Biomonitoring and Conservation of Freshwater & Marine Fishes

A special issue of Fishes (ISSN 2410-3888). This special issue belongs to the section "Biology and Ecology".

Deadline for manuscript submissions: closed (19 April 2024) | Viewed by 13714

Special Issue Editors


E-Mail Website
Guest Editor
Independent Researcher, Olympia, WA 98501, USA
Interests: fisheries; aquatic/riparian ecology; ecohydrology; multimetric indices; science philosophy

E-Mail Website
Guest Editor
1. Amnis Opes Institute, Corvallis, OR 97333, USA
2. Department of Fisheries, Wildlife, & Conservation Sciences, Oregon State University, Corvallis, OR 97331, USA
Interests: biomonitoring; bioassessment; landscape patterns; regional aquatic ecology; fish; macroinvertebrates

Special Issue Information

Dear Colleagues,

Globally, native migratory and resident fishes are declining due to aquatic and terrestrial ecosystem degradation caused by physicochemical habitat alteration, migration barriers, overexploitation, excessive hatchery supplementation, non-native species introductions, and climate heating—all driven by human overpopulation and excessive energy and material consumption. The loss of diadromous fishes reduces marine-derived nutrients that are important for freshwater and floodplain biota, including riparian trees that protect freshwater ecosystems from land use. The depletion of marine and freshwater fisheries threatens human food supplies. Healthy aquatic ecosystems have diverse habitats that house a diversity of fish species, including various trophic, habitat-use, and reproductive guilds. To better protect these fishery resources, which provide recreation and sustenance for millions of people, fishery monitoring is important for assessing fish assemblage and population health. Finally, the assessment of fish assemblage and population-limiting factors is important for mitigating these factors. This Special Issue focuses on ecological analyses based on large sample sizes, as well as review articles.

Dr. Robert L. Vadas Jr.
Dr. Robert M. Hughes
Guest Editors

Manuscript Submission Information

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Keywords

  • cumulative impacts
  • habitat diversity
  • ecological guilds
  • biotic indices
  • rehabilitation
  • fish populations
  • fish assemblages
  • risk assessment

Published Papers (10 papers)

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Research

16 pages, 4546 KiB  
Article
A Fish-Based Tool for the Quality Assessment of Portuguese Large Rivers
by António Tovar Faro, Maria Teresa Ferreira and João Manuel Oliveira
Fishes 2024, 9(5), 149; https://doi.org/10.3390/fishes9050149 - 23 Apr 2024
Viewed by 687
Abstract
Multimetric indices play a pivotal role in assessing river ecological quality, aligning with the European Water Framework Directive (EU WFD) requirements. However, indices developed specifically for large rivers are uncommon. Our objective was to develop a fish-based tool specifically tailored to assess the [...] Read more.
Multimetric indices play a pivotal role in assessing river ecological quality, aligning with the European Water Framework Directive (EU WFD) requirements. However, indices developed specifically for large rivers are uncommon. Our objective was to develop a fish-based tool specifically tailored to assess the ecological quality in Portuguese large rivers. Data were collected from seven sites in each of three Portuguese large rivers (Minho, Guadiana, and Tagus). Each site was classified using an environmental disturbance score, combining different pressure types, such as water chemistry, land use, and hydromorphological alterations. The Fish-based Multimetric Index for Portuguese Large Rivers (F-MMIP-LR) comprises four metrics: % native lithophilic individuals; % alien individuals; % migrant individuals; and % freshwater native individuals, representing compositional, reproductive, and migratory guilds. The index showed good performance in separating least- and most-disturbed sites. Least-disturbed sites were rated ‘high’ or ‘good’ by F-MMIP-LR, contrasting with no such classification for most-disturbed sites, highlighting index robustness. The three rivers presented a wide range of F-MMIP-LR values across the gradient of ‘bad’ to ‘high’, indicating that, on a large spatial extent, the biological condition was substantially altered. The F-MMIP-LR provides vital information for managers and decision-makers, guiding restoration efforts and strengthening conservation initiatives in line with the WFD. Full article
(This article belongs to the Special Issue Biomonitoring and Conservation of Freshwater & Marine Fishes)
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11 pages, 1469 KiB  
Article
A Cross-Decadal Change in the Fish and Crustacean Community of Lower Yaquina Bay, Oregon, USA
by Scott A. Heppell, Selina S. Heppell, N. Scarlett Arbuckle and M. Brett Gallagher
Fishes 2024, 9(4), 125; https://doi.org/10.3390/fishes9040125 - 30 Mar 2024
Viewed by 786
Abstract
Natural environmental change, anthropogenic development, and inter-annual variability can affect the ecology of estuarine fish and invertebrates. Yaquina Bay, Oregon, a well-studied estuary, has undergone intense development, as well as deep-draft dredging during the latter half of the 20th century, resulting in the [...] Read more.
Natural environmental change, anthropogenic development, and inter-annual variability can affect the ecology of estuarine fish and invertebrates. Yaquina Bay, Oregon, a well-studied estuary, has undergone intense development, as well as deep-draft dredging during the latter half of the 20th century, resulting in the alteration of ~45% of the lower estuary’s natural shoreline. In 1967, the United States Environmental Protection Agency (USEPA) conducted a 21-month survey of Yaquina Bay to characterize the demersal fishes and epibenthic crustaceans that occupy the bay. From 2003 to 2005, we conducted a 25-month survey to replicate that work and provide a comparative snapshot of the demersal fish and epibenthic crustacean community in the bay. A comparison of the trawl survey datasets reveals a 91% decline in total catch per unit effort (CPUE) between surveys, as well as a decline in multiple measures of biodiversity. Furthermore, the fishes and crustaceans of Yaquina Bay have experienced a shift in species dominance from demersal fishes in the late 1960s to epibenthic crustaceans in the 2000s, marked most notably by a nine-fold increase in the Dungeness crab CPUE. While this work does not establish a causal relationship between changes in the demersal communities of this West Coast estuary and human or natural events, it does document substantial changes in both the diversity and total abundance of animals in that community over a three-plus decade period of development and environmental variability. Hence, this forms a second baseline for continued long-term monitoring. Full article
(This article belongs to the Special Issue Biomonitoring and Conservation of Freshwater & Marine Fishes)
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16 pages, 3734 KiB  
Article
Integrative Taxonomy Clarifies the Historical Flaws in the Systematics and Distributions of Two Osteobrama Fishes (Cypriniformes: Cyprinidae) in India
by Boni Amin Laskar, Dhriti Banerjee, Sangdeok Chung, Hyun-Woo Kim, Ah Ran Kim and Shantanu Kundu
Fishes 2024, 9(3), 87; https://doi.org/10.3390/fishes9030087 - 27 Feb 2024
Viewed by 1078
Abstract
The taxonomy and geographical distributions of Osteobrama species have historically posed challenges to ichthyologists, leading to uncertainties regarding their native ranges. While traditional taxonomy has proven valuable in classification, the utility of an integrated approach is restricted for this particular group due to [...] Read more.
The taxonomy and geographical distributions of Osteobrama species have historically posed challenges to ichthyologists, leading to uncertainties regarding their native ranges. While traditional taxonomy has proven valuable in classification, the utility of an integrated approach is restricted for this particular group due to limitations in combining information from biogeography, morphology, and genetic data. This study addresses the taxonomic puzzle arising from the recent identification of Osteobrama tikarpadaensis in the Mahanadi and Godavari Rivers, casting doubt on the actual distribution and systematics of both O. tikarpadaensis and Osteobrama vigorsii. The research reveals distinctions among specimens resembling O. vigorsii from the Krishna and Godavari riverine systems. Notably, specimens identified as O. vigorsii from the Indian Museum exhibit two pairs of barbels, while those from the Godavari River in this study are identified as O. tikarpadaensis. Inter-species genetic divergence and maximum likelihood phylogeny provide clear delineation between O. vigorsii and O. tikarpadaensis. The study suggests that O. vigorsii may be limited to the Krishna River system in southern India, while O. tikarpadaensis could potentially extend from the Mahanadi River in central India to the Godavari River in southern India. Proposed revision to morphological features for both species, accompanied by revised taxonomic keys, aim to facilitate accurate differentiation among Osteobrama congeners. The data generated by this research provide a resource for future systematic investigations into cyprinids in India and surrounding regions. Further, the genetic diversity information obtained from various riverine systems for Osteobrama species will be instrumental in guiding aquaculture practices and formulating effective conservation action plans. Full article
(This article belongs to the Special Issue Biomonitoring and Conservation of Freshwater & Marine Fishes)
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31 pages, 4962 KiB  
Article
Sicklefin Chub (Macrhybopsis meeki) and Sturgeon Chub (M. gelida) Temporal and Spatial Patterns from Extant Population Monitoring and Habitat Data Spanning 23 Years
by Mark L. Wildhaber, Benjamin M. West, Kendell R. Bennett, Jack H. May, Janice L. Albers and Nicholas S. Green
Fishes 2024, 9(2), 43; https://doi.org/10.3390/fishes9020043 - 23 Jan 2024
Viewed by 1378
Abstract
Sicklefin (Macrhybopsis meeki) and sturgeon chub (M. gelida) historically occurred throughout the Missouri River (MR), in some tributaries, and Mississippi River downstream of the MR. They have been species of U.S. state-level conservation concern and U.S. Endangered Species Act [...] Read more.
Sicklefin (Macrhybopsis meeki) and sturgeon chub (M. gelida) historically occurred throughout the Missouri River (MR), in some tributaries, and Mississippi River downstream of the MR. They have been species of U.S. state-level conservation concern and U.S. Endangered Species Act listing candidates since the 1990s. We applied analytical approaches from occupancy modeling to correlation to monitoring data spanning 23 years to assess relationships between occupancy and time, space, environmental factors, habitat, and other species. Sicklefin chub occupancy appeared higher in the early to mid-2000s and mid-to-late 2010s. A potential decline in occupancy occurred for sturgeon chub in the mid-to-late 2010s. Spatially, chub occupancy was depressed for 159 to 438 km downstream of MR dams. Among macrohabitats, inside bends had relatively high occupancy for both species; secondary connected channels had relatively high values for sturgeon chub. Co-occurrence was likely between sicklefin and sturgeon chub and between chubs and shovelnose sturgeon (Scaphirhybchus platorybchus) and channel catfish (Ictalurus punctatus). The observed co-occurrence of chubs and pallid sturgeon (Scaphirhynchus albus; PS) was potentially higher than expected for adult PS. For juvenile PS, co-occurrence was lower than expected in the Lower MR and potentially higher than expected in the Upper MR, warranting future research. Results from this research suggest management for the improvement of sicklefin and sturgeon chub populations may benefit other MR fish populations. Full article
(This article belongs to the Special Issue Biomonitoring and Conservation of Freshwater & Marine Fishes)
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12 pages, 5526 KiB  
Article
Adaptation of the European Fish Index (EFI+) to Include the Alien Fish Pressure
by Enric Aparicio, Carles Alcaraz, Rafel Rocaspana, Quim Pou-Rovira and Emili García-Berthou
Fishes 2024, 9(1), 13; https://doi.org/10.3390/fishes9010013 - 29 Dec 2023
Viewed by 1374
Abstract
The European Fish Index EFI+ is the only fish-based multimetric index for the assessment of the ecological status of running waters that is validated and thus applicable across most countries of the European Union. Metrics of the index rely on several attributes of [...] Read more.
The European Fish Index EFI+ is the only fish-based multimetric index for the assessment of the ecological status of running waters that is validated and thus applicable across most countries of the European Union. Metrics of the index rely on several attributes of the species present in the fish assemblage, irrespective of their native/alien status. The abundance of alien fish, together with other anthropogenic impacts, is one of the most important threats to the conservation of native fish and ecosystem health and is also an indicator of degraded stream conditions. Therefore, to improve the performance of the EFI+ in regions with high incidence of alien species, the EFI+ was adapted to include alien fish pressure as a new metric that reflects the number of alien species as well as the proportional abundance of alien individuals. The application of the adapted index (A-EFI+) is illustrated with data from several Iberian Mediterranean basins and showed similar or stronger correlations than the original EFI+ with anthropogenic pressure (land-use variables and alterations in hydrology and river morphology) and with other regional fish indices. EFI+ has been invaluable to intercalibrate fish indices across Europe, and A-EFI+ is similar but explicitly includes alien pressure, thus helping to provide a more comprehensive assessment of ecosystem health and to communicate it to society. Full article
(This article belongs to the Special Issue Biomonitoring and Conservation of Freshwater & Marine Fishes)
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12 pages, 1614 KiB  
Article
Molecular Analysis of Two Endemic Squalius Species: Evidence for Intergeneric Introgression among Cyprinids and Conservation Issues
by Damir Valić, Matej Kristan Mirković, Višnja Besendorfer and Emin Teskeredžić
Fishes 2024, 9(1), 4; https://doi.org/10.3390/fishes9010004 - 20 Dec 2023
Viewed by 1237
Abstract
Conservation of indigenous species, especially endemic ones, is of the utmost importance. Morphological determination of species is usually not sufficient; therefore, molecular phylogenetic analyses of the Illyrian chub, Squalius illyricus, and the Zrmanja chub, Squalius zrmanjae, from the Krka River were performed. For [...] Read more.
Conservation of indigenous species, especially endemic ones, is of the utmost importance. Morphological determination of species is usually not sufficient; therefore, molecular phylogenetic analyses of the Illyrian chub, Squalius illyricus, and the Zrmanja chub, Squalius zrmanjae, from the Krka River were performed. For the genetic characterization of the mitochondrial gene cytochrome b and the non-coding nuclear region Cyfun P, 15 specimens from each species were subjected to analysis. The obtained sequences were aligned with similar ones from GenBank to determine the taxonomic and phylogenetic position of these species. The obtained molecular results imply that S. zrmanjae from the Krka River has a nuclear region that resembles Dalmatian rudd, Scardinius dergle. This result implies an introgression event and the transfer of genetic information between the two genera. The investigated species are on the IUCN Red List of Threatened Species, their biological data are scarce, and further investigation and protection are needed. Full article
(This article belongs to the Special Issue Biomonitoring and Conservation of Freshwater & Marine Fishes)
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18 pages, 7623 KiB  
Article
The Status of South Africa’s Freshwater Fish Fauna: A Spatial Analysis of Diversity, Threat, Invasion, and Protection
by Mohammed Kajee, Helen F. Dallas, Charles L. Griffiths, Cornelius J. Kleynhans and Jeremy M. Shelton
Fishes 2023, 8(12), 571; https://doi.org/10.3390/fishes8120571 - 22 Nov 2023
Viewed by 1831
Abstract
In South Africa, freshwater habitats are among the most threatened ecosystems, and freshwater fishes are the most threatened species group. Understanding patterns in freshwater fish diversity, threat, invasion, and protection status are vital for their management. However, few studies have undertaken such analyses [...] Read more.
In South Africa, freshwater habitats are among the most threatened ecosystems, and freshwater fishes are the most threatened species group. Understanding patterns in freshwater fish diversity, threat, invasion, and protection status are vital for their management. However, few studies have undertaken such analyses at ecologically and politically appropriate spatial scales, largely because of limited access to comprehensive biodiversity data sets. Access to freshwater fish data for South Africa has recently improved through the advent of the Freshwater Biodiversity Information System (FBIS). We used occurrence records downloaded from the FBIS to evaluate spatial patterns in distribution, diversity, threat, invasion, and protection status of freshwater fishes in South Africa. Results show that record density varies spatially, at both primary catchment and provincial scales. The diversity of freshwater fishes also varied spatially: native species hotspots were identified at a provincial level in the Limpopo, Mpumalanga, and KwaZulu-Natal provinces; endemic species hotspots were identified in the Western Cape; and threatened species hotspots in the Western Cape, Mpumalanga, Eastern Cape, and KwaZulu-Natal. Non-native species distributions mirrored threatened species hotspots in the Western Cape, Mpumalanga, Eastern Cape, and KwaZulu-Natal. Some 47% of threatened species records fell outside of protected areas, and 38% of non-native species records fell within protected areas. Concerningly, 58% of the distribution ranges of threatened species were invaded by non-native species. Full article
(This article belongs to the Special Issue Biomonitoring and Conservation of Freshwater & Marine Fishes)
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0 pages, 2706 KiB  
Article
Spatial Patterns in Fish Assemblages across the National Ecological Observation Network (NEON): The First Six Years
by Dylan Monahan, Jeff S. Wesner, Stephanie M. Parker and Hannah Schartel
Fishes 2023, 8(11), 552; https://doi.org/10.3390/fishes8110552 - 16 Nov 2023
Cited by 1 | Viewed by 1318 | Correction
Abstract
The National Ecological Observation Network (NEON) is a thirty-year, open-source, continental-scale ecological observation platform. The objective of the NEON project is to provide data to facilitate the understanding and forecasting of the ecological impacts of anthropogenic change at a continental scale. Fish are [...] Read more.
The National Ecological Observation Network (NEON) is a thirty-year, open-source, continental-scale ecological observation platform. The objective of the NEON project is to provide data to facilitate the understanding and forecasting of the ecological impacts of anthropogenic change at a continental scale. Fish are sentinel taxa in freshwater systems, and the NEON has been sampling and collecting fish assemblage data at wadable stream sites for six years. One to two NEON wadable stream sites are located in sixteen domains from Alaska to Puerto Rico. The goal of site selection was that sites represent local conditions but with the intention that site data be analyzed at a continental observatory level. Site selection did not include fish assemblage criteria. Without using fish assemblage criteria, anomalies in fish assemblages at the site level may skew the expected spatial patterns of North American stream fish assemblages, thereby hindering change detection in subsequent years. However, if NEON stream sites are representative of the current spatial distributions of North American stream fish assemblages, we could expect to find the most diverse sites in Atlantic drainages and the most depauperate sites in Pacific drainages. Therefore, we calculated the alpha and regional (beta) diversities of wadable stream sites to highlight spatial patterns. As expected, NEON sites followed predictable spatial diversity patterns, which could facilitate future change detection and attribution to changes in environmental drivers, if any. Full article
(This article belongs to the Special Issue Biomonitoring and Conservation of Freshwater & Marine Fishes)
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15 pages, 2343 KiB  
Article
Inadequate Sampling Frequency and Imprecise Taxonomic Identification Mask Results in Studies of Migratory Freshwater Fish Ichthyoplankton
by Paulo Santos Pompeu, Lídia Wouters, Heron Oliveira Hilário, Raquel Coelho Loures, Alexandre Peressin, Ivo Gavião Prado, Fábio Mineo Suzuki and Daniel Cardoso Carvalho
Fishes 2023, 8(10), 518; https://doi.org/10.3390/fishes8100518 - 19 Oct 2023
Cited by 1 | Viewed by 1458
Abstract
In South America, knowledge of major spawning sites is crucial for maintaining migratory fish populations. In this study, we aimed to understand the spatio-temporal distribution of fish eggs in the upper São Francisco River using high sampling frequency and DNA metabarcoding identification. We [...] Read more.
In South America, knowledge of major spawning sites is crucial for maintaining migratory fish populations. In this study, we aimed to understand the spatio-temporal distribution of fish eggs in the upper São Francisco River using high sampling frequency and DNA metabarcoding identification. We evaluated the possible effects of the non-molecular identification of eggs and decreased sampling frequency on the determination of spawning sites and major breeding periods. Collections were carried out every three days from November 2019 to February 2020. We found that, if we had assumed that all of the free and non-adhesive sampled eggs belonged to migratory species, as is usual in the literature, this assumption would have been wrong for both the spawning sites and the breeding periods. Moreover, any decrease in the frequency of sampling could dramatically affect the determination of the major spawning rivers, and the spawning events of some of the migratory species may not have been detected. Therefore, without the proper identification and adequate sampling frequency of eggs, important spawning sites may be overlooked, leading to ineffective or inappropriate conservation measures. Full article
(This article belongs to the Special Issue Biomonitoring and Conservation of Freshwater & Marine Fishes)
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17 pages, 2458 KiB  
Article
Environmental Impacts on Skin Microbiomes of Sympatric High Arctic Salmonids
by Erin F. Hamilton, Collin L. Juurakko, Katja Engel, Josh D. Neufeld, John M. Casselman, Charles W. Greer and Virginia K. Walker
Fishes 2023, 8(4), 214; https://doi.org/10.3390/fishes8040214 - 18 Apr 2023
Cited by 3 | Viewed by 1606
Abstract
In the region of King William Island, Nunavut, in the Canadian high Arctic, populations of salmonids including Arctic char (Salvelinus alpinus), cisco (Coregonus autumnalis and C. sardinella) as well as lake whitefish (C. clupeaformis) are diadromous, overwintering [...] Read more.
In the region of King William Island, Nunavut, in the Canadian high Arctic, populations of salmonids including Arctic char (Salvelinus alpinus), cisco (Coregonus autumnalis and C. sardinella) as well as lake whitefish (C. clupeaformis) are diadromous, overwintering in freshwater and transitioning to saline waters following ice melt. Since these fish were sampled at the same time and from the same traditional fishing sites, comparison of their skin structures, as revealed by 16S rRNA gene sequencing, has allowed an assessment of influences on wild fish bacterial communities. Arctic char skin microbiota underwent turnover in different seasonal habitats, but these striking differences in dispersion and diversity metrics, as well as prominent taxa involving primarily Proteobacteria and Firmicutes, were less apparent in the sympatric salmonids. Not only do these results refute the hypothesis that skin communities, for the most part, reflect water microbiota, but they also indicate that differential recruitment of bacteria is influenced by the host genome and physiology. In comparison to the well-adapted Arctic char, lake whitefish at the northern edge of their range may be particularly vulnerable, and we suggest the use of skin microbiomes as a supplemental tool to monitor a sustainable Indigenous salmonid harvest during this period of change in the high Arctic. Full article
(This article belongs to the Special Issue Biomonitoring and Conservation of Freshwater & Marine Fishes)
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