Genetic Structure and Diversity in Wild and Cultivated Populations of the Mangrove Oyster Crassostrea gasar from Southern Brazil.

The mangrove oyster (Crassostrea gasar) is Brazil's second most cultured species and presents a high potential for aquaculture. However, artificial selection in a highly fecund species and significant variance in reproductive success can result in the loss of genetic diversity and increases the inbreeding rate, especially in cultivated populations. In this study, we investigated the genetic structure and diversity of C. gasar in wild and cultivated populations using 14 microsatellites. Spatial genetic comparisons revealed the existence of two main genetic groups of C. gasar, one comprising the population in cultivation and the other formed by wild populations along the southern and southeastern Brazilian coasts. Although no common genetic structure exists among wild populations, it is possible to observe a distribution gradient based on discriminant analysis of principal components consistent with their geographic distribution. However, it is insufficient to differentiate them genetically. Despite artificial reproduction, the genetic diversity values of the cultivated population remained relatively high and did not show a reduction. Therefore, monitoring the cultivated population and establishing reference values for genetic diversity will allow the adoption of strategies both for the viability of the cultivated population and the management of wild populations.

An ancient truncated duplication of the anti-Müllerian hormone receptor type 2 gene is a potential conserved master sex determinant in the Pangasiidae catfish family.

The evolution of sex determination (SD) in teleosts is amazingly dynamic, as reflected by the variety of different master sex-determining genes identified. Pangasiids are economically important catfishes in South Asian countries, but little is known about their SD system. Here, we generated novel genomic resources for 12 Pangasiids and characterized their SD system. Based on a Pangasianodon hypophthalmus chromosome-scale genome assembly, we identified an anti-Müllerian hormone receptor type Ⅱ gene (amhr2) duplication, which was further characterized as being sex-linked in males and expressed only in testes. These results point to a Y chromosome male-specific duplication (amhr2by) of the autosomal amhr2a. Sequence annotation revealed that the P. hypophthalmus Amhr2by is truncated in its N-terminal domain, lacking the cysteine-rich extracellular part of the receptor that is crucial for ligand binding, suggesting a potential route for its neofunctionalization. Reference-guided assembly of 11 additional Pangasiids, along with sex-linkage studies, revealed that this truncated amhr2by duplication is a male-specific conserved gene in Pangasiids. Reconstructions of the amhr2 phylogeny suggested that amhr2by arose from an ancient duplication/insertion event at the root of the Siluroidei radiation that is dated to ~100 million years ago. Together these results bring multiple lines of evidence supporting that amhr2by is an ancient and conserved master sex-determining gene in Pangasiids, a finding that highlights the recurrent use of the transforming growth factor ß pathway, which is often used for the recruitment of teleost master SD genes, and provides another empirical case towards firther understanding of dynamics of SD systems.

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.

Anthropogenic river fragmentation reduces long-term viability of the migratory fish Salminus brasiliensis (Characiformes: Bryconidae) populations

Life-history, geographical barriers, and damming can shape the genetic diversity of freshwater migratory fish, which are particularly vulnerable to anthropogenic impacts. We investigated the genetic diversity of Salminus brasiliensis, a long-distance migratory species that is recognized as an important provider of ecosystem services. We implemented microsatellite analyses to assess genetic diversity and simulate future scenarios for evaluating the long-term viability of dammed and non-dammed populations from the Uruguay River. High levels of genetic diversity were detected for all sampled populations. However, effective population sizes were lower in the uppermost river stretches, where the landscape is highly fragmented. Population structure analysis indicated two spatial genetic populations. It is suggested that this genetic structure preserves populations partially isolated by an ancient natural barrier, instead of being a result of the presence of dams. The simulated genetic scenarios indicated that genetic variability of S. brasiliensis populations from upstream dams could collapse over the years, mainly due to the reduction in the number of alleles. Therefore, besides helping to better understand issues related to the influence of dams on the genetic diversity of migratory fish, our results are especially relevant for driving local fishery policies and management actions for the species conservation.'

História de vida, barreiras geográficas e barramento dos rios podem moldar a diversidade genética de grandes peixes migratórios de água doce, que são particularmente vulneráveis a impactos antrópicos. Nós investigamos a diversidade genética de Salminus brasiliensis, uma espécie migratória de longa distância que é reconhecida como um importante provedor de serviços ecossistêmicos. Realizamos análises de microssatélites para avaliar a diversidade genética e simular cenários futuros, possibilitando estimar a viabilidade em longo prazo de populações situadas em regiões com e sem represas do rio Uruguai. Altos níveis de diversidade genética foram detectados para todas as populações amostradas. Contudo, os tamanhos populacionais efetivos foram menores nos trechos superiores do rio, onde a paisagem é altamente fragmentada. A análise da estrutura populacional indicou duas populações genéticas espaciais. Sugere-se que esta estrutura genética preserva populações parcialmente isoladas por uma antiga barreira natural, ao invés de ser resultado da presença de barragens. Os cenários genéticos simulados indicaram que a variabilidade genética das populações de S. brasiliensis situadas a montante das barragens entraria em colapso ao longo dos anos, principalmente como resultado da redução do número de alelos. Portanto, além de ajudar a entender melhor questões relacionadas à influência de barragens na diversidade genética de peixes migradores, nossos resultados são especialmente relevantes para a condução de políticas pesqueiras locais e ações de manejo para a conservação das espécies.(AU)

A cascade of dams affects fish spatial distributions and functional groups of local assemblages in a subtropical river

Dams reduce the longitudinal connectivity of rivers and thereby disrupt fish migration and the spatial distribution of species, impacts that remain poorly studied for some Neotropical rivers from mega-diverse basins. We investigated the spatial distribution of fish species with different trophic and movement/reproductive/size characteristics to assess how functional groups have responded to a cascade of dams on the Uruguai River in southern Brazil. Fish abundance, biomass, and species composition were evaluated at eight locations along the longitudinal gradient. The fish assemblage in the upper stretch was mainly characterized by small and medium-sized species at higher trophic levels, whereas the sites located furthest downstream displayed more medium and large-sized species, including many carnivorous species. Species with high fecundity, seasonal migrants, and catfishes with internal fertilization were common in the river´s middle and lower reaches. Detritivorous species dominated areas distant from the dams. Overall, functional diversity of local fish assemblages was greater in lower reaches. The cascade of dams has impacted the distribution of functional groups of local fish assemblages of Uruguai River. The alteration of functional groups in upper reaches of the river has potential consequences for ecosystem processes and services, such as nutrient cycling and fisheries.(AU)

As barragens reduzem a conectividade longitudinal dos rios e interrompem a migração e a distribuição espacial das espécies, configurando impactos pouco estudados para alguns rios Neotropicais megadiversos. Investigamos a distribuição espacial de espécies de peixes com diferentes características tróficas e reprodutivas para avaliar como grupos funcionais responderam a uma cascata de reservatórios no rio Uruguai, sul do Brasil. Abundância de peixes, biomassa e composição de espécies foram avaliadas em oito locais ao longo do gradiente longitudinal. A assembleia de peixes no trecho superior foi caracterizada principalmente por espécies de pequeno e médio porte em níveis tróficos mais elevados, enquanto que os ambientes localizados mais a jusante apresentaram mais espécies de médio e grande porte, incluindo muitas espécies carnívoras. Espécies com alta fecundidade, migradores sazonais e bagres com fertilização interna foram comuns no curso médio e inferior. Espécies detritívoras dominaram áreas distantes das barragens. A diversidade funcional das assembleias de peixes locais foi maior nas partes inferiores. A cascata de barragens impactou a distribuição dos grupos funcionais das assembleias de peixes locais no rio Uruguai. A alteração da diversidade funcional no curso superior do rio tem consequências potenciais para a dinâmica e serviços do ecossistema, como ciclagem de nutrientes e pesca.(AU)

Limnoperna fortunei - Updating the geographic distribution in the Brazilian watersheds and mapping the regional occurrence in the Upper Uruguay River basin / Limnoperna fortunei - Atualização da distribuição geográfica nas bacias hidrográficas brasileiras e mapeamento da ocorrência regional na bacia do Alto Rio Uruguai

Abstract: Limnoperna fortunei is an invasive alien species (IAS) that cause serious ecological and economic problems in Brazilian freshwater environments. Due to its high dispersion capacity and the lack of new records in peer-reviewed journals we carried out an extensive survey to update the distribution of L. fortunei in the Brazilian hydrographic basins. We also performed a detailed investigation of its distribution in the Upper Uruguay River basin using a molecular method. We presented new records, showing the invasion in new basins and a wide distribution in the basins previously infested. Additionally, we confirmed that the Upper Uruguay River is fully colonized by the golden mussel, being distributed in the lentic, lotic, and transitional lotic/lentic environments presented in this region. This update is an important tool for the implementation of guidelines and the development of safety protocols and sanitary barriers to avoid the dispersion of this IAS to new environments..

Resumo: Limnoperna fortunei é uma espécie exótica invasora que causa sérios problemas ecológicos e econômicos em ambientes de água doce do Brasil. Devido à sua elevada capacidade de dispersão e à falta de novos registros em publicações científicas, o objetivo deste estudo foi realizar uma extensa pesquisa para entender e alertar sobre o atual cenário de distribuição de L. fortunei nas bacias hidrográficas brasileiras. Também realizamos uma investigação mais detalhada sobre a distribuição da espécie na bacia do Alto Rio Uruguai, utilizando um método molecular. Apresentamos novos registros de ocorrência da espécie, mostrando a invasão em novas bacias e uma ampla distribuição nas bacias anteriormente infestadas. Além disso, confirmamos que o Alto Rio Uruguai está totalmente colonizado pelo mexilhão-dourado, estando distribuído pelos ambientes lênticos, lóticos e de transição existentes na região. Esta atualização se mostra como uma importante ferramenta para a implementação de diretrizes e o desenvolvimento de protocolos de segurança e barreiras sanitárias para evitar a dispersão desta espécie invasora em novos ambientes.

Genetic evidence supports polygamous mating system in a wild population of Prochilodus lineatus (Characiformes: Prochilodontidae), a Neotropical shoal spawner fish

Behavioral observations made on fish have revealed remarkably diverse reproductive strategies, including polygamy by both sexes. Still, to date, most Neotropical species remain unstudied as to whether the observed reproductive behavior in natural populations correlates with their genetic mating systems. Here, we investigated the genetic mating system of a wild population of Prochilodus lineatus settled in the Middle Uruguay River basin. By using sibship reconstruction and parental inference methods based on microsatellites' genotypes, we inferred 45 females and 47 males as potential parents of the 87 larvae analyzed. We found evidence supporting polygamous mating in both sexes: while a high percentage of males (44.7%) fertilized the eggs of one female, 55.3% of the inferred males fertilized eggs of up to four females. Likewise, while 44.5% of the inferred females had their eggs fertilized by one only male, 55.5% of females were fertilized by multiple males. The estimated proxy of the effective population size (Nb) was 126, exhibiting moderate to high levels of genetic diversity. The genetic evidence contributed in this study complements earlier behavioral observations of formation of spawning nuclei of aggregating breeders, which may be promoting a polygamous mating strategy in this long-distance migratory fish.(AU)

Observações do comportamento de peixes neotropicais têm revelado estratégias reprodutivas marcadamente variáveis, incluindo poligamia nos dois sexos. Ainda assim, até então, a correlação entre comportamento reprodutivo observado em populações naturais e sistemas de acasalamento genético permanece pouco explorada para maioria de espécies Neotropicais. Neste estudo investigamos o sistema genético de acasalamento de Prochilodus lineatus em uma população natural estabelecida no Médio rio Uruguai. Utilizando métodos de reconstrução de grupos familiares e inferências parentais baseados em genótipos de microssatélites, inferimos 45 fêmeas e 47 machos como os possíveis parentais das 87 larvas amostradas. Encontramos evidência que permite apoiar a ocorrência de acasalamento poligâmico em ambos os sexos: enquanto uma percentagem alta de machos (44,7%) fertilizou somente uma fêmea, 55,3% dos machos inferidos fertilizaram mais de uma fêmea (até quatro por macho). Da mesma forma, enquanto que 44,5% das fêmeas inferidas tiveram seus ovos fertilizados por apenas um único macho, 55,5% das fêmeas tiveram ovos fertilizados por múltiplos machos. A estimativa do tamanho populacional efetivo (Nb) foi 126, exibindo níveis entre moderados e altos de diversidade genética. A evidência genética que apresentamos nesse estudo complementa observações iniciais da formação de núcleos de desova que podem promover estratégias de acasalamento poligâmico nessa espécie migratória de longa distância.(AU)

Genetic Variation of the Endangered Neotropical Catfish Steindachneridion scriptum (Siluriformes: Pimelodidae).

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.

Wide reproductive period of a long-distance migratory fish in a subtropical river, Brazil

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.(AU)

Salminus brasiliensis é uma espécie potamodroma que ocorre em rios da América do Sul. Apesar de sua importância ecológica e econômica, informações sobre a biologia reprodutiva de S. brasiliensis ainda são escassas. O presente estudo utilizou dados de 18 anos de amostragens contínuas na bacia do alto rio Uruguai, analisando 718 peixes adultos (307 machos, 243 fêmeas, 168 indefinidos) capturados em diferentes meses do ano. Os resultados mostraram que o período reprodutivo de S. brasiliensis é amplo na bacia do alto rio Uruguai, com a ocorrência de peixes maduros entre agosto e março, e de peixes desovados entre os meses de julho e maio do ano seguinte. A relação gonadossomática reforça essa observação, pois mostra um aumento a partir de agosto. O período reprodutivo de S. brasiliensis no alto rio Uruguai pode iniciar entre meados do inverno e início da primavera (entre final de julho e final de setembro), podendo se estender até o final do verão e meados do outono (entre meados de fevereiro e início de maio). Essas descobertas contribuem com informações sobre a biologia geral de S. brasiliensis e são relevantes para programas de gestão e para esforços de conservação desse recurso pesqueiro.(AU)

DNA barcoding confirms the occurrence of Rhamdia branneri and Rhamdia voulezi (Siluriformes: Heptapteridae) in the Iguaçu River Basin

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.(AU)

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.(AU)

Genetic characterization of the Neotropical catfish Pimelodus maculatus (Pimelodidae, Siluriformes) in the Upper Uruguay River.

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.

Individual contributions to pooled-milt fertilizations of silver catfish Rhamdia quelen

Supplementary stocking of fish in natural environments is a way to mitigate or compensate for the changes imposed on wild populations by river damming. Since little is known about the genetic composition of the supplementary stocks obtained by pooled-milt fertilization, the aim of this study was to determine the individual contributions of male jundiá Rhamdia quelen to offspring. Sperm from four males were mixed using equal volume of sperm from each of the males to fertilize eggs from only one female, kept in three blend with six males and three females. The proportions of larvae sired by the different males were quantified using five polymorphic DNA microsatellite loci. Analysis of these loci allowed paternal determination of 84 percent of the progeny, at a 0.972 combined exclusion probability. Broodstock milt had good fertilizing capacity when used alone, but when pooled the fertilizing capacities, its fertilizing possibility varied from 4 to 65 percent. Results show that milt pools favor gametes of some males over others, thus reducing the progeny's genetic variability.(AU)

A estocagem de suplementação de peixes em ambientes naturais é uma das maneiras de mitigar ou compensar as alterações impostas pelo represamento dos rios às populações selvagens. Pouco se conhece sobre a composição genética dos estoques repovoadores obtidos através do manejo reprodutivo com fertilizações com o uso de pool de sêmen, de maneira que este trabalho teve como objetivo verificar a contribuição individual de machos de jundiá (Rhamdia quelen) na progênie. O mesmo volume de sêmen de quatro machos foi misturado para fertilizar os ovócitos de uma única fêmea, sendo mantidos em três combinações com seis machos e três fêmeas. A proporção de larvas geradas de diferentes machos foi quantificada através de cinco marcadores microssatélites. A análise dos cinco locus permitiu a determinação da paternidade de 84 por cento da progênie, com 0,972 de probabilidade de exclusão combinada. O sêmen dos reprodutores apresentou boa capacidade de fertilização quando utilizados separadamente, porém, quando utilizados em pool apresentaram capacidade de fertilização entre 4 a 65 por cento. Os resultados revelam que o pool de sêmen favorece alguns machos sobre outros, reduzindo a variabilidade genética da progênie(AU)