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Juliana Araripe - One of the best experts on this subject based on the ideXlab platform.
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The Arapaima, an emblematic fishery resource: genetic diversity and structure reveal the presence of an isolated population in Amapá
Hydrobiologia, 2020Co-Authors: Fabrícia Nogueira, Iracilda Sampaio, Marilu Amaral, Gabryele Malcher, Natália Reis, Mauro A. D. Melo, Péricles S. Rêgo, Juliana AraripeAbstract:The Arapaima ( Arapaima gigas ) is one of the most emblematic species of the Amazon region, and has a long history of exploitation. The present study investigated the connectivity and genetic variability of the Arapaima in the region of the confluence of the Amazon and Araguaia-Tocantins basins, with emphasis on the population from the Lago Piratuba Biological Reserve, in the Brazilian state of Amapá. The study was based on the analysis of 11 microsatellite loci and the mtDNA control region sequences of 114 Arapaima collected at six localities in the region of the eastern Amazon. The genetic analysis found significant differentiation, which indicated the presence of three distinct populations, the Lower Amazon-Marajó, Lago Piratuba, and Lower Tocantins populations, which lacked any significant level of gene flow. All three populations presented evidence of recent bottlenecks and distinct levels of genetic diversity, which was high only in the Lower Amazon-Marajó population. The conservation strategies for this region should consider the specific characteristics of these three populations and the different patterns of diversity found. The genetic characterization of the Lago Piratuba reserve as a unique population reinforces the importance of the implementation of adequate management strategies in the region.
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Genetic diversity and structuring in the Arapaima (Osteoglossiformes, Osteoglossidae) population reveal differences between the Amazon and the Tocantins-Araguaia basins.
Anais da Academia Brasileira de Ciencias, 2020Co-Authors: Fabrícia Nogueira, Péricles Sena Do Rêgo, Helder Lima De Queiroz, Iracilda Sampaio, Horacio Schneider, Paulo Cesar Venere, Eduardo Sousa Varela, Juliana AraripeAbstract:Arapaima is a widely-distributed fish of enormous economic importance in the Amazon region. In the present study, a total of 232 specimens were sampled, 121 from five sites in the Amazon basin and 111 from five sites in the Tocantins-Araguaia basin. The analyses investigated fragments of the Cytochrome b, Control Region, Cytochrome Oxidase I, NADH dehydrogenase subunit 2 and seven loci microsatellites. The analyses revealed the existence of two mitochondrial lineages within the general area, with no haplotypes shared between basins, and genetic variability significantly higher in the Amazon than in the Tocantins-Araguaia basin. Two divergent, but sympatric mitochondrial lineages were found in the Amazon basin, but only a single lineage in the Tocantins-Araguaia basin. The existence of these two mitochondrial lineages indicates that past events, probably occurring during the Pleistocene, resulted in the separation of the populations of this species and molded its evolutionary history, which is reflected directly in its mitochondrial DNA. The analysis of the Arapaima population structure identified distinct levels of diversity within the distribution of the species, indicating specific geographic regions that will require special attention for the development of conservation and management strategies.
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genetic diversity and structure in Arapaima gigas populations from amazon and araguaia tocantins river basins
BMC Genetics, 2019Co-Authors: Juliana Araripe, Eduardo Sousa Varela, Lucas S Torati, John B Taggart, Stefanie Wehner, Herve MigaudAbstract:Arapaima gigas (Schinz, 1822) is the largest freshwater scaled fish in the world, and an emerging species for tropical aquaculture development. Conservation of the species, and the expansion of aquaculture requires the development of genetic tools to study polymorphism, differentiation, and stock structure. This study aimed to investigate genomic polymorphism through ddRAD sequencing, in order to identify a panel of single nucleotide polymorphisms (SNPs) and to simultaneously assess genetic diversity and structure in wild (from rivers Amazon, Solimoes, Tocantins and Araguaia) and captive populations. Compared to many other teleosts, the degree of polymorphism in A. gigas was low with only 2.3% of identified RAD-tags (135 bases long) containing SNPs. A panel of 393 informative SNPs was identified and screened across the five populations. Higher genetic diversity indices (number of polymorphic loci and private alleles, Shannon’s Index and HO) were found in populations from the Amazon and Solimoes, intermediate levels in Tocantins and Captive, and very low levels in the Araguaia population. These results likely reflect larger population sizes from less urbanized environments in the Amazon basin compared to Araguaia. Populations were significantly differentiated with pairwise FST values ranging from 0.086 (Amazon × Solimoes) to 0.556 (Amazon × Araguaia). Mean pairwise relatedness among individuals was significant in all populations (P < 0.01), reflecting a degree of inbreeding possibly due to severe depletion of natural stocks, the species sedentary behaviour and possible sampling biases. Although Mantel test was not significant (P = 0.104; R2 = 0.65), Bayesian analysis in STRUCTURE and discriminant analysis of principal components (DAPC) showed populations of Amazon and Solimoes to be genetically differentiated from Araguaia, with Tocantins comprising individuals from both identified stocks. This relatively rapid genotyping by sequencing approach proved to be successful in delineating Arapaima stocks. The approach and / or SNP panels identified should prove valuable for more detailed genetic studies of Arapaima populations, including the elucidation of the genetic status of described discrete morphotypes and aid in delivery of conservation programs to maintain genetic diversity in reservoirs across the Amazon region.
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Additional file 3: of Genetic diversity and structure in Arapaima gigas populations from Amazon and Araguaia-Tocantins river basins
2019Co-Authors: Lucas S Torati, Juliana Araripe, Stefanie Wehner, John Taggart, Eduardo Varela, Herve MigaudAbstract:A. Discriminant analysis of principal components (DAPC) using 392 SNP markers in Adegenet v. 2.0.1 [68] for the five Arapaima gigas populations sampled (n = 60 individuals). B. Selection of number of clusters was based on Bayesian Inference Criterion (BIC), which indicates 3 clusters for data summarization (elbow drop). C. Membership probabilities (red = 1, white = 0) for individuals into clusters, blue crosses indicate the prior cluster provided into DAPC. (TIF 2254 kb
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Additional file 1: of Genetic diversity and structure in Arapaima gigas populations from Amazon and Araguaia-Tocantins river basins
2019Co-Authors: Lucas S Torati, Juliana Araripe, Stefanie Wehner, John Taggart, Eduardo Varela, Herve MigaudAbstract:General information and summary data from the ddRAD study of Arapaima gigas: a) the combinatorial inline barcodes used for each individual - DNA samples were processed in duplicate, with a different barcode combination used for each RE digestion - ligation reaction, thus each individual is represented by two sets of identifiers; b) basic RAD locus statistics generated by STACKS for each of the 60 samples; c) mean observed heterozygosity within the 392 loci surveyed for each individual. (XLSX 14 kb
Leandro Castello - One of the best experts on this subject based on the ideXlab platform.
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Size‐structured habitat selection by Arapaima in floodplain lakes of the Lower Amazon
Aquatic Conservation: Marine and Freshwater Ecosystems, 2018Co-Authors: Jordan C. Richard, Leandro Castello, Daniel J. Gurdak, Brandon K. Peoples, Paul L. AngermeierAbstract:Human modification of floodplain ecosystems is widespread and a major threat to fish populations, particularly in the tropics where fish diversity and rates of floodplain degradation are high. Identifying measures to minimize the susceptibility of floodplain fishes to habitat modification requires understanding dry‐season lake habitat selection for species of conservation concern. This study examined the effects of environmental factors on dry‐season floodplain lake habitat selection by Arapaima (Arapaima spp.) and determined the extent to which they differed across three size classes. In floodplain lakes of the lower Amazon River, variables were measured at locations representing habitat availability and compared with measurements taken where Arapaima were observed during surface breathing. Regression models were used to account for between‐lake variation in the presence of Arapaima owing to nearby fishing communities. The probability of Arapaima presence at each sample location was modelled based on the variables measured. The results indicated that Arapaima expressed distinct habitat selection patterns, which differed significantly across size classes. The general pattern observed was that all Arapaima were more likely to be found in deeper, more turbid, and higher conductivity locations, whereas smaller Arapaima were more likely to remain near dense beds of floating macrophytes. The probability of Arapaima presence differed among fishing community territories, reflecting differences in management schemes. Deeper, macrophyte‐rich sections of floodplain lakes appear to provide key habitats for Arapaima and deserve consideration for becoming priority targets for conservation of the rich diversity of fish species in these systems.
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size structured habitat selection by Arapaima in floodplain lakes of the lower amazon
Aquatic Conservation-marine and Freshwater Ecosystems, 2018Co-Authors: Jordan C. Richard, Leandro Castello, Daniel J. Gurdak, Brandon K. Peoples, Paul L. AngermeierAbstract:Human modification of floodplain ecosystems is widespread and a major threat to fish populations, particularly in the tropics where fish diversity and rates of floodplain degradation are high. Identifying measures to minimize the susceptibility of floodplain fishes to habitat modification requires understanding dry‐season lake habitat selection for species of conservation concern. This study examined the effects of environmental factors on dry‐season floodplain lake habitat selection by Arapaima (Arapaima spp.) and determined the extent to which they differed across three size classes. In floodplain lakes of the lower Amazon River, variables were measured at locations representing habitat availability and compared with measurements taken where Arapaima were observed during surface breathing. Regression models were used to account for between‐lake variation in the presence of Arapaima owing to nearby fishing communities. The probability of Arapaima presence at each sample location was modelled based on the variables measured. The results indicated that Arapaima expressed distinct habitat selection patterns, which differed significantly across size classes. The general pattern observed was that all Arapaima were more likely to be found in deeper, more turbid, and higher conductivity locations, whereas smaller Arapaima were more likely to remain near dense beds of floating macrophytes. The probability of Arapaima presence differed among fishing community territories, reflecting differences in management schemes. Deeper, macrophyte‐rich sections of floodplain lakes appear to provide key habitats for Arapaima and deserve consideration for becoming priority targets for conservation of the rich diversity of fish species in these systems.
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trophic ecology of Arapaima sp in a ria lake river floodplain transition zone of the amazon
Ecology of Freshwater Fish, 2018Co-Authors: Felipe Pereira Camara Carvalho, Leandro Castello, Michael Power, B. Forsberg, Eduardo G. Martins, Carlos E. C. FreitasAbstract:Neotropical floodplains are usually productive systems that are maintained by the nutrient, detritus and sediment inputs provided by the main river channel flood pulse. Ria lakes represent a special feature and habitat in the Amazonian floodplains, being characterised by a dendritic morphology and dependence on terrestrial inputs provided by an intricate stream network. Our objective was to evaluate the trophic ecology of the Arapaima (Arapaima sp.). We combined stomach content analysis with measurements of carbon and nitrogen stable isotope values from dorsal muscle to infer the ontogenetic changes in trophic level and isotopic niche width in floodplain and ria lakes. Arapaima diet was dominated by fish from low trophic positions. While most of the stomachs sampled in the study ria lake were full, empty stomachs predominated in samples taken in the floodplain lakes. These differences indicate that ria lakes may provide better feeding grounds for Arapaima during the dry season, presumably because ria lakes are interconnected with a large stream network and the main river channel year round. Nitrogen stable isotope results further indicated an ontogenetic dietary shift in Arapaima, with piscivory increasing as a function of length in both environments. Carbon stable isotope analysis indicated that energy sources used by Arapaima varied by environment, with Arapaima using a greater diversity of food sources in ria lakes than in floodplain lakes. Information about the main carbon sources is useful for fishery management because stakeholders may choose to conserve key vegetal groups to ensure the productivity and diversity of aquatic ecosystems.
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Trophic Ecology of Arapaima sp. in a ria lake—river–floodplain transition zone of the Amazon
Ecology of Freshwater Fish, 2017Co-Authors: Felipe Pereira Camara Carvalho, Leandro Castello, Michael Power, B. Forsberg, Eduardo G. Martins, Carlos E. C. FreitasAbstract:Neotropical floodplains are usually productive systems that are maintained by the nutrient, detritus and sediment inputs provided by the main river channel flood pulse. Ria lakes represent a special feature and habitat in the Amazonian floodplains, being characterised by a dendritic morphology and dependence on terrestrial inputs provided by an intricate stream network. Our objective was to evaluate the trophic ecology of the Arapaima (Arapaima sp.). We combined stomach content analysis with measurements of carbon and nitrogen stable isotope values from dorsal muscle to infer the ontogenetic changes in trophic level and isotopic niche width in floodplain and ria lakes. Arapaima diet was dominated by fish from low trophic positions. While most of the stomachs sampled in the study ria lake were full, empty stomachs predominated in samples taken in the floodplain lakes. These differences indicate that ria lakes may provide better feeding grounds for Arapaima during the dry season, presumably because ria lakes are interconnected with a large stream network and the main river channel year round. Nitrogen stable isotope results further indicated an ontogenetic dietary shift in Arapaima, with piscivory increasing as a function of length in both environments. Carbon stable isotope analysis indicated that energy sources used by Arapaima varied by environment, with Arapaima using a greater diversity of food sources in ria lakes than in floodplain lakes. Information about the main carbon sources is useful for fishery management because stakeholders may choose to conserve key vegetal groups to ensure the productivity and diversity of aquatic ecosystems.
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Recovery of Arapaima sp. populations by community-based management in floodplains of the Purus River, Amazon.
Journal of fish biology, 2016Co-Authors: T. A. Petersen, S. M. Brum, F. Rossoni, G. F. V. Silveira, Leandro CastelloAbstract:In the present study a unique dataset on population abundance in various community-based management (CBM) and non-CBM areas is analysed to address the question of whether CBM can recover overexploited populations of Arapaima sp. in river-floodplain ecosystems. All non-CBM areas possessed depleted Arapaima sp. populations with a mean density of 0·01 individuals ha(-1) . Arapaima sp. population densities in all CBM areas changed over time from depleted to overexploited or well managed status, with a mean rate of increase of 77% year(-1) . Rates of Arapaima sp. population recovery in CBM areas differed, probably reflecting differences in ecosystem productivity and compliance with management regulations. These results indicate that CBM schemes can be effective tools for the recovery and conservation of fish populations with non-migratory life cycles in tropical river-floodplain ecosystems.
Iracilda Sampaio - One of the best experts on this subject based on the ideXlab platform.
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The Arapaima, an emblematic fishery resource: genetic diversity and structure reveal the presence of an isolated population in Amapá
Hydrobiologia, 2020Co-Authors: Fabrícia Nogueira, Iracilda Sampaio, Marilu Amaral, Gabryele Malcher, Natália Reis, Mauro A. D. Melo, Péricles S. Rêgo, Juliana AraripeAbstract:The Arapaima ( Arapaima gigas ) is one of the most emblematic species of the Amazon region, and has a long history of exploitation. The present study investigated the connectivity and genetic variability of the Arapaima in the region of the confluence of the Amazon and Araguaia-Tocantins basins, with emphasis on the population from the Lago Piratuba Biological Reserve, in the Brazilian state of Amapá. The study was based on the analysis of 11 microsatellite loci and the mtDNA control region sequences of 114 Arapaima collected at six localities in the region of the eastern Amazon. The genetic analysis found significant differentiation, which indicated the presence of three distinct populations, the Lower Amazon-Marajó, Lago Piratuba, and Lower Tocantins populations, which lacked any significant level of gene flow. All three populations presented evidence of recent bottlenecks and distinct levels of genetic diversity, which was high only in the Lower Amazon-Marajó population. The conservation strategies for this region should consider the specific characteristics of these three populations and the different patterns of diversity found. The genetic characterization of the Lago Piratuba reserve as a unique population reinforces the importance of the implementation of adequate management strategies in the region.
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Genetic diversity and structuring in the Arapaima (Osteoglossiformes, Osteoglossidae) population reveal differences between the Amazon and the Tocantins-Araguaia basins.
Anais da Academia Brasileira de Ciencias, 2020Co-Authors: Fabrícia Nogueira, Péricles Sena Do Rêgo, Helder Lima De Queiroz, Iracilda Sampaio, Horacio Schneider, Paulo Cesar Venere, Eduardo Sousa Varela, Juliana AraripeAbstract:Arapaima is a widely-distributed fish of enormous economic importance in the Amazon region. In the present study, a total of 232 specimens were sampled, 121 from five sites in the Amazon basin and 111 from five sites in the Tocantins-Araguaia basin. The analyses investigated fragments of the Cytochrome b, Control Region, Cytochrome Oxidase I, NADH dehydrogenase subunit 2 and seven loci microsatellites. The analyses revealed the existence of two mitochondrial lineages within the general area, with no haplotypes shared between basins, and genetic variability significantly higher in the Amazon than in the Tocantins-Araguaia basin. Two divergent, but sympatric mitochondrial lineages were found in the Amazon basin, but only a single lineage in the Tocantins-Araguaia basin. The existence of these two mitochondrial lineages indicates that past events, probably occurring during the Pleistocene, resulted in the separation of the populations of this species and molded its evolutionary history, which is reflected directly in its mitochondrial DNA. The analysis of the Arapaima population structure identified distinct levels of diversity within the distribution of the species, indicating specific geographic regions that will require special attention for the development of conservation and management strategies.
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The largest fish in the world's biggest river: Genetic connectivity and conservation of Arapaima gigas in the Amazon and Araguaia-Tocantins drainages.
PloS one, 2019Co-Authors: Izeni Pires Farias, Iracilda Sampaio, Stuart C. Willis, Adam Leão, Júlia Tovar Verba, Marcelo Crossa, Fausto Foresti, Fábio Porto-foresti, Tomas HrbekAbstract:Arapaima, pirarucu or paiche (Arapaima gigas) is one of the largest freshwater fish in the world, and has a long history of commercial exploitation in the Amazon region. To estimate levels of genetic variability and historical and recent connectivity in Arapaima, we examined variation in eleven microsatellite DNA markers in individuals from 22 localities in Brazil, Colombia, and Peru. The results of analysis of molecular variance, Bayesian clustering and discriminant analysis of principal components showed that Arapaima in our samples represents two major populations, one in the Amazonas and one in the Araguaia-Tocantins River basins. The Amazonas population is further structured by isolation-by-distance with the hydrologically largely unconnected Amapa locality representing the eastern-most extreme of this continuum; gene flow predominates at distances of less than 1500 km with localities separated by over 2000 km dominated by genetic drift and effectively forming different populations. We saw no evidence of multiple species of Arapaima in the Amazonas basin, and analysis of pairwise genetic divergence (FST) with Mantel tests and correlograms indicated that this largest population exhibits a large-scale pattern of isolation-by-distance, with which results from MIGRATE-N agreed. The degree and significance of genetic divergence indicates that most sampled localities represent demographically independent sub-populations, although we did identify several recent migration events between both proximal and more distant localities. The levels of genetic diversity were heterogeneous across sites, including low genetic diversity, effective population sizes, and evidence of genetic bottlenecks in several places. On average the levels of gene diversity and rarefied allelic richness were higher for localities along the Amazonas mainstem than in the tributaries, despite these being the areas of highest fishing pressure, while the lowest values were found in tributary headwaters, where landscape modification is a significant threat. We recommend that managers consider the regional and local threats to these populations and tailor strategies accordingly, strategies which should ensure the ability of young A. gigas to disperse through floodplain corridors to maintain genetic diversity among otherwise sedentary adult sub-populations.
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De novo transcriptome based on next-generation sequencing reveals candidate genes with sex-specific expression in Arapaima gigas (Schinz, 1822), an ancient Amazonian freshwater fish.
PloS one, 2018Co-Authors: Luciana Watanabe, Horacio Schneider, Fátima Gomes, João L.s.g. Vianez, Márcio Roberto Teixeira Nunes, Jedson Ferreira Cardoso, Clayton Pereira Silva De Lima, Iracilda SampaioAbstract:Background The Arapaima (Arapaima gigas) is one of the world's largest freshwater bony fish, and is found in the rivers of the Amazon basin. This species is a potential aquaculture resource, although reproductive management in captivity is limited in particular due to the lack of external sexual dimorphism. In this study, using the 454 Roche platform (pyrosequencing) techniques, we evaluated a major portion of the transcriptome of this important Amazonian species. Results Four libraries obtained from the liver and skin tissue of juvenile specimens (representing males and females separately) were sequenced, yielding 5,453,919 high-quality reads. The de novo transcriptome assembly resulted in 175,792 contigs, with 51,057 significant blast hits. A total of 38,586 transcripts were mapped by Gene Ontology using Blast2GO. We identified 20,219 genes in the total transcriptome (9,551 in the liver and 16,818 in the skin). The gene expression analyses indicated 105 genes in the liver and 204 in the skin with differentiated expression profiles, with 95 being over-expressed in the females and 214 in the males. The log2 Fold Change and heatmap based on Reads Per Kilobase per Million mapped reads (RPKM) revealed that the gene expression in the skin is highly differentiated between male and female Arapaima, while the levels of expression in the liver are similar between the sexes. Conclusion Transcriptome analysis based on pyrosequencing proved to be a reliable tool for the identification of genes with differentiated expression profiles between male and female Arapaima. These results provide useful insights into the molecular pathways of sexual dimorphism in this important Amazonian species, and for comparative analyses with other teleosts.
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Dispersal capacity and genetic structure of Arapaima gigas on different geographic scales using microsatellite markers.
PloS one, 2013Co-Authors: Juliana Araripe, Péricles Sena Do Rêgo, Helder Lima De Queiroz, Iracilda Sampaio, Horacio SchneiderAbstract:Despite the ecological and economic importance of the Arapaima gigas (Cuvier 1817), few data about its dispersal capacity are available. The present study was based on the analysis of microsatellite markers in order to estimate the dispersal capacity of the species on fine, meso, and large geographic scales. For this, 561 specimens obtained from stocks separated by distances of up to 25 km (fine scale), 100 km (meso scale), and 1300–2300 km (large scale) were analyzed. The fine scale analysis indicated a marked genetic similarity between lakes, with low genetic differentiation, and significant differences between only a few pairs of sites. Low to moderate genetic differentiation was observed between pairs of sites on a meso scale (100 km), which could be explained by the distances between sites. By contrast, major genetic differentiation was recorded in the large scale analysis, that is, between stocks separated by distances of over 1300 km, with the analysis indicating that differentiation was not related solely to distance. The genetic structuring analysis indicated the presence of two stocks, one represented by the Arapaimas of the Mamiraua Reserve, and the other by those of Santarem and Tucurui. The dispersal of Arapaimas over short distances indicates a process of lateral migration within the varzea floodplains, which may be the principal factor determining the considerable homogeneity observed among the varzea lakes. The populations separated by distances of approximately 100 km were characterized by reduced genetic differentiation, which was associated with the geographic distances between sites. Populations separated by distances of over 1300 km were characterized by a high degree of genetic differentiation, which may be related primarily to historical bottlenecks in population size and the sedentary behavior of the species. Evidence was found of asymmetric gene flow, resulting in increasing genetic variability in the population of the Mamiraua Reserve.
Herve Migaud - One of the best experts on this subject based on the ideXlab platform.
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GnRHa implants and size pairing effects on plasma and cephalic secretion sex steroids in Arapaima gigas.
General and comparative endocrinology, 2020Co-Authors: Lucas S Torati, John Taylor, Pedro E. C. Mesquita, Herve MigaudAbstract:Abstract Arapaima gigas, one of the world’s largest freshwater fish, is considered an emerging species for aquaculture development in Brazil given its high growth rate and meat quality. However, the lack of reproductive control in captivity has limited the expansion of Arapaima farming. This study aimed to test the effects of hormonal induction using mGnRHa implants and size pairing on broodstock reproduction through the analyses of sex steroids. To do so, broodstock of different sizes (large, small or mixed) were paired and implanted. Plasma and cephalic secretion profiles of testosterone (T), 11-ketotestosterone (11-KT) and 17β-oestradiol (E2) were analysed. Compared to control (non-implanted), implanted broodstock showed a significant increase in plasma 11-KT (large and small males) and T (large and mixed females) post GnRHa implantation. In females, a significant increase in plasma T levels was shown, however, E2 remained unchanged after implantation. Despite the lack of clear spawning induction, this study showed the potency of GnRHa on sex steroid production regardless of pairing groups. Interestingly, significant correlations between blood plasma and cephalic secretion levels of 11-KT in males and T in females were observed, indicating the possible release of pheromones through the cephalic canals of A. gigas.
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genetic diversity and structure in Arapaima gigas populations from amazon and araguaia tocantins river basins
BMC Genetics, 2019Co-Authors: Juliana Araripe, Eduardo Sousa Varela, Lucas S Torati, John B Taggart, Stefanie Wehner, Herve MigaudAbstract:Arapaima gigas (Schinz, 1822) is the largest freshwater scaled fish in the world, and an emerging species for tropical aquaculture development. Conservation of the species, and the expansion of aquaculture requires the development of genetic tools to study polymorphism, differentiation, and stock structure. This study aimed to investigate genomic polymorphism through ddRAD sequencing, in order to identify a panel of single nucleotide polymorphisms (SNPs) and to simultaneously assess genetic diversity and structure in wild (from rivers Amazon, Solimoes, Tocantins and Araguaia) and captive populations. Compared to many other teleosts, the degree of polymorphism in A. gigas was low with only 2.3% of identified RAD-tags (135 bases long) containing SNPs. A panel of 393 informative SNPs was identified and screened across the five populations. Higher genetic diversity indices (number of polymorphic loci and private alleles, Shannon’s Index and HO) were found in populations from the Amazon and Solimoes, intermediate levels in Tocantins and Captive, and very low levels in the Araguaia population. These results likely reflect larger population sizes from less urbanized environments in the Amazon basin compared to Araguaia. Populations were significantly differentiated with pairwise FST values ranging from 0.086 (Amazon × Solimoes) to 0.556 (Amazon × Araguaia). Mean pairwise relatedness among individuals was significant in all populations (P < 0.01), reflecting a degree of inbreeding possibly due to severe depletion of natural stocks, the species sedentary behaviour and possible sampling biases. Although Mantel test was not significant (P = 0.104; R2 = 0.65), Bayesian analysis in STRUCTURE and discriminant analysis of principal components (DAPC) showed populations of Amazon and Solimoes to be genetically differentiated from Araguaia, with Tocantins comprising individuals from both identified stocks. This relatively rapid genotyping by sequencing approach proved to be successful in delineating Arapaima stocks. The approach and / or SNP panels identified should prove valuable for more detailed genetic studies of Arapaima populations, including the elucidation of the genetic status of described discrete morphotypes and aid in delivery of conservation programs to maintain genetic diversity in reservoirs across the Amazon region.
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Additional file 3: of Genetic diversity and structure in Arapaima gigas populations from Amazon and Araguaia-Tocantins river basins
2019Co-Authors: Lucas S Torati, Juliana Araripe, Stefanie Wehner, John Taggart, Eduardo Varela, Herve MigaudAbstract:A. Discriminant analysis of principal components (DAPC) using 392 SNP markers in Adegenet v. 2.0.1 [68] for the five Arapaima gigas populations sampled (n = 60 individuals). B. Selection of number of clusters was based on Bayesian Inference Criterion (BIC), which indicates 3 clusters for data summarization (elbow drop). C. Membership probabilities (red = 1, white = 0) for individuals into clusters, blue crosses indicate the prior cluster provided into DAPC. (TIF 2254 kb
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Additional file 1: of Genetic diversity and structure in Arapaima gigas populations from Amazon and Araguaia-Tocantins river basins
2019Co-Authors: Lucas S Torati, Juliana Araripe, Stefanie Wehner, John Taggart, Eduardo Varela, Herve MigaudAbstract:General information and summary data from the ddRAD study of Arapaima gigas: a) the combinatorial inline barcodes used for each individual - DNA samples were processed in duplicate, with a different barcode combination used for each RE digestion - ligation reaction, thus each individual is represented by two sets of identifiers; b) basic RAD locus statistics generated by STACKS for each of the 60 samples; c) mean observed heterozygosity within the 392 loci surveyed for each individual. (XLSX 14 kb
Paulo Cesar Venere - One of the best experts on this subject based on the ideXlab platform.
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Genetic diversity and structuring in the Arapaima (Osteoglossiformes, Osteoglossidae) population reveal differences between the Amazon and the Tocantins-Araguaia basins.
Anais da Academia Brasileira de Ciencias, 2020Co-Authors: Fabrícia Nogueira, Péricles Sena Do Rêgo, Helder Lima De Queiroz, Iracilda Sampaio, Horacio Schneider, Paulo Cesar Venere, Eduardo Sousa Varela, Juliana AraripeAbstract:Arapaima is a widely-distributed fish of enormous economic importance in the Amazon region. In the present study, a total of 232 specimens were sampled, 121 from five sites in the Amazon basin and 111 from five sites in the Tocantins-Araguaia basin. The analyses investigated fragments of the Cytochrome b, Control Region, Cytochrome Oxidase I, NADH dehydrogenase subunit 2 and seven loci microsatellites. The analyses revealed the existence of two mitochondrial lineages within the general area, with no haplotypes shared between basins, and genetic variability significantly higher in the Amazon than in the Tocantins-Araguaia basin. Two divergent, but sympatric mitochondrial lineages were found in the Amazon basin, but only a single lineage in the Tocantins-Araguaia basin. The existence of these two mitochondrial lineages indicates that past events, probably occurring during the Pleistocene, resulted in the separation of the populations of this species and molded its evolutionary history, which is reflected directly in its mitochondrial DNA. The analysis of the Arapaima population structure identified distinct levels of diversity within the distribution of the species, indicating specific geographic regions that will require special attention for the development of conservation and management strategies.
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Low Genetic Diversity and Structuring of the Arapaima (Osteoglossiformes, Arapaimidae) Population of the Araguaia-Tocantins Basin.
Frontiers in genetics, 2017Co-Authors: Carla A. Vitorino, Juliana Araripe, Fabrícia Nogueira, Issakar Lima Souza, Paulo Cesar VenereAbstract:The Arapaima, Arapaima gigas, is a fish whose populations are threatened by both overfishing and the ongoing destruction of its natural habitats. In the Amazon basin, varying levels of population structure have been found in A. gigas, although no data are available on the genetic diversity or structure of the populations found in the Araguaia-Tocantins basin, which has a topographic profile, hydrological regime, and history of fishing quite distinct from those of the Amazon. In this context, microsatellite markers were used to assess the genetic diversity and connectivity of five wild A. gigas populations in the Araguaia-Tocantins basin. The results of the analysis indicated low levels of genetic diversity in comparison with other A. gigas populations, studied in the Amazon basin. The AMOVA revealed that the Arapaima populations of the Araguaia-Tocantins basin are structured significantly. No correlation was found between pairwise FST values and the geographical distance among populations. The low level of genetic variability and the evidence of restricted gene flow may both be accounted for by overfishing, as well as the other human impacts that these populations have been exposed to over the years. The genetic fragility of these populations demands attention, given that future environmental changes (natural or otherwise) may further reduce these indices and eventually endanger these populations. The results of this study emphasize the need to take the genetic differences among the study populations into account when planning management measures and conservation strategies for the Arapaima stocks of the Araguaia-Tocantins basin.
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Genetic diversity of Arapaima gigas (Schinz, 1822) (Osteoglossiformes: Arapaimidae) in the Araguaia-Tocantins basin estimated by ISSR marker
Neotropical Ichthyology, 2015Co-Authors: Carla A. Vitorino, Renata C. C. Oliveira, Vladimir Pavan Margarido, Paulo Cesar VenereAbstract:The genetic diversity of the specimens of four natural populations of Arapaima from Araguaia-Tocantins basin was assessed within and among these stocks, using five primers for ISSR. COI (cytochrome c oxidase subunit I ) partial sequences confirmed that the specimens belongs to Arapaima gigas . The ISSR provided 168 loci, of which 165 were polymorphic. However, the number of loci for each population and expected heterozygosity values were low. AMOVA showed 52.63% intra-population variation and 47.37% inter-population variation. The F ST was high among all populations (F ST ≥ 0.25), however, the cluster analysis (PCoA) and Bayesian inference showed three major groups: Araguaiana-MT + Sao Felix do Araguaia-MT, Novo Santo Antonio-MT and Itupiranga-PA. The genetic distance was not correlated with geographical distance. The ISSR marker revealed that the populations of the Araguaia-Tocantins are structured and have a low genetic diversity. These are the first data from a population analysis using molecular markers for A. gigas of Araguaia-Tocantins basins and may be used to define the best management strategies and conservation projects for this species.
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Feeding of juvenile pirarucu (Arapaima gigas, Arapaimidae) in their natural environment, lago Quatro Bocas, Araguaiana-MT, Brazil
Neotropical Ichthyology, 2005Co-Authors: Valdézio De Oliveira, Stephania Luz Poleto, Paulo Cesar VenereAbstract:The stomach content of samples of juvenile Arapaima gigas was analized to obtain information about feeding in natural environments. This species occurs in the Amazonian basin, predominantly in floodplain environment. This is the case of the valley of the middle rio Araguaia, where the lago Quatro Bocas is situated. Juveniles A. gigas prefered insects, microcrustaceans and gastropods, most of autochthonous origin. All the stomachs examined contained at least one food item.