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1.
  1. Freshwater ecosystems, providing valuable goods and services to humans, have been subjected to multiple human impacts, among which climate change plays a central role in threats to species. It is expected that protected areas, the cornerstone of biodiversity conservation efforts, will assume a decisive role in protecting freshwater species from the impacts of climate change.
  2. This study assessed the effects of climate change on migratory fish of the second largest neotropical river basin, evaluating the effectiveness of protected areas in safeguarding fish species, and hence the ecological functions that they perform and the ecosystem resources that they provide. The present range of 23 migratory fish of economic interest in the Paraná–Paraguay basin was estimated and the responses to future climatic shifts projected to the middle and end of the 21st century were examined, quantifying predictive uncertainties.
  3. Changes and losses of climatically suitable areas will trigger severe contractions in range, with the greatest impact on the most valuable species in commercial fishing, where range losses are likely to surpass 65% in the future. The main channel of the Upper Paraná River and tributaries of its left margin are projected to serve as climatic refuges for many species, and such regions are not affected by high predictive uncertainty. The results revealed that protected areas do not sufficiently protect migratory fish at present, and that they will continue to offer negligible protection in the face of climate change.
  4. This study alerts decision makers to the potential damage to inland fishery resources from climate change and provides useful information to guide conservation strategies spatially. We advocate that the creation of new protected areas and the redesign of the existing network to encompass regions that maximize current and future occupancy of migratory fish are crucial to conserve the valuable ecological, societal, and economic benefits that they provide.
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2.
  1. The Amazon Basin is being degraded at unprecedented rates, yet conservation efforts have implemented protected areas to curb deforestation, leaving freshwater ecosystems vulnerable to degradation. Amazon freshwater ecosystems are largely unprotected because a terrestrial bias has limited the ability of science to affect policy.
  2. Overcoming this bias requires increasing exchange of information among stakeholders across the basin to raise awareness of threats to Amazon freshwater ecosystems and promote discussions and access to conservation solutions. To help address this need, this Special Issue collates 15 synthetic articles that advance knowledge and identify conservation solutions.
  3. Three articles highlight the importance of considering the hydrological and limnological processes that control the integrity of these freshwater ecosystems and offer new insights on how to extrapolate them across the basin.
  4. Three articles on crocodilians, aquatic mammals, and migratory fishes document threats and knowledge gaps, and identify the missing role of governments as an impediment to conservation of their populations.
  5. Three articles evaluate the multi-faceted effects of hydropower dams on fish, birds, and floodplain trees. They reinforce perceptions that dams are key environmental threats and offer guidance for improving protocols for dam site selection and impact assessment.
  6. Three articles assessing the effectiveness of protected areas to safeguard fish and aquatic invertebrates show there is an urgent need to redesign the Amazon protected area network to adequately protect freshwater biota.
  7. Three forward-looking articles show that: (i) conservation initiatives by local communities are ‘bright spots’ for freshwater conservation; (ii) microchemistry analyses of the ear bones of fishes could boost the knowledge base needed to conserve them; and (iii) strengthening the Amazon conservation framework requires a reversal of Brazil's current governmental priorities, remobilization of stakeholders, investments in capacity building, and expanding protections to terrestrial and freshwater ecosystems.
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3.
  1. Amphidromy is a form of migratory life history typified by the reproduction of fish in freshwater environments, the early downstream dispersal of post‐hatch larvae to marine environments, and the return of small‐bodied young juveniles to freshwater environments for growth to adulthood. Island freshwater fish communities are frequently dominated by fish species with amphidromous life histories.
  2. Amphidromous life cycles leave fish communities highly susceptible to habitat modification and disruptions to connectivity across marine and freshwater environments. This means that managing waterway connectivity is fundamental to their conservation; however, the unique and often geographically restricted amphidromous communities that characterize many small island nations have received little consideration in the development of strategies for the management of fish passage.
  3. The ecology and locomotory capabilities of amphidromous species are often poorly studied, partly because their small size at migratory life stages renders current state‐of‐the‐art in situ biotelemetry methods unsuitable. The small size of fish also means that seemingly small obstructions can severely impede migrations.
  4. The steps necessary to advance the management of fish passage for island fish communities are: curating and maintaining barrier inventories; evaluating barrier permeability; developing effective barrier mitigation options; and prioritizing restoration and conservation efforts.
  5. New methods for understanding the ecology and locomotory capabilities and behaviour of amphidromous fishes are required to advance the management of fish passage for island fish communities. Fish passage solutions that imitate natural streams, such as those promoted in new guidelines in New Zealand, may be the most effective way of improving waterway connectivity; however, integrated approaches to freshwater fish conservation that account for meta‐population dynamics, in combination with the management of fish passage, are necessary to optimize conservation outcomes for amphidromous species.
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4.
  1. Freshwater ecosystems represent less than 0.01% of Earth's surface water but proportionately encompass the most species-rich environment on the planet, including nearly one-third of all vertebrate species. Even though inland continental waters are widely regarded as highly endangered ecosystems, their species assemblages are mostly ignored in conservation plans, largely because spatial patterns of freshwater species remain poorly understood. This is particularly severe throughout the Neotropics, most notably in the Amazon superbasin, where the sheer biotic diversity is coupled with a severe lack of biodiversity knowledge at several levels.
  2. Spatial patterns of Neotropical freshwater fishes focusing mainly on the Amazon superbasin were investigated. First, Endemic Amazonian Fish Areas (EAFAs) representing central units for the conservation of continental fishes were delimited. Interpolated maps were then analysed using alternative methodologies to delimit spatial patterns of diversity and endemicity across the Amazon superbasin. Several biogeographical analyses used a comprehensive dataset of species and geographical coordinates of Amazonian fishes.
  3. The results reveal well-defined spatial patterns of species richness and endemicity in the Amazonian fish fauna, showing that most protected areas are concentrated in a single bioregion (Amazon lowlands). Those areas are incongruent and insufficient to protect endemic and threatened species, which are mostly distributed in upland regions.
  4. Effective conservation of the Amazonian fish fauna should include EAFAs within protected areas, especially those undergoing deforestation and hydropower development pressure and containing a high concentration of threatened species.
  5. The following EAFAs should be considered as conservation priorities: Upper Araguaia, Upper Tocantins, Lower Teles Pires/Serra do Cachimbo, Chapada dos Parecis and Upper Marañon. These regions should be urgently protected to avert the loss of important trophic relationships and unique elements of the Amazonian fish fauna.
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5.
6.
  1. The Lake Victoria basin (LVB) and its tributary rivers are a major biodiversity hot spot, containing at least 234 native fish species, 135 native aquatic plant species, and 50 native freshwater mollusc species. Lake Victoria itself is home to around 500 fish species, most of which are haplochromine cichlids.
  2. The LVB is increasingly under threat from unsustainable land conversion and the intensification of agriculture. High population growth is driving the expansion of agriculture, urbanization, and freshwater abstractions, which have a profound impact on freshwater biodiversity. In addition, increased demand for agricultural crops from domestic and international markets are likely to lead to larger agricultural operations, further threatening freshwater biodiversity.
  3. This study explores these potential future impacts on the biodiversity found in freshwater rivers in the LVB as a result of projected future changes in land use.
  4. A newly developed database of land‐use impacts on freshwater biodiversity is introduced, with a focus on ecological community composition data from freshwater habitats under human pressures. Impacts on freshwater biodiversity are then projected under four different scenarios of land‐use change.
  5. Results show that land use has a significant impact on freshwater biodiversity. Freshwater biodiversity is projected to be at most risk in sub‐basins in the Tanzanian, Rwandan, and Burundian part of the LVB, such as the Kagera and Magoga/Isonga sub‐basins. Local species richness levels are particularly affected in the Magoga/Isonga sub‐basin in Tanzania, with an average loss of 10.8% across all scenarios.
  6. Model results show the potential to identify broad spatial patterns of likely threats and pressures on freshwater ecosystems under different socio‐economic futures. The analysis of these patterns, where they are consistent and where they differ, can support the production of policy that strives to find the optimal balance between development and conservation in an uncertain future.
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7.
  1. Mediterranean climate regions are globally recognized as hotspots of endemism in fishes; however, these unique assemblages are increasingly threatened by human mediated impacts including water abstraction, damming and non‐native species introductions.
  2. The Cape Fold aquatic ecoregion (CFR) of South Africa supports an assemblage of range‐restricted endemic freshwater fishes, the majority of which are conservation priorities because they are under severe threat of extinction. Effective conservation and management are constrained by the lack of readily available information on this imperilled group of fishes because research efforts over the last century have been temporally disjointed and relatively uncoordinated.
  3. This review provides an exhaustive appraisal of published literature on the taxonomy, biogeography, life history, ecology and physiology of freshwater fishes in the CFR, and the human impacts that affect them. Its aim is to direct future research needs for effective management and conservation of this imperilled group.
  4. Only 103 peer‐reviewed articles on CFR fishes were recorded and the majority of available research is on taxonomy and biogeography (40.8%), followed by ecological investigations (22.3%), conservation (19.4%) and human impacts (17.5%).
  5. Despite a plethora of studies on taxonomy and biogeography, recent genetic evidence suggests that fish diversity in the CFR has been severely underestimated and requires urgent attention. Human impacts severely threaten the existence of many native CFR fishes and require further study. Information on the biology and ecology of CFR fishes is limited to studies on selected species; of particular note is the lack of physiological information which is particularly pertinent given projected climate change scenarios.
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8.
9.
  1. Aquatic mammals worldwide are highly threatened in freshwater ecosystems where they are affected by direct human activities (e.g. hunting) as well as indirect human alteration of freshwater ecosystems (e.g. dams, mining activity). Although aquatic mammals of the Amazon Basin are experiencing many growing threats, little is known about the escalating impacts on them, current limitations in protection mechanisms, and possible strategies to ensure their conservation. This study synthesizes the available information on Amazonian aquatic mammals, including the ecological characteristics of these species, key threats, population status and conservation prospects.
  2. Amazonian aquatic mammals comprise seven species – Inia geoffrensis, Inia boliviensis, Inia araguaiaensis, Sotalia fluviatilis, Trichechus inunguis, Pteronura brasiliensis and Lontra longicaudis – which are characterized by low reproductive rates and keystone ecosystem roles. These species are endangered mainly by biological resource use, natural ecosystem modifications, energy production and mining, and climate change. Although information is sparse, there is evidence that these threats are inducing population declines of Inia spp., and hindering the recovery of populations of P. brasiliensis.
  3. Protection mechanisms for these species mostly include national and international laws and agreements, legislation governing environmental licensing and protected areas. Each of these protection mechanisms, however, has limited capacity to protect Amazonian aquatic mammals, largely because they are poorly enforced, lack transnational coordination or require population trend data that do not exist.
  4. Reversing the current state of affairs for Amazonian aquatic mammals requires an integrated research and policy approach that, at a minimum, substantially increases the present capacity to monitor their population responses to human impacts, establishes effective enforcement of existing legislation and prevents further impacts from hydropower development. To implement such an approach, information on the ecology of these species is necessary to create public and scientific awareness.
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10.
  1. Fish species that have no commercial or recreational value are often overlooked in conservation management, despite serious threats to their long‐term future. This can be termed the ‘small threatened freshwater fishes’ paradigm.
  2. Population viability analysis (PVA) is a useful technique to assess threatened species and conservation management options. While the development and use of population models and population viability analysis is common in conservation, and often used for larger fishes, this has not been so for small threatened freshwater species.
  3. This study uses the PVA process to develop a stochastic population model for Nannoperca australis (southern pygmy perch) in temperate south‐eastern Australia.
  4. The model was most sensitive to early life‐history survival rates, for which there were no estimates from field data, compared with other model uncertainty. This study also found that the oldest age class had the highest reproductive value, providing unique support to the value of big, old, fat and fecund fish (BOFFFs) in sustaining natural populations.
  5. Modelling indicated that a population in stable habitat supporting about 2000 female adults would likely to be viable, able to withstand some disturbance and possibly be used as a source population for reintroductions. In reality, however, there are few populations in the wild of sufficient size to withstand such take for translocations and hence the production of fish through hatchery means may be required.
  6. This type of approach should prove useful for the conservation management of many similar species globally.
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11.
  1. Assessing the effectiveness of protected areas for sustaining species and identifying priority sites for their conservation is vital for decision making, particularly for freshwater fishes in South America, the global centre of freshwater fish diversity. Several conservation planning studies have used threatened freshwater fishes or species that are vulnerable to climate change as conservation targets, but none has included both in priority‐setting analysis.
  2. The objectives of this study were to identify gaps in the coverage of the existing protected areas in representing the endemic freshwater fishes of the Tropical Andes region, and to identify conservation priority areas that adequately cover threatened species and species vulnerable to climate change.
  3. Data on 648 freshwater fishes from the Tropical Andes were used to identify gaps in the protected area coverage, and to identify conservation priority sites under three scenarios: (i) prioritize threatened species; (ii) prioritize species that are vulnerable to climate change; and (iii) prioritize both threatened species and species vulnerable to climate change.
  4. A total of 571 species (88% of all species) were not covered by any protected areas; most of them are restricted to ≤10 catchments. To represent both threatened species and species vulnerable to climate change in the third scenario, 635 catchments were identified as priority areas, representing 26.5% of the study area. The number of irreplaceable catchments for this scenario is 475, corresponding to 22.5% of the total area.
  5. The results of this study could be crucial for designing strategies for the effective protection of native fish populations in the Tropical Andes, and for planning proactive climate adaptation. It is hoped that the identification of priority areas, particularly irreplaceable catchments, will help to guide conservation and management decisions in the Andean region.
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12.
  1. Tetraodontiformes fishes play a critical role in benthic and demersal communities and are facing threats due to anthropogenic impacts and climate change. However, they are poorly studied worldwide. To improve knowledge on the socio‐ecological significance and conservation of Tetraodontiformes a review of literature addressing the diversity, ecology, use and trade, conservation, and main threats of Tetraodontiformes combined with a comprehensive in situ dataset from two broad‐range multidisciplinary oceanographic surveys performed along the Tropical Brazilian Continental Shelf was undertaken.
  2. Twenty‐nine species were identified, being primarily found on coral reefs and algal ecosystems. At these habitats, tetraodontids present highly diversified trophic categories and might play an important role by balancing the marine food web
  3. Coral reef ecosystems, especially those near to the shelf break, seem to be the most important areas of Tetraodontiformes fishes, concentrating the highest values of species richness, relative abundance and the uncommon and Near Threatened species.
  4. Ninety per cent of species are commonly caught as bycatch, being also used in the ornamental trade (69%) and as food (52%), serving as an important source of income for artisanal local fisheries.
  5. Tetraodontiformes are threatened by unregulated fisheries, overexploitation, bycatch, and habitat loss due to coral reef degradation and the potential effects of climate change. These factors are more broadly impacting global biodiversity, food security, and other related ecosystem functions upon which humans and many other organisms rely.
  6. We recommend the following steps that could improve the conservation of Tetraodontiformes along the tropical Brazilian Continental shelf and elsewhere: (i) data collection of the commercial, incidental, ornamental and recreational catches; (ii) improvement of the current legislation directed at the marine ornamental harvesting; (iii) increase efforts focused on the education and conservation awareness in coastal tourism and communities; and, most important, (iv) creation of marine reserves networks in priority areas of conservation, protecting either the species and key habitats for its survival.
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13.
  1. The five global Mediterranean-climate regions are experiencing alarming rates of freshwater biodiversity loss. Although freshwater mussels are recognized as important functional components in aquatic ecosystems, and are among the most threatened faunal groups globally, there has been no synthesis of the plight of this group within these regions.
  2. Data from the International Union for Conservation of Nature (IUCN) Red List were reviewed to compare the conservation status, threats, and conservation actions needed for freshwater mussel species occurring in Mediterranean-climate regions (med-mussels) with those of other freshwater mussel species globally. The first comprehensive catalogue of med-mussel species was compiled using existing taxonomic literature.
  3. There are 41 med-mussel species, 30 of which occur in the Mediterranean basin. Many regions have just a single species, and regions where multiple species occur generally only have between one and four species per river basin. Med-mussel species are almost twice as likely to be ‘Imperilled’, are affected by 2.4 times more threats, and require 3.5 times more conservation actions than non-med mussels. In many cases, the exact threats have not been identified.
  4. In combination with low species richness, this level of imperilment means that Mediterranean-climate regions are at risk of losing the benefits that mussels provide to broader ecosystem functioning. The conservation of med-mussels can be improved by increasing our knowledge of species distributions, including the identification of cryptic species and significant management units, through population genetic work. In addition, recognizing the potential of ‘novel’ habitats and refuge areas could augment the management of this important functional group.
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14.
  1. Freshwater environments host roughly half of the world’s fish diversity, much of which is concentrated in large, tropical river systems such as the Amazon. Fishes are critical to ecosystem functioning in the Amazon River basin but face increasing human threats. The basic biology of these species, and particularly migratory behaviour, remains poorly studied, in part owing to the difficulty associated with conducting tagging studies in remote tropical regions.
  2. Otolith microchemistry can circumvent logistical issues and is an increasingly important tool for studying fish life histories. However, this approach is still new in the Amazon, and its potential and limitations to inform fish conservation strategies remain unclear.
  3. Here, otolith microchemistry studies in the Amazon are reviewed, highlighting current possibilities, and several key factors that limit its use as a conservation tool in the Amazon are discussed. These include the dearth of spatiotemporal elemental data, poor understanding of environment–fish–otolith pathways, and insufficient funding, facilities, and equipment.
  4. A research initiative is proposed to harness the potential of this technique to support conservation in the Amazon. Key aspects of the proposal include recommendations for internal and external funding, which are critical to acquiring and maintaining technical staff, cutting-edge equipment, and facilities, as well as fostering regular scientific meetings and working groups. Meetings can facilitate a systematic approach to investigating environment–otolith pathways, broadening the chemical baseline for most Amazonian tributaries, and exploring potential valuable elements.
  5. These outcomes are urgently needed to conserve biodiversity and ecosystem functioning in the Amazon, especially given threats such as widespread hydroelectric damming. The initiative proposed here could make otolith microchemistry an important, cost-effective tool to inform and foster conservation in the Amazon, and act as a template for other imperilled tropical river basins, such as the Mekong and the Congo.
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15.
  1. Over the last two decades, systematic conservation planning has been increasingly applied in terrestrial and marine systems. The approach has traditionally been lagging in freshwater environments, partly because considering unique ecological processes, such as connectivity and propagation of threats along river networks, is a key factor for conservation success in freshwater landscapes. This review highlights advances in freshwater planning in the last decade, but also discusses areas in need of increased efforts.
  2. Including riverine connectivity and disturbances are largely resolved topics. Both processes have been included in major conservation planning software packages and applied globally. Theoretical advances to connectivity in wetlands and groundwater systems have started to appear, but no encompassing framework has emerged. Spatial solutions to conservation planning in lakes do not yet exist.
  3. Some headway has been made when dealing with functional connectivity and genetic processes. For the latter, approaches have been developed to deal with cryptic biodiversity and to investigate the adequacy of conservation plans to include genetic diversity. Functional connectivity has been included in conservation plans in ephemeral waterscapes, and initial steps have been made to include migratory species in conservation prioritizations.
  4. Conservation planning in socio‐ecological landscapes is catching up with biophysical prioritizations. Multiple protection tiers have been realized in river conservation planning frameworks, and freshwater scientists are leading the charge in both multi‐objective planning and in including direct functional responses. We conclude that tight integration between ecological sciences and optimization approaches is needed to further process‐based conservation planning.
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16.
17.
  1. The ecosystem services provided by freshwater biodiversity are threatened by development and environmental and climate change in the Anthropocene.
  2. Here, case studies are described to show that a focus on the shared dependence on freshwater ecosystem functioning can mutually benefit fisheries and conservation agendas in the Anthropocene.
  3. Meeting the threat to fish biodiversity and fisher livelihood is pertinent in developing regions where there is often a convergence between high biodiversity, high dependency on aquatic biota and rapid economic development (see Kafue River, Logone floodplain, Tonle Sap, and Rio Negro case studies).
  4. These case studies serve as evidence that biodiversity conservation goals can be achieved by emphasizing a sustainable fisheries agenda with partnerships, shared knowledge and innovation in fisheries management (see Kafue River and Kenai River case studies).
  5. In all case studies, aquatic biodiversity conservation and fisheries agendas are better served if efforts focused on creating synergies between fishing activities with ecosystem functioning yield long‐term livelihood and food security narratives.
  6. A unified voice from conservation and fisheries communities has more socio‐economic and political capital to advocate for biodiversity and social interests in freshwater governance decisions.
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18.
  1. Mahseer (Tor) fish species are critical components of locally adapted freshwater food webs across the Indian Himalayan biodiversity hotspot; however, multiple human stressors compounded by climate change have significantly depleted their populations over recent decades.
  2. Mahseer species are now considered locally vulnerable or endangered in many regions. Hydropower projects in particular have fragmented populations, impairing genetic exchange, obstructing migratory paths, and changing the structure and functioning of riverine habitats, especially of formerly fast‐flowing rivers.
  3. Worryingly, a literature survey and group discussions reveal that the increasing spread of non‐native fish species further compounds threats to mahseer and overall freshwater ecology. A better understanding of the current distribution, habitat requirement, and dispersal of non‐native fish is therefore essential to manage the growing threats to mahseer in the Indian Himalayan region.
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19.
  1. The Amazon basin has been subjected to extreme climatic events and according to climate change projections this hydrosystem could face changes in the natural dynamic of flood cycles that support the feeding and reproduction of many fish species, threatening aquatic biodiversity.
  2. Protected areas (PAs) are the main tools used to safeguard the biodiversity in the long term; however, they are fixed areas that could be subject to climate change, questioning their future efficiency in protecting biodiversity.
  3. The Amazon basin currently benefits from a relatively high level of protection as 52% of its catchment area is under the form of true PAs or indigenous lands. However, the capacity of these PAs to protect freshwater biodiversity remains unclear as they have generally been assessed with little regard to freshwater ecosystems and their hydrological connectivity. Here, the aim was to evaluate the effectiveness of PAs in representing the Amazon fish fauna under current and future climatic conditions.
  4. A macroecological approach was used to estimate the minimum size of the geographical range needed by each species to achieve long-term persistence, by a combined function of range size and body size, two ecological traits known to influence species extinction risk.
  5. In future the Amazon basin could risk losing 2% of its freshwater fish fauna owing to unsuitable climatic conditions, with a further 34% adversely affected. The present Amazon network of PAs will cover the minimum required range for species persistence for more than 60% of the freshwater fish species analysed under the future climate scenario. However, more than 25% of the future susceptible species are currently concentrated in large tributaries and in the central-lower Amazon floodplain where few PAs occur, highlighting the lack of appropriate conservation actions for these specific water bodies.
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20.
  1. Freshwater fishes have the distinction of being both a highly imperilled taxonomic group as well as one that has produced many invasive species with widespread ecological impacts. Faced with the difficult task of identifying those species with the greatest need for management action, ecologists have turned to using predictive suites of ecological and life‐history traits to provide reasonable estimates of fish invasion and extinction risk. Whether traits associated with invasiveness are the inverse of those associated with imperillment, known as the ‘two‐sides‐of‐the‐same‐coin’ hypothesis, remains unclear.
  2. A global trait analysis (including maximum total body size, longevity, size at maturation, age at maturation, fecundity and egg size) for 6293 freshwater fishes was conducted to examine the trait correlates of species proneness to invasion or extinction. A meta‐analytical procedure was deployed using univariate and multivariate trait analyses that accounted for the effects of shared phylogeny.
  3. Mean trait differences (measured as Hedges' d effect size) were found between invasive and threatened species when compared with native species, thus supporting the two‐sides‐of‐the‐same‐coin hypothesis for freshwater fish. Invasive species were characterized by larger body size, greater longevity, delayed maturation and higher fecundity than threatened species. Furthermore, invasive species were found to display greater trait variability compared with threatened species, suggesting that different traits may be selected at different stages of the invasion process (from pathway entrainment to establishment) whereas more specific trait combinations may predispose species to higher extinction risk.
  4. The present study demonstrated a strong trait basis to global‐scale invasion risk and extinction vulnerability for freshwater fishes. Given that both time and resources are too limited for detailed species‐by‐species assessments, the results suggest that trait correlates provide a reasonable estimate of invasion and extinction risk that can inform more targeted and proactive conservation strategies.
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