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Maxine P. Piggott Samuel C. Banks Ben T. Broadhurst Christopher J. Fulton Mark Lintermans 《水产资源保护:海洋与淡水生态系统》2021,31(1):173-184
- 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.
- 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.
- 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.
- 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.
- 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.
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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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近年来,环境DNA宏条形码技术(eDNA metabarcoding)在水生生态系统生物多样性评估等相关领域中得到广泛应用,因其具有快速测算群落中物种丰度的潜能,eDNA宏条形码技术成为资源保护和管理中颇具应用前景的调查工具。虽然大量证据表明eDNA高通量测序获得的reads数与自然环境中生物相对数量具有相关性,但一直不能得到明确的量化关系结果。eDNA的富集、扩增过程中的偏倚等诸多不确定因素,制约了该技术在生物资源调查领域的推广应用。假定水体中的eDNA全部回收,且PCR扩增时不存在引物偏倚性,这种理想状态下的水体中eDNA组成与其高通量测序reads数是否存在线性关系？为此,本研究在实验室可控条件下,选择2个同属近缘的凡纳滨对虾(Penaeus vannamei)和墨吉对虾(Penaeus merguiensis),对其DNA样品进行不同比例混合,模拟从自然水体中富集到的eDNA复合样品,既保证了样品的回收率,又降低了引物偏倚的干扰。以此为模板,探究eDNA宏条形码技术检测种群相对数量的准确性。结果显示,当2个物种DNA模板浓度比例为1∶1时,高通量测序结果注释得到的2个物种reads数比值为13/24(墨吉对虾/凡纳滨对虾),可见,即使是同属近缘种间依然存在轻微的引物偏倚现象,引物偏移率为1.5%。同时,根据7个实验组获得的高通量测序结果注释得到的2个物种reads数比值与对应模板中2个物种DNA浓度比值之间的线性回归分析表明,水体中eDNA组成与其高通量测序reads数间呈明显线性关系,即y=0.0716x+0.7043 (r²=0.9824)。综上所述,本研究为验证eDNA宏条形码技术监测水生生物资源量的可行性提供了直接证据,也为后续DNA宏条形码技术的定量研究提供了思路。 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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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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Elisabeth Lutz Philipp Emanuel Hirsch Karen Bussmann Joschka Wiegleb Hans‐Peter Jermann Roxane Muller Patricia Burkhardt‐Holm Irene Adrian‐Kalchhauser 《水产资源保护:海洋与淡水生态系统》2020,30(8):1566-1577
- Conservation of riverine fish often aims to improve access to spawning grounds and restore longitudinal connectivity by removing migration barriers, and involves substantial investments. However, these investments also enable non‐native predators to invade upstream into spawning areas and potentially adversely affect the recruitment of threatened freshwater fish through egg or fry predation.
- Detecting egg predation is often challenging. Visual inspections of fish gut contents may underestimate predation of soft materials such as eggs and fry, which limits the discovery of predators preying upon these life‐stages. DNA‐based detection assays may offer a more sensitive tool to assess predation of soft materials.
- A conservation issue was confirmed by developing and applying a species‐specific DNA‐based detection assay: invasive round goby (Neogobius melanostomus) prey on the eggs or fry of the threatened common nase (Chondrostoma nasus) in Switzerland.
- DNA‐based detection assays were also developed for five other valuable native fish species, including endangered salmonid and cyprinid river spawners. The applicability of the assays was confirmed in a series of laboratory and field feeding experiments involving eggs and fish tissue. In addition, this work provides a guiding framework for conservation managers regarding the use and applicability of different DNA‐based detection approaches for gut content analysis.
- The results of this study could inform local conservation measures – such as temporary reductions in the density of round goby at spawning sites prior to spawning – and demonstrate how targeted application of species‐specific molecular markers may advance freshwater fish management.
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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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- 1. Crucian carp Carassius carassius, which is native to south‐east England, has received little previous study in Britain but is threatened by introductions of goldfish Carassius auratus through hybridization and by frequent mis‐identification of brown goldfish as crucian carp. The present study provides the first data on back‐calculated growth, morphology and age‐at‐maturity of crucian carp in Britain.
- 2. The youngest mature crucian were female (age 2+), the smallest mature crucian were male (age 3+), with almost all fish mature at age 3+. Sex dimorphism in back‐calculated standard length at age was not observed except at age 2+ (juveniles longest). Shifts in morphological characters often associated with maturation (dorsal and ventral fin length, dorsal and anal fin depth, pre‐dorsal distance, body width) were observed between ages 4+ and 7+, which (in contrast to the relatively abrupt shift in maturity) suggests that age and size at maturation may not reflect the size and age of active (i.e. real) spawning.
- 3. Back‐calculated standard lengths at age for crucian carp were intermediate relative to other European populations, indicating that environmental conditions in England appear to be well suited to the species despite being at the westernmost extent of the species' native European range. The management of ornamental ponds specifically for crucian carp is discussed.
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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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Vanessa Modesto Ester Dias Martina Ilarri Manuel Lopes-Lima Amílcar Teixeira Simone Varandas Paulo Castro Carlos Antunes Ronaldo Sousa 《水产资源保护:海洋与淡水生态系统》2021,31(8):2058-2071
- Freshwater mussels (Order Unionida) are highly threatened. Interspecific competition for food sources with invasive alien species is considered to be one of the factors responsible for their decline because successful invaders are expected to have wider trophic niches and more flexible feeding strategies than their native counterparts.
- In this study, carbon (δ13C: 13C/12C) and nitrogen (δ15N: 15N/14N) stable isotopes were used to investigate the trophic niche overlap between the native freshwater mussel species, Anodonta anatina, Potomida littoralis, and Unio delphinus, and the invasive bivalve Corbicula fluminea living in sympatry in the Tua basin (south-west Europe).
- The species presenting the widest trophic niches were C. fluminea and A. anatina, which indicate that they have broader diets than U. delphinus and P. littoralis. Nonetheless, all the species assimilated microphytobenthos, sediment organic matter, and detritus derived from vascular plants, although with interspecific variability in the assimilated proportions of each source. The trophic niche of the invasive species overlapped with the trophic niche of all the native species, with the extent varying between sites and according to the species.
- From the three native species analysed, Potomida littoralis may be at a higher risk for competition for food with C. fluminea in the Tua basin, if food sources become limited, because this native mussel presented the narrowest trophic niche across sites and the highest probability of overlapping with the trophic niche of C. fluminea.
- Given the global widespread distribution of C. fluminea, the implementation of management measures devoted to the control or even eradication of this invasive alien species should be a conservation priority given its potential for competition with highly threatened native freshwater mussels.
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- The contribution of nearly three decades of research, much of it published in Aquatic Conservation: Marine and Freshwater Ecosystems (AQC), to the conservation of the crucian carp Carassius carassius in the East of England, including work coordinated by the Norfolk Crucian Project, is summarized.
- Although recent genetic studies indicate that this species was probably introduced to England about the same time as common carp Cyprinus carpio, the crucian carp is considered a cultural heritage species worthy of conservation in eastern England.
- This research covers the environmental biology of the species in the East of England, documentation of the species' decline in the county of Norfolk, and the pond management practices implemented in Norfolk to rehabilitate existing and fully terrestrialized pond habitat specifically for crucian carp conservation.
- The AQC papers that contributed to this line of research showed that England offers a particularly favourable environment for crucian carp growth and reproduction. These AQC articles provided the evidence base to complement crucian carp conservation initiatives in the London area (mainly the counties of Essex and Hertfordshire), as well as forming the basis for the designation of crucian carp as a Biodiversity Action Priority species in the county of Norfolk.
- The broader impact of the work in the East of England was to inspire the recently‐formed English National Crucian Conservation Project, which aims to promote the conservation of crucian carp and its habitat, and to encourage the development of well‐managed crucian fisheries.
- These evidence‐based conservation initiatives, perhaps the first throughout Europe, have witnessed a reversal of the species' fortunes in England, which is effectively an ideal geographical region in which to promote the conservation of this species within a wider, European context.
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Igor Christo Miyahira Maria Cristina Dreher Mansur Luiz Eduardo Macedo de Lacerda Isabela Cristina Brito Gonçalves Glauco Gil Sant'Anna Sonia Barbosa dos Santos 《水产资源保护:海洋与淡水生态系统》2023,33(1):102-114
- Bivalves are important components of freshwater ecosystems; however, they are also one of the most threatened animal groups, especially members of the order Unionida. The main threats to freshwater bivalves are habitat modification and invasive species. Protected areas are a common way to minimize impacts and preserve native species, but they are rarely designated with a focus on freshwater invertebrates.
- The main goal of this article was to describe the distribution of freshwater bivalves in the state of Rio de Janeiro, and the relationship between these species and bioclimatic areas, land use and protected areas.
- Five native and two invasive bivalve species have been reported in Rio de Janeiro. They occur mainly in bioclimatic areas related to the Paraíba do Sul River and Campista Lowlands. The few records of bivalves inside protected areas are in areas of sustainable use that offer a lower level of protection, and frequently in sympatry with invasive bivalves.
- Thus, the established protected areas in Rio de Janeiro are not adequately effective for freshwater bivalve conservation, and some species remain under threat even within them. Freshwater bivalves thus remain largely unprotected in the state.
- The development of new protected areas and management plans should consider other faunal groups that are usually ignored, such as freshwater bivalves, to achieve more inclusive and effective protection.