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1.
Madalyn K. Cooper Roger Huerlimann Richard C. Edmunds Alyssa M. Budd Agnès Le Port Peter M. Kyne Dean R. Jerry Colin A. Simpfendorfer 《水产资源保护:海洋与淡水生态系统》2021,31(8):2131-2148
- Pressures on coastal ecosystems are increasing and aquatic species that are restricted to these habitats are facing the threat of extinction. However, the true extent of many threatened and rare aquatic species, especially elasmobranchs, remains unclear due to high levels of data deficiency and poor efficacy of traditional survey methods. Sawfishes (Pristidae), a family of shark-like rays, are among the most threatened and rare elasmobranch species and are difficult to detect in turbid, coastal habitats. Reliable cost-effective tools to detect these species are urgently needed to increase their conservation potential.
- Characterization of environmental DNA (eDNA) extracted from water samples has garnered significant appeal for detection of rare and threatened species. To assist conservation and monitoring efforts for sawfishes using eDNA, species-specific TaqMan quantitative polymerase chain reaction assays were developed and validated to detect 1.25–5 copies of a 12S rRNA gene fragment. Filter samples were collected in Northern Territory, Australia to assess the utility of the developed eDNA assays and compare the efficacy of preservation and extraction workflows for detecting rare species.
- Dwarf sawfish (Pristis clavata) were detected in three of 20 sites, and there was a significant effect of preservation and extraction workflow on total eDNA yield and subsequent detection success. Longmire's preserved samples extracted using glycogen-aided precipitation yielded a significantly higher concentration of total eDNA (n = 60; β = 1.27, t(95) = 8.172, P < 0.0001) and yielded positive P. clavata eDNA detections compared to ethanol preserved samples extracted using QIAGEN DNeasy kit, which did not yield any positive detections.
- The optimized eDNA assays were developed to support monitoring efforts for endangered sawfishes. Importantly, this study demonstrates that choice of preservation and extraction workflow requires careful consideration, especially when detection of rare or threatened species can have important management and conservation outcomes.
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Jack Rojahn Dianne M. Gleeson Elise Furlan Tim Haeusler Jonas Bylemans 《水产资源保护:海洋与淡水生态系统》2021,31(4):990-997
- 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.
- 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.
- 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.
- 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.
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Karl A. Lamothe Jacob P. Ziegler Robin Gsprdy Jason Barnucz D. Andrew R. Drake 《水产资源保护:海洋与淡水生态系统》2020,30(4):691-700
- 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.
- 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.
- 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.
- 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.
- 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.
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- 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.
- 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.
- 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.
- 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.
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- Many conservation efforts for freshwater fishes have been undertaken; however, continuing the monitoring of both the distribution and the abundance of species to determine the effectiveness of these actions can be difficult. As species increase in rarity, they are more difficult to detect in the field, making inferences on occupancy less reliable.
- Conventional sampling methods, such as electrofishing and seining, require the physical handling of rare fishes, which may cause stress and mortality and, consequently, compromise conservation goals and limit monitoring programmes. Non‐invasive surveillance methods, including underwater video, are playing an increasingly important role.
- In this study, occupancy models were used to estimate the detection probability of underwater cameras as an alternative to the conventional sampling methods for rare stream fishes. Redside dace (Clinostomus elongatus), a small minnow listed as Endangered, was used as a model organism for rarity. A total of 69 historical redside dace sites were sampled using three sampling methods to determine the effect of gear type on detecting and identifying the habitat preferences of this rare minnow.
- On average, using multiple underwater cameras is as effective at detecting a rare minnow as conventional sampling methods (backpack electrofisher and seine) and causes no harm.
- The detection probability of both underwater cameras and backpack electrofishing were adversely affected by turbidity, whereas seining was positively affected by stream velocity. The probability of occupancy of redside dace is driven by open channels and sediment size, and this provides a strong basis for informing stream restoration projects.
- The use of multiple underwater cameras over conventional sampling methods is recommended when sampling for rare and endangered minnows in systems with low turbidity.
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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%. 相似文献
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- The use of environmental DNA (eDNA) is a promising approach for the detection of aquatic species, including species at risk. One freshwater mussel species of interest in Atlantic Canada, the brook floater (Alasmidonta varicosa), is listed as being of Special Concern under the Species at Risk Act in Canada and as Vulnerable on the International Union for Conservation of Nature Red List. Further scientific data regarding species distribution and critical habitat is needed for the protection and conservation of this species.
- The aim of this study was to design, optimize, and apply a species-specific quantitative polymerase chain reaction assay for the detection of brook floater from eDNA samples, and to assess temporal variability in brook floater eDNA quantities.
- Through an eDNA survey performed in New Brunswick rivers in 2017 and 2018, brook floater DNA was found at a total of 16 out of 56 sites sampled. The amount of brook floater DNA detected at all 16 sites was always below the theoretical limit of detection of the assay, and, as such, results were classified as either ‘inconclusive’ or ‘suspected’.
- The co-detection of eastern pearlshell (Margaritifera margaritifera), a more abundant freshwater mussel species in Atlantic Canada, was successfully used as a natural positive control.
- Temporal variability in the amount of eDNA found in the water was also assessed at a site with a known brook floater population and minimal variability in eDNA quantities was observed from May to September.
- These results provide researchers and managers with a new tool for the detection of the brook floater in support of conservation and monitoring efforts.
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Rowshyra A. Castaeda Nicholas E. Mandrak Stuart Barrow Olaf L. F. Weyl 《水产资源保护:海洋与淡水生态系统》2020,30(7):1424-1436
- 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.
- 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.
- 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.
- 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.
- 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.
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Jes Jessen Rasmussen Liselotte Wesley Andersen Trine Just Johnsen Jens Thaulow Marc Anglès d'Auriac Søren Nøhr Thomsen Martin Hesselsøe 《水产资源保护:海洋与淡水生态系统》2021,31(9):2506-2514
- Environmental DNA (eDNA) from water samples is increasingly used to detect the presence and distribution of species in aquatic ecosystems. However, before implementing eDNA in monitoring programmes, various species-specific sampling or analytical issues remain to be resolved in order to minimize frequencies of false-positive and -negative results. For example, empty shells from freshwater pearl mussels (Margaritifera margaritifera) contain extractable DNA (chemical extraction from ground-up shells) suggesting a risk of false-positive samples at stream sites with extinct populations but with empty shell material remaining.
- The aim of this study was to investigate whether empty and naturally degrading shells from M. margaritifera can cause false-positive eDNA signals in water samples.
- Water samples were collected from outdoor stream channels (in Lemming, Denmark) with living freshwater pearl mussels or empty shell material (density ~10 individuals m−2) during a 3-week experimental period. Living freshwater pearl mussels were collected from Hemgravs stream in Sweden and transported to Denmark according to permissions granted by the Swedish and Danish authorities.
- All water samples from stream channels containing empty shells were negative for eDNA indicating that eDNA traces in stream water are most likely to originate from living individuals located upstream of the sampling site. Water samples collected from stream channels containing living individuals of M. margaritifera were consistently positive for eDNA except for one sample (interpreted as a false negative).
- The study shows that positive eDNA signals for freshwater pearl mussels most likely reflect the presence of living individuals. Consequently, we suggest that eDNA should be used to locate remaining population fragments of M. margaritifera in deep and turbulent streams, providing a platform for faster and more efficient decision making when launching investigative and mitigation initiatives.
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- Habitat degradation and destruction arising from rapidly increasing urbanization represents one of the most significant threats to biodiversity. Human populations are continuing to increase around coastal regions, and as marine habitats are displaced by artificial structures it is important to understand how marine species may be impacted by these changes in habitat availability. The endangered seahorse Hippocampus whitei has been observed inhabiting protective swimming nets in Sydney Harbour, Sydney, Australia, even in the presence of natural habitats.
- This study tested whether the presence of a swimming net results in increased seahorse numbers at sites around Sydney Harbour, or whether seahorses are attracted away from natural habitats. Density surveys and mark–recapture population estimates were done at sites with pre-existing swimming nets and compared to control sites where only natural habitat was present. A manipulative experiment was conducted in which panels of swimming net material were installed at two sites in Sydney Harbour, with comparisons to control sites over a period of 14 months (April 2018 to June 2019) to test whether the installation of swimming nets would affect seahorses on surrounding natural habitat or increase site abundance.
- The pre-existing and installed swimming nets were found to support greater densities of H. whitei as well as some increases in site-scale abundance, with no effects on seahorse density on natural habitats. It is likely that increased seahorse production is occurring on the nets, with no evidence that seahorses are being attracted away from natural habitat; however, effects may vary across survey occasions and sites. Furthermore, swimming nets may serve as a useful replacement habitat in locations where natural habitat has become sparse or absent.
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Nicholas J. Rutter Julia H. Mynott Tiffani J. Howell Arthur A. Stukas Jack H. Pascoe Pauleen C. Bennett Nicholas P. Murphy 《水产资源保护:海洋与淡水生态系统》2021,31(4):984-989
- Professionally trained conservation detection dogs (CDDs) are taught to locate biological targets, including cryptic and low-density plant and animal species, but have been largely underused in detecting endangered invertebrates.
- This pilot study assessed the ability of four volunteer CDD/handler teams to detect the endangered Alpine stonefly (Eustheniidae: Thaumatoperla alpina). Once trained, all teams identified 100% of the targets when present in container line-up searches, with no false alerts.
- In the field, all available dog–handler teams (n = 3) alerted to the presence of numerous T. alpina individuals, including individuals that were not seen by experienced visual surveyors.
- Three of the four CDDs also spontaneously alerted (i.e. exhibited olfactory generalization) to a closely related species, the Stirling stonefly (Thaumatoperla flaveola), in an initial container search.
- These preliminary results demonstrate that volunteer dog–handler teams can be trained to detect T. alpina in situ. In addition, CDDs may be able to perform olfactory generalization effectively: from detecting a commonly occurring species to detecting a closely related, rare, or cryptic species.
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Alifa Bintha Haque Nidhi Gloria D'Costa Mahi Washim Amit Robert Baroi Nazia Hossain Mashrur Hafiz Sumaiya Rahman Karabi Farhana Biswas 《水产资源保护:海洋与淡水生态系统》2021,31(6):1392-1409
- Devil rays (Mobula spp.) are globally threatened cartilaginous fishes that have attracted global conservation concern owing to their high extinction risk and lack of protection in many countries. Limited resources and data on threatened marine species, including devil rays, impede conservation actions, particularly in developing countries, many of which have high biodiversity.
- Devil ray catch is a component of artisanal fisheries in Bangladesh, but data on their fisheries and trade are limited. To characterize devil ray fishing practices, fishers’ perception and trade, 230 fishers and traders were interviewed between 4 June 2018 and 22 June 2019, in four areas of south-east Bangladesh. Catch data were also opportunistically collected at landing sites.
- Six devil ray species were documented, caught in an array of gill nets, set-bag nets and longlines. All interviewed fishers reported life-long devil ray bycatch in some numbers, and also noted a decline in catch over the last decade. Bottom trawling, increased bycatch levels, increased demand for devil ray products and, in some cases, ecosystem changes were identified by fishers as threats to devil ray populations.
- Unregulated and undocumented trade and retained bycatch, especially by gill nets and set-bag nets, are fuelled by local consumption of devil ray meat and international trade in meat and gill rakers. Compliance with international trade control treaties for all Mobula spp. or the Bangladeshi law protecting Mobula mobular was low, with the majority of fishers (87%, n = 174) unaware of their existence.
- To manage devil ray fisheries, and prevent possible population declines, we propose a combination of legally enforced gear modifications, and catch and trade control through community-owned implementation strategies. Additionally, we propose the simultaneous implementation of inclusive, community-based awareness and stewardship projects in conjunction with a coast-wide ray monitoring programme. Finally, we emphasize that more research and action rooted in a sustainable fishery model is urgently needed to protect Bangladeshi devil ray populations.
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David L. Morgan Karissa O. Lear Emma Dobinson Adrian C. Gleiss Travis Fazeldean Richard D. Pillans Stephen J. Beatty Jeff M. Whitty 《水产资源保护:海洋与淡水生态系统》2021,31(8):2164-2177
- Sawfishes (Family: Pristidae) are one of the most imperilled fish families worldwide. There is an increasingly urgent need to better understand the biology, ecology, and population status of the five sawfish species to develop more effective conservation measures. The dwarf sawfish, Pristis clavata, is one of the least researched members of the pristids, with literature limited to analysing disparate datasets or collations of rare encounters in northern Australia.
- This study examined the spatial ecology of dwarf sawfish using targeted surveys and acoustic telemetry to determine its habitat use in a macrotidal estuary in northern Australia. Seventeen dwarf sawfish were tagged with acoustic transmitters and monitored in the Fitzroy River estuary and adjacent King Sound (Kimberley, Western Australia) between August 2015 and November 2017.
- Dwarf sawfish observed within the Fitzroy River estuary and King Sound were juveniles, ranging between 740 and 2,540 mm in total length. Catch per unit effort of dwarf sawfish in the late dry season was relatively high in the estuary, with the catch rate in 2015 being one of the highest reported for any sawfish species.
- Acoustic detections revealed a distinct seasonal pattern in the use of different parts of the estuary and King Sound, which was found to be driven by salinity. Dwarf sawfish predominately occupied a single large pool near the terminus of the tidal limit in the late dry season (August–November), before transitioning to regions in closer proximity to the river mouth or in King Sound in the wet and early dry seasons (December–July).
- Given the high abundance and residency of dwarf sawfish in the Fitzroy River estuary, this area is an important nursery for the species during the late dry season and should be formally recognized as a habitat protection area for the species.
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Kevin D. Friedland Michelle Bachman Andrew Davies Romain Frelat M. Conor McManus Ryan Morse Bradley A. Pickens Szymon Smoliński Kisei Tanaka 《水产资源保护:海洋与淡水生态系统》2021,31(6):1482-1498
- Species distribution models for marine organisms are increasingly used for a range of applications, including spatial planning, conservation, and fisheries management. These models have been constructed using a variety of mathematical forms and drawing on both physical and biological independent variables; however, what might be called first-generation models have mainly followed the form of linear models, or smoothing splines, informed by data collected in the context of fish surveys.
- The performance of different classes of variables were tested in a series of species occurrence models built with machine learning methods, specifically evaluating the potential contribution of lower trophic level data. Random forest models were fitted based on the classification of the absence/presence for fish and macroinvertebrates surveyed on the US Northeast Continental Shelf.
- The potential variables included physical, primary production, secondary production, and terrain variables. For accepted model fits, six variable importance measures were computed, which collectively showed that physical and secondary production variables make the greatest contribution across all models. In contrast, terrain variables made the least contribution to these models.
- Multivariable analyses that account for all performance measures reinforce the role of water depth and temperature in defining species presence and absence; however, chlorophyll concentration and some specific zooplankton taxa, such as Metridia lucens and Paracalanus parvus, also make important contributions with strong seasonal variations.
- Our results suggest that lower trophic level variables, if available, are valuable in the creation of species distribution models for marine organisms.
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Heather S. Galbraith Carrie J. Blakeslee Daniel E. Spooner William A. Lellis 《水产资源保护:海洋与淡水生态系统》2020,30(3):540-553
- Managing for threatened and endangered species under changing environmental conditions is a challenge faced by resource managers worldwide. Lack of basic knowledge of the biology and habitat requirements of these species can contribute to this difficulty but is exacerbated by the limitations of working with rare species (i.e. few individuals) or unrefined and non‐lethal methods for evaluating stress.
- A weight‐of‐evidence approach was used to evaluate the thermal biology of the federally endangered dwarf wedgemussel (Alasmidonta heterodon), using cumulative results from multiple experimental assessments, co‐occurring species, and their host fish to begin defining the thermal limits and optimal conditions for the species.
- Results suggest that dwarf wedgemussel and its host fish are thermally sensitive species compared with other Atlantic‐slope mussels, with a lower critical thermal maximum (CTM) and the selection of reduced temperatures during choice experiments.
- Physiological studies resulted in a lack of statistical significance, primarily owing to low power, which was a function of sample size – an unavoidable problem when studying rare species. Given these limitations, thermal choice and CTM may be more useful end points than physiological processes such as clearance and respiration rates when dealing with sample‐size limitations.
- These results suggest that management strategies that avoid exposing dwarf wedgemussel and its thermally sensitive host fish to extreme temperatures could be important for species conservation.
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- Fish assemblages in estuaries have a much lower species richness (number of taxa) when compared with the combined numbers of freshwater and marine species from adjacent aquatic ecosystems. This is primarily because of the relatively harsh and fluctuating physico-chemical conditions in estuaries compared with the more stable freshwater and marine environments.
- A comprehensive fish survey of estuaries in South Africa is used as a basis to determine fish species richness in subtropical, warm temperate, and cool temperate systems along the coast, and to assess the degree of redundancy in the different biogeographic regions.
- In general, only one or two species belonging to each of the detritivorous, piscivorous, zoobenthivorous, and zooplanktivorous fish guilds are numerically well represented in the larger cool temperate estuaries, but between four and 10 species in each of these guilds are usually recorded in the larger subtropical estuaries.
- Although the overall low redundancy of fish species groups in estuaries has already been formally recognized in the literature, this short note highlights the sensitivity of certain trophic guilds in temperate South African estuaries to any form of redundancy, a characteristic that may be equally applicable, based on declining species richness with increasing latitude, to temperate estuaries in other parts of the world.