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Carrion ecology, i.e. the decomposition and recycling of dead animals, has traditionally been neglected as a key process in ecosystem functioning. Similarly, despite the large threats that inland aquatic ecosystems (hereafter, aquatic ecosystems) face, the scientific literature is still largely biased towards terrestrial ecosystems. However, there has been an increasing number of studies on carrion ecology in aquatic ecosystems in the last two decades, highlighting their key role in nutrient recirculation and disease control. Thus, a global assessment of the ecological role of scavengers and carrion in aquatic ecosystems is timely. Here, we systematically reviewed scientific articles on carrion ecology in aquatic ecosystems to describe current knowledge, identify research gaps, and promote future studies that will deepen our understanding in this field. We found 206 relevant studies, which were highly biased towards North America, especially in lotic ecosystems, covering short time periods, and overlooking seasonality, a crucial factor in scavenging dynamics. Despite the low number of studies on scavenger assemblages, we recorded 55 orders of invertebrates from 179 families, with Diptera and Coleoptera being the most frequent orders. For vertebrates, we recorded 114 species from 40 families, with birds and mammals being the most common. Our results emphasise the significance of scavengers in stabilising food webs and facilitating nutrient cycling within aquatic ecosystems. Studies were strongly biased towards the assessment of the ecosystem effects of carrion, particularly of salmon carcasses in North America. The second most common research topic was the foraging ecology of vertebrates, which was mostly evaluated through sporadic observations of carrion in the diet. Articles assessing scavenger assemblages were scarce, and only a limited number of these studies evaluated carrion consumption patterns, which serve as a proxy for the role of scavengers in the ecosystem. The ecological functions performed by carrion and scavengers in aquatic ecosystems were diverse. The main ecological functions were carrion as food source and the role of scavengers in nutrient cycling, which appeared in 52.4% (N = 108) and 46.1% (N = 95) of publications, respectively. Ecosystem threats associated with carrion ecology were also identified, the most common being water eutrophication and carrion as source of pathogens (2.4%; N = 5 each). Regarding the effects of carrion on ecosystems, we found studies spanning all ecosystem components (N = 85), from soil or the water column to terrestrial vertebrates, with a particular focus on aquatic invertebrates and fish. Most of these articles found positive effects of carrion on ecosystems (e.g. higher species richness, abundance or fitness; 84.7%; N = 72), while a minority found negative effects, changes in community composition, or even no effects. Enhancing our understanding of scavengers and carrion in aquatic ecosystems is crucial to assessing their current and future roles amidst global change, mainly for water-land nutrient transport, due to changes in the amount and speed of nutrient movement, and for disease control and impact mitigation, due to the predicted increase in occurrence and magnitude of mortality events in aquatic ecosystems., (© 2024 The Authors. Biological Reviews published by John Wiley & Sons Ltd on behalf of Cambridge Philosophical Society.)

Expanding and managing current habitat and species protection measures is at the heart of the European biodiversity strategy. A structured approach is needed to gain insights into such issues is systematic conservation planning, which uses techniques from decision theory to identify places and actions that contribute most effectively to policy objectives given a set of constraints. Yet culturally and historically determined European landscapes make the implementation of any conservation plans challenging, requiring an analysis of synergies and trade-offs before implementation. In this work, we review the scientific literature for evidence of previous conservation planning approaches, highlighting recent advances and success stories. We find that the conceptual characteristics of European conservation planning studies likely reduced their potential in contributing to better-informed decisions. We outline pathways towards improving the uptake of decision theory and multi-criteria conservation planning at various scales, particularly highlighting the need for (a) open data and intuitive tools, (b) the integration of biodiversity-focused conservation planning with multiple objectives, (c) accounting of dynamic ecological processes and functions, and (d) better facilitation of entry-points and co-design practices of conservation planning scenarios with stakeholders. By adopting and improving these practices, European conservation planning might become more actionable and adaptable towards implementable policy outcomes. This article is part of the theme issue 'Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere'.

The latest report on the state of nature in Europe (2013-2018) shows that biodiversity is declining at an alarming rate, with most protected species and habitats in poor condition. Despite an increasing volume of collected biodiversity information, urgent action is needed to integrate biodiversity data and knowledge to improve conservation efforts. We conducted a study in Catalonia (NE Spain), where we collected management measures implemented between 2013 and 2018, including allocation, budget, pressures aimed, and habitats/species potentially benefiting. We integrated information on pressures and habitats/species with the measures to identify non-spatial management gaps. Then, we integrated the spatially explicit information to determine the spatial management gap, identifying geographical areas where species/habitats are under pressure without registered measures. We demonstrated the importance of integrating existing information. Our findings revealed that resources were often not distributed adequately across species/habitats, with biases towards certain taxa being a common issue. The non-spatial management gap analysis identified taxonomic groups, especially plants and mollusks with the wider management gaps. We also identified threatened areas, especially in the northeast of the region with the larger spatial management gaps. These results could guide priority objectives to optimize conservation efforts. Integrating different information sources provided a broader view of the challenges that conservation science is facing nowadays. Our study offers a path toward bending the curve of biodiversity loss by providing an integrative framework that could optimize the use of the available information and help narrow the knowing-doing gap. In the context of the EU, this example demonstrates how information can be used to promote some environmental policy instruments, such as the Prioritized Action Frameworks (PAFs). Additionally, our findings highlight the importance of supporting decision-making with systematic assessments to identify deficiencies in the conservation process, reduce the loss of critical ecosystems and species, and avoid biases among taxa., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Marine fungi are widely distributed in the ocean, playing an important role in the ecosystems, but only little information is available about their occurrence and activity. Seagrass bleaching is also a neglected phenomenon that seems to be linked to warm environments, even though the causes are still to be defined. In this study, the cultivable mycoflora associated to the leaf conditions (bleached, necrotic and live) and section (from the base to the tip) in the seagrass Posidonia oceanica was investigated in a Mediterranean warm-edge location (Cyprus). A total of 17 Ascomycota species/taxon were identified and results highlighted that mycoflora composition changed significantly in relation to both the leaf condition and section. A few known pathogens of terrestrial plants were detected only on bleached leaves, but it remains unknown whether they have any direct connections with P. oceanica bleaching phenomenon., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Authors. Published by Elsevier Ltd.. All rights reserved.)

The lack of high-resolution distribution maps for freshwater species across large extents fundamentally challenges biodiversity conservation worldwide. We devised a simple framework to delineate the distributions of freshwater fishes in a high-resolution drainage map based on stacked species distribution models and expert information. We applied this framework to the entire Chinese freshwater fish fauna (>1600 species) to examine high-resolution biodiversity patterns and reveal potential conflicts between freshwater biodiversity and anthropogenic disturbances. The correlations between spatial patterns of biodiversity facets (species richness, endemicity, and phylogenetic diversity) were all significant (r = 0.43-0.98, p < 0.001). Areas with high values of different biodiversity facets overlapped with anthropogenic disturbances. Existing protected areas (PAs), covering 22% of China's territory, protected 25-29% of fish habitats, 16-23% of species, and 30-31% of priority conservation areas. Moreover, 6-21% of the species were completely unprotected. These results suggest the need for extending the network of PAs to ensure the conservation of China's freshwater fishes and the goods and services they provide. Specifically, middle to low reaches of large rivers and their associated lakes from northeast to southwest China hosted the most diverse species assemblages and thus should be the target of future expansions of the network of PAs. More generally, our framework, which can be used to draw high-resolution freshwater biodiversity maps combining species occurrence data and expert knowledge on species distribution, provides an efficient way to design PAs regardless of the ecosystem, taxonomic group, or region considered., (© 2022 Society for Conservation Biology.)

As the number of introduced species keeps increasing unabatedly, identifying and prioritising current and potential Invasive Alien Species (IAS) has become essential to manage them. Horizon Scanning (HS), defined as an exploration of potential threats, is considered a fundamental component of IAS management. By combining scientific knowledge on taxa with expert opinion, we identified the most relevant aquatic IAS in the Iberian Peninsula, i.e., those with the greatest geographic extent (or probability of introduction), severe ecological, economic and human health impacts, greatest difficulty and acceptability of management. We highlighted the 126 most relevant IAS already present in Iberian inland waters (i.e., Concern list) and 89 with a high probability of being introduced in the near future (i.e., Alert list), of which 24 and 10 IAS, respectively, were considered as a management priority after receiving the highest scores in the expert assessment (i.e., top-ranked IAS). In both lists, aquatic IAS belonging to the four thematic groups (plants, freshwater invertebrates, estuarine invertebrates, and vertebrates) were identified as having been introduced through various pathways from different regions of the world and classified according to their main functional feeding groups. Also, the latest update of the list of IAS of Union concern pursuant to Regulation (EU) No 1143/2014 includes only 12 top-ranked IAS identified for the Iberian Peninsula, while the national lists incorporate the vast majority of them. This fact underlines the great importance of taxa prioritisation exercises at biogeographical scales as a step prior to risk analyses and their inclusion in national lists. This HS provides a robust assessment and a cost-effective strategy for decision-makers and stakeholders to prioritise the use of limited resources for IAS prevention and management. Although applied at a transnational level in a European biodiversity hotspot, this approach is designed for potential application at any geographical or administrative scale, including the continental one., Competing Interests: Declaration of competing interest Authors declare no conflict of interest., (Copyright © 2023 The Authors. Published by Elsevier B.V. All rights reserved.)

Information about biotic interactions (e.g. competition, predation, parasitism, diseases, mutualism, allelopathy) is fundamental to better understand species distribution and abundance, ecosystem functioning, and ultimately guide conservation efforts. However, conservation planning often overlooks these important interactions. Here, we aim to demonstrate a new framework to include biotic interactions into Marxan. For that, we use freshwater mussels and fish interaction (as mussels rely on fishes to complete their life cycle) in the Douro River basin (Iberian Peninsula) as a case study. While doing that, we also test the importance of including biotic interactions into conservation planning exercises, by running spatial prioritisation analysis considering either: 1) only the target species (freshwater mussels); 2) freshwater mussels and their obligatory hosts (freshwater fishes); 3) freshwater mussels, fishes and their interactions. With this framework we found that biotic interactions tend to be underrepresented when the data on both freshwater mussels and fishes is not simultaneously included in the spatial prioritisation. Overall, the priority areas selected across all scenarios are mostly located in the western part of the Douro River basin, where most freshwater mussels and fishes still occur. Given the low overlap of priority areas identified here and the current Natura 2000 network, our approach may be useful for establishing (or enlarging) protected areas, especially in light of the EU Biodiversity Strategy for 2030. Also, this work may provide guidance for future habitat restoration and management of main threats to freshwater biodiversity., Competing Interests: Declaration of competing interest The authors declare that they have no conflict of interest., (Copyright © 2022 Elsevier B.V. All rights reserved.)

River conservation efforts traditionally focus on perennial watercourses (i.e., those that do not dry) and their associated aquatic biodiversity. However, most of the global river network is not perennial and thus supports both aquatic and terrestrial biodiversity. We assessed the conservation value of nonperennial rivers and streams (NPRS) in one of Europe's driest regions based on aquatic (macroinvertebrates, diatoms) and terrestrial (riparian plants, birds, and carabid beetles) community data. We mapped the distribution of taxa at 90 locations and across wide environmental gradients. Using the systematic planning tool Marxan, we identified priority conservation sites under 2 scenarios: aquatic taxa alone or aquatic and terrestrial taxa together. We explored how environmental factors (runoff, flow intermittence, elevation, salinity, anthropogenic impact) influenced Marxan's site selection frequency. The NPRS were selected more frequently (over 13% on average) than perennial rivers when both aquatic and terrestrial taxa were considered, suggesting that NPRS have a high conservation value at the catchment scale. We detected an underrepresentation of terrestrial taxa (8.4-10.6% terrestrial vs. 0.5-1.1% aquatic taxa were unrepresented in most Marxan solutions) when priority sites were identified based exclusively on aquatic biodiversity, which points to a low surrogacy value of aquatic taxa for terrestrial taxa. Runoff explained site selection when focusing on aquatic taxa (all best-fitting models included runoff, r 2  = 0.26-0.27), whereas elevation, salinity, and flow intermittence were more important when considering both groups. In both cases, site selection frequency declined as anthropogenic impact increased. Our results highlight the need to integrate terrestrial and aquatic communities when identifying priority areas for conservation in catchments with NPRS. This is key to overcoming drawbacks of traditional assessments based only on aquatic taxa and to ensure the conservation of NPRS, especially as NPRS become more prevalent worldwide due to climate change and increasing water demands., (© 2022 The Authors. Conservation Biology published by Wiley Periodicals LLC on behalf of Society for Conservation Biology.)

Integrated management of biodiversity and ecosystem services (ES) in heterogeneous landscapes requires considering the potential trade-offs between conflicting objectives. The UNESCO's Biosphere Reserve zoning scheme is a suitable context to address these trade-offs by considering multiple management zones that aim to minimise conflicts between management objectives. Moreover, in Mediterranean ecosystems, management and planning also needs to consider drivers of landscape dynamics such as wildfires and traditional farming and forestry practices that have historically shaped landscapes and the biodiversity they host. In this study, we applied a conservation planning approach to prioritise the allocation of management zones under future landscape and climate scenarios. We tested different landscape management scenarios reflecting the outcomes of climate-smart and fire-smart policies. We projected the expected landscape dynamics and associated changes on the distribution of 207 vertebrate species, 4 ES and fire hazard under each scenario. We used Marxan with Zones to allocate three management zones, replicating the Biosphere Reserves zoning scheme ("Core area", "Buffer zone" and "Transition area") to address the various management objectives within the Biosphere Reserve. Our results show that to promote ES supply and biodiversity conservation, while also minimising fire hazard, the reserve will need to: i) Redefine its zoning, especially regarding Core Areas, which need a considerable expansion to help mitigate changes in biodiversity and accommodate ES supply under expected changes in climate and species distribution. ii) Revisit current management policies that will result in encroached landscapes prone to high intensity, uncontrollable wildfires with the potential to heavily damage ecosystems and compromise the supply of ES. Our results support that both climate- and fire-smart policies in the Meseta Ibérica can help develop multifunctional landscapes that help mitigate and adapt to climate change and ensure the best possible maintenance of biodiversity and ES supply under uncertain future climate conditions., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Degradation, fragmentation, and loss of tropical forests has exponentially increased in the last decades leading to unprecedented rates of species extinctions and loss of ecosystems functions and services. Forest restoration is key to recover ecosystems health and achieve the UN Sustainable Development Goals. However, restoring forests at the landscape scale presents many challenges, since it requires balancing conservation goals and economic development. In this study, we used a spatial planning tool (Marxan) to identify priority areas for restoration satisfying multiple objectives across a biological corridor in Costa Rica. Biological corridors are critical conservation instruments promoting forest connectivity while acknowledging human presence. Increasing forest connectivity requires restoration initiatives that will likely conflict with other land uses, some of them of high national economic importance. Our restoration plan sought to maximize the provision of forest-related services (i.e., seed dispersal, tourism and carbon storage) while minimizing the impact on current land uses and thus avoiding potential conflicts. We quantified seed dispersal and tourism services (birdwatching potential) using species distribution models. We used the carbon sequestration model of InVEST to quantify carbon storage potential. We tested different restoration scenarios that differed in whether land opportunity costs of current uses were considered or not when identifying potential restoration areas, or how these costs were estimated. We showed how a landscape-scale forest restoration plan accounting for only forest connectivity and ecosystem service provision capacity can greatly differ from a plan that considers the potential impacts on local livelihoods. Spatial planning tools can assist at designing cost-effective landscape-scale forest restoration plans, identifying priority areas where forest restoration can maximize ecosystem provision and increase forest connectivity. Special care must be paid to the use of adequate estimates of opportunity cost, to avoid potential conflicts between restoration goals and other legitimate land uses., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

Global freshwater biodiversity is declining dramatically, and meeting the challenges of this crisis requires bold goals and the mobilisation of substantial resources. While the reasons are varied, investments in both research and conservation of freshwater biodiversity lag far behind those in the terrestrial and marine realms. Inspired by a global consultation, we identify 15 pressing priority needs, grouped into five research areas, in an effort to support informed stewardship of freshwater biodiversity. The proposed agenda aims to advance freshwater biodiversity research globally as a critical step in improving coordinated actions towards its sustainable management and conservation., (© 2021 The Authors. Ecology Letters published by John Wiley & Sons Ltd.)

Freshwater biodiversity is declining, despite national and international efforts to manage and protect freshwater ecosystems. Ecosystem-based management (EBM) has been proposed as an approach that could more efficiently and adaptively balance ecological and societal needs. However, this raises the question of how social and ecological objectives can be included in an integrated management plan. Here, we present a generic model-coupling framework tailored to address this question for freshwater ecosystems, using three components: biodiversity, ecosystem services (ESS), and a spatial prioritisation that aims to balance the spatial representation of biodiversity and ESS supply and demand. We illustrate this model-coupling approach within the Danube River Basin using the spatially explicit, potential distribution of (i) 85 fish species as a surrogate for biodiversity as modelled using hierarchical Bayesian models, and (ii) four estimated ESS layers produced by the Artificial Intelligence for Ecosystem Services (ARIES) platform (with ESS supply defined as carbon storage and flood regulation, and demand specified as recreation and water use). These are then used for (iii) a joint spatial prioritisation of biodiversity and ESS employing Marxan with Zones, laying out the spatial representation of multiple management zones. Given the transboundary setting of the Danube River Basin, we also run comparative analyses including the country-level purchasing power parity (PPP)-adjusted gross domestic product (GDP) and each country's percent cover of the total basin area as potential cost factors, illustrating a scheme for balancing the share of establishing specific zones among countries. We demonstrate how emphasizing various biodiversity or ESS targets in an EBM model-coupling framework can be used to cost-effectively test various spatially explicit management options across a multi-national case study. We further discuss possible limitations, future developments, and requirements for effectively managing a balance between biodiversity and ESS supply and demand in freshwater ecosystems., (Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.)

There is a growing demand for holistic landscape planning to enhance sustainable use of ecosystem services (ESS) and maintenance of the biodiversity that supports them. In this context, the EU is developing policy to regulate the maintenance of ESS and enhance connectivity among protected areas (PAs). This is known as the network of Green Infrastructure (GI). However, there is not a working framework defined to plan the spatial design of such network of GI. Here, we use the software Marxan with Zones, to prioritize the spatial distribution of different management zones that accommodate the needs of a network of GI. These zones included a conservation zone, mainly devoted to protecting biodiversity, a GI zone, that aimed at connecting PAs and maintaining regulating and cultural ESS; and a management zone devoted to exploiting provisioning ESS. We performed four planning scenarios that distribute the targets for ESS and biodiversity in different ways across management zones. We also conducted a sensitivity analysis by increasing ESS targets to explore trade-offs that may occur when managing together biodiversity and ESS. We use Catalonia (northeastern Spain) as a case study. We found that the representation of ESS could be achieved for intermediate targets in all scenarios. There was, however, a threshold on these targets over which trade-offs appeared between maintaining regulating and cultural ESS and biodiversity versus getting access to provisioning ESS. These "thresholds values" were displaced towards higher ESS targets when we moved from more strict to more flexible planning scenarios (i.e., scenarios that allowed mixing representation of objectives for biodiversity and ESS within the same zone). This methodological approach could help design a framework to integrate biodiversity and ESS management in holistic plans and decision making and, at the same time, meeting European mandates concerning the design of GI networks, or similar needs elsewhere., (Copyright © 2018 Elsevier B.V. All rights reserved.)

The world´s largest network of protected areas-Natura 2000 (N2000)-has been implemented to protect Europe´s biodiversity. N2000 is built upon two cornerstones, the Birds Directive, which lists 691 bird species (plus one additional bird genus with no further classification) and the Habitats Directive, which lists next to a variety of species, 233 habitat types to be protected. There is evidence of the positive impact of the Directives on the EU´s biodiversity, although the overall improvement reported for species in favourable condition in the last assessment was low. However, most of the assessments are species focused, while habitats have received very little attention. Here we developed a generic workflow, which we exemplified for Germany, to assess the status of habitat coverage within the N2000 network combining information from publicly available data sources. Applying the workflow allows identification of gaps in habitat protection, followed by the prioritization of potential areas of high protection value using the conservation planning software Marxan. We found that, in Germany, N2000 covers all target habitats. However, common habitats were proportionally underrepresented relative to rare ones, which contrasts with studies focussing on the representation of species. Moreover, the German case study suggests that especially highly protected areas (i.e. covered by more than 90% with N2000 sites) build an excellent basis towards a cost-effective and efficient conservation network. Our workflow provides a generic approach to deal with the common problem of missing habitat distribution data outside of N2000 sites, information which is however crucial for managers to plan conservation actions appropriately across Europe. To avoid a biased representation of habitat types within N2000, our results underpin the importance of defining qualitative and quantitative conservation targets which will allow assesment of the trajectory of habitat protection in Europe as well as adjustment of the network accordingly-a future necessity in the light of climate change., Competing Interests: The authors have declared that no competing interests exist.

Securing access to energy for a growing population under the international commitment of reduction of greenhouse emissions requires increasing the contribution of renewable sources to the global share. Hydropower energy, which accounts for >80% of green energy, is experiencing a boom fostered by international investment mainly in developing countries. This boom could be further accelerated by the recent climate agreement reached in Paris. Despite its flexibility, hydropower production entails social, economic and ecological risks that need to be carefully considered before investing in the development of potentially thousands of planned hydropower projects worldwide. This is especially relevant given the weak or nonexistent legislation that regulates hydropower project approval and construction in many countries. I highlight the need for adequate policy to provide the Paris Agreement with new financial and planning mechanisms to avoid further and irreversible damage to freshwater ecosystem services and biodiversity., (© 2017 John Wiley & Sons Ltd.)

Understanding the drivers and implications of anthropogenic disturbance of ecological connectivity is a key concern for the conservation of biodiversity and ecosystem processes. Here, we review human activities that affect the movements and dispersal of aquatic organisms, including damming of rivers, river regulation, habitat loss and alteration, human-assisted dispersal of organisms and climate change. Using a series of case studies, we show that the insight needed to understand the nature and implications of connectivity, and to underpin conservation and management, is best achieved via data synthesis from multiple analytical approaches. We identify four key knowledge requirements for progressing our understanding of the effects of anthropogenic impacts on ecological connectivity: autecology; population structure; movement characteristics; and environmental tolerance/phenotypic plasticity. Structuring empirical research around these four broad data requirements, and using this information to parameterise appropriate models and develop management approaches, will allow for mitigation of the effects of anthropogenic disturbance on ecological connectivity in aquatic ecosystems., (Copyright © 2015 Elsevier B.V. All rights reserved.)

Freshwater ecosystems and biodiversity are among the most threatened at global scale, but efforts for their conservation have been mostly peripheral to terrestrial conservation. For example, Natura 2000, the world's largest network of protected areas, fails to cover adequately the distribution of rare and endangered aquatic species, and lacks of appropriate spatial design to make conservation for freshwater biodiversity effective. Here, we develop a framework to identify a complementary set of priority areas and enhance the conservation opportunities of Natura 2000 for freshwater biodiversity, using the Iberian Peninsula as a case study. We use a systematic planning approach to identify a minimum set of additional areas that would help i) adequately represent all freshwater fish, amphibians and aquatic reptiles at three different target levels, ii) account for key ecological processes derived from riverscape connectivity, and iii) minimize the impact of threats, both within protected areas and propagated from upstream unprotected areas. Addressing all these goals would need an increase in area between 7 and 46%, depending on the conservation target used and strength of connectivity required. These new priority areas correspond to subcatchments inhabited by endangered and range restricted species, as well as additional subcatchments required to improve connectivity among existing protected areas and to increase protection against upstream threats. Our study should help guide future revisions of the design of Natura 2000, while providing a framework to address deficiencies in reserve networks for adequately protecting freshwater biodiversity elsewhere., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

Mediterranean endemic freshwater fish are among the most threatened biota in the world. Distinguishing the role of different extinction drivers and their potential interactions is crucial for achieving conservation goals. While some authors argue that invasive species are a main driver of native species declines, others see their proliferation as a co-occurring process to biodiversity loss driven by habitat degradation. It is difficult to discern between the two potential causes given that few invaded ecosystems are free from habitat degradation, and that both factors may interact in different ways. Here we analyze the relative importance of habitat degradation and invasive species in the decline of native fish assemblages in the Guadiana River basin (southwestern Iberian Peninsula) using an information theoretic approach to evaluate interaction pathways between invasive species and habitat degradation (structural equation modeling, SEM). We also tested the possible changes in the functional relationships between invasive and native species, measured as the per capita effect of invasive species, using ANCOVA. We found that the abundance of invasive species was the best single predictor of natives' decline and had the highest Akaike weight among the set of predictor variables examined. Habitat degradation neither played an active role nor influenced the per capita effect of invasive species on natives. Our analyses indicated that downstream reaches and areas close to reservoirs had the most invaded fish assemblages, independently of their habitat degradation status. The proliferation of invasive species poses a strong threat to the persistence of native assemblages in highly fluctuating environments. Therefore, conservation efforts to reduce native freshwater fish diversity loss in Mediterranean rivers should focus on mitigating the effect of invasive species and preventing future invasions.