of American Eels ( Anguilla rostrata ) in Louisiana.

The American eel ( Anguilla rostrata) inhabits Louisiana waterways; however, little is known about their life history, population abundance, or behavior. Eels under 400 mm require histologic evaluation to determine sex. We have processed eel gonad samples from 40 sampling locations across Louisiana, as well as across size categories to aid in establishing a sex determination protocol. One hundred and eighteen (118) eel samples have been histologically analyzed to date. The histologic data compliments morphometric, location, and ageing data collected by the Louisiana Department of Wildlife and Fisheries to build an initial understanding of the biological characteristics of American eels in Louisiana.

RNA-seq analysis revealed the pathogenicity of Vibrio vulnificus to American eel (Anguilla rostrata) and the strategy of host anti-V. vulnificus infection

Vibrio vulnificus is a commonly pathogenic bacterium in cultivated eels, but its pathogenicity to American eel (Anguilla rostrata) and the molecular mechanism of host anti-V. vulnificus infection remains uncertain. In this study, American eels were infected with different dose of V. vulnificus to determine the LD50. Then, bacterial load in the liver and kidney histopathology were assessed post the LD50 of V. vulnificus infection. Additionally, gene expressions of 18 immune related genes in the liver, spleen and kidney were detected. Furthermore, transcriptome sequencing and enrichment of differentially expressed genes (DEGs) were analyzed in the eel spleens between pre-infection (Con_0), post-36 h (Vv_36), and post-60 h (Vv_60) infection. The results showed that LD50 of V. vulnificus to American eels was determined to be 5.0 × 105 cfu/g body weight, and the bacterial load peaked at 24 and 12 h post the infection (hpi) in the kidney and liver, respectively. The histopathology was highlighted by necrotic hepatocytes and splenic cells, congestion blood vessels in liver and spleen, atrophied glomeruli and vacuolization of renal tubular epithelial cells. The results of RT-PCR revealed that 18 host immune-related genes showed significantly up or downregulated expression post-infection compare to that of pre-infection. Finally, results of the RNA-seq revealed 16 DEGs play essential role to the immunosuppression in American eels, and the protein-protein interactions shed light on the widespread upregulation GEGs related to metabolism and immune response maintained the host cell homeostasis post the V. vulnificus infection, shedding new light on our understanding of the V. vulnificus pathogenesis towards understudied American eel and the host anti-V. vulnificus infection strategies in gene transcript.

To pool or not to pool data? Applying a generalized depletion model to assess American eel elver Anguilla rostrata fisheries from multiple rivers in Nova Scotia, Canada

AbstractSpatial scales are important for examining health of exploited fishery stocks and guiding management actions. However, information about the optimal spatial scale is still unclear for assessment of transit fisheries, such as elver fisheries of the American eel Anguilla rostrata. We applied a generalized depletion model to assess catch and effort data from three nearby rivers (within 50 km) to test the hypothesis that modeling on pooled and separate data from nearby rivers would give similar estimates of abundance and exploitation rate. Overall, pooling data from rivers within 50 km did not result in large differences (&lt;20% in relative difference) in estimates of abundance and exploitation rate with close mean abundance estimates and similar temporal trends in abundance, exploitation rate, and relative escapement. Pooling nearby river systems can greatly reduce modeling effort, at the cost of ignoring fine‐scale variability in elver recruitment and having coarser spatial scale for the management. When only an index of annual recruitment and exploitation rate are of interest, pooling data may be practical from different locations up to 50 km.

Widespread Deviant Patterns of Heterozygosity in Whole-Genome Sequencing Due to Autopolyploidy, Repeated Elements, and Duplication.

Most population genomic tools rely on accurate single nucleotide polymorphism (SNP) calling and filtering to meet their underlying assumptions. However, genomic complexity, resulting from structural variants, paralogous sequences, and repetitive elements, presents significant challenges in assembling contiguous reference genomes. Consequently, short-read resequencing studies can encounter mismapping issues, leading to SNPs that deviate from Mendelian expected patterns of heterozygosity and allelic ratio. In this study, we employed the ngsParalog software to identify such deviant SNPs in whole-genome sequencing (WGS) data with low (1.5×) to intermediate (4.8×) coverage for four species: Arctic Char (Salvelinus alpinus), Lake Whitefish (Coregonus clupeaformis), Atlantic Salmon (Salmo salar), and the American Eel (Anguilla rostrata). The analyses revealed that deviant SNPs accounted for 22% to 62% of all SNPs in salmonid datasets and approximately 11% in the American Eel dataset. These deviant SNPs were particularly concentrated within repetitive elements and genomic regions that had recently undergone rediploidization in salmonids. Additionally, narrow peaks of elevated coverage were ubiquitous along all four reference genomes, encompassed most deviant SNPs, and could be partially associated with transposons and tandem repeats. Including these deviant SNPs in genomic analyses led to highly distorted site frequency spectra, underestimated pairwise FST values, and overestimated nucleotide diversity. Considering the widespread occurrence of deviant SNPs arising from a variety of sources, their important impact in estimating population parameters, and the availability of effective tools to identify them, we propose that excluding deviant SNPs from WGS datasets is required to improve genomic inferences for a wide range of taxa and sequencing depths.