Abstract Molecular tools have been employed to improve the knowledge about freshwater Neotropical fishes. Such approaches supporting studies of groups including species complexes such as Astyanax, one of the most diversified and taxonomically complex genus of the family Characidae. Here, we employed species delimitation analyses in four Astyanax species described for the upper Paraguaçu River basin, a drainage within Northeastern Mata Atlântica freshwater ecoregion with high endemism. We implemented single and multilocus approaches based on two mitochondrial and one nuclear markers. Cytochrome c Oxidase I sequences previously available for Astyanax species were also added to our dataset. The single locus analyses showed A. epiagos, A. rupestris, and A. aff. rupestris as different Molecular Operational Taxonomic Units (MOTUs), while A. brucutu and A. lorien were grouped. However, the multilocus approach distinguished these two species and showed congruence for the remaining single locus results. Astyanax aff. rupestris was separated into two MOTUs using both approaches, highlighting the need for an integrative taxonomic revision including A. aff. rupestris. These findings contribute to a better understanding of the diversity of this fish group in the upper Paraguaçu, identifying hidden diversity and reinforcing the relevance of this hydrographic system as a notable hotspot for ichthyofauna biodiversity endemism.

Resumo Ferramentas moleculares têm sido empregadas para melhorar o conhecimento sobre os peixes Neotropicais. Tais abordagens apoiam estudos de grupos que incluem complexos de espécies, como Astyanax, um dos gêneros mais diversificados e taxonomicamente complexos dentro da família Characidae. Neste estudo, nós empregamos análises de delimitação de espécies em quatro espécies de Astyanax recentemente descritas da bacia do alto rio Paraguaçu, uma drenagem dentro da ecorregião Mata Atlântica Nordeste que apresenta alto endemismo. Nós realizamos abordagens de loco único e multilocos baseadas em dois marcadores mitocondriais e um nuclear. Sequências de Citocromo c Oxidase I anteriormente disponíveis para espécies de Astyanax foram adicionadas ao nosso conjunto de dados. As análises de loco único mostraram A. epiagos, A. rupestris e A. aff. rupestris como diferentes Unidades Taxonômicas Operacionais Moleculares (MOTUs), enquanto A. brucutu e A. lorien foram agrupadas. Entretanto, a abordagem multilocos distinguiu estas duas espécies e mostrou congruência com os demais resultados das análises de loco único. Astyanax aff. rupestris foi separada em duas MOTUs usando ambas as abordagens, sugerindo a necessidade de uma revisão taxonômica integrativa incluindo A. rupestris e ambas A. aff. rupestris. Esses achados contribuem para uma melhor compreensão da diversidade desse grupo de peixes na bacia do rio Paraguaçu, identificando diversidade oculta e reforçando a relevância desse sistema hidrográfico como um notável hotspot de endemismo da biodiversidade da ictiofauna.

Resumo 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.

Abstract 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.

Resumo: O objetivo deste trabalho foi avaliar polimorfismos em genes candidatos de Litopenaeus vannamei relacionados ao crescimento, e uma possível associação entre genótipos e fenótipos de peso em duas linhagens fechadas de camarão. Três SSR-EST (serina-arginina, 60S ribossomal e troponina) e um SNP-EST (crustacianina) foram selecionados e avaliados em L. vannamei e sete outras espécies de camarão marinho, além de duas espécies de água doce. Os genótipos não tiveram efeito significativo sobre o peso corporal total. Embora não tenham sido observadas associações na população amostrada, esses marcadores puderam ser amplificados para a maioria das espécies avaliadas e podem ser úteis em estudos genéticos adicionais em espécies de camarão.

Abstract: The objective of this work was to assess polymorphisms within Litopenaeus vannamei candidate genes related to growth performance, and a possible association between weight genotypes and phenotypes in two shrimp closed lines. Three EST-SSR (serine-arginine, 60S ribosomal, and troponin) and one EST-SNP (crustacyanin) were selected and evaluated in L. vannamei and seven other marine shrimp species, besides two freshwater species. Genotypes had no effect on total body weight. Although no association was observed in the sampled population, these markers showed amplification for most of the evaluated species and, therefore, may be useful in further genetic studies on shrimp species.

We performed an in silico analysis of all microsatellites so far described for penaeid shrimp and for which the polymorphic behavior has previously been analyzed. The objective of the study was to evaluate the structural characteristics of these microsatellites and identifying patterns which allow the characterization of the nature of these sequences in the penaeid genome. All data were compiled in a free-access database specially constructed for this study. Three hundred non-mononucleotide polymorphic microsatellite loci described for 12 shrimp species belonging to the family Penaeidae were analyzed and simple and compound microsatellites with di-, tri-, tetra-, penta- and hexanucleotide motifs were found. Dinucleotides and trinucleotides were the most frequent motifs among both the simple and the compound microsatellites. Although a certain bias related to different microsatellite isolation methodology could not be discarded, it is possible that part of this microsatellite abundance reflects some degree of conservation of microsatellite motifs among the different species. There was a pronounced motif variability within and between species, indicating high differentiation dynamism of these repetitions in this animal group. This study not only sheds light on the structure of the microsatellites present in the penaeid shrimp genome but also resulted in the free-access Penaeid Shrimp Microsatellite Database (available at http://www.shrimp.ufscar.br) which may be very useful for optimizing the use of these microsatellites.

The culture of the marine shrimp Litopenaeus vannamei has recently boosted the Brazilian shrimp industry. However, it is well known that selection methods based solely on phenotypic characteristics, a reduced number of breeders and the practice of inbreeding may promote a significant raise in the genetic similarity of the captive populations, leading to greater disease susceptibility and impairing both the growth and final size of the shrimps. We used four microsatellite loci to investigate genetic variation in three generations (F5, F6 and F7) of a closed and reared L. vannamei lineage. Although an accentuated heterozygosis deficit was detected, we also observed that the captive propagation of this lineage did not lead to a significant loss of genetic variability over the three generations studied. One possible reason for this is that the breeding conditions of this lineage were good enough to prevent any significant loss of genetic variability. However, three generations may have been insufficient to produce detectable changes in genetic frequencies in the loci studied. Alternatively, the microsatellite loci may have been non-neutral (biased) and related to the conditions in which the shrimps were kept, resulting in a similar allele pool in respect to these four microsatellites over the three generations studied. Any generalizations regarding microsatellite variation in closed shrimp lines may thus be incomplete and should be carefully analyzed.

The Pacific white shrimp, Litopenaeus vannamei (Penaeidae), represents about 95% of all Brazilian shrimp production. The Brazilian L. vannamei foundation broodstock was made up of specimens collected from different American Pacific sites, but little information was collected on the genetic structure of the broodstock. We used the fluorescence amplified fragment length polymorphism (fAFLP) method to study the genetic diversity of L. vannamei broodstock lines 03CMF1 and 03CBF1 originally produced by breeder-shrimps imported mainly from Panama and Ecuador, although wild individuals from other localities may also have been used in producing these two lines. Our results showed a total of 93 polymorphic bands ranging from 50 to 500 bp, the mean Nei's genetic diversity calculated for the total sample was 13.4% and identity and genetic distance analyses indicated high genetic homogeneity within and between both the broodstock lineages studied which suggests that they had similar genetic structure. These results may represent an important tool for the appropriate management of L. vannamei broodstocks.

The genetic variation in two farmed strains (F3-Panama and F17-Venezuela) of the shrimp Litopenaeus vannamei was examined based on DNA multiloci analyses. Eighteen adults of each strain were analyzed by PCR using a set of VNTR core sequence primers. Genetic similarity, mean allele frequency, mean heterozygosity and the frequency of polymorphic loci were determined for both strains. A dendrogram of genetic similarity was produced by UPGMA clustering. The results for three primers (INS, M13, YN73) revealed different levels of genetic variation within the strains. The higher genetic similarity seen within strain F17 was apparently related to inbreeding, although a bottleneck effect could not be discarded. The low level of genetic variability of this strain could account for the reduced adaptive advantage of these animals and their inability to adjust to breeding conditions in Brazil.