Fish biodiversity and conservation in South America

Global Patterns and Drivers of Freshwater Fish Extinctions: Can We Learn From Our Losses?

Nearly one-third of extant freshwater fish species, which account for over 50% of global fish diversity, are at risk of extinction. Despite their crucial ecological and socioeconomic importance, the extinction of freshwater fishes remains under-researched on a global scale. This is a comprehensive assessment of taxonomic, spatial, and temporal patterns of freshwater fish extinctions while identifying key extinction drivers and driver synergies. Using data from the International Union for Conservation of Nature Red List, 89 extinct freshwater fish and 11 extinct in the wild were analyzed. Taxonomic statistical analysis revealed the disproportionate impact on Cyprinidae, Leuciscidae, and Salmonidae. Estimated globally for the period 1851-2016, the modern extinction rate for freshwater fishes stands at 33.47 extinctions per million species-years (E/MSY), more than 100 times greater than the natural background extinction rate of 0.33 E/MSY. Extinction rates, when calculated per continent using the number of extinct species and the total number of species per continent, indicated that North America has the highest extinction rate (225.60 E/MSY), followed by Europe (220.26 E/MSY) and Asia (34.62 E/MSY). Although Africa is less affected, it still shows a 42-fold increase over the background rate. Bayesian modeling, reflecting cumulative species extinctions, indicated a strong association of North America and Asia with species loss (37 and 34 extinctions, respectively), a moderate one for Europe (20 extinctions) and a weak association of Africa (eight extinctions). Natural system modification, pollution, and invasive species emerged as the primary extinction drivers, often acting synergistically. Temporal trends indicate an acceleration in extinctions since the mid-20th century. This study highlights that, despite recent increases in conservation efforts, freshwater fish extinctions continue to rise, indicating the urgent need for integrated conservation strategies. Without immediate action, many species currently at risk may soon follow the same trajectory of extinction as the 100 extinct freshwater fishes of this study.

Inferring riverscape dispersal processes from fish biodiversity patterns

Dispersal patterns are recognized as determinants of biodiversity structure, particularly in rivers, where dendritic organization, waterflow direction, large distance immigrants from the outlet and fragmentation by dams combine to produce a complex dispersal scenario. Unravelling the role, magnitude and spatial scale at which these dispersal sources determine metacommunity diversity is challenging and requires a large amount of spatiotemporal information, which is rarely available. Here, we incorporate alternative dispersal hypotheses into metacommunity models, contrasting their predictions with the observed pattern of fish diversity (58 sampled sites) in the Negro River basin of Uruguay. Evidence supports: (i) a dispersal constrained by the river network, sharply decaying in upstream but not in downstream river directions; (ii) an outlet as a source of individuals that affects diversity even at distant communities; and (iii) a nonconclusive effect of dams, in which models with or without dam barriers are similarly supported. Observed alpha and beta diversity were well predicted by the metacommunity model (r = 0.55 and r = 0.56, respectively). Variation in diversity among simulations systematically decreased from headwaters to the outlet, evidencing a poorly recognized change in processes stochasticity along the landscape. Even without considering the well-recognized role of local filters in the assembly of the fish community, dispersal mechanisms were able to explain riverscape diversity. Dispersal patterns are made of several dispersal sources operating at different spatial scales, which are more complex than the arrival of individuals from species pool or than dispersal exchanges between neighbouring communities only. The non-conclusive effect of dams might stem from the long time lag of biotic relaxation following river fragmentation. Massive fragmentation of rivers challenges the preservation of their diversity and functioning due to disruptions in the different dispersal processes. However, demonstrating the actual and potential effect of dispersal disruption is limited by available information and the long time lags involved in faunal relaxation. Combining empirical information with the modelling of hypotheses emerges as a compelling approach for unravelling metacommunity mechanisms. Dispersal is here evidenced as a complex multi-scale phenomenon, a point that might be considered in theoretical and empirical studies and in ecosystem management.

Impacts of Belo Monte dam on fish co-occurrence and artisanal fishing

The operation of large hydroelectric dams, such as Belo Monte in the Brazilian Amazon, significantly disrupts local freshwater ecosystems, impacting the socio-economic fabric and food security of dependent communities. To investigate and simulate future dam-induced impacts on fish species crucial for subsistence and artisanal fishing, this study leveraged subsistence fishing data from four areas of the Xingu River: the reservoir, upstream, the de-watered reach, and downstream. Using network analysis and graph theory, we examined the temporal and spatial variations in fish species composition, focusing on species that co-occur in fishing catches and their ecological roles within the network. Results showed a 34 % reduction in total biomass, from 8442.51 kg (2012-2015) to 5537.42 kg (2016-2020). The analysis revealed marked changes in species diversity and catch composition, with substantial shifts in heavily altered regions. For instance, in the de-watered reach, traditional species such as curimatã (Prochilodontidae) were replaced by others like pacu (Serrasalmidae), reflecting ecological shifts and the replacement of a detritivorous species by an omnivorous one. Directed simulations projected the dynamics of species loss, revealing significant alterations in co-occurrence patterns and network centrality, particularly in the de-watered reach. These simulations demonstrated that species such as pacu, pescada (Sciaenidae), and tucunaré (Cichlidae) remained central to the network despite ongoing ecological transformations. While this study provides valuable insights into environmental shifts, the absence of direct socio-economic data highlights the need for future research to understand the broader impacts on artisanal fisheries better. These results underscore the profound transformations in fish diversity and emphasize the critical need for adaptive management strategies to mitigate these impacts, ensuring the resilience of local fishing communities. While our findings offer valuable ecological insights, the absence of direct socio-economic data highlights the need for future research to better understand the broader impacts of hydroelectric dams on artisanal fisheries.

Cost-effective alternatives to facilitate biomonitoring and bioassessment of neotropical streams

A reliable response of bioindicators to environmental variation is a cornerstone for effective bioassessment and biomonitoring. Fish and aquatic macroinvertebrates are widely used as bioindicators of different human impacts in freshwater ecosystems, but the cost-effectiveness of their usage can be improved through the use of surrogates. We investigated congruence patterns between using different taxonomic and numeric resolutions for aquatic macroinvertebrates and fish to assess community-environment relationships. We also tested whether dataset characteristics (e.g., area sampled, species pool) could explain the variation in the effectiveness of using different taxonomic and numerical resolutions. We used a Brazilian nationwide database encompassing multiple datasets with a gradient of riparian deforestation each. Our findings suggest that families and genera can effectively represent macroinvertebrate genera and fish species, respectively, when using community matrices for assessing community-environment relationships, with an acceptable loss of information. EPT (Ephemeroptera, Plecoptera, and Trichoptera) and Characiformes or Siluriformes may be used as a surrogate, in some cases, for the entire assemblages of macroinvertebrates and fish, respectively, but their use may result in higher loss of information. Presence-absence data also presented a minimal loss of information compared to abundance data, for both macroinvertebrates and fish. The variation in congruence levels among macroinvertebrate datasets was less predicted by dataset characteristics than fish. Across distinct resolutions, on average, 10 % and 19 % of the variation in community composition of macroinvertebrates and fish, respectively, was explained by broad-scale environmental variables, and the effect size was negatively affected by the dataset's sample size and spatial extent for fish. Whereas identification at species (fish) and genus (macroinvertebrates) level and quantification of all individuals still provide the best scenario, we provide evidence that coarser taxonomical resolution and presence-absence data can be used as cost-effective alternatives to facilitate biomonitoring and bioassessment of freshwaters in the Neotropical region impacted by deforestation.

Novel Amazonian Ceratomyxa species (Cnidaria: Myxozoa) with amoeboid plasmodial motility

Myxosporeans are a diverse group of cnidarian endoparasites of aquatic animals, with more than 2600 described species. The genus Ceratomyxa includes some 270 species that are mostly coelozoic and infect the gall bladders of mainly marine fish. During our survey in Tapajós River in the Brazilian Amazon, two Ceratomyxa species were discovered in the gallbladders of the anostomid fishes Schyzodon fasciatus and Schyzodon vittatus. Based on myxospore morphology and sequencing of small subunit ribosomal DNA, we propose that these are novel Ceratomyxa species. Ceratomyxa deformis n. sp. from S. fasciatus and Ceratomyxa anomala n. sp. from S. vittatus are similar in morphology, with mature myxospores slightly arcuate with rounded ends. Plasmodia are elongated, and can move by expanding and contracting the cytoplasm. This amoeboid-like motility is heretofore unreported in freshwater South American Ceratomyxa species. Ultrastructural analyses showed the plasmodial organization of both species comprised a cytoplasmic region harboring organelles and sporogonic stages and an internal large vacuole. Phylogenetic analysis corroborates monophyletic grouping of freshwater Ceratomyxa species from South America. Ceratomyxa deformis n. sp. and C. anomala n. sp., which are the first Ceratomyxa species described in anostomid fishes, grouped as sister taxa to C. gracillima and C. mandi, which infect bile in pimelodid fishes from the Amazon region.

Evolutionary dynamics of the B chromosomes in the fish species Prochiloduslineatus Valenciennes, 1837 of the Paraná River Basin

The fish species Prochiloduslineatus has an interesting B chromosome system, with three morphological types as acrocentric, metacentric, and submetacentric. However, most cytogenetic studies on this species are restricted to the natural population of the Mogi Guaçu River. Given this, the present work aimed to study the structure karyotypic profile as well as the occurrence of supernumeraries in P.lineatus in several localities in the Paraná River basin, where this species is abundant. The results obtained showed a predominantly conserved karyotypic macrostructure and the presence of B chromosomes in all the seven localities studied, with the exception of the Apa River. Additionally, new variants of morphological characteristics were found in the population of the Batalha River (Reginópolis). These results allow us to infer that there is a large occurrence of B chromosomes in this species, with important differences in B chromosome frequency between the populations, especially in acrocentric and submetacentric B variants. Considering the possible origin and evolution of B chromosomes in P.lineatus, our results allow us to describe the dispersion of metacentric B variants, in contrast with the elimination observed in acrocentric and submetacentric variants.

Integrative use of DNA barcode and morphology reveal high level of diversity in the ornamental fish on the lower Amazon basin

The Amazon basin is the world's largest hydrographic basin, in terms of both its total area and its species diversity, with more than 2,700 species of fish. Despite this diversity, the data available on the fish fauna of the Amazon basin are still relatively scant and incomplete, in particular from the streams and floodplain lakes of the lower Amazon, which may contain a large proportion of the still undescribed species of the basin. Many of these species are expected to be of interest to the ornamental fish market. The investigation of the diversity of potential ornamental fish using molecular tools is even more limited. Given this scenario, the present study employed DNA barcoding to investigate the diversity of ornamental fish found in two streams and a floodplain lake of the lower Amazon. The mitochondrially encoded cytochrome c oxidase I (MT-CO1) molecular marker was used to identify the taxa, in combination with morphological keys. A total of 51 ornamental species were identified, representing 13 families and three orders. A majority of the species were found at only one of the sampling points, which indicates that the distribution of the species is influenced by ecological factors. The most speciose order was the Characiformes, followed by the Cichliformes and Siluriformes, while the family with the greatest diversity of species was the Acestrorhamphidae (31.3% of the total number of species), followed by the Cichlidae (27.4%), and the Lebiasinidae (9.8%). One specie was registered in the region of the lower Amazon for the first time, and evidence was found of the possible existence of species not formally described of Aphyocharax, Astyanax, Apareiodon and Hemigrammus.

Time-calibrated phylogeny of neotropical freshwater fishes

Neotropical Freshwater Fish (NFF) fauna exhibits the greatest phenotypic disparity and species richness among all continental aquatic vertebrate faunas, with more than 6,345 species distributed across the mostly tropical regions of Central and South America. The last two decades have seen a proliferation of molecular phylogenies, often at the species level, covering almost all 875 valid NFF genera. This study presents the most comprehensive genome-wide, time-calibrated phylogenetic hypothesis of NFF species to date, based on DNA sequences generated over decades through the collaborative efforts of the multinational ichthyological research community. Our purpose is to build and curate an extensive molecular dataset allowing researchers to evaluate macroevolutionary hypotheses in the NFF while facilitating continuous refinement and expansion. Using thousands of DNA sequences from dozens of studies, we compiled a supermatrix of 51 markers for 5,984 taxa, representing 3,167 NFF species. Based on this dataset, we built the most species-rich time-calibrated phylogeny of the NFF taxa to date, summarizing the collective efforts of the ichthyological research community since the midpoint of the last century. We provide a summary review of this remarkable evolutionary history and hope this dataset provides a framework for forthcoming studies of the NFF fauna, documenting compelling, emergent patterns in the world's most diverse continental vertebrate fauna.

High resolution in turbid waters: Ampullae of Lorenzini in the daggernose shark Carcharhinus oxyrhynchus (Valenciennes, 1839) (Elasmobranchii: Carcharhinidae)

The present work aimed to analyse the distribution of the electrosensory pores of the daggernose shark Carcharhinus oxyrhynchus, identifying the organ's importance in the natural history of the species. By examining photographs and digital microscope videos, we found that C. oxyrhynchus possesses the highest abundance of pores among Carcharhiniformes. This suggests a well-developed electroreceptor system, which may have maximized its evolutionary success in high-turbidity environments. Furthermore, as a morphologically derived species, C. oxyrhynchus comprises a more complex and specialized electrosensory system. Notably, the species exhibits ontogenetic variation in pore abundance, highlighting the importance of a high-resolution system for adults. The higher density of pores in the ventral region indicates a preference for benthic prey, despite also feeding on pelagic items. Moreover, the species has a high-resolution electrosensory system and a high density of pores in the snout, which emphasizes the importance of the elongated snout that expands the electroreception search area coverage. Evolutionary convergence was observed in the development of the electrosensory system, as C. oxyrhynchus shares the characteristics of pore distribution and abundance with phylogenetically unrelated species.

Three new species of Demidospermus (Monopisthocotyla: Dactylogyridae) parasitizing Ageneiosus inermis (Siluriformes: Auchenipteridae) from western Amazon, Brazil

During a study on the helminth fauna of fishes in the Juruá and Moa Rivers, State of Acre, north Brazil, three new species of Demidospermus Suriano, 1983 were found parasitizing Ageneiosus inermis (Auchenipteridae). Demidospermus juruaensis sp. nov. is characterized by its accessory piece, which is robust and straight, anchor-shaped distally, as well as by morphology of its hooks, which have a delicate and expanded shaft with a spear-shape ending. Demidospermus bifurcatus sp. nov. is characterized by a male copulatory organ (MCO) composed of a robust tube, with a bisected tip at the distal end and a robust accessory piece, that embraces the MCO along its entire length. Demidospermus takemotoi sp. nov. differs from its congeners by its long, tubular and slender accessory piece, which is almost the same length as the MCO. These findings bring the number of valid Demidospermus species to 36. The results of this research on the helminth parasites of fishes in Acre State underscore the importance of carrying similar studies on other fish species, thereby enhancing understanding of biodiversity in the Neotropical Region.

Ethnoecology and use of fishes by the Cubeo people from the Cuduyarí River, Colombian Amazonia

BACKGROUND

Ethnoichthyology studies the knowledge of human communities about the uses, perception, and behavioral characteristics of fish, based on their cosmology, cosmogony, and culture. This study focused on the Cubeo (Pâmiwâ) ethnic group that inhabits the Cuduyarí River (Vaupés, Colombia) provides information on fishing activities, use of fishes, its ecological distributions (occurrence in rivers, pools, and/or streams) and seasonality (occurrence in low and/or high waters). Additionally, names in the Central Tukano language (Cubeo) are provided.

METHODS

The compilation of information was based on a visual catalog prepared from rapid ecological evaluations, previously carried out by the Amazon Institute of Scientific Research SINCHI. Workshops with the indigenous people were held in communities in the lower, middle, and upper sections of the basin to collect information. Network analyses were done to determine the fishing gear selectivity of the most common species and gears used regarding ecosystems. The coherence in the perception of fish resources among the three communities was assessed via multivariate analyses.

RESULTS

The results showed that a large percentage (89%) of the species are consumed. There is a generalized perception of resource decline, and there is no coherence regarding the ecological and seasonal distributions of fish reported by the three communities. These differences may be due to an effect of the structural characteristics of the basin in the different sectors where the communities are located.

CONCLUSIONS

Species consumed by the Cubeo in the Cuduyarí do not represent a high commercial value at the Amazon River basin scale. Nevertheless, locally, they are the main source of animal protein and most of the time, the sole source of income. The importance of these species must be recognized and must be a priority for conservation. Knowledge related to the fish resource by indigenous groups, including basic information and its usage, is essential to guide and implement management and conservation strategies specific to each region under study.

DNA barcode reveals a new lineage of Astyanax bimaculatus (Linnaeus 1758) in the basins of the Western Northeast Atlantic Region, Brazil

Astyanax bimaculatus are small characids known as piabas or lambaris that form a complex encompassing 18 species, including cryptic species. The present study aimed to use DNA barcode to analyze populations of A. bimaculatus found in Maranhão hydrographic basins, comparing molecular diversity indices between populations from the other Brazilian basins. The results revealed the formation of 32 haplotypes (h = 0.9289; π = 0.0523). Seven haplogroups were formed with intrapopulation genetic distance ranging from 0 to 2%. The Maranhão populations of the Western Northeast Atlantic Region basins separated from the other analyzed basins, corroborating with the groups generated in BAPS and with the Bayesian Inference tree. The occurrence of exclusive OTUs for the Maranhão populations of the Western Northeast Atlantic Region was confirmed through delimitation models. Thus, the data from this study provide information on the genetic diversity of the A. bimaculatus complex with the detection of a different lineage for the State of Maranhão, contributing to the understanding of the group's systematics.

Fishing for the gonadotropin releasing hormone from the genome of Salminus brasiliensis (Characiformes: Bryconidae)

The technological development of tools that enable the spawning of different native species is paramount to enable ex situ conservation initiatives, as well as providing means for commercial hatchery of threatened fish which, in turn, relieve fisheries pressure over wild stocks. Neotropical migratory freshwater fish depend on hormonal induction for spawning in hatcheries, through expensive methods of limited efficiency. Salminus brasiliensis is one of the largest Neotropical freshwater fish, a piscivorous top-predator, prized in angling, highly valued in the market, and appreciated in gastronomy. Teleost fish have either, two or three GnRH paralogous genes: GnRH1, GnRH2 and the GnRH3. The expression products of these paralogous isoforms consist of a larger prepro-GnRH polypeptide, which undergoes post-translational proteolytic processing to yield the active decapeptide hormone. There is increasing interest in characterizing and understanding these neuropeptides, because of its practical application in hatchery spawning. We present the characterization of GnRH1's coding sequence for the prepro-GnRH1 polypeptide of S. brasiliensis. An annotation from a genomic assembly was used for searching for GnRH paralogues, based on data from anonymous predicted transcripts. The sequence retrieved for GnRH1 was then used as a query for searching the uncharacterized GnRH paralogues from full genomes of Characiformes deposited at NCBI. The S. brasiliensis GnRH1 gene sequence retrieved was targeted for PCR and submitted to Sanger sequencing, allowing for its confirmation. It spans 423 bp (exon 1: 128 bp; intron: 161 bp; and exon 2: 1134 bp), with open reading frames coding for 264 and 88 amino acids, respectively. The different variants retrieved for the prepro-GnRH (1, 2 and 3) from Characiformes genomes and deposited sequences from NCBI grouped in three distinct clades in a neighbor joining tree, each forming a monophyletic branch and with the S. brasiliensis sequences nested within the expected groups. Here we observed a variation at a proteolytic site (GKR→GRR), reported as highly conserved in vertebrates up to now, that can potentially alter the cleavage site and modify the peptide topology. This work has characterized, for the first time, the sequence of the GnRH1 coding for its prepro-GnRH peptide, for a member of the Charaficormes order. This will help to promote research and development of tools for broodstock spawning and environmental management of S. brasiliensis and related migratory fish.

Traceability of primordial germ cells in three neotropical fish species aiming genetic conservation actions

Primordial germ cells (PGCs) are embryonic pluripotent cells that can differentiate into spermatogonia and oogonia, and therefore, PGCs are a genetic source for germplasm conservation through cryobanking and the generation of germline chimeras. The knowledge of PGC migration routes is essential for transplantation studies. In this work, the mRNA synthesized from the ddx4 3'UTR sequence of Pseudopimelodus mangurus, in fusion with gfp or dsred, was microinjected into zygotes of three neotropical species (P. mangurus, Astyanax altiparanae, and Prochilodus lineatus) for PGC labeling. Visualization of labeled PGCs was achieved by fluorescence microscopy during embryonic development. In addition, ddx4 and dnd1 expressions were evaluated during embryonic development, larvae, and adult tissues of P. mangurus, to validate their use as a PGC marker. As a result, the effective identification of presumptive PGCs was obtained. DsRed-positive PGC of P. mangurus was observed in the hatching stage, GFP-positive PGC of A. altiparanae in the gastrula stage, and GFP-positive PGCs from P. lineatus were identified at the segmentation stage, with representative labeling percentages of 29% and 16% in A. altiparanae and P. lineatus, respectively. The expression of ddx4 and dnd1 of P. mangurus confirmed the specificity of these genes in germ cells. These results point to the functionality of the P. mangurus ddx4 3'UTR sequence as a PGC marker, demonstrating that PGC labeling was more efficient in A. altiparanae and P. lineatus. The procedures used to identify PGCs in P. mangurus consolidate the first step for generating germinal chimeras as a conservation action of P. mangurus.

Henneguya patriciai n. sp. (Cnidaria: Myxosporea) parasitizing Leporinus friderici (Bloch 1794) from Tartarugalzinho river, eastern Amazon

The Amazon basin has the largest number of fish in the world, and among the most common fishes of the Neotropical region, the threespot (Leporinus friderici) is cited, which in relation to its microparasitic fauna, has described only 1 species of the genus Henneguya, Henneguya friderici. The Myxozoa class is considered an obligate parasite, being morphologically characterized by spores formed by valves connected by a suture line. This study describes a new species of Henneguya sp. in the Amazon region for L. friderici. This parasite was found in the host's pyloric caeca and caudal kidney, with mature spores with a total spore length of 38.4 ± 2.5 (35.9–40.9) μm; the spore body 14.4 ± 1.1 (13.3–15.5) μm and 7.3 ± 0.6 (6.7–7.9) μm wide. Regarding its 2 polar capsules, they had a length of 5.1 ± 0.4 (4.7–5.5) μm and a width of 2.0 ± 0.1 (1.9–2.1) μm in the same pear-shaped, and each polar capsule contained 9–11 turns. Morphological and phylogenetic analyses denote that this is a new species of the genus Henneguya.

A multi-evidence approach in an Amazonian river based on land use, water quality, histopathological effects and habitat selection behavior in fish

The Amazon rivers constitute the largest river basin in the world, with a high level of biodiversity. The Tocantins River is one of the most important rivers in this region, which has been impacted by different land uses. The objective of this study was to carry out a multi-evidence analysis focusing on the water quality of the Tocantins River, close to the municipality of Marabá-PA. We analyzed forest cover and water quality and, using the model organism Danio rerio, performed toxicity tests for histopathological effects, as well as the habitat selection approach by exposing fish to different river water samples in a multi-compartment device. The results showed that the studied area has already lost almost 30% of its forests in recent decades. Regarding water quality, the upstream (C1) and downstream (C5) points are the least impacted. On the other hand, the other points (C2-C4), closer to the city, greater input of pollutants was detected. Fish exposed to water samples from the most impacted sites showed several oedemas and hyperplastic cells in the gills. Regarding habitat selection behavior, there was a marked avoidance by samples with the highest contamination load. The results of this study lead to the understanding of the potential negative effects of human activities on local Amazonian biodiversity, since the potential toxicity of the environment, in conjunction with changes in the habitat selection process, could lead to a decline in populations of aquatic organisms, altering the environmental balance.

Southern marsh deer (Blastocerus dichotomus) populations assessed using Amplicon Sequencing on fecal samples

Populations in isolated and small fragments lose genetic variability very fast and are usually of conservation concern because they are at greater risk of local extinction. The largest native deer in South America, Blastocerus dichotomus (Illiger, 1815), is a Vulnerable species according to the IUCN categorization, which inhabits tropical and subtropical swampy areas. In Argentina, its presence has been restricted to four isolated fragments. Here we examine the genetic diversity and differentiation among three of them, including the three different patches that form the southernmost population, using 18 microsatellite markers genotyped by Amplicon Sequencing of DNA extracted from fecal samples. Genetic diversity was low (HE < 0.45) in all three populations studied. We found three genetic clusters compatible with the geographic location of the samples. We also found a metapopulation dynamics that involves the patches that make up the southernmost population, with evidence of a barrier to gene flow between two of them. Our results point to the creation of a corridor as a necessary and urgent management action. This is the first study, at the population level, employing microsatellite genotyping by Amplicon Sequencing with non-invasive samples in an endangered species.

SUPPLEMENTAL DESCRIPTION OF CABALLEROTREMA ANNULATUM (DIESING, 1850) OSTROWSKI DE NÚÑEZ AND SATTMANN, 2002 (DIGENEA: CABALLEROTREMATIDAE) FROM A NEW HOST (ELECTROPHORUS CF. VARII) AND LOCALITY (AMAZON RIVER, COLOMBIA) WITH PHYLOGENETIC ANALYSIS AND EMENDED GENERIC DIAGNOSIS

Herein, we provide a supplemental description of Caballerotrema annulatum (Diesing, 1850) Ostrowski de Núñez and Sattmann, 2002 (Digenea: Caballerotrematidae Tkach, Kudlai, and Kostadinova, 2016) based on specimens collected from the intestine of an electric eel, Electrophorus cf. varii (Gymnotiformes: Gymnotidae) captured in the Amazon River (Colombia). This caballerotrematid can be differentiated from its congeners by the following combination of morphological features: body surface spines forming contiguous transverse rows, concentric (wrapping dorso-ventrally around body), distributing into posterior body half (vs. restricted to anterior body half in Caballerotrema brasiliensePrudhoe, 1960; indeterminate for Caballerotrema aruanenseThatcher, 1980 and Caballerotrema piscicola [Stunkard, 1960] Kostadinova and Gibson, 2001); head collar lacking projections (vs. having them in C. brasiliense, C. aruanense, and C. piscicola), narrow (head collar more narrow than maximum body width vs. the head collar being obviously wider than the body in C. brasiliense, C. aruanense, and C. piscicola); corner spines clustered (vs. corner spines distributing as 2 separated pairs in C. brasiliense, C. aruanense, and C. piscicola); pharynx approximately at level of the corner spines (vs. pharynx far anterior to corner spines in C. brasiliense, C. aruanense, and C. piscicola); and testes ovoid and nonoverlapping (C. aruanense; vs. sinuous and overlapping in C. brasiliense and C. piscicola). Based on our results, we revise the diagnosis of CaballerotremaPrudhoe, 1960 to include features associated with the shape and distribution of body surface spines, orientation and position of head collar spines, cirrus sac, seminal vesicle, oviduct, Laurer's canal, oötype, vitellarium, and transverse vitelline ducts. We performed Bayesian inference analyses using the partial large subunit ribosomal (28S) DNA gene. Our 28S sequence of C. annulatum was recovered sister to that of Caballerotrema sp. (which is the only other caballerotrematid sequence available in GenBank) from an arapaima, Arapaima gigas (Schinz, 1822) (Osteoglossiformes: Arapaimidae) in the Peruvian Amazon. Our sequence of C. annulatum comprises the only caballerotrematid sequenced tethered to a morphological description and a voucher specimen in a lending museum. The present study is a new host record and new locality record for C. annulatum. The phylogeny comprises the most resolved and taxon-rich evolutionary hypothesis for Echinostomatoidea published to date.

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.

Electrosensory and metabolic responses of weakly electric fish to changing water conductivity

Weakly electric gymnotiform fishes use self-generated electric organ discharges (EODs) to navigate and communicate. The electrosensory range for these processes is a function of EOD amplitude, determined by the fish's electric organ (EO) output and the electrical conductivity of the surrounding water. Anthropogenic activity, such as deforestation, dams and industrial/agricultural runoff, are known to increase water conductivity in neotropical habitats, likely reducing the electrosensory range of these fish. We investigated whether fish modulate EO output as means of re-expanding electrosensory range after a rapid increase in water conductivity in the pulse-type Brachyhypopomus gauderio and the wave-type Eigenmannia virescens. Furthermore, because EOD production incurs significant metabolic costs, we assessed whether such compensation is associated with an increase in metabolic rate. Following the conductivity increase, B. gauderio increased EOD amplitude by 20.2±4.3% over 6 days but with no associated increase in metabolic rate, whereas the EOD amplitude of E. virescens remained constant, accompanied by an unexpected decrease in metabolic rate. Our results suggest that B. gauderio uses a compensation mechanism that requires no metabolic investment, such as impedance matching, or a physiological trade-off wherein energy is diverted from other physiological processes to increase EO output. These divergent responses between species could be the result of differences in reproductive life history or evolutionary adaptations to different aquatic habitats. Continued investigation of electrosensory responses to changing water conditions will be essential for understanding the effects of anthropogenic disturbances on gymnotiforms, and potential physiological mechanisms for adapting to a rapidly changing aquatic environment.

Integrative Taxonomy of Urocleidoides spp. (Monogenoidea, Dactylogyridae) Parasites of Pseudanos trimaculatus (Characiformes: Anostomidae) from Eastern Amazon, Brazil

Two new species of Urocleidoides are described from the gills of Pseudanos trimaculatus (Characiformes: Anostomidae) from the coastal drainages of the Eastern Amazon, Brazil. Urocleidoides itabocaensis n. sp. is characterized by having a sclerotized, tubular, sigmoid male copulatory organ (MCO), a circular sclerotized tandem brim associated with the base of the MCO; an accessory piece articulated with the MCO, a V-shaped, divided into two subunits, distal subunit spoon-shaped; and a vaginal pore dextroventral with opening marginal. Urocleidoides omphalocleithrum n. sp. is characterized by presenting a C-shaped or sigmoid MCO; an accessory piece articulated with the MCO, L-shaped, divided into two subunits, distal subunit gutter-shaped; a vaginal pore dextroventral with opening marginal; and a ventral bar broadly V-shaped, with anteromedial projection. Molecular phylogenetic analysis based on partial 28S rDNA and COI mtDNA genes indicate that U. itabocaensis n. sp. and U. omphalocleithrum n. sp. are closely related and appear as a sister group to other Urocleidoides species (U. paradoxus, U. digitabulum and U. sinus) parasitizing anostomid fishes. This study represents the first record of monogenoids from the gills of P. trimaculatus for the Eastern Amazon.

Genetic insights into Cyphocharax magdalenae (Characiformes: Curimatidae): Microsatellite loci development and population analysis in the Cauca River, Colombia

Cyphocharax magdalenae, a Colombian freshwater fish species, plays a vital role in nutrients distribution and serves as a significant food source for other fish species and local fishing communities. Considered a short-distance migratory species, C. magdalenae populations face substantial extinction risk due to human activities impacting their habitats. To address the lack of knowledge on genetic diversity and population structure, this study used next-generation sequencing technology to develop species-specific microsatellite loci and conducted a population genetics analysis of C. magdalenae in the middle and lower sections of the Cauca River, Colombia. Out of 30 pairs of microsatellite primers evaluated in 324 individuals, 14 loci were found to be polymorphic, at linkage equilibrium and, in at least one population, their genotypic frequencies were in Hardy-Weinberg equilibrium. Results showed high genetic diversity levels compared to other neotropical Characiformes, with inbreeding coefficients similar to those reported for phylogenetically related species. Moreover, C. magdalenae exhibits seasonal population structure (rainy-dry) consisting of two genetic stocks showing bottleneck signals and high effective population sizes. This information is essential for understanding the current species genetics and developing future management programs for this fishery resource.

Parasites (Monogenea) of tilapias Oreochromis niloticus and Coptodon rendalli (Cichlidae) in a river spring in Brazil

In the present study, we examined 30 individuals of introduced African cichlids, Oreochromis niloticus and Coptodon rendalli, collected in a river spring of the Pardo River, Paranapanema River basin, southeastern Brazil. Based on morphological and molecular analyses of the partial LSU rDNA gene, we identified four species of monogeneans, Cichlidogyrus tilapiae, C. thurstonae, C. mbirizei, and Scutogyrus longicornis on the gills of O. niloticus, whereas individuals of C. rendalli were infested only with C. papernastrema. This is the first record of C. mbirizei and C. papernastrema in tilapias from Brazil. The ecological consequences of the introduction of exotic species of tilapia such as O. niloticus and C. rendalli along with their monogenean parasites in a wild environment represented by a river spring are discussed. Our new molecular data on Cichlidogyrus and Scutogyrus contribute to the investigation of the phylogenetic interrelationships of these widely distributed genera of monogeneans since their species composition is still unsettled.

Increasing the species diversity of the monotypic genus Pariolius Cope 1872 (Siluriformes: Heptapteridae) after more than 150 years

Pariolius is a heptapterid genus represented by P. armillatus that is distributed along the upper Amazon River basin. A taxonomic integrative revision of Pariolius from Colombian Rivers revealed two new species. Several approaches as morphological, morphometric, meristic, osteology and molecular data were used to distinguish between Pariolius species. The two new species are distinguished from congeners by the caudal-fin shape and numbers of rays, colorations patterns and several morphometric characters. The two new species of Pariolius are restricted to tributaries of the Upper Orinoco and Upper Negro rivers in Colombia.

Improving the efficiency of adaptive management methods in multiple fishways using environmental DNA

Dams and weirs impede the continuity of rivers and transit of migratory fish. To overcome this obstacle, fishways are installed worldwide; however, management after installation is important. The Miyanaka Intake Dam has three fish ladders with different flow velocities and discharges and has been under adaptive management since 2012. Fish catch surveys, conducted as an adaptive management strategy, place a heavy burden on fish. Furthermore, a large number of investigators must be mobilized during the 30-day investigation period. Thus, a monitoring method using environmental DNA that exerts no burden on fish and requires only a few surveyors (to obtain water samples) and an in-house analyst was devised; however, its implementation in a fishway away from the point of analysis and with limited flow space and its effective water sampling frequency have not been reported. Therefore, in 2019, we started a trial aiming to evaluate the methods and application conditions of environmental DNA surveys for the continuous and long-term monitoring of various fish fauna upstream and downstream of the Miyanaka Intake Dam. To evaluate the fish fauna, the results of an environmental DNA survey (metabarcoding method) for 2019 to 2022 were compared to those of a catch survey in the fishway from 2012 to 2022. The results confirmed the use of environmental DNA surveys in evaluating the contribution of fishways to biodiversity under certain conditions and introduced a novel method for sample collection.

Characterizing functional morphology and trophic niches in a neotropical Characiforms (Actinopterygii: Teleostei) assemblage in middle Munim River basin, Maranhão, Brazil

Understanding how functionally similar species segregate resources to minimize competition is vital for predicting evolutionary factors and patterns of coexistence. We conducted a study in Mata de Itamacaoca, in the middle Munim River basin, Maranhão, northeastern Brazil, to characterize the functional morphology and trophic niches of five coexisting Characiform species in this area - including a recently described species, and to investigate whether their functional morphology is a key determinant of their trophic niches. Our analysis of functional morphology and diet, employing linear measurements to predict dietary specializations, showed that these species are predominantly generalist insectivores with a significant morphological overlap. This study underscores the influence of species' natural history on their ecological characteristics, contributing to more effective conservation strategies.

Phylogenomics of the narrowly endemic Eurycheilichthys (Siluriformes: Loricariidae): Sympatric species with non-sister relationships suggest mainly allopatric speciation

Armored catfishes of the genus Eurycheilichthys are endemic to Southern Brazil and Misiones (Argentina) comprising nine species of small size, with a high degree of sympatry and species diversity distributed in two river basins. Here we use new genome-wide data to infer a species phylogeny and test species boundaries for this poorly known group. We estimate 1) the phylogenetic relationships of the species of Eurycheilichthys based on 29,350 loci in 65 individuals of nine species plus outgroups, and 2) the population structure and differentiation based on 43,712 loci and 62 individuals to estimate how geography may have acted on speciation and formation of the sympatric species groups. Analyses support the monophyly of the genus and suggest two species-inclusive clades (East and West) with high support and very recently diverged species. Western clade contains E. limulus (from upper Jacuí River basin) that is sister to Western species of the Taquari-Antas basin plus E. paucidens. The Eastern clade contains E. pantherinus (from Uruguay River basin) sister to the Eastern species of the Taquari-Antas basin E. coryphaenus, plus the central-distributed species E. planus and E. vacariensis, and the more widely-distributed species E. luisae. Eurycheilichthys luisae is not monophyletic and may contain one or more cryptic species or hybrid individuals. A stronger diversity on structure of lineages on the Taquari-Antas, when compared to upper Uruguay and Jacuí River basins, and the fact that most of the sympatrically distributed taxa have non-sister relationships suggest a scenario of mainly allopatric speciation and may indicate a more dynamic landscape with headwater capture events among these tributaries.

Dactylogyrids (Platyhelminthes, Monogenea) from the gill lamellae of doradids (Siluriformes) with description of five new species of Cosmetocleithrum and new geographical distribution for known species from the Neotropical Region, Brazil

Five new species of Cosmetocleithrum were described parasitizing the gill filaments of neotropical doradid fishes. Cosmetocleithrum undulatum n. sp., Cosmetocleithrum brachylecis n. sp. and Cosmetocleithrum ludovicense n. sp. are described from Platydoras brachylecis from a market-place of São Luís, State of Maranhão, Brazil. Cosmetocleithrum sacciforme n. sp. and Cosmetocleithrum basicomplexum n. sp. are described from Oxydoras niger from Juruá River, State of Acre, Brazil. Cosmetocleithrum undulatum and Cosmetocleithrum brachylecis resemble Cosmetocleithrum falsunilatum Feronato, Razzolini, Morey & Boeger, 2022 mainly by the unique male copulatory organ (MCO) morphology but differ from these and all congeneric species mainly by the morphology of the MCO, accessory piece and hooks pairs. Cosmetocleithrum ludovicense is closer to Cosmetocleithrum confusus Kritsky, Thatcher & Boeger, 1986 and to Cosmetocleithrum akuanduba Soares, Santos Neto & Domingues, 2018 but differs from those mainly by the morphology of the accessory piece. Cosmetocleithrum sacciforme differs from all congeneric species mainly by the morphology of the accessory piece formed by a single plate of saccular appearance. Cosmetocleithrum basicomplexum also shares morphological characters with Cosmetocleithrum gigas Morey, Cachique & Babilonia, 2019 considering the size of the body and shape of the anchors, but differs mainly in the morphology of the bars and hooks. Besides the new species, new data are presented for Cosmetocleithrum leandroi Soares, Neto & Domingues, 2018, C. akuanduba and C. confusus regarding morphological characteristics and biogeography.

Freshwater fish diversity in the western Amazon basin shaped by Andean uplift since the Late Cretaceous

South America is home to the highest freshwater fish biodiversity on Earth, and the hotspot of species richness is located in the western Amazon basin. The location of this hotspot is enigmatic, as it is inconsistent with the pattern observed in river systems across the world of increasing species richness towards a river's mouth. Here we investigate the role of river capture events caused by Andean mountain building and repeated episodes of flooding in western Amazonia in shaping the modern-day richness pattern of freshwater fishes in South America, and in Amazonia in particular. To this end, we combine a reconstruction of river networks since 80 Ma with a mechanistic model simulating dispersal, allopatric speciation and extinction over the dynamic landscape of rivers and lakes. We show that Andean mountain building and consequent numerous small river capture events in western Amazonia caused freshwater habitats to be highly dynamic, leading to high diversification rates and exceptional richness. The history of marine incursions and lakes, including the Miocene Pebas mega-wetland system in western Amazonia, played a secondary role.

Comparison of seven complete mitochondrial genomes from Lamprologus and Neolamprologus (Chordata, Teleostei, Perciformes) and the phylogenetic implications for Cichlidae

In this study, mitochondrial genomes (mitogenomes) of seven cichlid species (Lamprologuskungweensis, L.meleagris, L.ornatipinnis, Neolamprologusbrevis, N.caudopunctatus, N.leleupi, and N.similis) are characterized for the first time. The newly sequenced mitogenomes contained 37 typical genes [13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs) and 22 transfer RNA genes (tRNAs)]. The mitogenomes were 16,562 ~ 16,587 bp in length with an A + T composition of 52.1~58.8%. The cichlid mitogenomes had a comparable nucleotide composition, A + T content was higher than the G + C content. The AT-skews of most mitogenomes were inconspicuously positive and the GC-skews were negative, indicating higher occurrences of C than G. Most PCGs started with the conventional start codon, ATN. There was no essential difference in the codon usage patterns of these seven species. Using Ka/Ks, we found the fastest-evolving gene were atp8. But the results of p-distance indicated that the fastest-evolving gene was nad6. Phylogenetic analysis revealed that L.meleagris did not cluster with Lamprologus species, but with species from the genus Neolamprologus. The novel information obtained about these mitogenomes will contribute to elucidating the complex relationships among cichlid species.

Inventory reveals non-native species and variation in spatial-temporal dynamics of fish community in a Brazilian protected area

The increase in the number of Brazilian protected areas has been progressive and, although it is essential for the conservation of biodiversity, it is important to monitor and properly manage these areas, as they present several cases of biological invasions. The Lençóis Maranhenses constitute the peculiar delta of the Americas and are under the consequences of the bioinvasion of tilapias and peacock bass. Collections were carried out in the Lençóis Maranhenses National Park from March/2016 to November/2020, with the aid of gill nets and cast nets. The species were identified with the help of specialized literature and a historical comparison with previous works was carried out. Cytochrome oxidase subunit I was sequenced to confirm identification of non-native species. We recorded the expansion of the occurrence of Oreochromis niloticus, and the first record of the species Oreochromis mossambicus and Cichla monoculus. A total of 31 species belonging to eight orders, eighteen families and twenty-nine genera were identified, indicating a lag in the diversity of species found in relation to previous studies. After 20 years of the first record of invasive fish, there is an expansion of bioinvasion and new cases that indicate a lack of monitoring and containment measures for the species, indicating the fragility of conservation in the area.

Speciation in Coastal Basins Driven by Staggered Headwater Captures: Dispersal of a Species Complex, Leporinus bahiensis, as Revealed by Genome-wide SNP Data

Past sea level changes and geological instability along watershed boundaries have largely influenced fish distribution across coastal basins, either by dispersal via palaeodrainages now submerged or by headwater captures, respectively. Accordingly, the South American Atlantic coast encompasses several small and isolated drainages that share a similar species composition, representing a suitable model to infer historical processes. Leporinus bahiensis is a freshwater fish species widespread along adjacent coastal basins over narrow continental shelf with no evidence of palaeodrainage connections at low sea level periods. Therefore, this study aimed to reconstruct its evolutionary history to infer the role of headwater captures in the dispersal process. To accomplish this, we employed molecular-level phylogenetic and population structure analyses based on Sanger sequences (5 genes) and genome-wide SNP data. Phylogenetic trees based on Sanger data were inconclusive, but SNPs data did support the monophyletic status of L. bahiensis. Both COI and SNP data revealed structured populations according to each hydrographic basin. Species delimitation analyses revealed from 3 (COI) to 5 (multilocus approach) MOTUs, corresponding to the sampled basins. An intricate biogeographic scenario was inferred and supported by Approximate Bayesian Computation (ABC) analysis. Specifically, a staggered pattern was revealed and characterized by sequential headwater captures from basins adjacent to upland drainages into small coastal basins at different periods. These headwater captures resulted in dispersal throughout contiguous coastal basins, followed by deep genetic divergence among lineages. To decipher such recent divergences, as herein represented by L. bahiensis populations, we used genome-wide SNPs data. Indeed, the combined use of genome-wide SNPs data and ABC method allowed us to reconstruct the evolutionary history and speciation of L. bahiensis. This framework might be useful in disentangling the diversification process in other neotropical fishes subject to a reticulate geological history.

Fish diversity in the rivers that drain the Baixada Maranhense and the Mearim basin in northeastern Brazil

The Baixada Maranhense Environmental Protection Area of the Brazilian state of Maranhão encompasses a biologically rich region that includes the basins of four principal rivers, the Mearim, Pericumã, Pindaré, and Turiaçu, which form a complex of wetlands. The present study provides a comprehensive inventory of the fish fauna of the rivers that drain the Baixada Maranhense based on the identification of voucher specimens that were deposited in a scientific collection. Expeditions were conducted between 2014 and 2020. The inventory identified a total of 100 fish species representing 79 genera, 34 families, and 11 orders, which are found in both freshwater and estuarine environments. Six (Potamotrygon orbignyi, Leporinus piau, Moenkhausia loweae, Serrasalmus spilopleura, Pachypops fourcroi and Peckoltia greedoi) of the 100 taxa identified here are considered to be new records for one or more of the basins surveyed during this study, based on the existing data, while four - Colossoma macropomum, Megaleporinus macrocephalus, Cichla sp. and Cichla kelberi - are not native. The most speciose orders were the Siluriformes and Characiformes, while the most diverse families were the Loricariidae, Characidae, Auchenipteridae, Cichlidae, and Serrasalmidae. These data are consistent with the findings of most of the previous studies of freshwater ecosystems in the Neotropical region, in particular those of the rivers of Maranhão. The results of the present study represent an important advance in the understanding of the diversity of the fish fauna of the Mearim, Pericumã, Pindaré, and Turiaçu rivers, which are still poorly studied, and have likely had their diversity underestimated up to now.

Metazoan parasites of Hoplias aff. malabaricus, Trachelyopterus galeatus and Schizodon borellii (Osteichthyes) from the Protected Area and its main tributary, Brazil

A study of the parasite-host interactions was conducted in the protected area popularly known as the "Refúgio Biológico de Santa Helena" and its tributary, the São Francisco Falso River. For each of the three host species, Schizodon borellii, Hoplias aff. malabaricus, and Trachelyopterus galeatus, 30 fish were collected from 2018 to 2019. A total of 2172 parasites were identified among the three host species. Among these, the Monogenea class had the highest number of species, with 26 taxa, followed by Copepoda with eight taxa, Digenea with six taxa, and Cestoda and Nematoda with one taxon each. Eleven new records of infection/infestation were found among the host species such as Urocleidoides paradoxus, Urocleidoides ramentacuminatus, Rhinoxenus arietinus, Mymarothecioides sp. (Monogenea), Ergasilus cf. bryconis, Lernaea devastatrix, and Brasergasilus sp. (Copepoda) parasitizing S. borellii. Trinigyrus sp., Vancleaveus sp. (Monogenea), Gamispinus diabolicus (Copepoda) present in T. galeatus, and Gamidactylus jaraquensis (Copepoda) present in H. aff. malabaricus. This study contributes to the record of parasite species occurrence in the vicinity of a protected area and helps fill gaps in the knowledge of fish parasitic fauna in the Neotropical region.

Influence of abiotic factors on the composition of fish assemblages in the Aracá-Demeni sub-basin of the middle Negro River

We evaluated the influence of flooding and receding comparison and spatial variation on the composition and structure of fish assemblages in blackwater and clearwater rivers of the Aracá-Demeni sub-basin in the middle Negro River, Amazonas state, Brazil. The collections were carried out during the falling-water period (November 2018) and the rising-water period (April 2019) using gillnets with meshes ranging from 30 to 120mm stretched mesh size. Ecological estimates of richness, equitability, the Shannon-Wiener diversity index, and the Berger-Parker index showed no significant differences between the periods. The composition of the ichthyofauna showed variations between the falling-water and rising-water periods. Beta diversity in the Aracá-Demeni sub-basin is almost completely caused by species substitution, with spatial turnover accounting for most of the estimate. The identification of these patterns and of the responsible factors are fundamental for the definition of conservation strategies, especially in an ecosystem whose dynamics can be influenced by climate change through changes in the intensity of the flood pulse and connectivity.

Integrating Genomic and Chromosomal Data: A Cytogenetic Study of Transancistrus santarosensis (Loricariidae: Hypostominae) with Characterization of a ZZ/ZW Sex Chromosome System

The plecos (Loricariidae) fish represent a great model for cytogenetic investigations due to their variety of karyotypes, including diploid and polyploid genomes, and different types of sex chromosomes. In this study we investigate Transancistrus santarosensis a rare loricariid endemic to Ecuador, integrating cytogenetic methods with specimens' molecular identification by mtDNA, to describe the the species karyotype. We aim to verify whether sex chromosomes are cytologically identifiable and if they are associated with the accumulation of repetitive sequences present in other species of the family. The analysis of the karyotype (2n = 54 chromosomes) excludes recent centric fusion and pericentromeric inversion and suggests the presence of a ZZ/ZW sex chromosome system at an early stage of differentiation: the W chromosome is degenerated but is not characterized by the presence of differential sex-specific repetitive DNAs. Data indicate that although T. santarosensis has retained the ancestral diploid number of Loricariidae, it accumulated heterochromatin and shows non-syntenic ribosomal genes localization, chromosomal traits considered apomorphic in the family.

Contrasts in riverscape patterns of intraspecific genetic variation in a diverse Neotropical fish community of high conservation value

Spatial patterns of genetic variation compared across species provide information about the predictability of genetic diversity in natural populations, and areas requiring conservation measures. Due to their remarkable fish diversity, rivers in Neotropical regions are ideal systems to confront theory with observations and would benefit greatly from such approaches given their increasing vulnerability to anthropogenic pressures. We used SNP data from 18 fish species with contrasting life-history traits, co-sampled across 12 sites in the Maroni- a major river system from the Guiana Shield -, to compare patterns of intraspecific genetic variation and identify their underlying drivers. Analyses of covariance revealed a decrease in genetic diversity as distance from the river outlet increased for 5 of the 18 species, illustrating a pattern commonly observed in riverscapes for species with low-to-medium dispersal abilities. However, the mean within-site genetic diversity was lowest in the two easternmost tributaries of the Upper Maroni and around an urbanized location downstream, indicating the need to address the potential influence of local pressures in these areas, such as gold mining or fishing. Finally, the relative influence of isolation by stream distance, isolation by discontinuous river flow, and isolation by spatial heterogeneity in effective size on pairwise genetic differentiation varied across species. Species with similar dispersal and reproductive guilds did not necessarily display shared patterns of population structure. Increasing the knowledge of specific life history traits and ecological requirements of fish species in these remote areas should help further understand factors that influence their current patterns of genetic variation.

Phylogeography and population genetic structure of the cardinal tetra (Paracheirodon axelrodi) in the Orinoco basin and Negro River (Amazon basin): evaluating connectivity and historical patterns of diversification

The Neotropics contain one of the most diverse assemblages of freshwater fishes worldwide. Part of this diversity is shared between the Orinoco and Amazon basins. These basins have been separated for a long time due to the Vaupes Arch, rising between 10-11 Ma. Today, there is only one permanent connection between the Orinoco and Negro (Amazon) basins, known as the Casiquiare Canal. However, alternative corridors allowing fish dispersion between both basins have been proposed. The cardinal tetra (Paracheirodon axelrodi), the most important fish in the ornamental world market, is distributed in both basins. Here we investigated P. axelrodi phylogeography, population structure, and potential routes of migration and connectivity between the two basins. A total of 468 bp of the mitochondrial gene (COI), 555 bp of the nuclear gene fragment (MYH6), and eight microsatellite loci were analyzed. As a result, we found two major genetic clusters as the most likely scenario (K = 2), but they were not discreetly distributed between basins. A gradient of genetic admixture was observed in Cucui and São Gabriel da Cachoeira, between the upper Negro River and the upper Orinoco. Samples from the middle-lower Negro River were highly structured. Cucui (Negro basin) was more similar to the Orinoco than to the rest of the Negro basin populations. However, substructure was also observed by the discriminant analysis, fixation indices and other hierarchichal structure analyses (K = 3 - 6), showing three major geographic clusters: Orinoco, Cucui, and the remaining Negro basin. Unidirectional migration patterns were detected between basins: via Cucui toward Orinoco and via the remaining of the Negro basin toward Orinoco. Results from the Relaxed Random Walk analysis support a very recent origin of this species in the headwater Orinoco basin (Western Guiana Shield, at late Pleistocene) with a later rapid colonization of the remaining Orinoco basin and almost simultaneously the Negro River via Cucui, between 0.115 until about 0.001 Ma. Historical biogeography and population genetic patterns observed here for Cardinal tetra, seem to be better explained by river capture, physical, or ecological barriers than due to the geographic distance.

Bridging archaeology and marine conservation in the Neotropics

Anthropogenic impacts on tropical and subtropical coastal environments are increasing at an alarming rate, compromising ecosystem functions, structures and services. Understanding the scale of marine population decline and diversity loss requires a long-term perspective that incorporates information from a range of sources. The Southern Atlantic Ocean represents a major gap in our understanding of pre-industrial marine species composition. Here we begin to fill this gap by performing an extensive review of the published data on Middle and Late Holocene marine fish remains along the southern coast of Brazil. This region preserves archaeological sites that are unique archives of past socio-ecological systems and pre-European biological diversity. We assessed snapshots of species compositions and relative abundances spanning the last 9500 years, and modelled differences in species' functional traits between archaeological and modern fisheries. We found evidence for both generalist and specialist fishing practices in pre-European times, with large body size and body mass caught regularly over hundreds of years. Comparison with modern catches revealed a significant decline in these functional traits, possibly associated with overfishing and escalating human impacts in recent times.

Fish response to the presence of hydrokinetic turbines as a sustainable energy solution

Hydrokinetic turbines such as vertical axis turbines (VATs) may provide decentralised, clean, sustainable energy for remote communities that lack access to the main energy grid or renewable resources. As traditional hydropower adversely alters aquatic ecosystems, it is essential to evaluate the environmental consequences of deploying VATs in riverine ecosystems to meet current and future energy needs. This study explores the implications of VATs on fish movement by observing fish swimming behaviour under two discharges, turbine operation states, and cross-sections confinements using scaled laboratory experiments. Our findings reveal that for cross-sectional confined conditions neither discharge, turbine presence, nor device operation, prevented fish from passing around and through the turbine both in the up- and downstream directions. However, fish spent the least time near the turbine vicinity and within the turbine's turbulent, low-velocity wake, indicating avoidance behaviour. Swimming in a less confined test section further reduced the time spent within the turbine's vicinity and wake, increasing the distance fish kept away from the device. Our results contribute to an understanding of VATs as low-risk hazards for fish swimming behaviour, advancing the potential of deploying VATs in rivers, estuaries or sea as a renewable energy solution for remote communities.

Genetic population structure of Pseudoplatystoma corruscans (Siluriformes: Pimelodidae) and evidence of temporal variation in structure

Surubim (Pseudoplatystoma corruscans, Pimelodidae) are migratory catfish native to the rivers in the La Plata and São Francisco basins. They are piscivores that attain considerable body sizes and are a valuable economic resource. Surubim exhibits extensive migrations during its life cycle that may affect the population structure at vast geographic scales. The authors examined the genetic diversity and population genetic structure of P. corruscans using microsatellite markers from a comprehensive sampling of 260 individuals from the Upper and Lower Paraná River. They identified two well-differentiated genetic clusters corresponding to a natural geographic barrier historically separating Upper and Lower Paraná regions. They also demonstrated temporal variation in population genetic structure at a site in Lower Paraná close to the confluence with the Paraguay River, most likely explained by the influx of migrant fishes at certain times of the year.

Application of a deep learning image classifier for identification of Amazonian fishes

Given the sharp increase in agricultural and infrastructure development and the paucity of widespread data available to support conservation management decisions, a more rapid and accurate tool for identifying fish fauna in the world's largest freshwater ecosystem, the Amazon, is needed. Current strategies for identification of freshwater fishes require high levels of training and taxonomic expertise for morphological identification or genetic testing for species recognition at a molecular level. To overcome these challenges, we built an image masking model (U-Net) and a convolutional neural net (CNN) to classify Amazonian fish in photographs. Fish used to generate training data were collected and photographed in tributaries in seasonally flooded forests of the upper Morona River valley in Loreto, Peru in 2018 and 2019. Species identifications in the training images (n = 3068) were verified by expert ichthyologists. These images were supplemented with photographs taken of additional Amazonian fish specimens housed in the ichthyological collection of the Smithsonian's National Museum of Natural History. We generated a CNN model that identified 33 genera of fishes with a mean accuracy of 97.9%. Wider availability of accurate freshwater fish image recognition tools, such as the one described here, will enable fishermen, local communities, and citizen scientists to more effectively participate in collecting and sharing data from their territories to inform policy and management decisions that impact them directly.

Diversidad, abundancia y dominancia de las especies ícticas en el río Churute, Ecuador

En esta investigación se evaluó la diversidad de especies nativas e introducidas en el río Churute, el cual atraviesa la Reserva Ecológica Manglares Churute, en Ecuador, utilizando para ello un enfoque empírico-inductivo, con diseño no experimental de corte transversal-explicativo. Las capturas se realizaron con atarraya, arte de pesca tradicional en época de sequía, a lo largo del río Churute. Se muestrearon 25 sitios, considerando 33 lances como esfuerzo de pesca por cada sitio, y los peces capturados fueron clasificados taxonómicamente, contados y pesados para estimar los índices ecológicos de riqueza, abundancia, diversidad y dominancia en el área de estudio. Se identificaron 20 especies ícticas (19 nativas y 1 introducida) distribuidas en 18 géneros de 13 familias y 5 órdenes; las familias con mayor número de especies fue CICHLIDAE con cuatro especies, BRYCONIDAE, CHARACIDAE, ELEOTRIDAE y HEPTAPTERIDAE con dos especies cada una. De las especies identificadas, siete calificaron como importantes, sobresaliendo la tilapia, pez introducido con un Índice de Importancia Relativa (IRI) de 40.075,58, dominando en los sitios de muestreo en un 61,13 %. Se concluye que la tilapia es una especie dominante, con tasas de reproducción superiores al de las especies nativas presentes en el río Churute, por lo que su presencia constituye una seria amenaza a la biodiversidad de este ecosistema.

Microplastics in fishes in amazon riverine beaches: Influence of feeding mode and distance to urban settlements

Microplastic (MP) pollution is a global problem and has affected several biological levels even in protected areas. In the present study, MP contamination was investigated in fish associated with sandy beaches in a permanent environmental protection area in the Amazon. In order to achieve this goal, the shape, color, abundance, richness, and chemical composition of MPs in the digestive tract of 29 fish species in 24 beaches of the Machado River, western Brazilian Amazon, were evaluated. Linear mixed models (LMMs) were adjusted to test the effects of local human modification (HMc), distance from urban settlements, distance from the closest affluent, and trophic categories of fish species on microplastic abundance and richness in their digestive tracts. From the 1082 fish analyzed, 332 (30 %) presented MPs in their digestive tracts. A total of 617 MPs was found (1.8 ± 1.6 MPs; 4.5 ± 1.9 MPs/g fish). Omnivorous and insectivorous fish presented more MPs in sandy beaches located closer to urban settlements. However, carnivorous fish presented a higher abundance of MPs in their digestive tracts compared with the other trophic guilds. This is the first study to analyze plastic contamination in fish associated with sandy beaches in the Amazon (Brazil), and it revealed contamination of the ichthyofauna mainly related to the distance from urban settlements. Our results reinforce the need for better management of landscape surrounding protected areas to mitigate MP pollution.

Checklist of the fish fauna of the Munim River Basin, Maranhão, north-eastern Brazil

Background

The Maranhão State harbours great fish diversity, but some areas are still undersampled or little known, such as the Munim River Basin in the northeast of the State. This lack of knowledge is critical when considering anthropogenic impacts on riverine systems especially in the face of major habitat destruction. These pressing threats mean that a comprehensive understanding of diversity is critical and fish checklists extremely relevant. Therefore, the present study provides a checklist of the fish species found in the Munim River Basin, Maranhão State, north-eastern Brazil, based on collected specimens.

New information

A total of 123 species were recorded for the Munim River Basin, with only two non-native species, Oreochromisniloticus and Colossomamacropomum, showing that the fish assemblage has relatively high ecological integrity. In addition, 29 species could not be identified at the species level, indicating the presence of species that are probably new to science in the Basin. A predominance of species belonging to the fish orders Characiformes and Siluriformes, with Characidae being recovered as the most species-rich family (21 species) agrees with the general pattern for river basins in the Neotropical Region. The total fish diversity was estimated by extensive fieldwork, including several sampling gears, carried out in different seasons (dry and rainy) and exploring different environments with both daily and nocturnal sampling, from the Basin's source to its mouth. A total of 84 sites were sampled between 2010 and 2022, resulting in 12 years of fieldwork. Fish assemblages were distinct in the Estuary and Upper river basin sections and more similar in the Lower and Middle sections indicating environmental filtering processes. Species were weakly nested across basin sections, but unique species were found in each section (per Simpsons Index). High variability of species richness in the Middle river basin section is likely due to microhabitat heterogeneity supporting specialist fish communities.

Identifying fish eggs and larvae: from classic methodologies to DNA metabarcoding

Studies involving fish eggs and larvae date back to the end of the nineteenth century. Since then, studies with ichthyoplankton have proved to be an essential tool, generating information for the knowledge of the ichthyofauna and the environmental inventory. Most of these studies reveal the difficulty of obtaining a precise taxonomic identification of the collected materials, making research with ichthyoplankton extremely challenging. With the advent of molecular biology, the use of markers such as COI enabled greater taxonomic precision, helping to understand events involving ichthyofauna. Now we can observe the evolution of the molecular identification tool for ichthyoplankton via DNA barcoding, which has been increasingly used over the last few decades. From 2000 to 2010, we found six publications; from 2011 to 2021, 75 papers were published, and in 2022 four studies. Our survey also showed the accuracy of molecular identification when compared to the taxonomic identification of these. In this review, we show the state of the art of studies that used barcode and DNA metabarcoding to identify fish eggs and larvae in different environments and discuss their importance as the best practice for working with these organisms.

Chromosomal rearrangements and the first indication of an ♀X1 X1 X2 X2 /♂X1 X2 Y sex chromosome system in Rineloricaria fishes (Teleostei: Siluriformes)

Rineloricaria is the most diverse genus within the freshwater fish subfamily Loricariinae, and it is widely distributed in the Neotropical region. Despite limited cytogenetic data, records from southern and south-eastern Brazil suggest a high rate of chromosomal rearrangements in this genus, mirrored in remarkable inter- and intraspecific karyotype variability. In the present work, we investigated the karyotype features of Rineloricaria teffeana, an endemic representative from northern Brazil, using both conventional and molecular cytogenetic techniques. We revealed different diploid chromosome numbers (2n) between sexes (33♂/34♀), which suggests the presence of an ♀X₁ X₁ X₂ X₂ /♂X₁ X₂ Y multiple sex chromosome system. The male-limited Y chromosome was the largest and the only biarmed element in the karyotype, implying Y-autosome fusion as the most probable mechanism behind its origination. C-banding revealed low amounts of constitutive heterochromatin, mostly confined to the (peri)centromeric regions of most chromosomes (including the X₂ and the Y) but also occupying the distal regions of a few chromosomal pairs. The chromosomal localization of the 18S ribosomal DNA (rDNA) clusters revealed a single site on chromosome pair 4, which was adjacent to the 5S rDNA cluster. Additional 5S rDNA loci were present on the autosome pair 8, X₁ chromosome, and in the presumed fusion point on the Y chromosome. The probe for telomeric repeat motif (TTAGGG)_n revealed signals of variable intensities at the ends of all chromosomes except for the Y chromosome, where no detectable signals were evidenced. Male-to-female comparative genomic hybridization revealed no sex-specific or sex-biased repetitive DNA accumulations, suggesting a presumably low level of neo-Y chromosome differentiation. We provide evidence that rDNA sites might have played a role in the formation of this putative multiple sex chromosome system and that chromosome fusions originate through different mechanisms among different Rineloricaria species.

Global trends, biases and gaps in the scientific literature about freshwater fish eggs and larvae

Syntheses of knowledge are important to reveal trends, biases and gaps in the scientific literature, indicating main data shortfalls and research needs. In this regard, the authors conducted a broad systematic review on the literature about freshwater fish eggs and larvae to investigate (a) temporal trends in the global scientific production, (b) the scope and habitat types, (c) the spatial distribution of studies, (d) the fish species contemplated and their respective conservation status and (e) the factors associated with the spatial distribution of studies. They analysed 654 studies published between 1950 and 2020. The number of studies has increased over time, but with a weak trend. Most studies investigated basic questions about biology and ecology and were carried out chiefly in rivers and lakes. These studies covered 95 freshwater ecoregions (22.3% of all ecoregions) and recorded 871 fish species (4.8% of all freshwater fish currently described). Most species were assessed by the IUCN and classified into six threat categories, but approximately 35% were not evaluated. The main drivers affecting the spatial distribution of studies were ecoregion area, road density, river volume and the number of hydroelectric plants. Results point to significant biases and gaps in the global scientific literature on fish eggs and larvae, especially associated with habitat type, spatial distribution and target species, emphasizing the need to address specific topics. Such biases and gaps indicate the existence of important data shortfalls, which compromise management and conservation planning, as information on fish eggs and larvae is basic and critical for the assessment of fish recruitment and population dynamics.

The freshwater fishes from the Costa Verde Fluminense region of southeastern Brazil

Abstract The region between the Brazilian Shield and the Atlantic Ocean is characterized by the presence of numerous hydrographic basins isolated by mountainous terrain that flow directly into the ocean without forming wide coastal plains. However, knowledge about the diversity and distribution of freshwater fish in several coastal areas is still incipient. One of these areas is the Costa Verde Fluminense region, situated between the municipalities of Mangaratiba and Paraty in the Brazilian State of Rio de Janeiro. In order to eliminate the gap of knowledge about the freshwater fish fauna of this region, we prepared a list of the species, and dichotomous identification keys and illustrations of all species. We examined material from expeditions carried out between 1942 and 2019, deposited in the Ichthyological Collection of the Museu Nacional, Universidade Federal do Rio de Janeiro, Brazil. The material comes from 29 continental coastal rivers and four drainages on Ilha Grande island. We recognized 54 fish species belonging to 16 families and 9 orders. The order Siluriformes was the most diverse with 18 species, followed by Characiformes with 14 species, Cyprinodontiformes with 10 species, Cichliformes with four species, Gobiiformes with three species, Syngnathiformes with two species, and Gymnotiformes, Salmoniformes and Synbranchiformes with one species each. These records include two putative undescribed species and four introduced species. Phalloceros anisophallos was the most widely distributed species, recorded in 24 drainages. More than a half (52 %) of the native species occur exclusively in coastal streams, demonstrating the importance of the area for biogeographic and conservation studies.