Native Fish Populations Research Articles

Rapid in-situ detection kit (RisK): Development of loop-mediated isothermal amplification (LAMP) assay for the rapid identification of selected invasive alien fish in Malaysian freshwaters

Invasive alien fish species have become a silent treat towards the ecosystem especially the native fish population in Malaysia. There has been a need to develop rapid identification methods that can aid management teams in identifying fish species that are not native to our ecosystem. Current visual identification methods are highly tedious and require time, delaying action towards curbing the invasion. The LAMP assay successfully identified six popular invasive fish species in Malaysia. None of the LAMP assays showed false positives and the Limit of Detection of the LAMP primers were highly sensitive and could detect DNA samples up to 1 × 10−15 ng/μl. The LAMP primers designed were highly specific to the target species and did not amplify non target species. DNA sequencing was done to ensure the accuracy of LAMP assay results. This study demonstrates that LAMP is a suitable tool in species identification efforts of invasive fish species in Malaysia.

In Memoriam

In Memoriam

First record of non-native platyfish, Xiphophorus maculatus (Günther, 1866) (Cyprinodontiformes, Poeciliidae), in the Jaguaribe River basin, northeastern Brazil

We provide the first record of Xiphophorus maculatus (Günther, 1866) in a river basin in the northeastern Brazil. Specimens were collected in the Jaguaribe River basin, João Pessoa, Paraíba state, Brazil. Two hundred eighty-one specimens, corresponding to 143 males and 138 females of X. maculatus, were collected at nine sites along the basin, from 2017 to 2019. Specimens total length ranged from 17.5 to 26.6 mm in males and from 11.7 to 32.7 mm in females. Introduction of non-native species greatly threatens the biological diversity worldwide. When introduced into a new habitat, X. maculatus usually decreases microcrustacean, macroinvertebrate and native fish populations.

Declining native fish, diminishing livelihood security: the predicament of Indian Himalayan communities

ABSTRACT Native fish species provide significant ecosystem services, including as food (provisioning services), as organisms with specific cultural and spiritual importance (cultural services), and contributions to supporting and regulatory services across the Indian Himalayan biodiversity hotspot. Fisheries in the Himalayan midhills and foothills, including in the Shivalik Hills and parts of the Terai (between the lower Himalayan foothills and the plains), provide livelihood security and cultural values for millions of people. Multiple anthropogenic stressors compounded by climate change have significantly depleted native fish populations over recent decades. Literature survey, focus group discussions and semi-structured interviews reveal that the decrease in native fish species undermines freshwater-dependent livelihood security in the region with ‘knock-on’ impacts on downstream ecosystem functions and services. Better understanding of the current distribution, habitat requirement and dispersal of native fish species important from a local perspective is essential to manage the growing threats to livelihoods in the Indian Himalayan region.

The effects of trophic interaction between the Patagonian native Percichthys trucha and the invasive Oncorhynchus mykiss during the juvenile period

Introduced salmonids have invaded almost all Patagonian freshwater environments, and yet the effect they have had on native fish populations is difficult to evaluate due to a lack of data prior to their introduction. In this study we focused on evaluating trophic interactions during the juvenile period of Oncorhynchus mykiss, and the ecologically similar native Percichthys trucha. For this purpose, we evaluated the diet and size range of juveniles of both species in the Caleufu River over one yearly cycle. The functional response (FR: the relationship between prey density and consumption rate) and functional response ratio (FRR = attack rate/handling time) were estimated for each species, in mono-specific and multi-specific trials. Comparison of the diet of these species by season showed high similarity for spring and summer. It was also found that juvenile sizes of these species overlap during early ontogeny. Additionally, both species presented a type II FR in mono-specific trials, with similar functional curves. In multi-specific experiments O. mykiss juveniles were dominant, leading to a reduction in P. trucha food intake. FRR was higher for O. mykiss than for P. trucha in mono-specific experiments, a difference which increased in multi-specific experiments, indicating the high potential ecological impact of O. mykiss. Our results show it is very likely that O. mykiss and native P. trucha compete in lotic environments, O. mykiss being competitively superior, highlighting the potential detrimental effect they may have during the juvenile period, especially in habitats and seasons where food resources are scarce.

Individual‐based simulations suggest mixed impacts of warmer temperatures and a nonnative predator on Chinook salmon

AbstractAs the climate changes, warmer water temperatures may stress populations of native coldwater fishes. Simultaneously, nonnative warmwater predators may expand their ranges and interact with already at‐risk native fish populations. To explore the independent and combined effects of these two stressors on threatened salmon, we present a case study of simulated Chinook salmon Oncorhynchus tshawytscha and largemouth bass Micropterus salmoides interacting under two thermal regimes in the Snoqualmie River, Washington, USA. We applied an individual‐based and spatially explicit model that tracks fish movement and growth. We evaluated changes in Chinook salmon emergence date, outmigration date, mass, and survival. We ran simulations for four scenarios: (1) Baseline, run without either stressor, (2) Warm, run with warmer temperatures, (3) Predator, run with largemouth bass, and (4) Warm‐Predator, run with both stressors. We assessed outcome metrics relative to the Baseline scenario. In the Warm scenario, salmon emerged 37 d and outmigrated 55 d earlier. There were 61% more subyearling migrants that were 31% smaller, and 72% fewer yearlings. In the Predator scenario, salmon survival decreased 64% for subyearlings and 69% for yearlings, and subyearlings were 7% smaller. In the Warm‐Predator scenario, salmon emerged 39 d and outmigrated 59 d earlier, subyearling survival increased 22%, subyearling mass decreased 37%, and 93% fewer yearlings survived. Our results suggest that warmer temperatures shift emergence and outmigration; predation by nonnative species is a threat to salmon survival; and life history strategies experience these stressors in different ways. Whereas subyearling production benefited from warmer temperatures more than it was hurt by predation, yearling production was depressed by both stressors independently and combined. Managers can use our individual‐based and spatially explicit approach to identify key times and areas to address exposure to extreme temperatures, overlap with nonnative species, and their interactive effects on threatened salmon. Our case study addressed three pressing needs identified in the literature: investigate impacts of nonnative species on threatened native salmon, build tools to evaluate management options where bass and salmon overlap, and explore how freshwater fishes will contend with multiple interactive stressors.

Morphological and trophic divergence of lake and stream minnows (Phoxinus phoxinus).

Phenotypic divergence in response to divergent natural selection between environments is a common phenomenon in species of freshwater fishes. Intraspecific differentiation is often pronounced between individuals inhabiting lakes versus stream habitats. The different hydrodynamic regimes in the contrasting habitats may promote a variation of body shape, but this could be intertwined with morphological adaptations to a specific foraging mode.Herein, I studied the divergence pattern of the European minnow (Phoxinus phoxinus), a common freshwater fish that has received little attention despite its large distribution. In many Scandinavian mountain lakes, European minnows are considered as being invasive and were found to pose threats to the native fish populations due to resource competition. Minnows were recently found to show phenotypic adaptations in lake versus stream habitats, but the question remained if this divergence pattern is related to differences in resource use. I therefore studied the patterns of minnow divergence in morphology (i.e., using geometric morphometrics) and trophic niches (i.e., using stomach content analyses) in the lake Ånnsjön and its tributaries to link the changes in body morphology to the feeding on specific resources. Lake minnows showed a strong reliance on benthic Cladocera and a more streamlined body shape with a more upward facing snout, whereas stream minnows fed on macroinvertebrates (larvae and adults) to a higher degree and had a deeper body with a snout that was pointed down. Correlations showed a significant relationship of the proportion of macroinvertebrates in the gut and morphological features present in the stream minnows. The results of this study highlight the habitat‐specific divergence pattern in morphology and resource use in this ubiquitous freshwater fish. Consequently, interspecific interactions of invasive minnows and the native fish population could differ in the respective food webs and resource competition could target different native fish species in the contrasting habitats.

Quantitative evaluation of intraspecific genetic diversity in a natural fish population using environmental DNA analysis.

Recent advances in environmental DNA (eDNA) analysis using high-throughput sequencing (HTS) enable evaluation of intraspecific genetic diversity in a population. As the intraspecific genetic diversity provides invaluable information for wildlife conservation and management, there is an increasing demand to apply eDNA analysis to population genetics and the phylogeography by quantitative evaluation of intraspecific diversity. However, quantitative evaluations of intraspecific genetic diversity using eDNA is not straightforward because the number of eDNA sequence reads obtained by HTS may not be an index of the quantity of eDNA. In this study, to quantitatively evaluate genetic diversity using eDNA analysis, we applied a quantitative eDNA metabarcoding method using the internal standard DNAs. We targeted Ayu (Plecoglossus altivelis altivelis) and added internal standard DNAs with known copy numbers to each eDNA sample obtained from three rivers during the library preparation process. The sequence reads of each Ayu haplotype were successfully converted to DNA copy numbers based on the relationship between the copy numbers and sequence reads of the internal standard DNAs. In all rivers, the calculated copy number of each haplotype showed a significant positive correlation with the haplotype frequency estimated by a capture-based survey. Furthermore, estimates of genetic indicators such as nucleotide diversity based on the eDNA copy numbers were comparable with those estimated based on a capture-based study. Our results demonstrate that eDNA analysis with internal standard DNAs enables reasonable quantification of intraspecific genetic diversity, and this method could thus be a promising tool in the field of population genetics and phylogeography.

Sumatran major lakes: limnological overviews

Sumatra’s major lakes are uniquely interesting because they were formed mainly by the Great Sumatra Fault and also affected by volcanic processes. Eight large Sumatran lakes, as major lakes, have played important roles for local people and been part of a significant study of Limnology in Indonesia. These lakes include Laut Tawar, Toba, Maninjau, Singkarak, Diatas, Dibawah, Kerinci, and Ranau. The utilization of lakes can be for several purposes: fisheries, tourism, and other activities that have developed rapidly in the last decade, such as aquaculture in floating net cages. Activities in the waters and the surrounding areas of the lake have had impacts on the trophic status and the decrease of native fish populations. In this paper, the environmental conditions of the lake were comprehensively reviewed.

Factors Related to Age-0 Native Fish Catch per Unit Effort in the South Dakota Missouri River Reservoirs

AbstractThe Missouri River in South Dakota was dammed in the 1950s and 1960s, altering the biotic and abiotic factors that potentially affect native species in the mainstem reservoirs. Little research has been conducted regarding what factors regulate age-0 catch per unit effort (CPUE) of native fish species since the damming occurred. Thus, we examined age-0 CPUE for 13 native fish species in the four Missouri River mainstem reservoirs. We analyzed data from 1995 to 2015 in Lake Oahe, 2002 to 2016 in Lake Sharpe, 1998 to 2008 in Lake Francis Case, and 2000 to 2013 in Lewis and Clark Lake. Not all species were sampled in all reservoirs. We evaluated potential environmental (inflow, gauge height, peak flow, precipitation, air temperature) and biological (CPUE of other native species, nonnative species, and predators) factors that have documented impacts on age-0 native fish. Significant relationships existed between age-0 native fish CPUE and both biotic and abiotic factors in all four reservoirs, but were species- and reservoir-dependent. Age-0 CPUE was either stable or increasing in all species examined in all reservoirs except age-0 Emerald Shiner Notropis atherinoides in Lewis and Clark Lake. Age-0 Emerald Shiner CPUE in Lewis and Clark Lake was most supported by biological models (e.g., total age-0 nonnative and adult White Bass Morone chrysops CPUE), and a positive relationship existed between age-0 Emerald Shiner and both factors. We believe our findings provide valuable insight into successful management of native fish populations.

Small-Bodied Fish Surveys Demonstrate Native Fish Dominance Over 300 Kilometers of the Colorado River Through Grand Canyon, Arizona

The Colorado River in Grand Canyon is highly regulated, with hypolimnetic releases that are generally unfavorable for endemic native fishes. However, both long-term drought and changes in dam operations have led to changes in river conditions, including the addition of approximately 125 km of riverine environment due to the contraction of Lake Mead. Through sampling of small-bodied fish, we were able to describe the Grand Canyon fish community and define the current native fish distribution from near Bright Angel Creek downstream to Pearce Ferry. Beginning in 2014 and continuing through 2018, we sampled the fish community via seining and documented a fish community that was dominated (>95%) by native fish through approximately 300 km of river. Nonnative species that were once commonly captured, such as Red Shiner Cyprinella lutrensis, Common Carp Cyprinus carpio, and Channel Catfish Ictalurus punctatus, were rarely encountered in Grand Canyon during this more recent sampling, which makes the Colorado River in Grand Canyon National Park a rare contemporary example of native fish populations regaining dominance over invasive fishes in the desert southwest.

Fish predation on a landscape scale

AbstractPredator–prey dynamics can have landscape‐level impacts on ecosystems, and yet, spatial patterns and environmental predictors of predator–prey dynamics are often investigated at discrete locations, limiting our understanding of the broader impacts. At these broader scales, landscapes often contain multiple complex and heterogeneous habitats, requiring a spatially representative sampling design. This challenge is especially pronounced in California’s Sacramento–San Joaquin River Delta, where managers require information on the landscape‐scale impacts of non‐native fish predators on multiple imperiled native prey fish populations. We quantified relative predation risk in the southern half of the Delta (South Delta) in 2017 using floating baited tethers that record the exact time and location of predation events. We selected 20 study sites using a generalized random tessellation stratified survey design, which allowed us to infer relationships between key environmental covariates and predation across a broader spatial scale than previous studies. Covariates included distance‐to‐nearest predators, water temperature, turbidity, depth, bottom slope, bottom roughness, water velocity, and distance‐to‐nearest riverbank and nearest aquatic vegetation bed. Model selection determined the covariates that best predicted relative predation risk: water temperature, time of day, mean predator distance, and river bottom roughness. Using this model, we estimated predation risk for the South Delta landscape at a 1‐day and 1‐km resolution. This effort identified hot spots of predation risk and allowed us to generate predicted survival for migrating fish transiting the South Delta. This methodology can be applied to other systems to evaluate spatio‐temporal dynamics in predation risk, and their biotic and abiotic predictors.

Integrating Studies of Anatomy, Physiology, and Behavior into Conservation Strategies for the Imperiled Cyprinid Fishes of the Southwestern United States.

Over the last 100 years, fishes native to the Southwestern United States have faced a myriad of biotic and abiotic pressures which has resulted in most being federally listed as endangered or threatened. Most notably, water diversions and the introduction of non-native fishes have been the primary culprits in causing the downfall of native fish populations. We describe how recent studies of morphology, physiology, and behavior yield insights into the failed (occasionally successful) management of this vanishing biota. We describe how understanding locomotor morphologies, physiologies, and behaviors unique to Southwestern native fishes can be used to create habitats that favor native fishes. Additionally, through realizing differences in morphologies and behaviors between native and non-native fishes, we describe how understanding predator-prey interactions might render greater survivorship of native fishes when stocked into the wild from repatriation programs. Understanding fundamental form-function relationships is imperative for managers to make educated decisions on how to best recover species of concern in the Southwestern United States and worldwide.

A Decade in Review: Alaska’s Adaptive Management of an Invasive Apex Predator

Northern pike are an invasive species in southcentral Alaska and have caused the decline and extirpation of salmonids and other native fish populations across the region. Over the last decade, adaptive management of invasive pike populations has included population suppression, eradication, outreach, angler engagement, and research to mitigate damages from pike where feasible. Pike suppression efforts have been focused in open drainages of the northern and western Cook Inlet areas, and eradication efforts have been primarily focused on the Kenai Peninsula and the municipality of Anchorage. Between 2010 and 2020, almost 40,000 pike were removed from southcentral Alaska waters as a result of suppression programs, and pike have been successfully eradicated from over 20 lakes and creeks from the Kenai Peninsula and Anchorage, nearly completing total eradication of pike from known distributions in those areas. Northern pike control actions are tailored to the unique conditions of waters prioritized for their management, and all efforts support the goal of preventing further spread of this invasive aquatic apex predator to vulnerable waters.

Transposable DNA Elements in Amazonian Fish: From Genome Enlargement to Genetic Adaptation to Stressful Environments

Transposable elements have driven genome evolution and plasticity in many ways across a range of organisms. Different types of biotic and abiotic stresses can stimulate the expression or transposition of these mobile elements. Here, we cytogenetically analyzed natural fish populations of the same species living under different environmental conditions to test the influence and organization of transposable elements in their genome. Differential behavior was observed for the markers Rex 1, Rex 3, and Rex 6 in the chromosomes of individuals of the same species but coming from different environments (polluted and unpolluted). An increase in the number of Rex transposable elements in the chromosomes and their influence on the genome of populations living in a polluted environment indicates that they must be under constant adaptive evolution.

Killing One Trout to Save Another: A Hegemonic Political Ecology with Its Biopolitical Basis in Yellowstone’s Native Fish Conservation Plan

Yellowstone National Park implements a native fish conservation plan to control translocated trout species competing with native cutthroat trout. Under the plan, millions of lake trout are removed from Yellowstone Lake and park streams are poisoned to eradicate other translocated trout species. Killing trout introduced by officials decades earlier is a significant reversal in fisheries management. This article employs a biopolitical analysis of data derived qualitatively from semistructured interviews, relevant documents, and participant observation in the field. Results reveal a diversity of sometimes antagonistic stakeholders subjecting themselves to the practice of killing formerly revered fish based on truth claims circulating around the crisis-based conservation of native fish populations and ecosystem health. Stakeholders support logics of killing in relation to their varied engagements with fish, leading to a multiplicity of biopolitical motivations endorsing nativism in Yellowstone. From this multiplicity emerges a conservation hegemon where power over life and death is enacted in many corners of the biosocial collective but trends toward dominant knowledge and practice vested in the National Park Service. Theorizing killing for conservation as a hegemonic political ecology reconceptualizes the place of species outside of problematic dichotomies like native and nonnative. Instead, species are either hegemonic or counterhegemonic based on their lively positions relative to the conservation hegemon, leading to more honestly articulated motivations behind resource management goals associated with the practice of killing for conservation.

Fish inhabiting rice fields: Bioaccumulation, oxidative stress and neurotoxic effects after pesticides application

Abstract The present study aimed to evaluate the biological effects triggered by the application of a current-use mixture of pesticides (the herbicide glyphosate, the insecticide bifenthrin, BF, and the fungicides azoxystrobin, AZ, and cyproconazole, CYP) on two native fish (Markiana nigripinnis and Astyanax lacustris) inhabiting a rice field. We analyzed pesticide residues in water, sediment and fish samples 21 days before and after a fumigation event. Additionally, organismic indices, oxidative stress and neurotoxicity biomarkers in fish at both sampling periods were compared. After fumigation, glyphosate, BF, AZ and CYP were detected in water and sediment samples, being also bioaccumulated in both fish species. A decreasing condition factor in A. lacustris and a higher liver somatic index in M. nigripinnis were observed as well. Overall, results showed that, after the application of the pesticide mixture, antioxidant mechanisms failed to prevent oxidative damage in the liver and gills of M. nigripinnis. Meanwhile, A. lacustris showed a different response: an inhibition of the antioxidant defenses without tissue lipid oxidative damage. Furthermore, acetylcholinesterase activity after spraying was significantly reduced in brain and muscle tissues of A. lacustris and in the brain of M. nigripinnis. Our results show that current-use pesticides, like glyphosate, BF, AZ and CYP, pose health risks on native fish populations inhabiting rice fields.

Native bighead carp Hypophthalmichthys nobilis and silver carp Hypophthalmichthys molitrix populations in the Pearl River are threatened by Yangtze River introductions as revealed by mitochondrial DNA.

Bighead carp Hypophthalmichthys nobilis and silver carp Hypophthalmichthys molitrix have been two economically important aquaculture species in China for centuries. In the past decades, bighead and silver carp have been introduced from the Yangtze River to many river systems in China, including the Pearl River, in annual, large-scale, stocking activities to enhance wild fisheries. Nonetheless, few studies have assessed the ecological or genetic impacts of such introductions on native conspecific fish populations. An mtDNA D-loop segment of 978 bp from 213 bighead carp samples from 9 populations and a 975 bp segment from 204 silver carp samples from 10 populations were obtained to evaluate genetic diversity and population integrity. Results from a haplotype network analysis revealed that most haplotypes of the Pearl River clustered with those of Yangtze River origin and only a small proportion were distinct, suggesting that both the native Pearl River bighead and silver carp populations are currently dominated by genetic material from the Yangtze River. The genetic diversity of Pearl River populations is high in both species because of this inter-population gene flow, but the diversity of native Pearl River populations is low. To preserve the native genetic diversity, stocking of non-native fingerlings should cease immediately and native Pearl River bighead and silver carp fish farms should be established. This research demonstrates the danger to native biodiversity across China because of the substantial, ongoing stock-enhancement activities without prior genetic assessment.

What is needed to restore native fishes in Australia’s Murray–Darling Basin?

The Murray–Darling Basin (MDB) is Australia’s food bowl, contributing 40% of agricultural production and supporting a population of over 4 million people. Historically, the MDB supported a unique native fish community with significant cultural, subsistence, recreational, commercial and ecological values. Approximately one-quarter of the MDB’s native species are endemic. Changes to river flows and habitats have led to a >90% decline in native fish populations over the past 150 years, with almost half the species now of conservation concern. Commercial fisheries have collapsed, and important traditional cultural practices of First Nations People have been weakened. The past 20 years have seen significant advances in the scientific understanding of native fish ecology, the effects of human-related activities and the recovery measures needed. The science is well established, and some robust restoration-enabling policies have been initiated to underpin actions. What is now required is the political vision and commitment to support investment to drive long-term recovery. We present a summary of 30 priority activities urgently needed to restore MDB native fishes.

The effects of cold shock on freshwater fish larvae and early-stage juveniles: implications for river management.

Temperature is essential to the maintenance of optimal physiological functioning in aquatic organisms. Fish can manage natural fluctuations in temperature; however, in freshwater ecosystems acute and rapid temperature changes can originate from sources such as large dams and industrial effluents. These rapid temperature changes may induce several physiological and behavioural responses that can result in lethal and sub-lethal consequences. The present study assessed immediate sub-lethal and short-term (10days) lethal responses of three species of Australian freshwater fish larvae and early-stage juveniles to a range of different 'field-relevant' cold shocks (-4, -6, -8 and -10°C). Murray cod (Maccullochella peelii), silver perch (Bidyanus bidyanus) and golden perch (Macquaria ambigua) were tested at two age groups to elucidate the interaction between ontogeny and sensitivity to cold shock. Cold shock caused mortality and reductions in swimming ability (time to exhaustion and lines crossed) in all species of fish at both age groups. Sensitivity was correlated to the magnitude of cold shock; a 10°C drop in temperature caused the highest mortalities. Ontogeny interacted with the severity of cold shock; the younger fish experienced higher mortalities and greater impairment to swimming ability. This study demonstrates the potential lethal and sub-lethal impacts of cold shock on freshwater fish at a critical life-history stage. Understanding the impacts of cold shock will aid management of freshwater ecosystems for the benefit of fish populations, with the current study identifying critical life stages to be considered in remediation and guiding thresholds necessary to reduce the impact of cold shock on native fish populations.