DNA barcoding is a widely utilized molecular-based identification of species and taxonomic resolutions. Until recently, Rhamdia voulezi and Rhamdia branneri were considered species synonyms of Rhamdia quelen; however, morphological and cytogenetic analyses have suggested the validity of distinct species. Due to the absence of molecular taxonomy of R. voulezi and R. branneri, the objective of this study was to test its validity through traditional DNA barcoding and the GMYC (General Mixed Yule Coalescent) COI-based analyses in 19 specimens from the Iguaçu River Basin. In both methodologies, three MOTUs (Molecular Operational Taxonomic Units) were identified based on the estimated optimum threshold (OT = 0.77). The average inter-MOTU distance (NJ, K2P) between R. branneri and R. voulezi was 1.4%, and 0% intra-MOTU distance in both species. The two species identified as R. branneri and R. voulezi showed correspondence with taxonomic and morphological identifications. With regard to R. quelen, the average intra-MOTU distance was greater than OT (2.7%), indicating that this species can be formed by different MOTUs. We suggest that molecular and taxonomic studies should be employed concurrently in R. quelen, to prevent contamination of wild species by hybridizations. O DNA barcoding é uma ferramenta molecular precisa para a identificação de espécies e resoluções taxonômicas. Até recentemente, Rhamdia voulezi e Rhamdia branneri eram consideradas sinônimas de Rhamdia quelen, contudo caracteres morfológicos e citogenéticos têm apontado à validade de ambas. Devido à escassez de informações sobre a taxonomia molecular de R. voulezi e R. branneri, o objetivo do presente estudo foi testar a validade das mesmas através do método de DNA barcoding tradicional e GMYC (General Mixed Yule Coalescent), por meio da análise do gene COI em 19 espécimes do rio Iguaçu. Em ambos os métodos, três MOTUs (Unidades Taxonômicas Operacionais Moleculares) foram identificadas com base no ótimo threshold (OT = 0,77). A média inter-MOTU (NJ, K2P) entre R. branneri e R. voulezi foi 1,4%, com valores de 0% intra-MOTUs em ambas espécies. As duas espécies identificadas como R. voulezi e R. branneri apresentaram correspondência com a identificação taxonômica e morfológica dos respectivos vouchers. No que se refere a R. quelen, os resultados intra-MOTU foram superiores ao OT (2,7%), evidenciando a possibilidade de existirem diferentes MOTUs denominadas como R. quelen. Sugerimos que estudos moleculares e taxonômicos sejam empregados em R. quelen, para evitar a contaminação de espécies selvagens por hibridizações.Palavras-chave: Aquicultura, COI, Complexo de espécies, Jundiá, MOTU.

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Salminus brasiliensis is a potamodromous fish species that occurs in southern South American rivers. In spite of its ecological and economic relevance, information regarding the reproductive biology of S. brasiliensis is still scarce. This study used data from 18 years of continuous sampling in the Upper Uruguay River Basin, analyzing 718 adult fish (307 males, 243 females, 168 undefined) captured at different months of the year. The results showed that the reproductive timing for S. brasiliensis is wide in the Upper Uruguay River, with the occurrence of mature fish between the month of August and March and spawned individuals between July and May of the next year. These results were sustained by the increase of gonadal somatic relationship (GSR) from August. The reproductive timing of S. brasiliensis in the Upper Uruguay River may start between the middle winter and early spring (from late July to late September), and may extend until the late summer and middle fall (from the middle February to early May). These findings contribute to information on the general biology of S. brasiliensis and provide valuable knowledge to management programs and to conservation efforts of this fisheries resource.

Freshwater fish present unique challenges when one attempts to understand the factors that determine the structure of their populations. Habitat fragmentation is a leading cause of population decline that threatens ecosystems worldwide. In this study, we investigated the conservation status of genetic variability in the Neotropical catfish (Pimelodus maculatus). Specifically, we examined the structure and genetic diversity of this species in a region of the Upper Uruguay River fragmented by natural barriers and dams. There was no genetic structure among the four sites analyzed, indicating the existence of only one population group. A combination of environmental management and genetic monitoring should be used to minimize the impact of impoundment on panmitic populations of migratory fish species.

Rhamdia quelen is the most produced native freshwater fish in fish farms in South Brazil. Until recently, Rhamdia branneri and Rhamdia voulezi were synonyms of R. quelen, and all the species are commercialized as silver catfish (locally called jundiá or bagre sapo) by the aquaculture industry. In fact, because these species are morphologically very similar, interspecific crosses easily might occur in fish farming. We employed standard DNA barcoding to identify jundiá molecular operational taxonomic units (MOTUs) in fish cultivated and commercialized in the industry and in possible escapees in the natural environment in southern Brazil. We analysed 48 individuals from six fish farms and 48 individuals from three rivers (Uruguay, Benedito Novo and Itapocu Rivers) using the mitochondrial cytochrome oxidase subunit I (COI). Four MOTUs were identified based on the estimated optimum threshold (OT = 0.77), and these MOTUs were concordant with Bayesian Inferece (BI) and Neighbour‐Joining (NJ) trees. Our results support the existence of at least three species in our dataset: R. branneri, R. voulezi, and R. quelen 1 and R. quelen 2. The interspecific genetic divergence ranged from 1.1% to 5.1% (mean = 3.5%), and the intraspecific distance ranged from 0% to 1.4% (mean = 0.24%). The presence of cultivated fish in the Uruguay and Benedito Novo Rivers provides evidence of genetic contamination in native populations. These results show the need to regulate aquaculture activities and to characterize the species and commercial lineages of silver catfish that are cultivated in South Brazil.

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Aim Aquaculture plays an important role in the world and in Brazil. Artificial construction of water bodies, such as ponds and reservoirs, has allowed for fish culture in cages in those environments, generating conflicts over the use of these public waters. The producers are seeking to increase production, and the ecosystem is susceptible to the impacts caused by production activity. The aim of this review was to identify questions about these conflicts (productivity × environment) and to indicate possible solutions to the main problems related to fish farming in reservoirs. Methods A bibliographical survey was carried out on the main aspects of cage fish farming in Brazilian reservoirs. Studies from 1977 to 2018 (scientific journals, books, and thesis) were revised using seven databases, the CAPES periodicals portal and Google Scholar websites. The main keywords used were “aquaculture”, “reservoir”, “cage”, “eutrophication”, “carrying capacity”, “impacts”, “oligotrophic”, “escapes”, “hybrids”, and “pollution”. Results We accessed approximately 330 and cited 151 documents. Conclusions The negative aspects associated with cage fish farming, as escapes of cultivated fish, and the possible solutions of this and others negative impacts were addressed, identifying mechanisms for reducing conflicts between environmental impacts and aquaculture production. Potential solutions include the use of native fish species or sterile species, implementation of monitoring systems of the surrounding area, adoption of measures to reduce the accidental escape of fish, use of multitrophic culture systems, use of highly digestible diets with appropriate food management, and use of computer programs that incorporate current and historical environmental data to calculate carrying capacity and choose the most appropriate location for production.

Steindachneridion scriptum is an important species as a resource for fisheries and aquaculture; it is currently threatened and has a reduced occurrence in South America. The damming of rivers, overfishing, and contamination of freshwater environments are the main impacts on the maintenance of this species. We accessed the genetic diversity and structure of S. scriptum using the DNA barcode and control region (D-loop) sequences of 43 individuals from the Upper Uruguay River Basin (UUR) and 10 sequences from the Upper Paraná River Basin (UPR), which were obtained from GenBank. S. scriptum from the UUR and the UPR were assigned in two distinct molecular operational taxonomic units (MOTUs) with higher inter-specific K2P distance than the optimum threshold (OT = 0.0079). The COI Intra-MOTU distances of S. scriptum specimens from the UUR ranged from 0.0000 to 0.0100. The control region indicated a high number of haplotypes and low nucleotide diversity, compatible with a new population in recent expansion process. Genetic structure was observed, with high differentiation between UUR and UPR basins, identified by BAPS, haplotype network, AMOVA (FST = 0.78, p < 0.05) and Mantel test. S. scriptum from the UUR showed a slight differentiation (FST = 0.068, p < 0.05), but not isolation-by-distance. Negative values of Tajima’s D and Fu’s Fs suggest recent demographic oscillations. The Bayesian skyline plot analysis indicated possible population expansion from beginning 2,500 years ago and a recent reduction in the population size. Low nucleotide diversity, spatial population structure, and the reduction of effective population size should be considered for the planning of strategies aimed at the conservation and rehabilitation of this important fisheries resource.