Underwater video analysis as a non‐destructive alternative to electrofishing for sampling imperilled headwater stream fishes

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Estimating local and regional population sizes for an endangered minnow,redside dace (Clinostomus elongatus), in Canada

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Fish biodiversity sampling in stream ecosystems: a process for evaluating the appropriate types and amount of gear

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Occupancy dynamics of rare cyprinids after invasive fish eradication

1. The eradication of invasive species is a management strategy implemented to eliminate adverse impacts of invaders on native species communities. After eradications, follow‐up studies are done to confirm eradication of the invasive species and the short‐term recovery of the native species, but long‐term monitoring to confirm full population recovery and stability is often not completed.
2. In this study, long‐term monitoring of native fishes was carried out over 5 years after the eradication of an invasive fish from the Rondegat River, South Africa. Forty‐six sites distributed along four river sections were sampled for presence/absence using underwater cameras and snorkel surveys. Density data were collected by snorkel surveys.
3. Using multi‐season occupancy models, the annual probability of colonization and local extinction of the native fishes and annual rate of change in occupancy along the river were estimated. Changes in native fish densities across time and across the control and treatment sections were analysed using Kruskal–Wallis analysis, followed by Dunn's post‐hoc test.
4. Probability of colonization and local extinction differed for each native fish species and may have been affected by extrinsic factors, such as rainfall, and intrinsic density‐dependent factors, hypothesized from the density data. The occupancy rates of change revealed that the two Near Threatened fish species have reached an occupancy dynamic equilibrium but the Endangered fish has not, suggesting that other conservation efforts may be needed.
5. Long‐term monitoring of native fishes after an eradication programme has confirmed the successful removal of the invader and the recovery and stability of the community. However, successful eradication was not sufficient for full recovery of all species; additional conservation management strategies are needed to secure the population stability and persistence of endangered fishes. We recommend that eradication programmes, regardless of locality, should employ long‐term monitoring to ensure full recovery of a native fish community.

     

Comparison of traditional and environmental DNA survey methods for detecting rare and abundant freshwater fish

1. Detecting rare species is often a necessity for conservation and management, yet challenging for many field survey methods. Environmental DNA (eDNA) is a highly promising solution that has been shown to outperform many established survey methods.
2. Macquarie perch (Macquaria australasica) is an endangered native species that has declined significantly in range and abundance. Detection of M. australasica was compared with an abundant alien fish species (Oncorhynchus mykiss) using eDNA and three conventional survey methods: gill nets, electrofishing and fyke nets.
3. eDNA occupancy estimates for both fish species were compared using four different models to investigate what effect these differences have on false positives and false negatives for the rare and common fish species. These models used unadjusted eDNA detections in water samples, eDNA detections that have been screened using a limit of detection method to remove potential false positives, eDNA data supplemented with a second survey method, or eDNA data augmented with sequencing of positive polymerase chain reaction replicates.
4. eDNA surveying as a single detection method was found to be more efficient and sensitive compared with each capture method separately and combined. Occupancy estimates for the common and rare species did not vary significantly between the four site occupancy-detection models, suggesting that supplementary data may not have as much effect on occupancy estimates compared with other approaches such as temporal or spatial sampling.
5. We conclude that eDNA outperforms the three established survey methods for both a rare and common freshwater fish species. Although there was no significant effect of augmenting eDNA survey methods with other survey data, additional data may improve confidence in detection, and provide confirmatory evidence for unexpected or new detections of a species.

     

Connectivity and flow regime direct conservation priorities for pelagophil fishes

1. Dam construction threatens global aquatic biodiversity by fragmenting stream networks and altering flow regimes. The negative effects of dams are exacerbated by increased drought periods and associated water withdrawals, especially in semi-arid regions. Stream fishes are particularly threatened owing to their mobile nature and requirement for multiple habitats to complete their life cycles. An understanding of relationships with fragmentation and flow regimes, particularly as coarse-scale (e.g. catchment) constraints on species distributions, is essential for stream fish conservation strategies.
2. Prairie chub (Macrhybopsis australis) is a small-bodied minnow (Cyprinidae) with poorly understood ecology endemic to the North American Great Plains. Suspected declines in abundance and extirpations have resulted in conservation interest for prairie chub at state and federal levels. Prairie chub is thought to share its reproductive strategy with pelagic-broadcast spawning minnows (pelagophils). Freshwater pelagic-broadcast spawning fishes have been disproportionately affected by fragmentation and streamflow alteration globally.
3. Relationships of prairie chub occurrence with coarse-scale fragmentation and streamflow metrics were examined in the upper Red River catchment. Occurrence probability was modelled using existing survey data, while accounting for variable detection. The modelled relationships were used to project the distribution of prairie chub in both a wet and dry climatic period.
4. The probability of prairie chub occurrence was essentially zero at sites with higher densities of upstream dams, but increased sharply with increases in flow magnitude, downstream open mainstem, and flood duration. The projected distribution of prairie chub was broader than indicated by naïve occurrence, but similar in both climatic periods. The occurrence relationships are consistent with the hypotheses of pelagic broadcast spawning and represent coarse-scale constraints that are useful for identifying areas of the stream network with higher potential for finer-scale prairie chub conservation and recovery efforts. In addition to informing pelagophil conservation, the relationships are also applicable to pelagic-broadcast spawning fishes in marine environments.

     

Factors associated with distributions of six fishes of greatest conservation need in streams in midwestern USA

1. Many fish species of greatest conservation need (SGCN) in Iowa and Minnesota, USA, have been in decline for decades. A key reason for the decline is the alteration and degradation of naturally flowing streams owing to land use changes resulting from agricultural practices. Populations of several fishes have been adversely affected by widespread stream channelization that has resulted in more homogeneous stream habitats throughout Iowa and Minnesota.
2. The goal of this study was to determine the abiotic and fish assemblage characteristics associated with the presence of these rare fishes. Electrofishing and seining were used to sample fish assemblages and 43 abiotic characteristics were measured at 111 sites in the North Raccoon and Boone River basins in central Iowa and the Rock River and Beaver Creek basins in north-west Iowa and south-west Minnesota during 2016 and 2017.
3. Six SGCN, including the federally endangered Topeka shiner (Notropis topeka), were included in statistical modelling to determine habitat and fish assemblage characteristics associated with their presence.
4. Species-specific nonmetric multidimensional scaling ordinations indicated that abiotic characteristics and fish assemblages often differed between sites where SGCN were present and absent. Random forest and logistic regression models suggested that the presence of four of six SGCN were positively associated with species richness, whereas all other 10 important abiotic and fish assemblage variables were unique to only one or two of the six SGCN.
5. Topeka shiners were present at 36% of sites and were positively associated with orangespotted sunfish (Lepomis humilis) catch per unit effort while being negatively associated with canopy cover and fantail darter (Etheostoma flabellare) catch per unit effort.

     

Improving benthic biodiversity assessments in turbid aquatic environments

1. Biodiversity in turbid aquatic environments is commonly assessed using extractive sampling methods that damage the seabed. Underwater cameras equipped with clear liquid optical chambers (CLOCs) for the assessment of seabed habitats and species are a non-extractive alternative and have been applied in turbid environments globally. A CLOC is a body of clear liquid positioned in front of a camera to reduce the scattering of light that would otherwise occur when passing through the turbid water it displaces. Here, we test and quantify the effectiveness of a CLOC for marine benthic biodiversity assessments over gradients of increasing turbidity.
2. The addition of a CLOC to a conventional benthic camera system significantly enhanced the quality of information gathered. Images acquired using the CLOC system consistently recorded statistically higher values of image quality (49% increase, based on the clarity of the image), seabed visible within the drop-down frame (34% increase), and European Nature Information System habitat level identification (49% increase). Furthermore, it was found that the ‘annotation success’ of taxa (classification of a specimen to family level or higher) was found to increase between individual experts in the presence of a CLOC. A reduced sampling effort was also identified when using a CLOC. Taxonomic richness increased by 27% when comparing the same number of image stills collected with and without the CLOC.
3. By reducing the limitations of underwater visibility previously attributed to underwater cameras, this concept extends the potential for use of non-destructive survey techniques and allows for future users to collect robust information of an area, making better informed management decisions.

     

Improving the detection of rare native fish species in environmental DNA metabarcoding surveys

1. The presence of threatened or endangered species often strongly influences management and conservation decisions. Within the Murray–Darling Basin (MDB), Australia, the presence of threatened native fish affects the management and allocation of water resources. In New South Wales, these decisions are currently based on traditional fisheries data and a predictive MaxEnt model. However, it is important to verify the model's predictive power given the implication it may have, but this requires methods with a high detection sensitivity for rare species.
2. Although the use of environmental DNA (eDNA) monitoring, in particular eDNA metabarcoding, achieves a higher detection sensitivity compared with traditional methods, earlier surveys in the MDB have shown that the highly abundant and invasive common carp (Cyprinus carpio) can reduce detection probabilities for rare species. Consequently, a polymerase chain reaction (PCR) blocking primer designed to block the amplification of carp eDNA could increase the detection probabilities for rare native species while simultaneously reducing the required sampling effort and survey costs. Although PCR blocking primers are often used in ancient DNA and dietary studies, no aquatic eDNA metabarcoding study to date has evaluated the potential benefits of using PCR blocking primers.
3. A laboratory and field-based pilot study was used to address this knowledge gap and assess the impact of a blocking primer, targeting cyprinid fishes (including carp), on the detection probabilities of native species and the minimum sampling effort required.
4. Results showed that the inclusion of the blocking primer increased the detection probabilities for native species by 10–20% and reduced the minimum required sampling effort by 25–50%. These findings provide important insights into possible methods for optimizing eDNA metabarcoding surveys for the detection of rare aquatic species.

     

Physical habitat utilization of fish in a Sonoran Desert stream, Arizona, southwestern United States

Abstract– The physical habitat utilization of 7 species of native fishes in a Sonoran Desert stream, Aravaipa Creek, Arizona is described. The species occupied significantly different depths and velocities of water. Longfin dace ( Agosia chrysogaster ), speckled dace ( Rhinichthys osculus ) and loach minnow ( Tiaroga cobitis ) used similar depths and velocities. Two of the three larger species (Sonora sucker [ Catostomus insignis ] and roundtail chub [ Gila robusta ]) used areas of greater depth and reduced velocity. Desert sucker ( Catostomus clarki ) grouped with loach minnow and speckled dace in the velocity of water occupied, but utilized deeper waters. The spikedace ( Meda fulgida ) aligned very closely with desert sucker in use of all 3 physical habitat variables.     

Abiotic and biotic associations between the round goby Neogobius melanostomus and tubenose goby Proterorhinus marmoratus with the endangered northern madtom Noturus stigmosus in Canada

1. Quantifying habitat associations and threats to the persistence of imperilled species is a fundamental step for initiating species recovery efforts, but the traits associated with species imperillment (e.g. rarity and vulnerability to stressors) also limit the ability to empirically inform recovery strategies. Novel sampling designs and modelling approaches are therefore needed to quantitatively assess habitat associations and the threats to species persistence.
2. To improve the understanding of habitat associations and threats for one of the rarest endangered freshwater fish species in Canada, northern madtom (Noturus stigmosus), two‐species occupancy models were developed with two invasive gobies: round goby (Neogobius melanostomus) and tubenose goby (Proterorhinus marmoratus). Models were parameterized with data from a multi‐year benthic trawling survey of two large Great Lakes tributaries in southern Ontario, Canada, and subsequently used to evaluate the need for reducing measurement error with future sampling efforts.
3. The probability of detecting northern madtom in the St. Clair (0.163) and Thames (0.194) rivers was low compared with round goby (St. Clair, 0.827; Thames, 0.833) and tubenose goby (St. Clair, 0.297). The best occupancy models indicated a negative association between northern madtom and round goby in the St. Clair River and the importance of gravel substrate for northern madtom.
4. Up to 16 repeated non‐detections using benthic trawls are needed to be 95% confident that northern madtom is absent at a site, indicating that current sampling approaches are likely inadequate.
5. Despite low detection probabilities, intensive trawling surveys combined with the two‐species occupancy modelling framework provided vital information for describing habitat associations for northern madtom and identified a significant negative association with round goby. Nonetheless, alternative sampling methods to improve the detection probability of northern madtom would allow a more robust evaluation of habitat associations and would provide more information on the negative association with round goby.

     

Detecting North American signal crayfish (Pacifastacus leniusculus) in riffles

• 1. The spread of the invasive signal crayfish (Pacifastacus leniusculus) outside its natural range is of widespread concern due to the threats posed to native biodiversity. To date, there is no standard protocol for determining signal crayfish presence or absence in a watercourse.
• 2. For the purposes of this investigation, the crayfish detection ability of active sampling methods — hand‐netting, electrofishing (one, two and three runs), kick sampling and Surber sampling — was tested at 30 sites along the River Clyde, southern central Scotland.
• 3. No single technique was successful in detecting crayfish in 100% of the sites known to contain crayfish and so the application of combinations of techniques was considered. The combination of techniques that resulted in a 100% detection rate was electrofishing (three runs) together with kick sampling. These results suggest that three‐run electrofishing and kick sampling are the best candidates for incorporation into a crayfish detection protocol.
• 4. The mean time taken to apply electrofishing (three runs) was significantly greater than the mean time to apply kick sampling. Given the lower effort required for its application, kick sampling is recommended as the preliminary technique: if kick sampling yields a negative result, the application of electrofishing will decrease the chance of recording a false negative presence. If both kick sampling and electrofishing fail to detect crayfish, trapping may further decrease the risk of a false negative result.
• 5. These findings have assisted in the development of a crayfish detection protocol, which will be applied across Scotland to determine the current distribution of signal crayfish. Copyright © 2010 John Wiley & Sons, Ltd.

     

Influences of in-stream habitat and upstream land-use on site occupancy of the Kanawha darter (Etheostoma kanawhae): A narrowly distributed species from the New River (Upper Kanawha Basin)

1. Freshwater communities are threatened by the conversion of natural landscapes for urban and agricultural purposes. Changes to land use may disrupt stream nutrient and geomorphological processes and reduce water quality, increase sedimentation, and decrease habitat heterogeneity eventually leading to species loss and decreases in ecosystem productivity. Endemic species are frequently at greater risk of habitat-mediated fragmentation and extirpation due to their constrained distributions.
2. The Kanawha darter (Etheostoma kanawhae) is an understudied fish endemic to the New River Drainage in North Carolina and Virginia, USA. To investigate the potential effect(s) of land-use change on Kanawha darters, naïve occupancy was modelled using instream habitat characteristics and upstream forest cover.
3. Generalized linear models revealed that instream habitat and forest cover are reliable predictors of Kanawha darter site occupancy. Specifically, models demonstrated that occupancy increased in reaches with reduced stream width, velocity, and bedrock substrate but higher concentrations of coarse woody material. Kanawha darter occupancy was also positively associated with the extent of forest cover in upstream catchments.
4. Although Kanawha darters are not currently considered imperilled, most populations occurred in isolated reaches separated by large sections of unoccupied habitat. Continuing ex-urban development in riparian zones is likely to be the primary threat to Kanawha darters and other endemic species in this catchment. Resource managers and stakeholders should preserve forest cover in headwaters and occupied tributaries and protect or restore riparian zones along the main-stem South and North Forks of the New River to preserve high-quality habitat and enhance connectivity among isolated Kanawha darter populations.
5. As human populations in montane regions continue to grow, there is a need to understand how land-use change affects endemic freshwater species. This study further supports the importance of retaining forest cover as an effective strategy for protecting and restoring populations of endemic fishes in high-gradient streams.

     

A conservation trade‐off? Interspecific differences in seahorse responses to experimental changes in fishing effort

• 1. A 2‐year experimental seining programme and underwater visual censuses were undertaken to quantify the direct effects of active demersal fishing on the population structure and relative abundance of two sympatric seahorse species of conservation concern: the European long‐snouted seahorse, Hippocampus guttulatus Cuvier 1829 and the short‐snouted seahorse, Hippocampus hippocampus L. The influence of habitat preference on population‐level responses to changes in habitat structure following a reduction in fishing effort was also investigated.
• 2. It was predicted that the benthic habitat would be more structurally complex after fishing ceased and that seahorse densities would increase in response to reduced fishing mortality. Furthermore, it was predicted that the magnitude of the increase in density would be greater for H. guttulatus than for H. hippocampus, because the former species prefers complex vegetated habitats while the latter species uses sparsely vegetated habitats.
• 3. As predicted, the amount of habitat cover increased significantly when seining ceased, primarily through increases in the abundance of drifting macroalgae and unattached invertebrates. Despite similarities in life histories, the two seahorse species responded differently in terms of magnitude and direction to reduced fishing effort: the abundance of H. guttulatus increased significantly while H. hippocampus decreased in abundance.
• 4. Results suggest that active demersal fishing may influence the magnitude and direction of the responses of benthic marine fishes to exploitation through its impacts on habitat structure. An increase in habitat cover appeared to favour higher densities of H. guttulatus when seining effort was reduced. By contrast, repeated seining, which maintained less complex habitats, appeared to favour greater abundances of H. hippocampus.
• 5. Given differences in habitat preference among benthic marine fishes subject to incidental capture in fisheries, simultaneous attempts to manage populations of sympatric species may require complementary strategies that support the persistence of diverse habitat types.

Copyright © 2006 John Wiley & Sons, Ltd.     

Nearshore fish assemblages associated with introduced predatory fishes in lakes

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Persistence of native fishes in small streams of the urbanized San Francisco Estuary,California: acknowledging the role of urban streams in native fish conservation

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Accounting for variation in species detection in fish community monitoring

Long‐term fish assemblage monitoring requires investigators account for within‐year variation in species' detection. An occupancy modelling framework is presented that accounts for variation in species presence and estimates the effort required to minimise within‐year variation. Species detections from snorkelling surveys and an electrofishing survey were used in single‐species occupancy models to determine the importance of site and sampling covariates on species' occupancy (psi) and detection probabilities (p). Community occupancy models estimated species richness in light of undetected species. For most species, models including patch size and reach as psi‐covariates had higher support whereas models including patch size and sampling method as p‐covariates had higher support. The number of sites and repeated surveys required to estimate occupancy accurately varied among fish species. Community models suggested that the observed number of species underestimated actual richness as much as 27% and the addition of an electrofishing survey increased estimated richness by 13%.     

Multiple survey methods reveal greater abundance of endangered pupfish in restored habitats

1. Freshwater organisms inhabiting arid ecosystems are imperilled by human alterations to water-limited landscapes. This is especially true among desert-dwelling cyprinodontid fishes, 90% of which are imperilled by habitat destruction within limited or shrinking ranges. Constructing habitats that mimic natural habitat form and function may provide a tool for species conservation, especially within freshwater protected areas. However, pupfish population assessments within degraded compared with restored habitats are infrequent, and few comparisons among survey methods exist.
2. Density estimates were developed for Endangered Comanche Springs pupfish Cyprinodon elegans throughout altered and restored habitats in a freshwater protected area by using mark–recapture and N-mixture models fitted to data collected using minnow trap and visual count survey methods. This allowed comparison of habitats, survey methods, and statistical methods commonly used to generate population size estimates for imperilled pupfish.
3. Population estimates varied across major habitat types and were largest among habitats constructed to mimic naturally occurring ciénegas. Estimates using visual counts were higher than estimates from minnow traps where water was deeper and where macroalgae cover was highest. N-mixture models generally estimated higher abundances than mark–recapture and were not limited by recapture ability.
4. The results provide strong evidence that restored habitats house greater abundances of pupfish, but survey and statistical methods commonly used to detect these differences have trade-offs in performance according to the habitats surveyed. This work benefits the field of conservation biology by providing guidance for existing and emerging monitoring programmes assessing abundance-based fish responses to habitat improvements.

     

Feeding ecology of redside dace, Clinostomus elongatus

Abstract– Redside dace, Clinostomus elongatus (Kirtland), from two populations in New York, USA, consumed adult Diptera; over 85% of the prey taken between April and November was in this order. Adult Hilara spp. (Empididae) were the dipterans consumed most frequently; individuals of this genus represented 70% and 60% of the items consumed by fishes from populations in Allcgheny and Hudson River drainages, respectively. Over 98% of the prey consumed by redside dace was in ten insect orders. Adult and larval chironomids and adult trichopterans were the next most frequently consumed prey. Adult chironomids made up 9% of the diet, by number, in both populations. Adult trichopterans accounted for 2–3% of the items taken. Adult empidids were selected by individuals in both populations. The dominance of flying insects in the diet of redside dace is related to their foraging behavior. These data show that adjacent terrestrial environments may be important to some stream-dwelling organisms.     

Detection efficiency and habitat use to inform inventory and monitoring efforts: juvenile coho salmon in the Knik River basin,Alaska

Imperfect detection associated with sampling gear presents challenges for wildlife inventory and monitoring efforts. We examined occupancy dynamics and habitat use of juvenile coho salmon, Oncorhynchus kisutch, in shallow lake environments over a summer and early fall season in the Knik River area of south central Alaska using models which control for and estimate sampling gear detection efficiency. In addition, we present statements for the probability that observed absences at a survey site or from a survey area (a collection of sites) are true absences given some amount of sampling effort and analysts' beliefs about site occupancy and sampling gear detection efficiency which can be used to guide inventory and monitoring efforts for juvenile salmon or other wildlife and plant species. Occupancy modelling results demonstrate that minnow traps were effective at sampling juvenile coho in shallow lake environments, with a mean probability of detection across the study period of 0.68 (i.e., probability of detecting the presence of juvenile coho given that they are present at a trap site; SE = 0.03). Juvenile coho salmon migrated into shallow water lakes in late summer and early fall, presumably to seek out overwinter habitat. N‐mixture modelling examination of habitat use demonstrated that once in shallow lake environments, juvenile coho were widely distributed across a range of microhabitats, with some evidence for preference for shallower depths and warmer water temperatures.