A database of freshwater fish species of the Amazon Basin

Fishers' ecological knowledge points to fishing-induced changes in the Peruvian Amazon

Scientists increasingly draw on fishers' ecological knowledge (FEK) to gain a better understanding of fish biology and ecology, and inform options for fisheries management. We report on a study of FEK among fishers along the Lower Ucayali River in Peru, a region of exceptional productivity and diversity, which is also a major supplier of fish to the largest city in the Peruvian Amazon. Given a lack of available scientific information on stock status, we sought to identify temporal changes in the composition and size of exploited species by interviewing fishers from 18 communities who vary in years of fishing experience since the mid-1950s. We develop four FEK-based indicators to assess changes in the fish assemblage and compare findings with landings data. We find an intensification of fishing gear deployed over time and spatiotemporal shifts in the fish assemblage and reported declines in species weight, which point to a fishing-down process with declines across multiple species. This finding is reflected in a shifting baseline among our participants, whereby younger generations of fishers have different expectations regarding the distribution and size of species. Our study points to the importance of spillover effects from the nearby Pacaya-Samira National Reserve and community initiatives to support the regional fishery. Reference to fishers' knowledge also suggests that species decline is likely underreported in aggregated landings data. Despite the dynamism and diversity of Amazonian floodplain fisheries, simple FEK-based indicators can provide useful information for understanding fishing-induced changes in the fish assemblage. Fishers hold valuable knowledge for fishery management and conservation initiatives in the region.

Fishes (Actinopterygii) of the rapids and associated environments in the lower Vaupés River Basin: an undiscovered Colombian Amazon diversity

The Vaupés River stands out as one of the few within the Amazon basin due to its numerous rapids. These riverine fast-flowing sections not only provide habitat to highly specialized fishes but also function as natural barriers hindering the movement of fish along its course. During a fish-collecting expedition in the lower Vaupés River basin in Colombia, 95 species were registered belonging to 30 families and seven orders. Despite recent inventories in the region, our comprehensive sampling efforts particularly focused on the rapids and associated rheophilic fauna, allowing us to contribute the first records of four fish species in Colombia (Mylopluslucienae Andrade, Ota, Bastos & Jégu, 2016, Tometesmakue Jégu, Santos & Jégu, 2002, also first record of the genus, Leptodoraspraelongus (Myers & Weitzman, 1956), and Eigenmanniamatintapereira Peixoto, Dutra & Wosiacki, 2015) and six presumably undescribed species (i.e., Jupiaba sp., Moenkhausia sp., Phenacogaster sp., Bunocephalus sp., Hemiancistrus sp., and Archolaemus sp.). In this study, a commented list of the ichthyofauna of these environments is presented, as well as a photographic catalog of fish species integrated into the CaVFish Project - Colombia.

Local trade, spatial occurrence and conservation of hypostomus soniae (siluriformes, loricariidae), an ornamental fish endemic to the tapajos river, Brazil

Hypostomus soniae is a small sized armored catfish endemic to the Tapajos River basin and ranked as one of the most exploited ornamental fish in the Santarem export marketplace. This study aims to evaluate distributional patterns of Hypostomus soniae and contribute to the species conservation in the face of development of the ornamental fish trade in the Amazon region. We compiled data associated with geographic coordinates in public repositories, supplemented with original field records. We compared our data to published records in the literature and museum collections to check for accuracy. To investigate the fishery and commercialization of H. soniae, we conducted interviews with ornamental fish stakeholders from the local trade. We also made direct observations in the fishing sites and export facilities in Santarem. A cluster analysis of the geolocation data was carried out to explore the spatial distribution patterns. The volume of captures and exportation of H. soniae decreased during the period 2020-2023. The occurrence of H. soniae was associated with annual rainfall ranging from 2,000 mm to 2,500 mm and concentrated in two municipalities of the State of Mato Grosso and two of the Para State. The species distribution area has been threatened, unfortunately, by fishermen who do not respect the laws that support artisanal fishing in the Amazon.

Human exposure to elements through consumption of raw and cooked fish in an urban region of the central Brazilian Amazon biome: Health risks

Fish is an important source of animal protein for local communities in the Amazon basin, whose food safety must be assured. However, certain potential toxicants elements, can bioaccumulate in fish species, which inhabit anthropogenically polluted waters, ultimately posing a risk to human health. In the present study, the concentrations of nine elements (Al, As, Cd, Cr, Cu, Hg, Ni, Pb and Zn) were determined in raw and cooked samples of eight fish species consumed in Santarém (northern Brazil, Amazon biome). The potential for non- carcinogenic human health risks linked to the consumption of cooked fish were evaluated for adults and children in two different scenarios. Four carnivores, three omnivores and one detritivore, all of them regularly marketed and consumed by the Santarém population, were the target species. The safety reference values set by national and international guidelines for humans, in both raw and cooked preparations, were used. In most cases, the cooking process showed a trend to increase elements concentrations compared to raw samples, however the differences were not significant. Moreover, the risk assessment showed danger for children in relation to Hg from the consumption of fish, in both scenarios evaluated. For adults, in one of the scenarios, there was a health risk associated to Hg as a result of carnivorous fish consumption. In a context of combined exposure to all elements, children were at risk when consuming fish, especially carnivorous and omnivorous species. For adults, the mixture of elements posed a risk to health human only for carnivorous fish consumption. The results reveal an environmental scenario of Hg contamination, which requires monitoring actions to preserve the aquatic biodiversity and human health in the Brazilian Amazon biome.

Dearomatization drives complexity generation in freshwater organic matter

Dissolved organic matter (DOM) is one of the most complex, dynamic and abundant sources of organic carbon, but its chemical reactivity remains uncertain1-3. Greater insights into DOM structural features could facilitate understanding its synthesis, turnover and processing in the global carbon cycle4,5. Here we use complementary multiplicity-edited 13C nuclear magnetic resonance (NMR) spectra to quantify key substructures assembling the carbon skeletons of DOM from four main Amazon rivers and two mid-size Swedish boreal lakes. We find that one type of reaction mechanism, oxidative dearomatization (ODA), widely used in organic synthetic chemistry to create natural product scaffolds6-10, is probably a key driver for generating structural diversity during processing of DOM that are rich in suitable polyphenolic precursor molecules. Our data suggest a high abundance of tetrahedral quaternary carbons bound to one oxygen and three carbon atoms (OCqC3 units). These units are rare in common biomolecules but could be readily produced by ODA of lignin-derived and tannin-derived polyphenols. Tautomerization of (poly)phenols by ODA creates non-planar cyclohexadienones, which are subject to immediate and parallel cycloadditions. This combination leads to a proliferation of structural diversity of DOM compounds from early stages of DOM processing, with an increase in oxygenated aliphatic structures. Overall, we propose that ODA is a key reaction mechanism for complexity acceleration in the processing of DOM molecules, creation of new oxygenated aliphatic molecules and that it could be prevalent in nature.

New records of native and introduced fish species in a river basin of Western Ecuador, the Chocó-Darien Ecoregion, using DNA barcoding

DNA barcoding, based on mitochondrial markers, is widely applied in species identification and biodiversity studies. The aim of this study was to establish a barcoding reference database of fishes inhabiting the Cube River from Western Ecuador in the Chocó-Darien Global Ecoregion (CGE), a threatened ecoregion with high diversity and endemism, and evaluate the applicability of using barcoding for the identification of fish species. Barcode sequences were obtained from seven orders, 17 families, 23 genera and 26 species, which were validated through phylogenetic analysis, morphological measurements, and literature review. Our results showed that 43% of fish species in this region are endemic, confirmed the presence of known species in the area, and included the addition of three new records of native (Hoplias microlepis, Rhamdia guatemalensis and Sicydium salvini) and an introduced species (Xiphophorus maculatus) to Ecuador. In addition, eight species were barcoded for the first time. Species identification based on barcoding and morphology showed discrepancy with species lists from previous studies in the CGE, suggesting that the current baseline of western fishes of Ecuador is still incomplete. Because this study analyzed fishes from a relatively small basin (165 km2), more molecular-based studies focusing on fish are needed to achieve a robust sequence reference library of species inhabiting Western Ecuador. The new sequences of this study will be useful for future comparisons and biodiversity monitoring, supporting the application of barcoding tools for studying fish diversity in genetically unexplored regions and to develop well-informed conservation programs.

'From the sky to the ground': fishers' knowledge, landscape analysis and hydrological data indicate long-term environmental changes in Amazonian clear water rivers

Fishers possess detailed local ecological knowledge (LEK) which can be a valuable resource for tracking long-term environmental changes in less studied tropical rivers. Our goal was to investigate such changes in three clear water rivers in the Brazilian Amazon, focusing on hydrology, water quality and land cover. Additionally, we aimed to compare these changes among three rivers (Trombetas, Tapajós and Tocantins) representing a potential gradient of environmental changes. We interviewed 129 fishers (67 in Tapajós, 33 in Tocantins and 29 in Trombetas), and analyzed temporal series on land cover and hydrology respectively through maps produced by the project MapBiomas, and data from the Brazilian National Water Agency across the last 34 years (from 1985 to 2019). The complementary analyses of these three databases (mapping, hydrological data and fishers' knowledge) revealed environmental changes in the studied rivers. The maps showed a gradient of anthropic changes on land cover, from the less altered Trombetas river, the moderately altered Tapajós and the more intensely changed landscape in the Tocantins River. Fishers from the Tocantins River reported a greater variety of negative changes in water quality related to anthropic actions, such as dams, deforestation, and pollution. Additionally, most fishers indicated hydrological changes making the Tocantins River drier in more recent years, which would cause negative effects on fish populations. In the Tapajós River, fishers mentioned more varied hydrological patterns and negative effects on water quality linked to mining activities, whereas in Trombetas fishers perceived increased floods. The changes mentioned by the interviewed fishers matched observed trends from hydrological data indicating a trend of increasing droughts in the more impacted Tocantins River. Fishers' knowledge provided exclusive 'on the ground' data to track long-term changes on local hydrology and water quality, as well as inform the effects of these changes on fish and fisheries.

The effects of simulated hydropower turbine rapid decompression on two Neotropical fish species

Barotrauma is a major cause of injury and mortality of fish as they pass through hydropower turbines. Current understanding of hydropower related barotrauma is biased towards northern temperate and southern subtropical species with single chambered swim bladders, specifically North American and Australian species, respectively. Today, unprecedented hydropower development is taking place in Neotropical regions where many species have complex multi-chambered swim bladder architecture. This study investigated barotrauma in two dual-chambered physostomous Neotropical fish (pacu, Piaractus mesopotamicus, and piracanjuba, Brycon orbignyanus) exposed to rapid (< 1 s) decompression at different Ratios of Pressure Change (RPC), using a hypo-hyperbaric chamber. The incidence and intensity (percentage surface area of organ affected) of injury and physiological and behavioural response (hereafter just response) of each species immediately after decompression was assessed. Twenty-two injury types (e.g. gill haemorrhage and exophthalmia) and eight response categories (e.g. rising to the surface and loss of orientation) were identified and the influence of: 1) species, 2) RPC, and 3) swim bladder rupture on each was quantified. There was considerable interspecific difference with emboli type injuries occurring more frequently in piracanjuba, but injury intensity tending to be higher in pacu. Both swim bladder chambers tended to rupture in piracanjuba but only the anterior chamber in pacu. RPC was positively correlated with response, incidence and intensity of several injury types for both species with some injuries occurring at very low RPC (e.g. 50 % probability of swim bladder rupture at 2.2 and 1.75 for piracanjuba and pacu, respectively). Multiple responses (e.g. loss of orientation) and injuries (e.g. eye haemorrhage) were correlated with swim bladder rupture suggesting gas venting into the body cavity likely causes secondary injury. When directly comparing our results with those available in the published literature, both pacu and piracanjuba appear to be more susceptible to barotrauma than previously studied subtropical and temperate species.

A new species of rheophilic armored catfish of Rineloricaria (Siluriformes: Loricariidae) from the Vaupés River, Amazonas basin, Colombia

A new rheophilic species of the genus Rineloricaria is described for the Amazon basin in Colombia. Rineloricaria cachivera n. sp. differs from its congeners by having anterior to the first predorsal plate, an inconspicuous saddle-like mark; the presence of dark, diffuse blotches, present as unified dark colouration along most of the dorsal portion of the head, without bands or spots on the head; a long snout that occupies more than half the head length (HL), between 58.0% and 66.3% HL; a naked portion on the cleithral area from the border of lower lip reaching the origin of pectoral fin; and by having five series of lateral plates in longitudinal rows below the dorsal fin. The new species is morphologically similar to Rineloricaria daraha; however, it can be distinguished by the presence of six branched pectoral fin rays (vs. seven) and the lower lip surface with short thick papillae (vs. long finger papillae). An identification key to the Rineloricaria species of the Amazon River basin in Colombia is provided. The new species is herein categorized as Least Concern, following the IUCN criteria.

Cytogenetic characterization of the golden mussel (Limnoperna fortunei) reveals the absence of sex heteromorphic chromosomes

The golden mussel (Limnoperna fortunei) is an aggressive invasive species in South America, where it endangers native species and freshwater ecosystems, in addition to causing extensive economic losses, mainly to the hydroelectric sector. Currently, there's no efficient control method available and the invasion has progressed across the continent. Its high reproduction rate is one of the key factors of the golden mussel's high invasive potential and, recently, efforts have been done in order to understand the reproduction and the sexual features of this species. However, its cytogenetics characterization is incipient and the possible occurrence of sex-specific cytogenetic features was never investigated. In this study, we aimed to characterize the chromosomal morphometry, the distribution profile of heterochromatin, and to detect possible sex-related epigenetic marks in the golden mussel. Results revealed that the karyotypic structure is similar in both sexes and no chromosome heteromorphism was observed between males and females specimens. The data increment the cytogenetic characterization of Limnoperna fortunei and contribute for future studies that aim to further investigate its reproduction and underlying sex determination processes.

Knodus borari, a new species from the lower Rio Tapajós basin (Characiformes: Characidae)

A new species of Knodus from the Rio Cupari, a right-bank tributary of the lower Rio Tapajós, is described. Among its congeners, the new species shares exclusively with K. figueiredoi the presence of only uni-tricuspid teeth in the premaxilla, maxilla and dentary. Knodus borari differs from K. figueiredoi by the colour pattern and morphological characteristics. The new species is the fifth species of the genus described from the Rio Tapajós basin, and the second restricted to the lower portion of the basin. This is additional evidence that the lower Rio Tapajós basin is a region of ichthyofaunal endemism.

Species invasiveness and community invasibility of North American freshwater fish fauna revealed via trait-based analysis

While biological invasions are recognized as a major threat to global biodiversity, determining non-native species' abilities to establish in new areas (species invasiveness) and the vulnerability of those areas to invasions (community invasibility) is challenging. Here, we use trait-based analysis to profile invasive species and quantify the community invasibility for >1,800 North American freshwater fish communities. We show that, in addition to effects attributed to propagule pressure caused by human intervention, species with higher fecundity, longer lifespan and larger size tend to be more invasive. Community invasibility peaks when the functional distance among native species was high, leaving unoccupied functional space for the establishment of potential invaders. Our findings illustrate how the functional traits of non-native species determining their invasiveness, and the functional characteristics of the invaded community determining its invasibility, may be identified. Considering those two determinants together will enable better predictions of invasions.

Lista de especies de peces de la cuenca del Río Ucayali, Perú

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.

Connections among Land Use, Water Quality, Biodiversity of Aquatic Invertebrates, and Fish Behavior in Amazon Rivers

Rivers in the Amazon have among the greatest biodiversity in the world. The Xingu River, one of the tributaries of the Amazon River, has a length of 1640 km, draining 510,000 km2 in one of the most protected regions on the planet. The Middle Xingu region in Brazil has been highly impacted by mining and livestock farming, leading to habitat fragmentation due to altered water quality. Therefore, comparing two rivers (the preserved Xingu River and the impacted Fresco River) and their confluence, the aims of the present study were to (1) assess the land uses in the hydrographic basin; (2) determine the water quality by measurements of turbidity, total solids, and metals (Cd, Cu, Fe, Mn, Pb, Zn, and Hg); (3) compare the zooplankton biodiversity; and (4) to evaluate the avoidance behavior of fish (Astyanax bimaculatus) when exposed to waters from the Xingu and Fresco Rivers. Zooplankton were grouped and counted down to the family level. For the analysis of fish avoidance, a multi-compartment system was used. The forest class predominated at the study locations, accounting for 57.6%, 60.8%, and 63.9% of the total area at P1XR, P2FR, and P3XFR, respectively, although since 1985, at the same points, the forest had been reduced by 31.3%, 25.7%, and 27.9%. The Xingu River presented almost 300% more invertebrate families than the Fresco River, and the fish population preferred its waters (>50%). The inputs from the Fresco River impacted the water quality of the Xingu River, leading to reductions in local invertebrate biodiversity and potential habitats for fish in a typical case of habitat fragmentation due to anthropic factors.

Two novel species of Myxobolus parasitizing the gills of Semaprochilodus insignis in the Brazilian Amazon

The present study describes two new Myxobolus species infecting the gills of Semaprochilodus insignis, the most consumed freshwater fish species in the Brazilian Amazon. The fish specimens were caught in the Tapajós River, in the state of Pará, and the morphological, ultrastructural, small subunit ribosomal DNA (ssrDNA), and phylogenetic data of the myxosporean species were obtained. Two species of Myxobolus were found in the gills of S. insignis. Myxobolus maiai n. sp. developed in the gill filaments, and mature myxospores were round-shaped from the frontal view, measuring 12.5-14.8 (13.9 ± 0.5) μm in length, 11.4-13.8 (12.3 ± 0.5) μm in width, and have a thickness of 6.4-7.7 (6.9 ± 0.6) μm in the lateral view, with symmetric values. Its polar capsules were 4.4-6.6 (5.5 ± 0.5) μm in length and 2.3-3.7 (3.0 ± 0.3) μm in width, and the polar tubules had 4 - 5 coils. Myxobolus iarakiensis n. sp. was found infecting the gill arch. Mature myxospores were oval-shaped from the frontal view, and measured 6.7-8.6 (8.0 ± 0.4) μm in length, 4.5-6.3 (5.6 ± 0.4) μm in width, and had a thickness of 2.7-4.7 (3.8 ± 0.5) μm in the lateral view, with symmetric values. Its polar capsules were 2.1-3.7 (2.9 ± 0.3) μm in length and 1.1-2.0 (1.5 ± 0.2) μm in width, and its polar tubules had 4 - 5 coils. The ssrDNA based phylogeny showed these two novel species as grouping in a clade composed of parasite species of Prochilodontidae hosts.

Reducing adverse impacts of Amazon hydropower expansion

Proposed hydropower dams at more than 350 sites throughout the Amazon require strategic evaluation of trade-offs between the numerous ecosystem services provided by Earth's largest and most biodiverse river basin. These services are spatially variable, hence collective impacts of newly built dams depend strongly on their configuration. We use multiobjective optimization to identify portfolios of sites that simultaneously minimize impacts on river flow, river connectivity, sediment transport, fish diversity, and greenhouse gas emissions while achieving energy production goals. We find that uncoordinated, dam-by-dam hydropower expansion has resulted in forgone ecosystem service benefits. Minimizing further damage from hydropower development requires considering diverse environmental impacts across the entire basin, as well as cooperation among Amazonian nations. Our findings offer a transferable model for the evaluation of hydropower expansion in transboundary basins.

Unveiling biogeographical patterns of the ichthyofauna in the Tuichi basin, a biodiversity hotspot in the Bolivian Amazon, using environmental DNA

To date, more than 2400 valid fish species have been recorded in the Amazon basin. However, some regions remain poorly documented. This is the case in the Beni basin and in particular in one of its main sub-basins, the Tuichi, an Andean foothills rivers flowing through the Madidi National Park in the Bolivian Amazonia. The knowledge of its ichthyological diversity is, however, essential for the management and protection of aquatic ecosystems, which are threatened by the development of infrastructures (dams, factories and cities), mining and deforestation. Environmental DNA (eDNA) has been relatively little used so far in the Amazon basin. We sampled eDNA from water in 34 sites in lakes and rivers in the Beni basin including 22 sites in the Tuichi sub-basin, during the dry season. To assess the biogeographical patterns of the amazonian ichthyofauna, we implemented a metabarcoding approach using two pairs of specific primers designed and developed in our laboratory to amplify two partially overlapping CO1 fragments, one of 185bp and another of 285bp. We detected 252 fish taxa (207 at species level) among which 57 are newly identified for the Beni watershed. Species compositions are significantly different between lakes and rivers but also between rivers according to their hydrographic rank and altitude. Furthermore, the diversity patterns are related to the different hydro-ecoregions through which the Tuichi flows. The eDNA approach makes it possible to identify and complete the inventory of the ichthyofauna in this still poorly documented Amazon basin. However, taxonomic identification remains constrained by the lack of reference barcodes in public databases and does not allow the assignment of all OTUs. Our results can be taken into account in conservation and management strategies and could serve as a baseline for future studies, including on other Andean tributaries.

Spatial and seasonal variation of benthic fish assemblages in whitewater rivers of Central Amazon

Abstract Despite the high number of fish species described for the Amazon region, the ichthyofauna that inhabits the depths of the main channels of large tropical rivers is one of the least known. In order to know the diversity patterns of these fish in whitewater rivers of the Central Amazon, we used data from the main channel benthic fish assemblage of the Japurá, Purus and Madeira rivers and tested the hypothesis that there are marked spatial and seasonal differences in the composition of the fish community among them. For this, we used a multivariate dispersion test, total β diversity and its decomposition into local (LCBD) and species contribution to β diversity (SCBD). Additionally, we tested for relationships between LCBD values and richness, total abundance, and environmental variables. We categorized species with higher SCBD values into resident or migratory to investigate the potential importance of floodplains to benthic fish assemblage of the main channel of whitewater rivers. Our results corroborate the proposed hypothesis, showing that there are seasonal and inter-river differences in benthic ichthyofauna, being more evident for the Purus River. LCBD showed strong negative relationships with species richness and total abundance, particularly in the Japurá and Madeira rivers in rising season, indicating that rivers and season with high uniqueness in their composition also had low richness and abundance. LCBD was negatively correlated with conductivity and pH, which increased with declining these environmental variables, as observed mainly in Japurá River in both seasons. Approximately one third of the species had higher than average SCBD values and were considered major contributors to β diversity, as well as classified as migratory. This demonstrates the importance of conducting studies that use spatial and seasonal variables, in addition to including the background fish fauna in conservation studies, expanding the protected area and taking into account the different patterns of diversity between rivers. Furthermore, these differences in assemblage composition might be explained by the asymmetrical spatial use of habitats during different seasons, strongly suggesting the importance of the flood-pulse cycle for maintaining diversity in this environment.

Fishes from the Colombian Amazonia region: species composition from the river systems within the rainforest biome

Abstract The Colombian Amazon region is part of the Neotropical rainforest (humid forest biome) covering an area of 483,163 km2 and includes tributaries of both the Amazon and Orinoco River basins. The aquatic ecosystems found there include: rivers and alluvial plains originating in Andean headwaters, on eroded soils of tropical forests in the lowlands, and Guiana Shield formations, comprising a dense fluvial drainage network in the lowlands, with Paleogene/Neogene geological formations (terra firme streams in higher places that don’t usually flood) and Paleozoic (shield streams); and Andean and Guiana Shield streams above 200–250 m a.s.l. We present here an exhaustive compilation of published information, supported by fish collections, consisting of a list of 1104 species distributed in 375 genera, 53 families, and 16 orders. We include occurrence data of these species in each sub-basin. The presence/absence species matrix was analyzed using a dendrogram and non-metric multidimensional scaling (NMDS) analysis to identify patterns of similarity between basins and sub-basins. We evaluated species composition between basins and among the different geological origins using PERMANOVA. The dendrogram shows co-occurrences of 404 species in the two basins. It also shows two clear groupings of the sub-basins of the Amazon (except Guainía-Negro drainages) and those of the Orinoco. Within the Amazon Basin, there are two nodes according to the geological origin: systems of Andean origin and those of the lowlands. The dendrogram results are consistent with the NMDS analysis, which shows a clear grouping according to the connectivity of the basins; the Guainía-Negro is included in the Amazon basin. Species distribution patterns were supported by the PERMANOVA, and differed significantly between basins (F = 4.3, R = 0.26, P = 0.003) and geological origin (F = 3.6, R = 0.23, P = 0.003). The number of species in this study represents almost a fifth of the ichthyofauna of the Neotropics and about a third of that of the Amazon River basin; clearly supporting Colombia’s status among the countries with the greatest diversity of freshwater fish species of the planet. We include here a significant number of new records (75 spp), provide a first approximation of the distribution patterns, and a framework for future biogeographical studies.

Description of a new species of miniature catfish of the genus Ammoglanis (Siluriformes: Trichomycteridae) from rio Tapajós basin, Brazil

Abstract A new species of Ammoglanis is described from the rio Aruri Grande, rio Jamanxim drainage, a right bank tributary to the middle rio Tapajós, Pará State, Brazil. The new species is identified and defined through morphological characters such as color pattern, consisting of eight or nine transverse dark bars regularly spaced along the dorsum; skeletal morphology; numbers of premaxillary teeth, vertebrae, and dorsal- and pectoral-fin rays; presence of cranial fontanel and two small, finger-like papillae on chin anterior to the gular apex. The new species probably is an additional example of endemism in the rio Tapajós basin.

Conservation threats and future prospects for the freshwater fishes of Ecuador: A hotspot of Neotropical fish diversity

Freshwater fish communities in Ecuador exhibit some of the highest levels of diversity and endemism in the Neotropics. Unfortunately, aquatic ecosystems in the country are under serious threat and conditions are deteriorating. In 2018-19, the government of Ecuador sponsored a series of workshops to examine the conservation status of Ecuador's freshwater fishes. Concerns were identified for 35 species, most of which are native to the Amazon region, and overfishing of Amazonian pimelodid catfishes emerged as a major issue. However, much of the information needed to make decisions across fish groups and regions was not available, hindering the process and highlighting the need for a review of the conservation threats to Ecuador's freshwater fishes. Here, we review how the physical alteration of rivers, deforestation, wetland and floodplain degradation, agricultural and urban water pollution, mining, oil extraction, dams, overfishing, introduced species and climate change are affecting freshwater fishes in Ecuador. Although many of these factors affect fishes throughout the Neotropics, the lack of data on Ecuadorian fish communities is staggering and highlights the urgent need for more research. We also make recommendations, including the need for proper enforcement of existing environmental laws, restoration of degraded aquatic ecosystems, establishment of a national monitoring system for freshwater ecosystems, investment in research to fill gaps in knowledge, and encouragement of public engagement in citizen science and conservation efforts. Freshwater fishes are an important component of the cultural and biological legacy of the Ecuadorian people. Conserving them for future generations is critical.

Genome assembly and annotation of the tambaqui (Colossoma macropomum): an emblematic fish of the Amazon River Basin

Colossoma macropomum, known as "tambaqui", is the largest Characiformes fish in the Amazon River Basin and a leading species in Brazilian aquaculture and fisheries. Good quality meat and excellent adaptability to culture systems are some of its remarkable farming features. To support studies into the genetics and genomics of the tambaqui, we have produced the first high-quality genome for the species. We combined Illumina and PacBio sequencing technologies to generate a reference genome, assembled with 39× coverage of long reads and polished to a consensus quality value (QV) of 36 with 130× coverage of short reads. The genome was assembled into 1269 scaffolds (a total of 1,221,847,006 bases), with a scaffold N50 size of 40 Mb, where 93% of all assembled bases were placed in the largest 54 scaffolds corresponding to the diploid karyotype of the tambaqui. Furthermore, the NCBI Annotation Pipeline annotated genes, pseudogenes, and non-coding transcripts using the RefSeq database as evidence, guaranteeing a high-quality annotation. A Genome Data Viewer for the tambaqui was produced, which will benefit groups interested in exploring the unique genomic features of the species. The availability of a highly accurate genome assembly for tambaqui provides the foundation for the discovery of novel ecological and evolutionary insights, and is a helpful resource for aquaculture.

The critical role of natural history museums in advancing eDNA for biodiversity studies: a case study with Amazonian fishes

Ichthyological surveys have traditionally been conducted using whole-specimen, capture-based sampling with varied but conventional fishing gear. Recently, environmental DNA (eDNA) metabarcoding has emerged as a complementary, and possible alternative, approach to whole-specimen methodologies. In the tropics, where much of the diversity remains undescribed, vast reaches continue unexplored, and anthropogenic activities are constant threats; there have been few eDNA attempts for ichthyological inventories. We tested the discriminatory power of eDNA using MiFish primers with existing public reference libraries and compared this with capture-based methods in two distinct ecosystems in the megadiverse Amazon basin. In our study, eDNA provided an accurate snapshot of the fishes at higher taxonomic levels and corroborated its effectiveness to detect specialized fish assemblages. Some flaws in fish metabarcoding studies are routine issues addressed in natural history museums. Thus, by expanding their archives and adopting a series of initiatives linking collection-based research, training and outreach, natural history museums can enable the effective use of eDNA to survey Earth's hotspots of biodiversity before taxa go extinct. Our project surveying poorly explored rivers and using DNA vouchered archives to build metabarcoding libraries for Neotropical fishes can serve as a model of this protocol.

Corydoras fulleri (Siluriformes: Callichthyidae), a new catfish species from the rio Madeira basin, Peru

A new long-snouted Corydoras species is described from two tributaries of the río Manuripe and a tributary of the río Madre de Dios, rio Madeira basin, Peru. Corydoras fulleri can be distinguished from its congeners by having the following features: (a) branch of the temporal sensory canal at sphenotic, which gives rise to the supraorbital canal, with two pores; (b) upper tooth plate of branchial arch with three series of teeth; (c) area at the corner of the mouth, ventral to the maxillary barbel, with a small fleshy flap; (d) two moderate-sized dark-brown or black blotches on caudal-fin base, one on its lateral portion and another one on its dorsal portion, blotches variably diffuse and/or fused with each other; (e) absence of a dark-brown or black stripe transversally crossing the orbit; (f) a longitudinal dark-brown or black stripe on the postdorsal region of flank midline, variably fused with the lateral peduncular blotch, some specimens with slender, longitudinally elongated, dark-brown or black blotch on flank midline, forming a dash-like marking, stripe or dash-like blotch diffuse in some specimens; and (g) region around dorsal-fin origin generally lacking dark brown or black blotch, or displaying diffuse blotch.

Health Risk Assessment of Mercury Exposure from Fish Consumption in Munduruku Indigenous Communities in the Brazilian Amazon

Fish serves as the principal source of animal protein for the indigenous people of the Amazon, ensuring their food and nutritional security. However, gold mining causes mercury (Hg) contamination in fish, and consequently increases health risks associated with fish consumption. The aim of this study was to assess the health risk attributed to the consumption of mercury-contaminated fish by Munduruku indigenous communities in the Middle-Tapajós Region. Different fish species were collected in the Sawré Muybu Indigenous Land to determine mercury levels. The health risk assessment was carried out according to the World Health Organization (WHO 2008) methodology and different scenarios were built for counterfactual analysis. Eighty-eight fish specimens from 17 species and four trophic levels were analyzed. Estimates of Hg ingestion indicated that the methylmercury daily intake exceeds the U.S. EPA (United States Environmental Protection Agency) (2000) reference dose from 3 to 25-fold, and up to 11 times the FAO (Food and Agriculture Organization)/WHO (2003) dose recommendation. In all situations analyzed, the risk ratio estimates were above 1.0, meaning that the investigated Munduruku communities are at serious risk of harm as a result of ingestion of mercury-contaminated fish. These results indicate that, at present, fish consumption is not safe for this Munduruku population. This hazardous situation threatens the survival of this indigenous population, their food security, and their culture.

Species-level ichthyoplankton dynamics for 97 fishes in two major river basins of the Amazon using quantitative metabarcoding

The Amazon basin holds the world's largest freshwater fish diversity. Information on the intensity and timing of reproductive ecology of Amazonian fish is scant. We use a metabarcoding method by capture using a single probe to quantify species-level ichthyoplankton dynamics. We sampled the Marañón and the Ucayali rivers in Peru monthly for 2 years. We identified 97 species that spawned mainly during the flood start, the flood end or the receding periods, although some species had spawning activity in more than one period. This information was new for 40 of the species in the Amazon basin and 80 species in Peru. Most species ceased spawning for a month during a strong hydrological anomaly in January 2016, demonstrating the rapidity with which they react to environmental modifications during the breeding season. We also document another unreported event in the Amazon basin, the inverse phenology of species belonging to one genus (Triportheus). Overall larval flow in the Marañón was more than twice that of the Ucayali, including for most commercial species (between two and 20 times higher), whereas the Ucayali accounts for ~80% of the fisheries landings in the region. Our results are discussed in the light of the main anthropogenic threats to fishes, hydropower dam construction and the Hidrovía Amazónica, and should serve as a pre-impact baseline.

Threats of global warming to the world's freshwater fishes

Climate change poses a significant threat to global biodiversity, but freshwater fishes have been largely ignored in climate change assessments. Here, we assess threats of future flow and water temperature extremes to ~11,500 riverine fish species. In a 3.2 °C warmer world (no further emission cuts after current governments’ pledges for 2030), 36% of the species have over half of their present-day geographic range exposed to climatic extremes beyond current levels. Threats are largest in tropical and sub-arid regions and increases in maximum water temperature are more threatening than changes in flow extremes. In comparison, 9% of the species are projected to have more than half of their present-day geographic range threatened in a 2 °C warmer world, which further reduces to 4% of the species if warming is limited to 1.5 °C. Our results highlight the need to intensify (inter)national commitments to limit global warming if freshwater biodiversity is to be safeguarded.

Climate change is a threat to global biodiversity, but the potential effects on freshwater fishes have not been well studied. Here the authors model future flow and water temperature extremes and predict that increases in water temperature in particular will pose serious threats to freshwater fishes

Climate vulnerability of South American freshwater fish: Thermal tolerance and acclimation

Freshwater fish are restricted by their physiology to rivers and lakes, and are generally limited in their capacity to disperse across basins. As a result, there is often a close match between the evolutionary history of river basins and their natural history. Thus, the regional landscape and ecological features, such as temperature, have shaped the evolution and adaptation of local fish assemblages. Climate change is expected to affect fish diversity and increase extinction, especially in low latitudes, and it has been suggested that species that inhabit low latitude species are more susceptible since they live close to their maximum thermal limits and have low capacity for acclimation. To understand the mechanisms of variation in thermal tolerance across a broad-scale of South American fishes is fundamental to be able to assess the vulnerability of species and habitat to global warming. Herein, we present the first attempt to analyze the vulnerability of South American freshwater fish species, based on the review of upper thermal limits of 106 species from a broad range of latitudinal habitats. Our findings show that upper thermal limits decrease with latitude, while the thermal safety margin (TSM) increase. Furthermore, the latitude has little effects on the acclimation response ratio, and the TSM decreased with rising temperatures. These data suggest that thermal phenotypic acclimation has low potential for mitigating global warming. These results indicate that South American fish species living in tropical areas are more susceptible to global warming since they are already living close to their maximum habitat temperature.

Integrative taxonomy reveals disjunct distribution and first record of Hoplias misionera (Characiformes: Erythrinidae) in the Amazon River basin: morphological, DNA barcoding and cytogenetic considerations

Abstract The Hoplias malabaricus group encompasses six valid species and still is believed to harbors cryptic diversity. In this work, an integrative approach including morphological, DNA barcoding, and cytogenetic considerations was conducted to characterize a population of H. malabaricus from the Amazon basin that was recently allocated in the same mitochondrial lineage with H. misionera, a species originally described from La Plata basin. The DNA barcoding analysis revealed that the Amazon population nested together with H. misionera specimens from the La Plata basin (BIN AAB1732) in the same cluster. The intragroup distance (0.5%) was 12 times lower than the nearest neighbor (6%) distance. The morphometric analysis demonstrated slightly variation between Amazon and La Plata populations, being the former composed by larger specimens. Further morphological data supported the molecular evidence of H. misionera inhabiting Amazon basin. The karyotype characterization of H. misionera in the Amazon population showed 2n=40 and karyotypic formulae 20m+20sm, that added to C-banding, Ag-NOR and 18S results are suggestive of the similarity to karyomorph C of H. malabaricus. This work reveals the first record of H. misionera outside of La Plata basin and expands the species distribution for 2500 km northward until the Marajó Island, estuary of Amazonas River.

Fish Community Responses to Human-Induced Stresses in the Lower Mekong Basin

The Mekong River is one of the world’s largest rivers and has an annual captured fish production of about 2.3 million tonnes, equivalent to around 11 billion USD. Although the Mekong provides important ecological and socioeconomic benefits to millions of people, it is facing intensive change due to anthropogenic stressors. Therefore, it is necessary to understand the changes to the spatiotemporal fish communities to inform sustainable fisheries management. Here, we aimed to characterize patterns of the fish communities and identify the ecological status of each fish community using daily catch data from 2007 to 2018 at 25 monitoring sites in the Lower Mekong Basin (LMB). The collected data were classified by a self-organizing map into four main groups. Group 4 represented the lower Vietnam Mekong Delta (VMD), while groups 1, 2, and 3 were subdivided into subgroups 1a (upper LMB), 1b (upper and middle LMB), 2a (Mekong River below the Khone Falls and Sesan River), 2b (Mekong River below the Khone Falls and Sekong, Sesan and Srepok (3S) Rivers), 3a (Floodplain-Tonle Sap and Songkhram) and 3b (upper VMD). Among the 571 species recorded, 119 were identified as indicator species. Based on the abundance and biomass comparison curves, the fish community of 2b was in a healthier condition with a positive W-statistic value while the rest had a negative W-statistic value. The highest species richness and diversity were observed in 3a and 2b, so these subgroups deserve high management and conservation priority. Likewise, 1a should also be considered as a high priority area since it harbors several endangered and long-distant migratory fishes. It was also noticed that the fish communities of groups 3 and 4, located far from the hydropower dams, remained mostly unchanged compared to those of groups 1 and 2, close to the mainstream and tributary dams in the upper LMB and 3S Rivers.

A new species of Odontostilbe cope (Characiformes: Cheirodontinae) from rio Madeira basin diagnosed based on morphological and molecular data

A new species of Odontostilbe is described from the rio Jaciparaná, rio Madeira basin, Rondônia, Brazil. Odontostilbe pacaasnovos differs from all its congeners, except O. pequira, by the colour pattern. Additionally, it differs from its congeners by the terminal mouth, number of cusps in the teeth of the premaxilla (5-7), number of branched rays in the anal fin (19-22), by the shape of dentary teeth (5-7 cusps with central cusp larger and longer than laterals cusps) and by the number of lamellae of the olfactory rosette (17-18 in male and 14 in female). Morphological and molecular comparisons corroborate the distinctiveness between O. pacaasnovos and its congeners, justifying its recognition as a new species.

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.

High-Resolution Surface Water Classifications of the Xingu River, Brazil, Pre and Post Operationalization of the Belo Monte Hydropower Complex

We describe a new high spatial resolution surface water classification dataset generated for the Xingu river, Brazil, from its confluence with the Iriri river to the Pimental dam prior to construction of the Belo Monte hydropower complex, and after its operationalization. This river is well-known for its exceptionally high diversity and endemism in ichthyofauna. Pre-existing datasets generated from moderate resolution satellite imagery (e.g., 30 m) do not adequately capture the extent of the river. Accurate measurements of water extent are important for a range of applications utilizing surface water data, including greenhouse gas emission estimation, land cover change mapping, and habitat loss/change estimates, among others. We generated the new classifications from RapidEye imagery (5 m pixel size) for 2011 and PlanteScope imagery (3 m pixel size) for 2019 using a Geographic Object Based Image Analysis (GEOBIA) approach.

Participatory Research with Fishers to Improve Knowledge on Small-Scale Fisheries in Tropical Rivers

Freshwater small-scale fisheries sustain millions of livelihoods worldwide, but a lack of monitoring makes it difficult to check the sustainability of these fisheries. We aim to compare and describe participatory research methods used in studies with fishers in the Tapajos River, a poorly known tropical river in the Brazilian Amazon. We address three interview approaches, two ways to do fisheries monitoring and two approaches for georeferenced mapping based on fishers’ knowledge, which can provide data about at least 16 topics related to fisheries. We highlight major advantages and shortcomings of these methods and illustrate their potential with examples of results on fisheries and fish biology of Peacock bass (Cichla spp. tucunaré in Brazil), an important commercial fish in the Brazilian Amazon. The interviews, participatory monitoring and mapping revealed which fish are more valued by local communities, how fish abundance and sizes varied over time, when fish are more often caught and show reproductive activity, and which sites or habitats fish need to reproduce. In addition to providing useful data from many sites in a cost-effective way, participatory methods can bring the additional benefit of including local stakeholders in the monitoring, management, and research activities.

Ichthyofauna of sandy beaches along the Acre river, Brazil

Abstract: Despite increasing efforts in recent years to catalog the fish diversity of Amazonian rivers, many regions are still under-sampled, and sandy beach environments are particularly poorly understood. The present study focused on a 300 km stretch of the Acre river, in the southwestern Amazon basin, where we sampled 30 sandy beaches separated by a mean interval of 10 km. We collected 15,329 fish representing 80 species, 26 families, and nine orders. The Characiformes were the most abundant order, providing 88.24% of the individuals collected, followed by the Siluriformes, with 10.03%, while the Siluriformes had the highest species richness, with 37 species (45.0%), followed by the Characiformes, with 30 (37.5%). The most abundant species were the characiforms Knodus orteguasae and Creagruto barrigai. Reliable data on a region’s biota is fundamental for the evaluation of patterns of biodiversity, and the occurrence and management of threatened species. As fish are directly affected by pollutants and the degradation of aquatic environments, further research in areas that are still poorly sampled will be essential for the elaboration of effective conservation strategies.