Abstract Identifying the main taxonomic, phylogenetic and trait dimensions of beta diversity, and evaluating their prospective drivers, advances our understanding of patterns and processes involved in the evolution of biological assemblages. Using comprehensive databases on the distribution, phylogeny, and morphological traits of Amazonian freshwater fishes, we analyzed turnover beta diversity patterns of these three dimensions to evaluate prospective historical and contemporary drivers using multiple regression on distance matrices.We found mean taxonomic beta diversity about two times higher than mean phylogenetic and six times higher than species traits beta diversity, and coincident spatial patterns in Taxoβsim and Phyloβsim dimensions, whereas Traitβsim seemed more diffuse and heterogeneous across space. We find prominent influence of sub-basins geographic distances, habitat harshness and water color types on the taxonomic and phylogenetic dimensions of beta diversity, together with smaller individual effects of current temperature and habitat types, historical sub-basins connections and marine incursions, and sampling effort. By contrast, Traitβsim was weakly explained only by sampling effort and current sub-basins hydro-morphological conditions.These results point to leading effects of dispersal limitation, environmental filtering and historical contingencies in explaining Amazonian fish assemblages taxonomic and phylogenetic beta diversity patterns, but not functional traits turnover.

About one hundred subterranean catfish species have been described, resulting from repeated colonization of cave environments by multiple surface lineages. Most cave-dwelling species are found in the Americas, in particular in South America, but a few species also live in Central and North America. Despite the availability of high-quality genome assemblies for two cave species, the Mexican blind catfish Prietella phreatophila and the Colombian blind catfish Trichomycterus rosablanca, genomic approaches to investigate genetic changes associated with subterranean life or to estimate cave colonization times remain largely unexplored. To fill this gap, we additionally sequenced the genomes of four blind and depigmented subterranean catfishes from Peru (three Trichomycterus and one Astroblepus), as well as the genomes of four close surface relatives. We first extracted a large set of light-related genes, such as phototransduction and crystallin genes, and found contrasting decays of these sequences in different cave species, from 1% of pseudogenes in T. rosablanca to 48% in P. phreatophila. Two independent molecular dating methods gave congruent ages, indicating that these catfishes colonized subterranean habitats at different times, ranging from Early Pliocene to Late Pleistocene, supporting the hypothesis that surface catfishes repeatedly and rapidly adapted to subterranean habitats. The oldest cave species, P. phreatophila, appears to have been thriving in the dark for over 3.5 million years. Moreover, a genome-wide analysis of protein-coding genes suggests weaker purifying selection on mildly deleterious mutations in this cavefish than in other catfish lineages, likely reflecting a long-term small effective population size.

The Amazon Basin, the largest on Earth, hosts an exceptionally rich fish fauna shaped by its ancient evolutionary history, vast environmental heterogeneity, and steep altitudinal gradient. Despite this diversity, major taxonomic gaps persist, including the Linnean shortfall—the large number of undescribed species—and the Wallacean shortfall, reflecting limited knowledge of species distributions. During the past two decades, DNA barcoding using the mitochondrial COI gene has helped uncover substantial cryptic diversity in Amazonian fishes, particularly along the Andean slope, where Siluriformes exhibit striking levels of undocumented diversity. In this study, we investigated catfish communities from the families Astroblepidae and Loricariidae in the headwaters of the Madre de Dios and Huallaga rivers in Peru, spanning elevations from 500 to 2,500 m. Using DNA barcoding and multiple species-delimitation methods, we identified 27 MOTUs, most of which could not be assigned to recognized species. Our aim was to examine diversity patterns, species co-occurrence, and phylogenetic community structure along the Andean slope. This framework allows us to evaluate how ecological processes—such as competition, niche partitioning, and ecological specialization—shape community assembly. Combined with evidence of close phylogenetic relationships among MOTUs, our results highlight the likely importance of in situ diversification in driving species turnover and structuring catfish biodiversity across Andean elevational gradients.

Unlike most rivers globally, nearly all lowland Amazonian rivers have unregulated flow, supporting seasonally flooded floodplain forests. Floodplain forests harbor a unique tree species assemblage adapted to flooding and specialized fauna, including fruit-eating fish that migrate seasonally into floodplains, favoring expansive floodplain areas. Frugivorous fish are forest-dependent fauna critical to forest regeneration via seed dispersal and support commercial and artisanal fisheries. We implemented linear mixed effects models to investigate drivers of species richness among specialized frugivorous fishes across the ~6,000,000 km 2 Amazon Basin, analyzing 29 species from 9 families (10,058 occurrences). Floodplain predictors per subbasin included floodplain forest extent, tree species richness (309,540 occurrences for 2,506 species), water biogeochemistry, flood duration, and elevation, with river order controlling for longitudinal positioning along the river network. We observed heterogeneous patterns of frugivorous fish species richness, which were positively correlated with floodplain forest extent, tree species richness, and flood duration. The natural hydrological regime facilitates fish access to flooded forests and controls fruit production. Thus, the ability of Amazonian floodplain ecosystems to support frugivorous fish assemblages hinges on extensive and diverse seasonally flooded forests. Given the low functional redundancy in fish seed dispersal networks, diverse frugivorous fish assemblages disperse and maintain diverse forests; vice versa, diverse forests maintain more fish species, underscoring the critically important taxonomic interdependencies that embody Amazonian ecosystems. Effective management strategies must acknowledge that access to diverse and hydrologically functional floodplain forests is essential to ensure the long-term survival of frugivorous fish and, in turn, the long-term sustainability of floodplain forests.

This study presents an updated checklists of the fish species recorded in the Ucayali River basin, Peru, from published and unpublished data. Ucayali River basin shows a rich and diversified ichthyofauna, with 734 species distributed in 15 orders, 49 families and 292 genera. It is composed by miniature fishes (4 %, < 2.6 cm of standard length), small fishes (39 %), medium fishes (41 %), large fishes (13 %) and giants (3 %). The dominant groups are Characiformes (312 species, 43.0 %), Siluriformes (270 species, 36.8 %), Gymnotiformes (51 species, 6.9 %) and Cichliformes (50 species, 6.8 %). Part of the ichthyofauna is shared with the adjacent basins as Maranon and Amazon, mainly in the confluence area, which contribute to the highest diversity of fishes in the Ucayali basin. High diversity of fishes with restricted distribution was observed, among them Orestias, Astroblepus, Trichomycterus, Hemibrycon genera that occur in the headwaters. Estimates of species richness considering their distribution per 100 m of altitude, show that the Ucayali basin is underestimated, expecting to find up to 1125 species. The results presented here are background information that will contribute to decision-making for conservation and sustainable development purposes in the Amazon region.

Despite decades of investigation, there are few ecological studies on the Amazonian fish fauna that have looked both at the main factors shaping the fish assemblages at a regional scale and used environmental, spatial and historical approaches simultaneously. The current study aimed to measure the relative influence of environmental aspects, spatial distance and historical processes on fish genera assemblages in the upper Amazon basin (Peru and Ecuador). Climate, slope and elevation were used as environmental variables; watercourse was used to represent the spatial distance between sites and phylogenetic relationships were used as a proxy for historical processes. A partial Redundancy Analysis (pRDA) was used to compute the influence of each group of factors (environment, space and historical processes) on the fish genera assemblage. Our analysis indicated historical processes had the greatest influence on fish genera assemblages, followed by spatial distance and environment. Such patterns are most likely due to the extinction processes caused by environmental filters generated by the Andean orogeny and possible speciation in each sub-basin. The results suggest that the use of phylogeny, in addition to environment and space, provides a useful tool with which to assess the drivers responsible for fish assemblages at a regional scale.

ABSTRACTAimCommunity phylogenetics provides important information about the evolutionary and ecological factors help structure regional species assemblages. Here, we analyze phylogenetic diversity (phylodiversity) patterns among fish species in 97 sub-drainages of the Amazon basin, to evaluate the roles of historical and contemporary processes in generating and maintaining the exceptional richness and endemism of Amazonian fish species assemblages.LocationAmazon River basinTaxonFreshwater fishesMethodsUsing a large comprehensive database of freshwater fish species distributions, and a well-sampled molecular phylogeny of ray-finned (actinopterygian) fishes, we develop of multivariate statistical model to correlate estimated historical and contemporary environmental parameters with sub-drainage phylodiversity patterns. The model employs three phylogenetic metrics: i.e.: phylogenetic diversity (PD) sensu stricto, mean pairwise phylogenetic distance (MPD) between species capturing phylodiversity variation at older evolutionary timescales), and mean nearest taxon distance (MNTD) capturing variation in phylodiversity at younger evolutionary timescales.ResultsThe model recovered significant effects of elevation gradients, contemporary climate, habitat fragmentation, water types, and past marine incursions on assemblage phylodiversity patterns. The model also found significantly negative relationships among the three phylogenetic metrics, and between these metrics and distance to mouth of the Amazon, representing a West-East longitudinal gradient.Main conclusionsOur study revealed a highly non-random spatial and environmental distribution of our three phylogenetic diversity metrics across the 97 sub-drainages of the Amazon basin. Beyond significant regional effects of several environmental and historical drivers, we also found a significant West-East gradient of increasing phylogenetic diversity and phylogenetic relatedness, both patterns suggesting deeper evolutionary divergences among taxa located to the east, and more diverse, more recent radiations in the western sub-drainages. We conclude that western Amazonia can be seen as an evolutionary “cradle” of biodiversity for freshwater fishes in the Amazon basin as a whole.Significance StatementThis manuscript reveals spatial patterns of freshwater fish phylogenetic diversity and relatedness and explains its major contemporary and historical drivers in the Amazon basin. Amazon basin contains the highest freshwater biodiversity on Earth, as so investigate phylogenetic dimension of diversity is extremally relevant from the perspective of understanding the information on the evolutionary processes that had shaped Amazonian contemporary fish assemblages.

En este trabajo se presenta una lista actualizada de los registros de especies de peces de la cuenca del río Ucayali, Perú, provenientes de datos publicados y no publicados. Los resultados muestran que la cuenca del Ucayali presenta una ictiofauna rica y diversificada con el registro de 734 especies distribuidas en 15 órdenes, 49 familias y 292 géneros. La Ictiofauna está compuesta por peces miniatura (4%), peces pequeños (39%), medianos (41%), grandes (13%) y gigantes (3%). Los grupos dominantes son los Characiformes (312 especies, 43.0 %), Siluriformes (270 especies, 36.8%), Gymnotiformes (51 especies, 6.9%), y Cichliformes (50 especies, 6.8%). Parte de la ictiofauna es compartida con cuencas adyacentes como Marañón, y Amazonas peruano, principalmente en la región de confluencia, lo que contribuye a la notable diversidad de peces en la cuenca. Se observó una alta riqueza de especies con distribución restricta de los géneros Orestias, Astroblepus, Trichomycterus, Hemibrycon, entre otras especies, que ocurren en la región de cabeceras. Estimativos de riqueza de especies considerando su distribución por cada 100 m de altitud, indican que la cuenca del Ucayali esta subestimada, esperándose encontrar hasta 1125 especies. Los resultados aquí presentados son antecedentes que coadyuvaran a la toma de decisiones con fines de conservación y desarrollo sustentable en la región amazónica.

This study presents an extensive review of published and unpublished occurrence records of fish species in the Loreto department. Located in the northeast of the country, Loreto is the most geographically extensive region in the Peruvian territory. Despite the increase in fish collections in Loreto in recent years, the ichthyofauna of this department needs to be more documented. Based on a database of scientific collections and bibliographic information, an updated checklist of the freshwater fishes from Loreto is presented. The results reveal a rich and diversified ichthyofauna, with 873 species distributed in 331 genera, 50 families and 15 orders. The main groups are Characiformes (42.6%), Siluriformes (34.8%), Gymnotiformes (8.6%) and Cichliformes (7.4%). Part of the ichthyofauna has restricted distribution for Loreto (4.7%). In addition, 9.0% of species from Loreto are used in fisheries. Meanwhile, 219 species (25%) were categorized according to the IUCN criteria where only six species (0.7%) are currently considered threatened species (CR, EN or VU). The results presented in this work indicate that this department needs more studies to know the biodiversity of fish, likewise, the information presented constitutes a contribution to the knowledge of fish diversity that would support environmental management actions and decision-making aimed at conserving one of the most diverse departments of Peru.

Meeting international commitments to protect 17% of terrestrial ecosystems worldwide will require >3 million square kilometers of new protected areas and strategies to create those areas in a way that respects local communities and land use. In 2000-2016, biological and social scientists worked to increase the protected proportion of Peru's largest department via 14 interdisciplinary inventories covering >9 million hectares of this megadiverse corner of the Amazon basin. In each landscape, the strategy was the same: convene diverse partners, identify biological and sociocultural assets, document residents' use of natural resources, and tailor the findings to the needs of decision-makers. Nine of the 14 landscapes have since been protected (5.7 million hectares of new protected areas), contributing to a quadrupling of conservation coverage in Loreto (from 6 to 23%). We outline the methods and enabling conditions most crucial for successfully applying similar campaigns elsewhere on Earth.

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.

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.

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.

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.

We described herein a new Hemigrammus from the río Madre de Dios and rio Mamoré basins in southeastern Peru and Bolivia. The new species possess a color pattern similar to those belonging to the Hemigrammus lunatus species-group, i.e., a broad longitudinal dark stripe across the eye and a conspicuous, narrow dark stripe along the anal-fin basis. It can be easily diagnosed from the species belonging to this group by presenting the combination of the following characters: an oval, horizontally elongated humeral blotch, 6-7 upper branch and 10-12 lower branch gill-rakers, up to five cusps on broader maxillary teeth, and by lacking a midlateral dark stripe. Comments on its putative relationships are provided. Additionally, we updated the geographical distribution of Hemigrammus lunatus and H. machadoi based on an exhaustive survey of material deposited in collections. [Species Zoobank registration: urn:lsid:zoobank.org:act:A2ED5D61-8434-4A0F-BC5B-B496FB3DC191].

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.

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. 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. 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. 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. 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.

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.

El libro es la continuacion de una iniciativa de hace ya unos anos (2012), donde varios paises del area de distribucion de la familia, decidieron unirse al ver como este recurso estaba disminuyendo o bien, era practicamente desconocido. Este grupo tiene un gran impacto principalmente por su importancia como recurso pesquero ornamental, aunque tambien se usa como alimento, en la pesca deportiva y tiene incidencia en la salud publica. Para poder mitigar la posible sobreexplotacion, surgio la necesidad de regular el comercio e intentar convertir la pesca ornamental de rayas en una actividad sostenible. Por ello, desde 2012 el IAvH junto a varios paises propusieron la inclusion de varias especies al Apendice III de Cites. Una de las limitantes de esta propuesta y por la cual no prospero en su inicio, fue la falta de informacion sobre las especies.