Global freshwater fish invasion linked to the presence of closely related species.

In the Anthropocene, non-native freshwater fish introductions and translocations have occurred extensively worldwide. However, their global distribution patterns and the factors influencing their establishment remain poorly understood. We analyze a comprehensive database of 14953 freshwater fish species across 3119 river basins and identify global hotspots for exotic and translocated non-native fishes. We show that both types of non-native fishes are more likely to occur when closely related to native fishes. This finding is consistent across measures of phylogenetic relatedness, biogeographical realms, and highly invaded countries, even after accounting for the influence of native diversity. This contradicts Darwin's naturalization hypothesis, suggesting that the presence of close relatives more often signifies suitable habitats than intensified competition, predicting the establishment of non-native fish species. Our study provides a comprehensive assessment of global non-native freshwater fish patterns and their phylogenetic correlates, laying the groundwork for understanding and predicting future fish invasions in freshwater ecosystems.

Major shifts in biogeographic regions of freshwater fishes as evidence of the Anthropocene epoch.

Animals and plants worldwide are structured in global biogeographic regions, which were shaped by major geologic forces during Earth history. Recently, humans have changed the course of events by multiplying global pathways of introduction for nonindigenous species and propagating local species extirpations. Here, we report on how introductions and extirpations have changed the distributions of freshwater fishes worldwide and how it affected their natural biogeographic regions. We found major shifts in natural regions, with the emergence of an intercontinental region arising from the fusion of multiple faunas, which we named Pan-Anthropocenian Global North and East Asia (PAGNEA). The PAGNEA region is evocative of the Pangea supercontinent, as flows of introductions show that dispersal has become possible again across multiple continents, suggesting that human activities have superseded natural geological forces. Our results constitute evidence on the expected modification of biostratigraphic boundaries based on freshwater fish, which are abundant in the fossil record, thereby supporting the concept of the Anthropocene epoch.

Same process, different patterns: pervasive effect of evolutionary time on species richness in freshwater fishes.

Tropical lands harbour the highest number of species, resulting in the ubiquitous latitudinal diversity gradient (LDG). However, exceptions to this pattern have been observed in some taxa, explained by the interaction between the evolutionary histories and environmental factors that constrain species' physiological and ecological requirements. Here, we applied a deconstruction approach to map the detailed species richness patterns of Actinopterygian freshwater fishes at the class and order levels and to disentangle their drivers using geographical ranges and a phylogeny, comprising 77% (12 557) of all described species. We jointly evaluated seven evolutionary and ecological hypotheses posited to explain the LDG: diversification rate, time for speciation, species-area relationship, environmental heterogeneity, energy, temperature seasonality and past temperature stability. We found distinct diversity gradients across orders, including expected, bimodal and inverse LDGs. Despite these differences, the positive effect of evolutionary time explained patterns for all orders, where species-rich regions are inhabited by older species compared to species-poor regions. Overall, the LDG of each order has been shaped by a unique combination of factors, highlighting the importance of performing a joint evaluation of evolutionary, historical and ecological factors at different taxonomic levels to reach a comprehensive understanding on the causes driving global species richness patterns.

Scale of population synchrony confirms macroecological estimates of minimum viable range size.

Global ecosystems are facing a deepening biodiversity crisis, necessitating robust approaches to quantifying species extinction risk. The lower limit of the macroecological relationship between species range and body size has long been hypothesized as an estimate of the relationship between the minimum viable range size (MVRS) needed for species persistence and the organismal traits that affect space and resource requirements. Here, we perform the first explicit test of this assumption by confronting the MVRS predicted by the range-body size relationship with an independent estimate based on the scale of synchrony in abundance among spatially separated populations of riverine fish. We provide clear evidence of a positive relationship between the scale of synchrony and species body size, and strong support for the MVRS set by the lower limit of the range-body size macroecological relationship. This MVRS may help prioritize first evaluations for unassessed or data-deficient taxa in global conservation assessments.

Climate and land-use changes interact to drive long-term reorganization of riverine fish communities globally.

As climate change unfolds, changes in population dynamics and species distribution ranges are expected to fundamentally reshuffle communities worldwide. Yet, a comprehensive understanding of the mechanisms and extent of community reorganization remains elusive. This is particularly true in riverine systems, which are simultaneously exposed to changing temperature and streamflow, and where land-use change continues to be a major driver of biodiversity loss. Here, we use the most comprehensive compilation of fish abundance time series to date to provide a global synthesis of climate- and LU-induced effects on riverine biota with respect to changes in species thermal and streamflow affinities. We demonstrate that fish communities are increasingly dominated by thermophilic (warm-water) and limnophilic (slow-water) species. Despite being consistent with trends in water temperature and streamflow observed over recent decades, these community changes appear largely decoupled from each other and show wide spatial variation. We further reveal a synergy among climate- and land use-related drivers, such that community thermophilization is heightened in more human-modified systems. Importantly, communities in which species experience thermal and flow regimes that approach or exceed their tolerance thresholds (high community sensitivity), as well as species-poor communities (low community resilience), also display faster rates of compositional change. This research illustrates that quantifying vulnerability of riverine systems to climate change requires a broadening from a narrower thermal focus to more integrative approaches that account for the spatially varying and multifaceted sensitivity of riverine organisms to the interactive effects of water temperature, hydrology, and other anthropogenic changes.

The geography of metapopulation synchrony in dendritic river networks.

Dendritic habitats, such as river ecosystems, promote the persistence of species by favouring spatial asynchronous dynamics among branches. Yet, our understanding of how network topology influences metapopulation synchrony in these ecosystems remains limited. Here, we introduce the concept of fluvial synchrogram to formulate and test expectations regarding the geography of metapopulation synchrony across watersheds. By combining theoretical simulations and an extensive fish population time-series dataset across Europe, we provide evidence that fish metapopulations can be buffered against synchronous dynamics as a direct consequence of network connectivity and branching complexity. Synchrony was higher between populations connected by direct water flow and decayed faster with distance over the Euclidean than the watercourse dimension. Likewise, synchrony decayed faster with distance in headwater than mainstem populations of the same basin. As network topology and flow directionality generate fundamental spatial patterns of synchrony in fish metapopulations, empirical synchrograms can aid knowledge advancement and inform conservation strategies in complex habitats.

Protecting the downstream migration of salmon smolts from hydroelectric power plants with inclined racks and optimized bypass water discharge.

The sustained development of hydropower energy in the last century has caused important ecological impacts, promoting recent advances in efficient mitigation measures to be implemented in existing and future hydropower plants. Although upstream fish migration has been largely addressed with the development of fish-pass infrastructures, downstream passage solutions are often missing or inefficient, strengthening the need for their improvement and efficiency assessment. The efficiency of horizontally inclined (26°) low bar spacing racks associated to a bypass was assessed using salmon smolts radiotelemetry along three successive hydropower plants (HPP) in the Ariège River (southern France). In average, nearly 90% of the smolts were successfully protected by the racks and rapidly guided to the bypass, within few minutes in most cases. Furthermore, we detected a significant positive influence of the bypass discharge (Qbp% expressed as the proportion of concurrent HPP discharge) on the probability of successful bypass passage, reaching 85% of successful passage with a Qbp% of only 3%, and more than 92% when the Qbp% exceeded 5%. The probability of bypass passage without hesitation (e.g. passage within the first 5 min) also increased with Qbp%, and reached 90% with 5% of Qbp%. Passage without hesitation was especially detected on the site having larger bypass entrances and transversal currents, providing better guidance into the bypass. High-efficiency results of inclined racks yielded with reduced Qbp% confirmed their relevance to mitigate some of the HPP ecological impacts, re-establishing safe downstream salmon migration with lower impact on energy production than older less efficient solutions.

Quantifying the relative performance of two undetected-extinction models.

Extinctions of undiscovered species (undetected extinctions) constitute a portion of biodiversity loss that is often ignored. We compared the performance of 2 models of undetected extinctions - Tedesco and SEUX - when estimating undetected extinctions with both simulated and real-world data. We generated simulated data by considering a birth-death process in which less abundant species were more likely to go extinct. When detection rates were higher for common species, the 2 models underestimated the true number of undetected extinctions by up to 88.7%, and when detection rates were independent of abundance, the 2 models performed better; the SEUX model had an average bias of +3.1% and the Tedesco model had an average bias of -62.3%. We applied the models to 8 real-world data sets (e.g., Australian amphibians, Australian birds, North American bivalves) and found that true extinctions may be from 15% to 180% higher than observed values. For 6 of the 8 data sets, the SEUX model yielded absolute estimates that were 5.7-66.8% lower than those of the Tedesco model. We mainly attributed this difference to the SEUX model's assumption that there are no undetected extant species currently. We assessed the accuracy of the models' estimates with a logistic regression to test whether detection and extinction rates were uncorrelated across species. Rates were correlated for 3 of the 8 data sets; species discovered later had a higher probability of being extinct, suggesting that extinction numbers could be even higher for these groups. Despite caveats associated with the models, the evidence from both show biodiversity loss in these groups may be more severe than what has been documented.

Cuantificación del Desempeño Relativo de Dos Modelos de Extinción No Detectada Resumen Las extinciones no detectadas constituyen una porción de la pérdida de la biodiversidad que comúnmente pasa desapercibida. Comparamos el desempeño de dos modelos de extinciones no detectadas - Tedesco y SEUX - durante su estimación de extinciones no detectadas tanto con datos simulados como reales. Generamos datos simulados mediante la consideración de un proceso de nacimiento-muerte en el cual las especies menos abundantes tenían una mayor probabilidad de extinguirse. Cuando las tasas de detección fueron mayores para las especies comunes, los dos modelos subestimaron el número real de extinciones no detectadas hasta en un 88.7%; cuando las detecciones fueron independientes a la abundancia, ambos modelos tuvieron un mejor desempeño. El modelo SEUX tuvo un sesgo promedio de +3.1% y el modelo Tedesco uno de -62.3%. Aplicamos estos modelos en ocho conjuntos de datos reales (p. ej.: anfibios australianos, aves australianas, bivalvos norteamericanos) y descubrimos que las extinciones verdaderas podrían ser desde 15% a 180% más altas que los valores observados. Para seis de los ocho conjuntos de datos, el modelo SEUX produjo estimaciones absolutas que fueron entre 5.7% y 66.8% más bajas que las producidas por el modelo Tedesco. Esta diferencia la atribuimos principalmente a la suposición del modelo SEUX de que actualmente no existen especies no detectadas. Evaluamos la certeza de las estimaciones de cada modelo con una regresión logística para comprobar si las tasas de detección y extinción no tenían correlación en todas las especies. Las tasas tuvieron correlación en tres de los ocho conjuntos de datos; las especies descubiertas más tarde tuvieron una probabilidad más alta de estar extintas, lo que sugiere que los datos de extinción podrían ser mayores para estos grupos. A pesar de las salvedades asociadas a estos modelos, la evidencia de ambos muestra que la pérdida de biodiversidad en estos grupos podría ser más severa de lo que se ha documentado hasta ahora.

The combined effects of climate change and river fragmentation on the distribution of Andean Amazon fishes.

Upstream range shifts of freshwater fishes have been documented in recent years due to ongoing climate change. River fragmentation by dams, presenting physical barriers, can limit the climatically induced spatial redistribution of fishes. Andean freshwater ecosystems in the Neotropical region are expected to be highly affected by these future disturbances. However, proper evaluations are still missing. Combining species distribution models and functional traits of Andean Amazon fishes, coupled with dam locations and climatic projections (2070s), we (a) evaluated the potential impacts of future climate on species ranges, (b) investigated the combined impact of river fragmentation and climate change and (c) tested the relationships between these impacts and species functional traits. Results show that climate change will induce range contraction for most of the Andean Amazon fish species, particularly those inhabiting highlands. Dams are not predicted to greatly limit future range shifts for most species (i.e., the Barrier effect). However, some of these barriers should prevent upstream shifts for a considerable number of species, reducing future potential diversity in some basins. River fragmentation is predicted to act jointly with climate change in promoting a considerable decrease in the probability of species to persist in the long-term because of splitting species ranges in smaller fragments (i.e., the Isolation effect). Benthic and fast-flowing water adapted species with hydrodynamic bodies are significantly associated with severe range contractions from climate change.

A database of freshwater fish species of the Amazon Basin.

The Amazon Basin is an unquestionable biodiversity hotspot, containing the highest freshwater biodiversity on earth and facing off a recent increase in anthropogenic threats. The current knowledge on the spatial distribution of the freshwater fish species is greatly deficient in this basin, preventing a comprehensive understanding of this hyper-diverse ecosystem as a whole. Filling this gap was the priority of a transnational collaborative project, i.e. the AmazonFish project - https://www.amazon-fish.com/. Relying on the outputs of this project, we provide the most complete fish species distribution records covering the whole Amazon drainage. The database, including 2,406 validated freshwater native fish species, 232,936 georeferenced records, results from an extensive survey of species distribution including 590 different sources (e.g. published articles, grey literature, online biodiversity databases and scientific collections from museums and universities worldwide) and field expeditions conducted during the project. This database, delivered at both georeferenced localities (21,500 localities) and sub-drainages grains (144 units), represents a highly valuable source of information for further studies on freshwater fish biodiversity, biogeography and conservation.

Freshwater fish diversity hotspots for conservation priorities in the Amazon Basin.

Conserving freshwater habitats and their biodiversity in the Amazon Basin is a growing challenge in the face of rapid anthropogenic changes. We used the most comprehensive fish-occurrence database available (2355 valid species; 21,248 sampling points) and 3 ecological criteria (irreplaceability, representativeness, and vulnerability) to identify biodiversity hotspots based on 6 conservation templates (3 proactive, 1 reactive, 1 representative, and 1 balanced) to provide a set of alternative planning solutions for freshwater fish protection in the Amazon Basin. We identified empirically for each template the 17% of sub-basins that should be conserved and performed a prioritization analysis by identifying current and future (2050) threats (i.e., degree of deforestation and habitat fragmentation by dams). Two of our 3 proactive templates had around 65% of their surface covered by protected areas; high levels of irreplaceability (60% of endemics) and representativeness (71% of the Amazonian fish fauna); and low current and future vulnerability. These 2 templates, then, seemed more robust for conservation prioritization. The future of the selected sub-basins in these 2 proactive templates is not immediately threatened by human activities, and these sub-basins host the largest part of Amazonian biodiversity. They could easily be conserved if no additional threats occur between now and 2050.

Puntos Calientes de Diversidad de Peces de Agua Dulce para las Prioridades de Conservación en la Cuenca del Amazonas Resumen Cada día, la conservación de los hábitats de agua dulce y su biodiversidad en la cuenca del Amazonas es un reto creciente de cara a los rápidos cambios antropogénicos. Usamos la base de datos de presencia de peces más completa que existe (2,355 especies válidas; 21,248 puntos de muestreo) y tres criterios ecológicos (carácter irremplazable, representatividad y vulnerabilidad) para identificar los puntos calientes de biodiversidad con base en seis patrones de conservación (tres proactivos, uno reactivo, uno representativo y uno balanceado) y así proporcionar un conjunto de soluciones alternativas para la planeación de la protección de peces de agua dulce en la cuenca del Amazonas. Identificamos para cada patrón de manera empírica el 17% de las subcuencas que deberían conservarse y realizamos un análisis de priorización identificando amenazas actuales y a futuro (2050) (es decir, grado de deforestación y fragmentación del hábitat causado por presas). Dos de nuestros tres patrones proactivos tuvieron alrededor del 65% de su superficie cubierta por áreas protegidas; niveles altos de carácter irremplazable (60% de especies endémicas) y de representatividad (71% de la fauna ictiológica del Amazonas); y una vulnerabilidad baja actual y a futuro. Entonces, estos dos patrones parecen estar más completos para la priorización de la conservación. El futuro de las subcuencas en estos dos patrones proactivos no está amenazado por las actividades humanas a corto plazo. Además, estas subcuencas albergan la mayor parte de la biodiversidad amazónica. Se podrían conservar fácilmente si ninguna amenaza adicional sucede entre ahora y el 2050.

Unexpected fish diversity gradients in the Amazon basin.

Using the most comprehensive fish occurrence database, we evaluated the importance of ecological and historical drivers in diversity patterns of subdrainage basins across the Amazon system. Linear models reveal the influence of climatic conditions, habitat size and sub-basin isolation on species diversity. Unexpectedly, the species richness model also highlighted a negative upriver-downriver gradient, contrary to predictions of increasing richness at more downriver locations along fluvial gradients. This reverse gradient may be linked to the history of the Amazon drainage network, which, after isolation as western and eastern basins throughout the Miocene, only began flowing eastward 1-9 million years (Ma) ago. Our results suggest that the main center of fish diversity was located westward, with fish dispersal progressing eastward after the basins were united and the Amazon River assumed its modern course toward the Atlantic. This dispersal process seems not yet achieved, suggesting a recent formation of the current Amazon system.

Drainage network position and historical connectivity explain global patterns in freshwater fishes' range size.

Identifying the drivers and processes that determine globally the geographic range size of species is crucial to understanding the geographic distribution of biodiversity and further predicting the response of species to current global changes. However, these drivers and processes are still poorly understood, and no ecological explanation has emerged yet as preponderant in explaining the extent of species' geographical range. Here, we identify the main drivers of the geographic range size variation in freshwater fishes at global and biogeographic scales and determine how these drivers affect range size both directly and indirectly. We tested the main hypotheses already proposed to explain range size variation, using geographic ranges of 8,147 strictly freshwater fish species (i.e., 63% of all known species). We found that, contrary to terrestrial organisms, for which climate and topography seem preponderant in determining species' range size, the geographic range sizes of freshwater fishes are mostly explained by the species' position within the river network, and by the historical connection among river basins during Quaternary low-sea-level periods. Large-ranged fish species inhabit preferentially lowland areas of river basins, where hydrological connectivity is the highest, and also are found in river basins that were historically connected. The disproportionately high explanatory power of these two drivers suggests that connectivity is the key component of riverine fish geographic range sizes, independent of any other potential driver, and indicates that the accelerated rates in river fragmentation might strongly affect fish species distribution and freshwater biodiversity.

Modelling built infrastructure heights to evaluate common assumptions in aquatic conservation.

Built infrastructure, such as dams and weirs, are some of the most impactful stressors affecting aquatic ecosystems. However, data on the distribution and characteristics of small built infrastructure that often restrict fish movement, impede flows, and retain sediments and materials, remain limited. Collection of this necessary information is challenged by the large number of built infrastructure with unknown dimensions (e.g., height), which means scientists and practitioners need to make assumptions about these characteristics in research and decision-making. Evaluating these common assumptions is essential for advancing conservation that is more effective. We use a statistical modelling approach to double the number of small (≤5 m high) built infrastructure with height values in France. Using two scenarios depicting common assumptions (all infrastructure without height data are impassable, or all are passable for all species) and one based on our modelled heights, we demonstrate how assumptions can influence our understanding of river fragmentation. Assuming all built infrastructure without height data are passable results in a 5-fold reduction in estimated river fragmentation for fish species that cannot pass built infrastructure ≥1.0 m. The opposite is true for fish species that cannot pass ≥2.0 m, where assuming all built infrastructure without height data are impassable results in a 7-fold increase in fragmentation compared to the scenario with modelled heights to attribute built infrastructure passability. Our findings suggest that modelled height data leads to better understanding of river fragmentation, and that knowledge of different fish species' abilities to pass a variety of built infrastructure is essential to guide more effective management strategies. Our modelling approach, and results, are of particular relevance to regions where efforts to both remediate and remove built infrastructure is occurring, but where gaps in data on characteristics of built infrastructure remain, and limit effective decision making.

Non-native species led to marked shifts in functional diversity of the world freshwater fish faunas.

Global spread of non-native species profoundly changed the world biodiversity patterns, but how it translates into functional changes remains unanswered at the world scale. We here show that while in two centuries the number of fish species per river increased on average by 15% in 1569 basins worldwide, the diversity of their functional attributes (i.e. functional richness) increased on average by 150%. The inflation of functional richness was paired with changes in the functional structure of assemblages, with shifts of species position toward the border of the functional space of assemblages (i.e. increased functional divergence). Non-native species moreover caused shifts in functional identity toward higher body sized and less elongated species for most of assemblages throughout the world. Although varying between rivers and biogeographic realms, such changes in the different facets of functional diversity might still increase in the future through increasing species invasion and may further modify ecosystem functioning.

Fragmentation of Andes-to-Amazon connectivity by hydropower dams.

Andes-to-Amazon river connectivity controls numerous natural and human systems in the greater Amazon. However, it is being rapidly altered by a wave of new hydropower development, the impacts of which have been previously underestimated. We document 142 dams existing or under construction and 160 proposed dams for rivers draining the Andean headwaters of the Amazon. Existing dams have fragmented the tributary networks of six of eight major Andean Amazon river basins. Proposed dams could result in significant losses in river connectivity in river mainstems of five of eight major systems-the Napo, Marañón, Ucayali, Beni, and Mamoré. With a newly reported 671 freshwater fish species inhabiting the Andean headwaters of the Amazon (>500 m), dams threaten previously unrecognized biodiversity, particularly among endemic and migratory species. Because Andean rivers contribute most of the sediment in the mainstem Amazon, losses in river connectivity translate to drastic alteration of river channel and floodplain geomorphology and associated ecosystem services.

A global database on freshwater fish species occurrence in drainage basins.

A growing interest is devoted to global-scale approaches in ecology and evolution that examine patterns and determinants of species diversity and the threats resulting from global change. These analyses obviously require global datasets of species distribution. Freshwater systems house a disproportionately high fraction of the global fish diversity considering the small proportion of the earth's surface that they occupy, and are one of the most threatened habitats on Earth. Here we provide complete species lists for 3119 drainage basins covering more than 80% of the Earth surface using 14953 fish species inhabiting permanently or occasionally freshwater systems. The database results from an extensive survey of native and non-native freshwater fish species distribution based on 1436 published papers, books, grey literature and web-based sources. Alone or in combination with further datasets on species biological and ecological characteristics and their evolutionary history, this database represents a highly valuable source of information for further studies on freshwater macroecology, macroevolution, biogeography and conservation.

Bushmeat genetics: setting up a reference framework for the DNA typing of African forest bushmeat.

The bushmeat trade in tropical Africa represents illegal, unsustainable off-takes of millions of tons of wild game - mostly mammals - per year. We sequenced four mitochondrial gene fragments (cyt b, COI, 12S, 16S) in >300 bushmeat items representing nine mammalian orders and 59 morphological species from five western and central African countries (Guinea, Ghana, Nigeria, Cameroon and Equatorial Guinea). Our objectives were to assess the efficiency of cross-species PCR amplification and to evaluate the usefulness of our multilocus approach for reliable bushmeat species identification. We provide a straightforward amplification protocol using a single 'universal' primer pair per gene that generally yielded >90% PCR success rates across orders and was robust to different types of meat preprocessing and DNA extraction protocols. For taxonomic identification, we set up a decision pipeline combining similarity- and tree-based approaches with an assessment of taxonomic expertise and coverage of the GENBANK database. Our multilocus approach permitted us to: (i) adjust for existing taxonomic gaps in GENBANK databases, (ii) assign to the species level 67% of the morphological species hypotheses and (iii) successfully identify samples with uncertain taxonomic attribution (preprocessed carcasses and cryptic lineages). High levels of genetic polymorphism across genes and taxa, together with the excellent resolution observed among species-level clusters (neighbour-joining trees and Klee diagrams) advocate the usefulness of our markers for bushmeat DNA typing. We formalize our DNA typing decision pipeline through an expert-curated query database - DNA BUSHMEAT - that shall permit the automated identification of African forest bushmeat items.

Global imprint of historical connectivity on freshwater fish biodiversity.

The relative importance of contemporary and historical processes is central for understanding biodiversity patterns. While several studies show that past conditions can partly explain the current biodiversity patterns, the role of history remains elusive. We reconstructed palaeo-drainage basins under lower sea level conditions (Last Glacial Maximum) to test whether the historical connectivity between basins left an imprint on the global patterns of freshwater fish biodiversity. After controlling for contemporary and past environmental conditions, we found that palaeo-connected basins displayed greater species richness but lower levels of endemism and beta diversity than did palaeo-disconnected basins. Palaeo-connected basins exhibited shallower distance decay of compositional similarity, suggesting that palaeo-river connections favoured the exchange of fish species. Finally, we found that a longer period of palaeo-connection resulted in lower levels of beta diversity. These findings reveal the first unambiguous results of the role played by history in explaining the global contemporary patterns of biodiversity.