Fish biodiversity and conservation in South America

Fine-scale genetic structure of suckermouth Hypostomus ancistroides populations: the importance of Neotropical streams for fish conservation

In the Neotropics, freshwater streams harbour high fish diversity and are constantly threatened by anthropogenic disturbance. However, there are few studies on the genetic diversity of fish populations inhabiting these streams. We aimed to assess, based on microsatellite and mitochondrial DNA markers, the population structure and genetic diversity of the suckermouth catfish, Hypostomus ancistroides, a Neotropical species widely distributed across the Upper Paraná River Basin in South America. Twenty-five locations were sampled, distributed across 18 sites in six tributary streams and another seven sites in the main river channel. Our analyses revealed a spatial heterogeneity in genetic diversity within the basin, indicating fine-scale genetic structuring. Samples from all streams showed exclusive haplotypes and private alleles, reinforcing the importance of preserving the tributaries for the conservation of the genetic diversity of the studied populations. The fine-scale genetic structuring of H. ancistroides is probably related to the limited displacement capacity of this species.

Patterns of Pelagic Fish Diversity in Floodplain Lakes of Whitewater and Blackwater Drainage Systems Within the Central Amazon River Basin of Brazil

The Amazon River Basin, one of the world’s most threatened ecosystems, has an enormous diversity of fish species, a result of temporally and spatially complex habitat containing biogeochemically different river systems. The annual hydrologic cycle results in floodplain lakes during low water and inundates forests during high water, exposing fish to different resources and environmental conditions. The two principal river systems in the central Brazilian Amazon are blackwater, with nutrient-poor acidic water, and nutrient-rich whitewater. Although species-rich, the Amazon Basin is data-poor in terms of comparative studies on a regional scale. We analyzed data sets from independent sampling studies of pelagic fish in 16 floodplain lakes, nine whitewater (Rio Solimões) and seven blackwater (Rio Negro), in the central Amazon Basin of Brazil. Our findings suggest striking similarities in pelagic fish diversity patterns. Species richness was virtually equal (165 in whitewater and 168 in blackwater). Both species richness, and number of migratory species, per lake increased toward the confluence of the rivers in both systems in our study. The proportion of unique species was also similar in whitewater lakes and blackwater (41 and 43%, respectively), boosting total regional richness to 237 species. However, species composition in whitewater lakes was more homogenous (lower β diversity), and species composition was associated with conductivity and pH in whitewater, but with dissolved oxygen and transparency in blackwater. Therefore, regional fish diversity cannot be represented by sampling one lake or even one drainage system, but must include multiple lakes from both systems. These two systems may differ in sensitivity to anthropogenic stressors such as damming and deforestation.

Cryptic diversity and diversification processes in three cis-Andean Rhamdia species (Siluriformes: Heptapteridae) revealed by DNA barcoding

The wide distribution of the Neotropical freshwater catfish Rhamdia offers an excellent opportunity to investigate the historical processes responsible for modeling South America’s hydrogeological structure. We used sequences from cis-Andean and Mesoamerican Rhamdia species to reconstruct and estimate divergence times among cis-Andean lineages, correlating the results with known geological events. Species delimitation methods based on distance (DNA barcoding and BIN) and coalescence (GMYC) approaches identified nine well-supported lineages from the cis-Andean region from sequences available in the BOLD dataset. The cis-Andean Rhamdia lineages diversification process began in Eocene and represented the split between cis-Andean and Mesoamerican clades. The cis-Andean clade contains two principal groups: Northwest clade (MOTUs from Amazon, Essequibo, Paraguay, and Itapecuru basins) and Southeast clade (Eastern Brazilian shield basins (Paraná, Uruguay, Iguaçu, and São Francisco) plus eastern coastal basins). The diversification of the cis-Andean Rhamdia lineages results from vicariance and geodispersion events, which played a key role in the current intricate distribution pattern of the Rhamdia lineages. The wide geographical distribution and large size of the specimens make it attractive to cultivate in different countries of the Neotropical region. The lineages delimitation minimizes identification mistakes, unintentional crossings by aquaculture, and reduces natural stocks contamination.

Qualitative and quantitative study of parasites of Pimelodus maculatus and Rhamdia quelen from the Jacaré-Pepira River, state of São Paulo, Brazil

In the freshwater ecosystems of Brazil can be found high biodiversity of fish, about 5160 species. However, the Jacaré-Pepira River, located in the state of São Paulo, Brazil, presents a diversity of fish still to be explored in ichthyological studies. Metazoan parasites of Pimelodus maculatus and Rhamdia quelen were qualitatively and quantitatively diagnosed. Ten species of parasites (Demidospermus sp., D. majusculus, D. bidiverticulatum, D. paravalenciennesi, Ameloblastella paranaensis, Scleroductus sp., Riggia sp., Austrodiplostomum compactum, Helobdella sp. and Neochinorhynchus pimelodi) were collected in P. maculatus and eight species of parasites (Aphanoblastella robustus, A. mastigatus, Phyllodistomum rhamdiae, Crocodilicola pseudostoma, Henneguya jundiai, Contracaecum sp., Rhabdochona sp. and Capillariidae gen. sp.) were collected in R. quelen. All parasites presented aggregate distribution. A significant correlation was observed in P. maculatus concerning the weight with the prevalence of ectoparasite D. majusculus; however, R. quelen showed a relation to the length and weight with the abundance of ectoparasite A. mastigatus and endoparasites. The parasitic community of P. maculatus and R. quelen was characterized by high diversity, high richness, and low uniformity.

The Silent Threat of Non-native Fish in the Amazon: ANNF Database and Review

Non-native fish (NNF) can threaten megadiverse aquatic ecosystems throughout the planet, but limited information is available for the Amazon Region. In this study we review NNF data in the Amazonian macroregion using spatiotemporal records on the occurrence and the richness of NNF from a collaborative network of 35 regional experts, establishing the Amazon NNF database (ANNF). The NNF species richness was analyzed by river basin and by country, as well as the policies for each geopolitical division for the Amazon. The analysis included six countries (Brazil, Peru, Bolivia, Ecuador, Venezuela, and Colombia), together comprising more than 80% of the Amazon Region. A total of 1314 NNF occurrence records were gathered. The first record of NNF in this region was in 1939 and there has been a marked increase in the last 20 years (2000–2020), during which 75% of the records were observed. The highest number of localities with NNF occurrence records was observed for Colombia, followed by Brazil and Bolivia. The NNF records include 9 orders, 17 families and 41 species. Most of the NNF species are also used in aquaculture (12 species) and in the aquarium trade (12 species). The most frequent NNF detected were Arapaima gigas, Poecilia reticulata and Oreochromis niloticus. The current data highlight that there are few documented cases on NNF in the Amazon, their negative impacts and management strategies adopted. The occurrence of NNF in the Amazon Region represents a threat to native biodiversity that has been increasing “silently” due to the difficulties of large-scale sampling and low number of NNF species reported when compared to other South American regions. The adoption of effective management measures by decision-makers is urgently needed and their enforcement needed to change this alarming trend and help protect the Amazon’s native fish diversity.

Accelerated Diversification Explains the Exceptional Species Richness of Tropical Characoid Fishes

The Neotropics harbor the most species-rich freshwater fish fauna on the planet, but the timing of that exceptional diversification remains unclear. Did the Neotropics accumulate species steadily throughout their long history, or attain their remarkable diversity recently? Biologists have long debated the relative support for these museum and cradle hypotheses, but few phylogenies of megadiverse tropical clades have included sufficient taxa to distinguish between them. We used 1,288 ultraconserved element loci (UCE) spanning 293 species, 211 genera and 21 families of characoid fishes to reconstruct a new, fossil-calibrated phylogeny and infer the most likely diversification scenario for a clade that includes a third of Neotropical fish diversity. This phylogeny implies paraphyly of the traditional delimitation of Characiformes because it resolves the largely Neotropical Characoidei as the sister lineage of Siluriformes (catfishes), rather than the African Citharinodei. Time-calibrated phylogenies indicate an ancient origin of major characoid lineages and reveal a much more recent emergence of most characoid species. Diversification rate analyses infer increased speciation and decreased extinction rates during the Oligocene at around 30 million years ago (Ma) during a period of mega-wetland formation in the proto-Orinoco-Amazonas. Three species-rich and ecomorphologically diverse lineages (Anostomidae, Serrasalmidae, and Characidae) that originated more than 60 Ma in the Paleocene experienced particularly notable bursts of Oligocene diversification and now account collectively for 68% of the approximately 2,150 species of Characoidei. In addition to paleogeographic changes, we discuss potential accelerants of diversification in these three lineages. While the Neotropics accumulated a museum of ecomorphologically diverse characoid lineages long ago, this geologically dynamic region also cradled a much more recent birth of remarkable species-level diversity.

Ichthyofauna in the last free-flowing river of the Lower Iguaçu basin: the importance of tributaries for conservation of endemic species

The fish fauna from the Lower Iguaçu River and tributaries upstream of the Iguaçu Falls, the last free-flowing river stretch, were investigated. Twenty five sites in tributaries and the main channel were sampled between 2010 and 2016 using several kinds of fishing gear. The species were categorized according to their size, origin, and conservation status. Species richness and abundance in the main channel and tributaries were compared. In total, 87,702 specimens were recorded, comprising 76 species, 25 families, 53 genera, and eight orders. Characiformes and Siluriformes were the richest orders, representing 92% of the total specimens; Characidae, Cichlidae, Pimelodidae, and Loricariidae were the richest families. The fish fauna was composed of small and medium-sized species and included endemic (42%), autochthonous (24%), allochthonous (21%), and exotic (9%) species, as well as hybrids (4%). Significant differences in the relative numerical abundance of species were found among sites. Ancistrusmullerae and Rhamdiabranneri (endemic) were indicator species for tributaries inside of Iguaçu National Park (INP), while Phallocerosharpagos (autochthonous) and Ictaluruspunctatus (exotic) for tributaries outside of INP and Odontesthesbonariensis (allochthonous) for the main channel. The last dam-free stretch of the Lower Iguaçu River and tributaries upstream the Iguaçu Falls exhibits a rich endemic fish fauna, including some rare, endangered species (Steindachneridionmelanodermatum, Gymnogeophagustaroba, and Psalidodongymnogenys). These findings are essential to predict and understand the effects caused by the new Baixo Iguaçu Hydroelectric Power Plant and highlight the importance of tributaries and Iguaçu National Park for conservation of endemic species.

Molecular and morphological evidence of a new species of Crassicutis Manter 1936 (Digenea), a parasite of cichlids in South America

A new species of Crassicutis Manter, 1936 (Digenea: Megaperidae) is described from the intestine of Satanoperca jurupari (Cichlidae) in the Amazon River basin, Brazil. The genus Crassicutis currently contains eight species. Crassicutis manteri n. sp. is morphologically very similar to Crassicutis cichlasomae Manter, 1936, a parasite of cichlids reported from Mexico, the Antilles, and Central and South America. Molecular data revealed that C. cichlasomae represents a species complex in Middle American cichlids. The new species can be readily distinguished from C. cichlasomae sensu lato, and the other congeners, by a combination of morphological traits such as a narrow, elongate mouth opening (versus spherical in other species), the tandem position of testes (symmetrical or oblique in most congeners), narrow body widening towards its posterior end (versus widely oval, leaf-like in other species), and short intestinal caeca ending close to the posterior end of the posterior testis (versus reaching more posteriorly in other species). Six novel sequences of 28S rDNA, ITS1, and cox1 were generated for two isolates of the new species. Sequences of the 28S rRNA gene were used to corroborate that Crassicutis is sister taxa of Homalometron Stafford, 1904. Mitochondrial DNA corroborated the distinction of the new species with previously sequenced congeners in Middle American cichlids; the interspecific divergence between the new species and the genetic lineages of C. cichlasomae was very high, varying between 23.7 and 27.2%. Biogeographical implications of our findings are briefly discussed including questionable validity of records of C. cichlasomae from South America.

Heat-induced triploids in Brycon amazonicus: a strategic fish species for aquaculture and conservation

Triploidization plays an important role in aquaculture and surrogate technologies. In this study, we induced triploidy in the matrinxã fish (Brycon amazonicus) using a heat-shock technique. Embryos at 2 min post fertilization (mpf) were heat shocked at 38°C, 40°C, or 42°C for 2 min. Untreated, intact embryos were used as a control. Survival rates during early development were monitored and ploidy status was confirmed using flow cytometry and nuclear diameter analysis of erythrocytes. The hatching rate reduced with heat-shock treatment, and heat-shock treatments at 42°C resulted in no hatching events. Optimal results were obtained at 40°C with 95% of larvae exhibiting triploidy. Therefore, we report that heat-shock treatments of embryos (2 mpf) at 40°C for 2 min is an effective way to induce triploid individuals in B. amazonicus.

Broad but restricted detection of malacosporeans in a Neotropical cradle of diversification

This study undertook the first investigation of malacosporean infections in Neotropical fish. We used polymerase chain reaction detection with a primer set generally targeting known malacosporeans to assay for infection in the kidney of 146 fish in 21 species belonging to 12 families collected from two areas in the Amazon Basin. Infections were found in 13 fish variously belonging to seven species in six families and included the first identification of a malacosporean infection in cartilaginous fish (a freshwater stingray). Based on ssrDNA, all infections represented a single Buddenbrockia species (Buddenbrockia sp. E) that demonstrates an exceptionally broad range of fish species infected, and countered our expectations of high Neotropical malacosporean diversity. Infections were characterized at varying and often high prevalences in fish species but sample sizes were small. Ascertaining whether highly divergent malacosporeans have not been detected by current primers, and more comprehensive sampling may reveal whether malacosporeans are truly as species poor in the Amazon Basin as present data suggest. Our results prompt speculations about evolutionary scenarios including introduction via marine incursions and patterns of host use over time.

A combined molecular and morphological phylogeny of the Loricariinae (Siluriformes: Loricariidae), with emphasis on the Harttiini and Farlowellini

We present a combined molecular and morphological phylogenetic analysis of the Loricariinae, with emphasis on the Harttiini (Cteniloricaria, Harttia, and Harttiella) and Farlowellini (Aposturisoma, Farlowella, Lamontichthys, Pterosturisoma, Sturisoma, and Sturisomatichthys). Character sampling comprised seven molecular markers (the mitochondrial Cytb, nd2, 12S and 16S, and the nuclear MyH6, RAG1 and RAG2) and 196 morphological characters. A total of 1,059 specimens, and 159 tissue samples were analized, representing 100 species. A Bayesian Inference analysis was performed using the concatenated data matrix, which is comprised of 6,819 characters. The Loricariinae were found to comprise the tribes (Hartiini (Loricariini, Farlowellini)), the latter two elevated from subtribes. A Maximum Parsimony analysis was also performed using the same data matrix in order to reveal phenotypical synapomorphies to diagnose each clade. Two MP trees were found with a length of 14,704 steps, consistency index of 0.29 and retention index of 0.61, which were summarized in a strict consensus tree. Harttiini includes (Harttiella (Cteniloricaria, Harttia), and Farlowellini includes (Lamontichthys (Pterosturisoma (Sturisoma (Sturisomatichthys, Farlowella)))). Aposturisoma was recovered nested within Farlowella and is synonymyzed to the latter. Sturisoma was corroborated as strictly cis-Andean, while Sturisomatichthys encompasses, besides the valid species already included in the genus, the trans-Andean species once belonging to Sturisoma sensu lato. Identification keys and phylogenetic diagnoses of family-group taxa and genera of both the Harttiini and the Farlowellini are provided.

Ellipsomyxa tucujuensis n. sp. (Myxozoa: Ceratomyxidae), a parasite of Satanoperca jurupari (Osteichthyes: Cichlidae) from the Brazilian Amazon

The present study describes a new coelozoic, eukaryotic microparasite of the genus Ellipsomyxa Køie, 2003 (Ceratomyxidae: Myxozoa) found parasitizing the gallbladder of Satanoperca jurupari Heckel, 1840 collected in the Curiaú River Environmental Protection Area in Macapá, Amapá state, Brazil. The fish were collected using mesh cast net. The gallbladders were examined, preserved in 80% alcohol for molecular analysis (SSU rDNA gene), and fixed in Davidson for histological slide preparation. The new parasite had a prevalence of 81% in the gallbladder, asymmetric plasmodia, irregular free spores in the bladder fluid, with no cyst formation. The spores are elliptical, with characteristics of the genus Ellipsomyxa, and they had a mean length of 10.11 (8.56-10.5) μm, mean width of 7.81 (5.96-9.56) μm, and thick walls. The polar capsules are sub-spherical in shape, slightly asymmetrical, with a mean length of 3.12 (2.31-3.99) μm and mean width of 2.5 (2.22-2.95) μm, containing polar filament with five or six coils perpendicular to the longitudinal axis of the capsule. The Bayesian Inference assigned the new species to a subclade formed by a lineage of Ellipsomyxa species from the Amazon region. Ellipsomyxa tucujuensis n. sp. is the sixth species of this genus described in fish from the Amazon region, and the first for the state of Amapá.

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.

Multilocus phylogeny and historical biogeography of Hypostomus shed light on the processes of fish diversification in La Plata Basin

Distribution history of the widespread Neotropical genus Hypostomus was studied to shed light on the processes that shaped species diversity. We inferred a calibrated phylogeny, ancestral habitat preference, ancestral areas distribution, and the history of dispersal and vicariance events of this genus. The phylogenetic and distribution analyses indicate that Hypostomus species inhabiting La Plata Basin do not form a monophyletic clade, suggesting that several unrelated ancestral species colonized this basin in the Miocene. Dispersal to other rivers of La Plata Basin started about 8 Mya, followed by habitat shifts and an increased rate of cladogenesis. Amazonian Hypostomus species colonized La Plata Basin several times in the Middle Miocene, probably via the Upper Paraná and the Paraguay rivers that acted as dispersal corridors. During the Miocene, La Plata Basin experienced marine incursions, and geomorphological and climatic changes that reconfigured its drainage pattern, driving dispersal and diversification of Hypostomus. The Miocene marine incursion was a strong barrier and its retraction triggered Hypostomus dispersal, increased speciation rate and ecological diversification. The timing of hydrogeological changes in La Plata Basin coincides well with Hypostomus cladogenetic events, indicating that the history of this basin has acted on the diversification of its biota.

Equilibrium reproductive strategy of the peacock bass Cichla kelberi facilitates invasion into a Neotropical reservoir

The reproductive strategy of the non-native predator cichlid Cichla kelberi was determined to explain its success after more than 60 years of being introduced into an isolated reservoir in southeastern Brazil. This was one of the first-known translocations of the genus Cichla out of its natural range. Macro- and microscopy characteristics of the gonadal development stages and the maturation phases, along with the reproductive features (size at first maturation size, gonado-somatic index and sex ratio), were described. It was hypothesized that the stable conditions of the reservoir, with low connectivity, weakly defined spatial gradient and slight seasonal changes in environmental variables, favour the equilibrium strategy that enables predators to have high offspring survivorship because of great parental investment in individual progeny. Sex ratio was well balanced, with males and females reaching first maturity between 30.0 and 28.6 cm total length (L_T ), respectively. The stages of oocyte (primary and secondary growth, vitellogenic and atresia) and spermatocyte (spermatogonia, spermatocytes, spermatids and spermatozoa) development were identified. Five phases of gonadal development (immature, developing, spawning capable, regressing and regenerating) were described for both sexes. A long reproductive season was found, with spawning peaks in August/September and, to a lesser extent, in April/May. Parental care and spawns in parcels (batch spawns) corroborated the raised equilibrium strategy that was effective in this isolated reservoir. This species developed reproductive mechanisms that fit to different environmental conditions, with multiple spawning being associated with lentic environments and asynchronous development of oocytes, which are released over long periods. The reproductive plasticity in reservoirs may be one of the main factors inherent to the successful of colonization and establishment of the peacock bass in the environments in which they were introduced.

Phylogenetic relationships, genetic diversity and biogeography of menhadens, genus Brevoortia (Clupeiformes, Clupeidae)

Brevoortia Gill 1861 is a genus of the Clupeidae (Teleostei) that includes six species of fishes commonly known as menhadens in eastern North America and "savelhas" or "saracas" in southeastern South America. Species of Brevoortia are important components of the marine food web of coastal ecosystems in the Atlantic and contribute significantly to fisheries. In this study, the first phylogenetic and biogeographic hypotheses including all species of Brevoortia are presented. A total of 113 specimens were analyzed using three molecular markers (two mitochondrial: COI and 16s; and one nuclear: RAG2). Maximum Parsimony, Maximum Likelihood and Bayesian Inference were employed to estimate phylogenetic relationships. A Bayesian multispecies coalescent approach was used to estimate a dated phylogeny, which supported biogeographic analyses of ancestral geographic ranges. Results corroborate previous hypotheses that the four North Atlantic species are grouped in two clades, one composed of B. tyrannus (Latrobe, 1802) and B. patronus Goode, 1878, and the second including B. smithi Hildebrand, 1941 and B. gunteri Hildebrand, 1948. The South Atlantic B. aurea (Spix and Agassiz, 1829) and B. pectinata (Jenyns, 1842) form a third clade, which is sister to the clade composed of B. smithi and B. gunteri. The monophyly and validity of the six nominal species of Brevoortia were not supported. Results also indicate that Brevoortia originated in the North Atlantic during the middle Miocene (about 15 Mya). A cooling event of the tropical Atlantic at around 10 Mya likely facilitated the range expansion of the genus to the South Atlantic, whereas a significant warming of the tropical Atlantic waters during the late Miocene at 6-7 Mya possibly promoted the isolation between the northern and southern counterparts of that ancestral lineage. The relevance of the Florida Peninsula in association with sea level fluctuations for the diversification within Brevoortia is also discussed.

Reproduction of Hypoptopoma inexspectatum (Holmberg, 1893) (Siluriformes, Loricariidae) in the Southern Pantanal Floodplain, Upper Paraguay River Basin, Brazil

This work aimed to describe the reproductive biology of Hypoptopoma inexspectatum in southern Pantanal. A total of 538 individuals were sampled and analyzed from February 2009 through January 2011 in southern Pantanal. We did not observe differences in sex-ratio, and both sexes presented positive allometric length/weight relationship (LWR). Reproduction occurs mainly from January to February. Females reached first maturation (L50) with 37.80 mm and males with 45.80 mm. Absolute fecundity is estimated in mean=177.43 (sd±127.06) oocytes and relative fecundity in 3.12 (sd±2.23) oocytes/mg. Fecundity is positively correlated with standard length (Spearman r= 0.43; p=0.013), and total spawning is a used spawning strategy for H. inexspectatum.

High Genetic Diversity despite Conserved Karyotype Organization in the Giant Trahiras from Genus Hoplias (Characiformes, Erythrinidae)

In the fish genus Hoplias, two major general groups can be found, one of which is formed by the “common trahiras” (Hoplias malabaricus group) and the other by the “giant trahiras” (Hoplias lacerdae group, in addition to Hoplias aimara), which usually comprises specimens of larger body size. Previous investigations from the giant trahiras group recovered 2n = 50 meta/submetacentric chromosomes and no sex chromosome differentiation, indicating a probable conservative pattern for their karyotype organization. Here, we conducted comparative cytogenetic studies in six giant trahiras species, two of them for the first time. We employed standard and advanced molecular cytogenetics procedures, including comparative genomic hybridization (CGH), as well as genomic assessments of diversity levels and phylogenetic relationships among them. The results strongly suggest that the giant trahiras have a particular and differentiated evolutionary pathway inside the Hoplias genus. While these species share the same 2n and karyotypes, their congeneric species of the H. malabaricus group show a notable chromosomal diversity in number, morphology, and sex chromosome systems. However, at the same time, significant changes were characterized at their inner chromosomal level, as well as in their genetic diversity, highlighting their current relationships resulting from different evolutionary histories.

Space-time dynamics in monitoring neotropical fish communities using eDNA metabarcoding

The biodiverse Neotropical ecoregion remains insufficiently assessed, poorly managed, and threatened by unregulated human activities. Novel, rapid and cost-effective DNA-based approaches are valuable to improve understanding of the biological communities and for biomonitoring in remote areas. Here, we evaluate the potential of environmental DNA (eDNA) metabarcoding for assessing the structure and distribution of fish communities by analysing water and sediment from 11 locations along the Jequitinhonha River catchment (Brazil). Each site was sampled twice, before and after a major rain event in a five-week period and fish diversity was estimated using high-throughput sequencing of 12S rRNA amplicons. In total, 252 Molecular Operational Taxonomic Units (MOTUs) and 34 fish species were recovered, including endemic, introduced, and previously unrecorded species for this basin. Spatio-temporal variation of eDNA from fish assemblages was observed and species richness was nearly twice as high before the major rain event compared to afterwards. Yet, peaks of diversity were primarily associated with only four of the locations. No correlation between β-diversity and longitudinal distance or presence of dams was detected, but low species richness observed at sites located near dams might that these anthropogenic barriers may have an impact on local fish diversity. Unexpectedly high α-diversity levels recorded at the river mouth suggest that these sections should be further evaluated as putative "eDNA reservoirs" for rapid monitoring. By uncovering spatio-temporal changes, unrecorded biodiversity components, and putative anthropogenic impacts on fish assemblages, we further strengthen the potential of eDNA metabarcoding as a biomonitoring tool, especially in regions often neglected or difficult to access.

The most important fishery resource in the Amazon, the migratory catfish Brachyplatystoma vaillantii (Siluriformes: Pimelodidae), is composed by an unique and genetically diverse population in the Solimões-Amazonas River System

ABSTRACT The migratory catfish Brachyplatystoma vaillantii is one of the most important fishery resources in the Amazon. Intense capture occurs associated to its life cycle. In order to know the genetic status, we sequenced the mitochondrial DNA control region from 150 individuals of B. vaillantii, collected in five fishing landing locations, covering the length of the Solimões-Amazonas River in Brazil. Genetic diversity parameters suggest there is no genetic differentiation between the five localities. Population’s expansion indicated by R 2 and Fu’s Fs tests was also confirmed by the high number of unique haplotypes found. The Analyses of molecular variance indicated that nearly all variability was contained within locations (99.86%), and estimates of gene flow among B. vaillantii were high (F ST = 0.0014). These results suggest that Brachyplatystoma vaillantii forms a panmitic population along the Solimões-Amazonas River and, has greater genetic variability than other species of the Brachyplatystoma genus available so far. Although the influence of different tributaries on B. vaillantii migration patterns remains uncertain, a single population in the main channel should be consider in future policies for management of this resource. However, since the species’ life cycle uses habitats in several countries, its management and conservation depend greatly of internationally joined efforts.

Human impacts and the loss of Neotropical freshwater fish diversity

Abstract Neotropical Ichthyology promotes the Special Issue (SI) “Human impacts and the loss of Neotropical freshwater fish diversity” with the purpose of publishing relevant scientific articles on the current biodiversity crisis and the loss of Neotropical freshwater fishes in the Anthropocene. The SI is composed of 22 publications, being two review articles and 20 original articles. A total of 107 researchers contributed to these papers, involving 44 institutions based in Brazil and six other countries. Published articles investigated main anthropic activities and their impacts on fish diversity, with special focus on river regulation, mining, land use changes, aquaculture, and fisheries. Studies provided evidence about the loss of fish diversity in the Neotropics, including fish kill events, demographic changes, contamination, changes in assemblage structure, loss of taxonomic and functional diversity, besides the degradation of ecosystem functions and services, and the lack of effective protection and conservation. Studies were conducted in rivers, streams, lakes, and reservoirs from different Neotropical systems. The studies published in this SI represent a relevant sample of the current worrisome situation of freshwater fishes in the Neotropical region and call for urgent revision in environmental policies, management and conservation initiatives, and socioeconomic priorities.

Integrative taxonomy reveals a new species of Neotropical headstanding fish in genus Schizodon (Characiformes: Anostomidae)

Abstract Schizodon encompasses approximately 15 species of Neotropical headstanding fishes. Integrative taxonomy, combining molecular and morphometric analyses with traditional taxonomic methods, was used to investigate Schizodon vittatus and its potential new sister species. Molecular differences between the two species in the barcode are greater than intra-specific variation recovered in species of Schizodon, and the two species represent distinct lineages for approximately one million years. The two species are morphologically very similar, and the meristic data showed great overlap. Morphometric analyses also showed overlap among the putative species but indicated differences in caudal-peduncle depth, orbital diameter, and length of anal-fin rays. Color pattern seems to provide a clear diagnostic feature for the two species. Schizodon vittatus usually has four dark brown transversal bars on body, and its sister species has three conspicuous bars, with the fourth, if present, inconspicuous and dorsal to the lateral line. Schizodon vittatus is redescribed based on the type and recently collected specimens, its type locality is revisited, and its known distribution restricted to the Araguaia and Tocantins drainages. The new species, sister to S. vittatus, distributed in the Xingu and Tapajós drainages, is described. A key for the identification of the Amazon clade species of Schizodon is provided.

Population genetics of the endangered catfish Pseudoplatystoma magdaleniatum (Siluriformes: Pimelodidae) based on species-specific microsatellite loci

ABSTRACT The Neotropical catfish genus Pseudoplatystoma comprises eight species of large size, widely distributed in South American basins. The endangered species P. magdaleniatum is endemic to Magdalena basin (Colombia), experiences high fishing pressure and its population genetics is relatively unknown. To study the genetic status and structure of P. magdaleniatum, 25 species-specific polymorphic microsatellite loci were developed using next-generation sequencing and then tested in samples collected in the Magdalena-Cauca basin. Based on 15 of these loci, P. magdaleniatum showed a high number of alleles per locus (9-10), high values of observed (0.762-0.798) and expected (0.770-0.791) heterozygosities, recent reduction of population size and gene flow. These findings constitute a baseline to measure potential changes in genetic diversity and structure of this commercially important species in a basin undergoing high anthropogenic activities.

Long-term trends of fishery landings and target fish populations in the lower La Plata basin

Abstract The La Plata basin is the second largest basin of South America and has supported important river fisheries for more than a century. In this paper, we evaluate for the first time the historical trends of landings of 21 fish taxa and the recent population trends of 27 species of commercial fishes in the lower La Plata basin (Argentina). We compiled three kinds of data sets: Total fishery landings (between 1934 and 1986) and exports (1994‒2019), fisheries monitoring programs of Chaco and Santa Fe provinces in the Paraná River (2009‒2019), and surveys of fish populations in the Upper (Corrientes, 1993‒2020) and Middle (EBIPES, 2005‒2020) Paraná River. The analysis of the historical landings showed more species declining in the lower portion of the basin than in the upper basin. Regarding recent population trends, Pimelodus spp., Hoplias spp., Salminus brasiliensis, Luciopimelodus pati, and Ageneiosus spp. declined in more than one region, while Megaleporinus spp., Pterodoras granulosus, and Oxydoras kneri showed stable to positive trends, with the other species varying in their trends between regions. These tendencies could be associated to a combination of factors such as overfishing and environmental changes that would require an ecosystem approach for their adequate management.

Assessing extinction risk from geographic distribution data in Neotropical freshwater fishes

Abstract The IUCN Red List (RL) provides high-quality conservation assessments for individual species, yet the rate and scale of environmental deterioration globally challenges the conservation community to develop expedited methods for risk assessment. Here we compare threat assessments for 3,001 species of Neotropical freshwater fishes (NFF) in the IUCN–RL using readily accessible data types as proxies for extinction risk: geographic range, elevation, and species publication date. Furthermore, using geographic and taxonomic data alone, we generated preliminary conservation assessments for 2,334 NFF species currently awaiting IUCN assessment, identifying an additional 671 NFF species as potentially threatened. This number of potentially threatened species represents an increase of 59% over the number of species currently assigned to threat categories by the IUCN–RL. These results substantially expand the number of threatened NFF species from 422 currently on the IUCN RL to 1,093 species as threatened or potentially threatened, representing about 18% of all NFF species. Extinction risk is greater in species with smaller geographic ranges, which inhabit upland rivers, and which were described more recently. We propose the Central and Southern Andes, and Eastern Guiana Shield as priorities in the upcoming IUCN RL assessment of NFF species conservation risk.

Composition and distribution of fishes from the Perequê-Açu river basin, Paraty, Rio de Janeiro, Southeastern Brazil

Abstract The large number of less-known coastal drainages in the Atlantic Forest still represents an important gap in the knowledge of ichthyofauna. It is evaluated the taxonomic diversity, frequency and constancy of occurrence, and the distribution of species in the various segments of the Perequê-Açu river basin, state of Rio de Janeiro, Brazil. Twelve sampling campaigns resulted in 13,423 individuals, belonging to seven orders, 10 families, 21 genera, and 23 native species. Cyprinodontiformes and Siluriformes represented about 87.2% of the total abundance, mainly due to the contribution of Phalloceros anisophallos and Schizolecis guntheri, which account for 63.2% of the total sampled individuals. The analysis of constancy of occurrence reveals that 78.3% of the drainage species are residents, with approximately 93% of the residents of the Carrasquinho River sub-basin. The Sertões River sub-basin had the largest number of species in total: 18. The rarefaction curve did not reach an asymptote, although Chao 2 and bootstrap estimate the richness of 23.9 species and 23.7 species, respectively. The results of PERMANOVA, PCoA, and SIMPER indicate that the fish composition along the catchment is not homogeneous. The conservation status of species is also discussed, regionally, nationally, and globally.

Chromosome analysis in Saccodon wagneri (Characiformes) and insights into the karyotype evolution of Parodontidae

ABSTRACT Parodontidae is a relatively small group of Neotropical characiform fishes consisting of three genera (Apareiodon, Parodon, and Saccodon) with 32 valid species. A vast cytogenetic literature is available on Apareiodon and Parodon, but to date, there is no cytogenetic data about Saccodon, a genus that contains only three species with a trans-Andean distribution. In the present study the karyotype of S. wagneri was described, based on both conventional (Giemsa staining, Ag-NOR, C-bands) and molecular (repetitive DNA mapping by fluorescent in situ hybridization) methods. A diploid chromosome number of 2n = 54 was observed in both sexes, and the presence of heteromorphic sex chromosomes of the ZZ/ZW type was detected. The W chromosome has a terminal heterochromatin band that occupies approximately half of the long arm, being this band approximately half the size of the Z chromosome. The FISH assay showed a synteny of the 18S-rDNA and 5S-rDNA genes in the chromosome pair 14, and the absence of interstitial telomeric sites. Our data reinforce the hypothesis of a conservative karyotype structure in Parodontidae and suggest an ancient origin of the sex chromosomes in the fishes of this family.

Fish fauna of small-order streams of savannah and forest fragments landscape in the lower Tapajós River basin, Amazonia

Abstract: To better understand the fish fauna of Amazonian streams, we assessed small streams in a landscape of forest fragments and savannah in the region of the lower Tapajós River, Brazil. We sampled the fish fauna using a well-tested active capture method during two dry seasons (October 2006 and 2018) and one rainy season (March to May 2018). Species richness was calculated using an abundance matrix and first-order jackknife estimator. Using qualitative and quantitative data, we present a cluster analysis in which each stream corresponds to a sampling unit. We collected 6,094 individuals of 43 species distributed in six orders. The sampling effort represents 73% of the estimated richness (58.69 ± 7.65). The most abundant species were Copella nattereri, Iguanodectes variatus and Laimosemion dibaphus that together represent almost half of the total sample (48.7%). The most frequent species were Aequidens epae, Helogenes marmoratus and Laimosemion dibaphus, which were collected in 11 of the 13 sampled streams. This is the first fish fauna list for small-order streams of savannah and forest fragments landscape in Amazonian Brazil. The richness of fish and the presence of many rare species underscore the contribution of small streams to the regional fish fauna composition, even in dynamic and spatially restricted landscapes.

Negative impacts of mining on Neotropical freshwater fishes

Abstract Mining activities have significantly affected the Neotropical freshwater ichthyofauna, the most diverse in the world. However, no study has systematized knowledge on the subject. In this review, we assembled information on the main impacts of mining of crude oil, gold, iron, copper, and bauxite on aquatic ecosystems, emphasizing Neotropical freshwater fishes. The information obtained shows that mining activities generate several different disturbances, mainly via input of crude oil, metals and other pollutants, erosion and siltation, deforestation, and road construction. Mining has resulted in direct and indirect losses of fish diversity in several Neotropical waterbodies. The negative impacts on the ichthyofauna may change the structure of communities, compromise entire food chains, and erode ecosystem services provided by freshwater fishes. Particularly noteworthy is that mining activities (legal and illegal) are widespread in the Neotropics, and often located within or near protected areas. Actions to prevent and mitigate impacts, such as inspection, monitoring, management, and restoration plans, have been cursory or absent. In addition, there is strong political pressure to expand mining; if – or when – this happens, it will increase the potential of the activity to further diminish the diversity of Neotropical freshwater fishes.

Molecular species delimitation of the genera Anodus, Argonectes, Bivibranchia and Micromischodus (Ostariophysi: Characiformes)

ABSTRACT A good taxonomic assessment of specimens is an essential task to many biological studies and DNA data have provided additional sources of information to assist in the disentanglement of taxonomic problems among living organisms, as has been the case of some taxa of the megadiverse Neotropical ichthyofauna. Here we assessed all valid species in the Neotropical freshwater fish genera Anodus, Argonectes, Bivibranchia and Micromischodus of the family Hemiodontidae to establish molecular species boundaries among them. All species delimitation methods defined exactly only one MOTU for Anodus elongatus, Argonectes longiceps, A. robertsi, Bivibranchia bimaculata, B. notata, B. velox, and Micromischodus sugillatus, resulting in total congruence between nominal species and MOTUs for these seven taxa. The three species having discordant results across analyses: Anodus orinocensis, Bivibranchia fowleri, and Bivibranchia simulata, matched more than one MOTU per species in some methods, meaning that cryptic diversity may exist within these taxa. Overall, this great correspondence among morphological and molecular boundaries for thae species analysed seem to be indicative of a reasonably stable taxonomy within these Hemiodontidae genera.

Fish fauna in low-order streams of the Piquiri River, Upper Paraná River basin, Brazil

Abstract The South America ichthyofauna encompasses the highest diversity of the world, however is highly threatened by anthropogenic actions. The fish fauna of nine low-order streams, tributaries of the Piquiri River and impacted by aquaculture, agriculture and urbanization were sampled in the present study. Samplings were done quarterly from December 2017 to September 2018 at three sites in each stream, using a portable electric fishing device in 50-meter segments. A total of 14,507 individuals were collected, belonging to six orders, 20 families, 46 genera, and 70 species. The highest richness and abundance were found for the orders Characiformes and Siluriformes. In this study, nine species that had not been recorded were found, totaling 163 for the basin. In addition, 14 non-native species were captured. The presented list of species contributes to the existing database of ichthyofauna distribution in Neotropical streams, denoting that it is underestimated in the region, mainly in low-order tributaries. The present study reinforces the importance of inventories and monitoring in environments with high biodiversity and sensitive to anthropogenic actions.

Streams fish from Upper Araguaia and Middle Rio da Mortes basin, Brazil: generating subsidies for preservation and conservation of this critical natural resource

Abstract: The Araguaia River basin has the highest fish biodiversity within the Cerrado biome (Brazilian savannah), with many endemic and threatened species by human activities. Despite growing efforts to catalog Neotropical freshwater fish biodiversity, many regions are still undersampled. Our objective is to complement the information about stream fish in two hydrographic basins in the Cerrado. We sampled 72 streams with 50 m stretch in the Upper Araguaia (n = 32) and Middle Rio das Mortes (n = 40) basins. We collected 14,887 individuals distributed in 137 species, 81 genera, 30 families, and six orders. Characidae, Loricariidae, and Cichlidae were the families richer in species. We found a high diversity of rare fish species in the streams sampled, ca. 71.5% of the species had at least five individuals collected, and 18 species had only one collected specimen. The most frequent species were Astyanax cf. goyacensis, Knodus cf. breviceps, and Characidium cf. zebra. Both basins shared around 43% of the species. We caught 76 species in Upper Araguaia and 120 species in Middle Rio das Mortes. Seventeen exclusive fish species occurred in Upper Araguaia, whereas 61 were found in the Middle Rio das Mortes basin. Our analysis showed lower diversity of fish in Upper Araguaia than in the Middle Rio das Mortes basin. Considering the exclusive fish species of both basins, the human threats in those regions, and the few existent protected areas, we need a better look at the aquatic biodiversity conservation of this ecosystem.

Deep-sea anglerfishes (Lophiiformes: Ceratioidei) from off northeastern Brazil, with remarks on the ceratioids reported from the Brazilian Exclusive Economic Zone

Abstract The deep-sea anglerfishes of the suborder Ceratioidei (Lophiiformes) are represented by about 170 valid species with some of the most extraordinary morphological and reproductive adaptations among vertebrates, including extreme sexual dimorphism and male parasitism. Here we report on the diversity and distribution of rare ceratioids collected during the ABRACOS (Acoustics along the BRAzilian COaSt) expeditions off northeastern Brazil and the Fernando de Noronha Ridge (Rocas Atoll, Fernando de Noronha Archipelago, and associated seamounts). Chaenophryne ramifera, Oneirodes anisacanthus, O. carlsbergi, Gigantactis watermani, and unidentified specimens of Caulophryne, Dolopichthys, and Rhynchactis are recorded for the first time in the Brazilian Exclusive Economic Zone. Ceratias uranoscopus, Melanocetus johnsonii, and Chaenophryne draco have their distributions extended in Brazilian waters. Caulophryne, O. anisacanthus, and G. watermani are also recorded for the first time in the western South Atlantic. The specimen of G. watermani reported here represents the third known specimen of the species, and variations of its escal anatomy in relation to the holotype are described. Based on specimens examined and a review of records in the literature, 20 species of the Ceratioidei, in addition to unidentified species of Caulophryne, Dolopichthys, and Rhynchactis, are confirmed in the Brazilian Exclusive Economic Zone.

A new, narrowly distributed, and critically endangered species of Characidium (Characiformes: Crenuchidae) from the Distrito Federal, Central Brazil

ABSTRACT A new species of Characidium is described from the Cerrado biome, in Brasília, Distrito Federal, Central Brazil. The new species can be readily diagnosed by the presence of two or three longitudinal rows of dots along the body sides, absence of bars, by the short pectoral fin, which does not reach the vertical through the dorsal fin origin. Additional useful diagnostic characters are the scaled isthmus, absence of the adipose fin, and the terminal mouth. The new species is only known from the córrego Taquara and its tributaries, a tributary of ribeirão do Gama, upstream from lago Paranoá, in the upper rio Paraná basin. In accordance to the IUCN Red List Categories and Criteria, the new species is categorized as Critically Endangered.

DNA barcoding in the Southeast Pacific marine realm: Low coverage and geographic representation despite high diversity

The Southeast Pacific comprises two Large Marine Ecosystems, the Pacific Central-American Coastal and the Humboldt Current System; and is one of the less well known in the tropical subregions in terms of biodiversity. To address this, we compared DNA barcoding repositories with the marine biodiversity species for the Southeast Pacific. We obtained a checklist of marine species in the Southeast Pacific (i.e. Colombia, Ecuador, Chile, and Peru) from the Ocean Biodiversity Information System (OBIS) database and compared it with species available at the Barcoding of Life Data System (BOLD) repository. Of the 5504 species records retrieved from OBIS, 42% of them had at least one registered specimen in BOLD (including specimens around the world); however, only 4.5% of records corresponded to publicly available DNA barcodes including specimens collected from a Southeast Pacific country. The low representation of barcoded species does not vary much across the different taxonomic groups or within countries, but we observed an asymmetric distribution of DNA barcoding records for taxonomic groups along the coast, being more abundant for the Humboldt Current System than the Pacific Central-American Coastal. We observed high-level of barcode records with Barcode Index Number (BIN) incongruences, particularly for fishes (Actinopterygii = 30.27% and Elasmobranchii = 24.71%), reflecting taxonomic uncertainties for fishes, whereas for Invertebrates and Mammalia more than 85% of records were classified as data deficient or inadequate procedure for DNA barcoding. DNA barcoding is a powerful tool to study biodiversity, with a great potential to increase the knowledge of the Southeast Pacific marine biodiversity. Our results highlight the critical need for increasing taxonomic sampling effort, the number of trained taxonomic specialists, laboratory facilities, scientific collections, and genetic reference libraries.

Ecological impacts of pesticides on Astyanax jacuhiensis (Characiformes: Characidae) from the Uruguay river, Brazil

Brazilian freshwater ecosystems are continuously exposed to pesticides and domestic sewage. The Uruguay River was chosen for this study because of its international importance, as it flows through Brazil, Argentina, and Uruguay. It receives contaminants such as pesticides and domestic residues. Thus, the aim of this study to assess the accumulation of pesticides in muscle of the fish Astyanax jacuhiensis, its biochemical responses, and the presence of pesticides in water. In total, seven pesticides were registered in water from both river sites. Eight pesticides were detected in fish muscle. The biochemical responses showed that brain lipid peroxidation (LPO) and protein carbonyl (PC) in A. jacuhiensis were higher in the summer. Muscle showed the highest LPO levels in the spring and the highest PC in the summer. Liver LPO and PC levels were higher in the spring and summer. In the gills, the PC was higher in the spring and the LPO in the spring and winter. In the brain and in the gills, glutathione-S-transferase activity was high in the summer and autumn. Catalase activity was lower during the winter and spring. Non-protein thiol (NPSH) levels were lower in the brain in the winter and spring. Muscle tissue showed lower NPSH in the winter (site 1). Liver NPSH showed increased levels in liver in the spring and winter (site 2). The biochemical results clearly is related to pesticides and/or to the presence of other contaminants in the water such as metals or domestic sewage. The accumulation of pesticides in fish muscle added evidence that pesticides have been used in the area surrounding the Uruguay River. In conclusion, the biomarkers assayed in the present study could be used in future investigations considering other sampling sites along Uruguay River.

Diversification of Neotropical Freshwater Fishes

Neotropical freshwater fishes (NFFs) constitute the most diverse continental vertebrate fauna on Earth, with more than 6,200 named species compressed into an aquatic footprint <0.5% of the total regional land-surface area and representing the greatest phenotypic disparity and functional diversity of any continental ichthyofauna. Data from the fossil record and time-calibrated molecular phylogenies indicate that most higher taxa (e.g., genera, families) diversified relatively continuously through the Cenozoic, across broad geographic ranges of the South American platform. Biodiversity data for most NFF clades support a model of continental radiation rather than adaptive radiation, in which speciation occurs mainly in allopatry, and speciation and adaptation are largely decoupled. These radiations occurred under the perennial influence of river capture and sea-level oscillations, which episodically fragmented and merged portions of adjacent river networks. The future of the NFF fauna into the Anthropocene is uncertain, facing numerous threats at local, regional, and continental scales.

Species composition and invasion risks of alien ornamental freshwater fishes from pet stores in Klang Valley, Malaysia

The ornamental fish trade has been considered as one of the most important routes of invasive alien fish introduction into native freshwater ecosystems. Therefore, the species composition and invasion risks of fish species from 60 freshwater fish pet stores in Klang Valley, Malaysia were studied. A checklist of taxa belonging to 18 orders, 53 families, and 251 species of alien fishes was documented. Fish Invasiveness Screening Test (FIST) showed that seven (30.43%), eight (34.78%) and eight (34.78%) species were considered to be high, medium and low invasion risks, respectively. After the calibration of the Fish Invasiveness Screening Kit (FISK) v2 using the Receiver Operating Characteristics, a threshold value of 17 for distinguishing between invasive and non-invasive fishes was identified. As a result, nine species (39.13%) were of high invasion risk. In this study, we found that non-native fishes dominated (85.66%) the freshwater ornamental trade in Klang Valley, while FISK is a more robust tool in assessing the risk of invasion, and for the most part, its outcome was commensurate with FIST. This study, for the first time, revealed the number of high-risk ornamental fish species that give an awareness of possible future invasion if unmonitored in Klang Valley, Malaysia.