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Japanese eel (Anguilla japonica) constitutes one of the most important food fish in Japan; accordingly, genome sequencing and linkage mapping have been conducted for the purpose of artificial cultivation. In the next stage, integration of genomic sequences within linkage groups (LG) is required to construct higher-resolution genetic markers for quantitative trait loci mapping and selective breeding of beneficial traits in farming. In order to identify LG1-linked scaffolds from the draft genome assembly (323,776 scaffolds) reported previously, we attempted to isolate chromosomes corresponding to LG1 by flow sorting and subsequent analyses. Initially, single chromosomes were randomly collected by chromosome sorting and subjected to whole-genome amplification (WGA). A total of 60 WGA samples were screened by PCR with primers for a known LG1-linked scaffold, and five positive WGA samples were sequenced by next-generation sequencing (NGS). Following reference mapping analysis of the NGS reads, four of the five WGA samples were found to be enriched by LG1-linked sequences. These samples were cytogenetically assigned to chromosome 5 by fluorescence in situ hybridization. Using blastn searches with 82,081 contigs constructed from the NGS reads of the four WGA samples as queries, 2323 scaffolds were identified as putative LG1-linked scaffolds from the draft genome assembly. The total length of the putative LG1-linked scaffolds was 99.0 Mb, comparable to the estimated DNA amounts of chromosome 5 (91.1 Mb). These results suggest that the methodology developed herein is applicable to isolate specific chromosome DNAs and integrate unanchored scaffold sequences onto a particular LG and chromosome even in teleost fishes, in which isolation of specific chromosomes by flow sorting is generally difficult owing to similar morphologies, sizes, and GC-contents among chromosomes in the genome. The putative LG1-linked scaffolds of Japanese eel contain a total of 6833 short tandem repeats which will be available for higher-resolution linkage mapping.

Catadromous anguillid eels (genus Anguilla) migrate from their freshwater or estuarine habitats to marine spawning areas. Evidence from satellite tagging studies indicates that tropical and temperate eel species exhibit pronounced diel vertical migrations, from between 150–300 m nighttime depths to 600–800 m during the day. Collections of eggs and larvae of Japanese eels A. japonica suggest they may spawn at these upper nighttime migration depths. How anguillid eels navigate through the ocean and find their spawning areas remains unknown; thus, this study describes the salinity, temperature and geostrophic currents between 0 and 800 m depths within 2 confirmed and 3 hypothetical anguillid spawning areas during likely spawning seasons. Within the 4 ocean gyres in which these spawning areas are located, many eels would encounter subducted ‘Subtropical Underwater’ water masses during their nighttime ascents that could provide odor plumes as signposts. Four of the spawning areas are located near the western margins of where subducted water masses form cores of elevated salinities (~35.0 to 36.8) around 150 m depths, and one is located near the center of subduction. Low salinity surface waters and fronts are present in some of the areas above the high-salinity cores. Spawning may occur at temperatures between 16 and 24°C where the thermocline locally deepens. At spawning depths, weak westward currents (~0 to 0.1 m s−1) prevail, and eastward surface countercurrents are present. Anguillid eels possess acute sensory capabilities to detect these hydrographic features as potential signposts, guiding them to their spawning areas.

Freshwater eels (Anguillidae) are facing numerous anthropogenic impacts that have led to declines in abundance for nearly all species. They have a complex life history that includes obligate migration and flexible habitat use, characteristics which have generated much research interest in the family. Eels also have high cultural and economic value, further incentivizing the study of key species. We reviewed the scientific literature on anguillids from the last four decades, analyzing research trends among and within species of the genus Anguilla. We identified a shift in research focus from largely biological towards more applied management and conservation topics, an increased emphasis on migration and fish passage considerations, and a tendency towards research on glass eels and silver eels over other life stages. We also identified a significant disparity in research effort between temperate species and tropical species, with a scarcity of knowledge on the latter. Finally, we described several key knowledge gaps about community-based interactions of eels, notably their roles as predator, prey, and ecosystem connector, and highlight opportunities for early career researchers to establish research programs within the field of anguillid research.

Habitat connectivity is vital to the persistence of migratory fishes. Native tropical island stream fish assemblages composed of diadromous species require intact corridors between ocean and riverine habitats. High dams block fish migration, but low-head artificial barriers are more widespread and are rarely assessed for impacts. Among all 46 drainages in Puerto Rico, we identified and surveyed 335 artificial barriers that hinder fish migration to 74.5% of the upstream habitat. We also surveyed occupancy of native diadromous fishes (Anguillidae, Eleotridae, Gobiidae, and Mugilidae) in 118 river reaches. Occupancy models demonstrated that barriers 2 meters (m) high restricted nongoby fish migration and extirpated those fish upstream of 4-m barriers. Gobies are adapted to climbing and are restricted by 12-m barriers and extirpated upstream of 32-m barriers. Our findings quantitatively illustrate the extensive impact of low-head structures on island stream fauna and provide guidance for natural resource management, habitat restoration, and water development strategies.

Background Fish injury and mortality resulting from entrainment and/or impingement during downstream passage over/through hydropower infrastructure has the potential to cause negative effects on fish populations. The primary goal of this systematic review was to address two research questions: (1) What are the consequences of hydroelectric dam fish entrainment and impingement on freshwater fish productivity in temperate regions?; (2) To what extent do various factors like site type, intervention type, and life history characteristics influence the consequences of fish entrainment and impingement? Methods The review was conducted using guidelines provided by the Collaboration for Environmental Evidence and examined commercially published and grey literature. All articles found using a systematic search were screened using a priori eligibility criteria at two stages (title and abstract, and full-text, respectively), with consistency checks being performed at each stage. The validity of studies was appraised and data were extracted using tools explicitly designed for this review. A narrative synthesis encompassed all relevant studies and a quantitative synthesis (meta-analysis) was conducted where appropriate. Review findings A total of 264 studies from 87 articles were included for critical appraisal and narrative synthesis. Studies were primarily conducted in the United States (93%) on genera in the Salmonidae family (86%). The evidence base did not allow for an evaluation of the consequences of entrainment/impingement on fish productivity per se; therefore, we evaluated the risk of freshwater fish injury and mortality owing to downstream passage through common hydropower infrastructure. Our quantitative synthesis suggested an overall increased risk of injury and immediate mortality from passage through/over hydropower infrastructure. Injury and immediate mortality risk varied among infrastructure types. Bypasses resulted in decreased injury risk relative to controls, whereas turbines and spillways were associated with the highest injury risks relative to controls. Within turbine studies, those conducted in a lab setting were associated with higher injury risk than field-based studies, and studies with longer assessment time periods (≥ 24–48 h) were associated with higher risk than shorter duration assessment periods (< 24 h). Turbines and sluiceways were associated with the highest immediate mortality risk relative to controls. Within turbine studies, lab-based studies had higher mortality risk ratios than field-based studies. Within field studies, Francis turbines resulted in a higher immediate mortality risk than Kaplan turbines relative to controls, and wild sourced fish had a higher immediate mortality risk than hatchery sourced fish in Kaplan turbines. No other associations between effect size and moderators were identified. Taxonomic analyses revealed a significant increased injury and immediate mortality risk relative to controls for genera Alosa (river herring) and Oncorhynchus (Pacific salmonids), and delayed mortality risk for Anguilla (freshwater eels). Conclusions Our synthesis suggests that hydropower infrastructure in temperate regions increased the overall risk of freshwater fish injury and immediate mortality relative to controls. The evidence base confirmed that turbines and spillways increase the risk of injury and/or mortality for downstream passing fish compared to controls. Differences in lab- and field-based studies were evident, highlighting the need for further studies to understand the sources of variation among lab- and field-based studies. We were unable to examine delayed mortality, likely due to the lack of consistency in monitoring for post-passage delayed injury and mortality. Our synthesis suggests that bypasses are the most “fish friendly” passage option in terms of reducing fish injury and mortality. To address knowledge gaps, studies are needed that focus on systems outside of North America, on non-salmonid or non-sportfish target species, and on population-level consequences of fish entrainment/impingement.

Scientific naming rules of animals are strictly defined by the International Code of Zoological Nomenclature, while those for common names are vague and not well defined. Specifically, the common names of freshwater eels of the genus Anguilla have become confused among scientific papers, pictorial books, and online resources in recent years. This disordered use of common names among freshwater eels demonstrates the urgent need for the standardization of common names for these species. In addition, freshwater eel populations have drastically decreased worldwide over the past few decades, resulting in their listing as endangered species. In the present study, we defined the following five rules for the common names of freshwater eels: to (1) use a representative locality name of the geographic distribution of the species or subspecies, (2) distinguish two sympatric species or subspecies as longfin or shortfin, (3) select a name that would enable the scientific name to be easily recalled, (4) value longstanding former common names if they adhere to the above three rules, and (5) use the shortest name possible. Based on current scientific knowledge and on these rules, we proposed 22 common names for all known 19 species and subspecies of the genus. As a result, 21, 6, 13, and 3 species and subspecies were named based on Rules (1), (2), (3), and (4), respectively.

The possible effect of directional larval swimming on the recruitment success of the Japanese eel, Anguilla japonica, was examined with a three-dimensional particle-tracking ocean circulation model using horizontal northwestward swimming and diel vertical migration (DVM). Four separate experiments included virtual larvae (v-larvae) movement from the spawning area over 290 days (total migration) and 160 days (stage A), from the STCC eddy region in 70 days (stage B), and from the origin of the Kuroshio in 60 days (stage C) to evaluate the effect of directional swimming and DVM compared to simple drifting. Passive or random swimming were not the most effective strategies for larvae dispersing from the spawning area because most v-larvae remained south of 20°N without entering the Kuroshio. Northwestward swimming resulted in wider dispersion and a better chance of successful recruitment, with v-larvae becoming widely distributed in the STCC eddy zone, arriving at the east coast of the Philippines (stage A), escaping the STCC eddy area and reaching the Kuroshio (stage B), and crossing the Kuroshio into the East China Sea shelf (stage C). DVM slightly shortened the migration period due to faster shallow layer ocean currents during nighttime. The NEC transported non-swimming v-larvae westward to the Kuroshio and occasionally northward into the Subtropical Countercurrent (STCC) area where eddies transported v-larvae westward into the Kuroshio, but less than with swimming. Directional swimming increased recruitment success, northwestward swimming was more effective than other directions, and a slower swimming speed was still better than no/random swimming in sensitivity tests. The present study demonstrated a first view of the possibility that Japanese eel larvae might be able to use a strategy of single-direction swimming to increase arrival at their recruitment areas.

Yilan, Taiwan is the first place in East Asia where freshwater glass eels, the juvenile stage of Anguilla species, arrive by ocean currents. We collected glass eels by fyke net in Lanyang River estuary twice a month from July 2010 to November 2023. By morphological examination and sequencing of the mitochondrial cytochrome b gene, we identified seven species of Anguilla . Most of the glass eels captured in Yilan belonged to the species A. japonica , A. marmorata , and A. bicolor pacifica . Only a few were A. luzonensis , and two A. celebesensis were recorded. In addition, two species were recorded for the time time from Taiwan; A. interioris and A. borneensis were confirmed by cytochrome b sequencing. Thus, we increase the number of Anguilla species in Taiwan from five to seven.

The current study represents the first molecular characterization of freshwater fish species in Egypt from two major fish resources; the River Nile and Lake Nasser. A total of 160 DNA barcodes using a 655-bp-long fragment of the mitochondrial cytochrome oxidase subunit I (COI) gene were generated from 37 species belonging to 32 genera that represent 15 families from nine orders. The studied species were identified using different molecular-based identification approaches, in addition to the morphological identification, including neighbor-joining (NJ) trees, Barcode Index Number, and Automatic Barcode Gap Discovery (ABGD). The average genetic divergence based on the Kimura two-parameter model (K2P) within orders, families, genera, and species were 0.175, 0.067, 0.02, and 0.008, respectively. The minimum and maximum K2P distance-based genetic divergences were 0.0 and 0.154, respectively. Nucleotide diversity ( π ) varied among families and ranged between 0.0% for families Malapteruridae, Auchenoglanididae, Schilbeidae, Anguillidae, Centropomidae and Tetraodontidae and 17% for family Cyprinidae. The current study cautions against the lack of species coverage at public databases which limits the accurate identification of newly surveyed species and recommends that multiple methods are encouraged for accurate species identification. The findings of the current study also support that COI barcode enabled effective fish species identification in River Nile and Lake Nasser. Moreover, the results of the current study will establish a comprehensive DNA barcode library for freshwater fishes along the River Nile in Egypt. Egyptian freshwater fish DNA barcodes will contribute substantially to future efforts in monitoring, conservation, and management of fisheries in Egypt.

ABSTRACT   This study is the first to document glass American Eels Anguilla rostrata in Texas, and it provides critical information about recruitment timing along the northern Gulf Coast. The American Eel is a facultative catadromous fish. Data are lacking related to juvenile (glass eel and elver) recruitment into the bays and estuaries of the Gulf of Mexico. Objective The goal of the study was to document glass and elver recruitment timing and distribution for American Eels in Texas. Methods The study implemented year-round monitoring in rivers and streams using eel ramps and environmental DNA (eDNA) to increase the likelihood of detecting even highly sporadic recruitment events. Thirteen sites were identified based on their connectivity to coastal estuarine waters and the ability to support a gravity-fed eel ramp. Ramps were deployed during June–July 2022 and were checked weekly for 1 year. A subset of nine ramp sites was also monitored for eDNA during each ramp check. Results American Eels were caught in one of the 13 eel ramps. In total, 26 juvenile eels (19 glass and 7 elvers) were captured. Captures of glass eels began in January, and captures of elvers ended in May. American Eel DNA was detected at eight of the nine sites that were monitored for eDNA. Environmental DNA detection rates were highest for the only ramp site where eels were captured. Conclusions Positive eDNA samples were temporally associated with the recruitment window observed through captures in the ramps. Continued deployment of eel ramps during the estimated recruitment window are planned for 2024 and 2025, with more frequent checks. Continued monitoring will be conducted with the goal of assisting natural resource agencies in determining the conservation and management needs of American Eels in Texas. Lay Summary American Eels have a complex life history, and little is known about when and where juvenile eels arrive to coastal water bodies in the Gulf of Mexico. This study is the first to document glass American Eels in Texas, and it provides critical information about recruitment timing along the northern Gulf Coast.