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Claudio Oliveira - One of the best experts on this subject based on the ideXlab platform.
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phylogenomic incongruence hypothesis testing and taxonomic sampling the monophyly of characiform fishes
Evolution, 2019Co-Authors: Claudio Oliveira, Richard P Vari, Ricardo Betancurr, Dahiana Arcila, Lily C Hughes, Mark H SabajAbstract:: Phylogenomic studies using genome-wide datasets are quickly becoming the state of the art for systematics and comparative studies, but in many cases, they result in strongly supported incongruent results. The extent to which this conflict is real depends on different sources of error potentially affecting big datasets (assembly, stochastic, and systematic error). Here, we apply a recently developed methodology (GGI or gene genealogy interrogation) and data curation to new and published datasets with more than 1000 exons, 500 ultraconserved element (UCE) loci, and transcriptomic sequences that support incongruent hypotheses. The contentious non-monophyly of the order Characiformes proposed by two studies is shown to be a spurious outcome induced by sample contamination in the transcriptomic dataset and an ambiguous result due to poor taxonomic sampling in the UCE dataset. By exploring the effects of number of taxa and loci used for analysis, we show that the power of GGI to discriminate among competing hypotheses is diminished by limited taxonomic sampling, but not equally sensitive to gene sampling. Taken together, our results reinforce the notion that merely increasing the number of genetic loci for a few representative taxa is not a robust strategy to advance phylogenetic knowledge of recalcitrant groups. We leverage the expanded exon capture dataset generated here for Characiformes (206 species in 23 out of 24 families) to produce a comprehensive phylogeny and a revised classification of the order.
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Isolation and characterization of microsatellite loci in the Neotropical fish Astyanax altiparanae (Teleostei: Characiformes) and cross-species amplification
Journal of Genetics, 2012Co-Authors: Rosângela Lopes Zaganini, Claudio Oliveira, Diogo Teruo Hashimoto, Luiz Henrique Garcia Pereira, Fernando Fernandes Mendonça, Fausto Foresti, Fábio Porto-forestiAbstract:We isolated and characterized 11 polymorphic microsatellite loci from the Neotropical fish Astyanax altiparanae, considered of economic interest, whose stocks have been seriously endangered by the introduction of predatory fishes. The analyses in a population of 33 specimens detected a large number of alleles (ranging from 4 to 11) and high levels of heterozygosity (0.64–0.88) at these loci, indicating their usefulness in population genetic studies. Cross-species amplification was successful only in species of Astyanax, 43% of which were polymorphic. The Characiformes constitute one of the dominant and more diverse orders among tropical fishes, with more than 1800 species, among which the family Characidae is the most diverse, with species spread throughout the Neotropical region. However, the interrelationships among the Characidae are poorly known (Reis et al. 2003) and remain under discussion (Javonillo et al. 2010; Mirande 2010). The genus Astyanax (Characiformes, Characidae) comprises 163 described species (Froese and Paulay 2010), and its systematics are very complex and several studies have currently shown that the genus needs to be more thoroughly characterized. A. altiparanae, encountered along the south and southeast Brazilian rivers, was formerly included in the complex ‘A. bimaculatus’ (Garutti and Britski 2000), which is widely distributed in South America. A. altiparanae is of great economic interest, also being utilized as bait in
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phylogenetic relationships within the speciose family characidae teleostei ostariophysi Characiformes based on multilocus analysis and extensive ingroup sampling
BMC Evolutionary Biology, 2011Co-Authors: Claudio Oliveira, Gleisy S. Avelino, Tatiane C Mariguela, Ricardo C. Benine, Richard P Vari, Guillermo Orti, Ricardo M. C. CastroAbstract:Background With nearly 1,100 species, the fish family Characidae represents more than half of the species of Characiformes, and is a key component of Neotropical freshwater ecosystems. The composition, phylogeny, and classification of Characidae is currently uncertain, despite significant efforts based on analysis of morphological and molecular data. No consensus about the monophyly of this group or its position within the order Characiformes has been reached, challenged by the fact that many key studies to date have non-overlapping taxonomic representation and focus only on subsets of this diversity.
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Phylogenetic relationships within the speciose family Characidae (Teleostei: Ostariophysi: Characiformes) based on multilocus analysis and extensive ingroup sampling
BMC evolutionary biology, 2011Co-Authors: Claudio Oliveira, Gleisy S. Avelino, Tatiane C Mariguela, Ricardo C. Benine, Richard P Vari, Guillermo Orti, Kelly T. Abe, Ricardo M. C. CastroAbstract:With nearly 1,100 species, the fish family Characidae represents more than half of the species of Characiformes, and is a key component of Neotropical freshwater ecosystems. The composition, phylogeny, and classification of Characidae is currently uncertain, despite significant efforts based on analysis of morphological and molecular data. No consensus about the monophyly of this group or its position within the order Characiformes has been reached, challenged by the fact that many key studies to date have non-overlapping taxonomic representation and focus only on subsets of this diversity. In the present study we propose a new definition of the family Characidae and a hypothesis of relationships for the Characiformes based on phylogenetic analysis of DNA sequences of two mitochondrial and three nuclear genes (4,680 base pairs). The sequences were obtained from 211 samples representing 166 genera distributed among all 18 recognized families in the order Characiformes, all 14 recognized subfamilies in the Characidae, plus 56 of the genera so far considered incertae sedis in the Characidae. The phylogeny obtained is robust, with most lineages significantly supported by posterior probabilities in Bayesian analysis, and high bootstrap values from maximum likelihood and parsimony analyses. A monophyletic assemblage strongly supported in all our phylogenetic analysis is herein defined as the Characidae and includes the characiform species lacking a supraorbital bone and with a derived position of the emergence of the hyoid artery from the anterior ceratohyal. To recognize this and several other monophyletic groups within characiforms we propose changes in the limits of several families to facilitate future studies in the Characiformes and particularly the Characidae. This work presents a new phylogenetic framework for a speciose and morphologically diverse group of freshwater fishes of significant ecological and evolutionary importance across the Neotropics and portions of Africa.
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Ultrastructure of spermiogenesis and spermatozoa of Gymnotus cf. anguillaris and Brachyhypopomus cf. pinnicaudatus (Teleostei: Gymnotiformes).
Tissue & cell, 2007Co-Authors: Gisleine Fernanda França, Claudio Oliveira, Irani Quagio-grassiottoAbstract:The ultrastructure of spermiogenic stages and spermatozoa of representatives of two gymnotiform families, Gymnotus cf. anguillaris (Gymnotidae) and Brachyhypopomus cf. pinnicaudatus (Hypopomidae) were studied. Spermiogenesis of both species is characterized by lateral development of the flagellum and formation of a nuclear fossa. Some differences were found between these species, such as whether (B. cf. pinnicaudatus) or not (G. cf. anguillaris) nuclear rotation occurs, permanence of the cytoplasmic channel, and type and localization of the nuclear fossa. In the G. cf. anguillaris spermatozoon the nucleus is spherical with highly condensed chromatin. The nuclear fossa is shallow and lateral and is associated with the centriolar complex through stabilizing fibrils. The midpiece is short, with many vesicles, a cytoplasmic channel, and elongate mitochondria. In the B. cf. pinnicaudatus spermatozoon the ovoid nucleus is elongated lateral and posterior to the centriolar complex, and has highly condensed chromatin. The eccentric nuclear fossa is of the moderate type, and contains the entire centriolar complex. The midpiece is long, with numerous vesicles, elongate mitochondria, and no cytoplasmic channel. In both species the flagella are laterally disposed in relation to the nucleus and comprise of the classical 9+2 axoneme. Most of the characteristics found in the spermatozoa of these two species of Gymnotiformes are shared with species of Characiformes, whereas only a few are also found in Siluriformes. This suggests that Gymnotiformes and Characiformes may be more closely related than previously proposed.
Ricardo M. C. Castro - One of the best experts on this subject based on the ideXlab platform.
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The brain of Brycon orbignyanus (Valenciennes, 1850) (Teleostei: Characiformes: Bryconidae): gross morphology and phylogenetic considerations
Neotropical Ichthyology, 2016Co-Authors: Thiago Nilton Alves Pereira, Ricardo M. C. CastroAbstract:The brain of Brycon orbignyanus is described as a model for future studies of the gross morphology of the central nervous system in Characiformes. The study of brain gross morphology of 48 distinct taxa of Characiformes, one of Cypriniformes, two of Siluriformes and two of Gymnotiformes, allowed us to propose, for the first time, six putative brain synapomorphies for the Characiformes and also two possibly unique gross brain morphology characters for the Siluriformes. A detailed protocol for the extraction of the brain in Characiformes is also provided.
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phylogenetic relationships within the speciose family characidae teleostei ostariophysi Characiformes based on multilocus analysis and extensive ingroup sampling
BMC Evolutionary Biology, 2011Co-Authors: Claudio Oliveira, Gleisy S. Avelino, Tatiane C Mariguela, Ricardo C. Benine, Richard P Vari, Guillermo Orti, Ricardo M. C. CastroAbstract:Background With nearly 1,100 species, the fish family Characidae represents more than half of the species of Characiformes, and is a key component of Neotropical freshwater ecosystems. The composition, phylogeny, and classification of Characidae is currently uncertain, despite significant efforts based on analysis of morphological and molecular data. No consensus about the monophyly of this group or its position within the order Characiformes has been reached, challenged by the fact that many key studies to date have non-overlapping taxonomic representation and focus only on subsets of this diversity.
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Phylogenetic relationships within the speciose family Characidae (Teleostei: Ostariophysi: Characiformes) based on multilocus analysis and extensive ingroup sampling
BMC evolutionary biology, 2011Co-Authors: Claudio Oliveira, Gleisy S. Avelino, Tatiane C Mariguela, Ricardo C. Benine, Richard P Vari, Guillermo Orti, Kelly T. Abe, Ricardo M. C. CastroAbstract:With nearly 1,100 species, the fish family Characidae represents more than half of the species of Characiformes, and is a key component of Neotropical freshwater ecosystems. The composition, phylogeny, and classification of Characidae is currently uncertain, despite significant efforts based on analysis of morphological and molecular data. No consensus about the monophyly of this group or its position within the order Characiformes has been reached, challenged by the fact that many key studies to date have non-overlapping taxonomic representation and focus only on subsets of this diversity. In the present study we propose a new definition of the family Characidae and a hypothesis of relationships for the Characiformes based on phylogenetic analysis of DNA sequences of two mitochondrial and three nuclear genes (4,680 base pairs). The sequences were obtained from 211 samples representing 166 genera distributed among all 18 recognized families in the order Characiformes, all 14 recognized subfamilies in the Characidae, plus 56 of the genera so far considered incertae sedis in the Characidae. The phylogeny obtained is robust, with most lineages significantly supported by posterior probabilities in Bayesian analysis, and high bootstrap values from maximum likelihood and parsimony analyses. A monophyletic assemblage strongly supported in all our phylogenetic analysis is herein defined as the Characidae and includes the characiform species lacking a supraorbital bone and with a derived position of the emergence of the hyoid artery from the anterior ceratohyal. To recognize this and several other monophyletic groups within characiforms we propose changes in the limits of several families to facilitate future studies in the Characiformes and particularly the Characidae. This work presents a new phylogenetic framework for a speciose and morphologically diverse group of freshwater fishes of significant ecological and evolutionary importance across the Neotropics and portions of Africa.
Richard P Vari - One of the best experts on this subject based on the ideXlab platform.
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phylogenomic incongruence hypothesis testing and taxonomic sampling the monophyly of characiform fishes
Evolution, 2019Co-Authors: Claudio Oliveira, Richard P Vari, Ricardo Betancurr, Dahiana Arcila, Lily C Hughes, Mark H SabajAbstract:: Phylogenomic studies using genome-wide datasets are quickly becoming the state of the art for systematics and comparative studies, but in many cases, they result in strongly supported incongruent results. The extent to which this conflict is real depends on different sources of error potentially affecting big datasets (assembly, stochastic, and systematic error). Here, we apply a recently developed methodology (GGI or gene genealogy interrogation) and data curation to new and published datasets with more than 1000 exons, 500 ultraconserved element (UCE) loci, and transcriptomic sequences that support incongruent hypotheses. The contentious non-monophyly of the order Characiformes proposed by two studies is shown to be a spurious outcome induced by sample contamination in the transcriptomic dataset and an ambiguous result due to poor taxonomic sampling in the UCE dataset. By exploring the effects of number of taxa and loci used for analysis, we show that the power of GGI to discriminate among competing hypotheses is diminished by limited taxonomic sampling, but not equally sensitive to gene sampling. Taken together, our results reinforce the notion that merely increasing the number of genetic loci for a few representative taxa is not a robust strategy to advance phylogenetic knowledge of recalcitrant groups. We leverage the expanded exon capture dataset generated here for Characiformes (206 species in 23 out of 24 families) to produce a comprehensive phylogeny and a revised classification of the order.
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Arrhinolemur scalabrinii Ameghino, 1898, of the late Miocene - a taxonomic journey from the Mammalia to the Anostomidae (Ostariophysi: Characiformes)
Neotropical Ichthyology, 2012Co-Authors: Sergio Bogan, Richard P Vari, Brian L. Sidlauskas, Frederico AgnolinAbstract:The fossil species Arrhinolemur scalabrinii, which was described from late Miocene deposits of Entre Rios, Argentina, is reevaluated. Whereas the species was originally placed in the Primates (Mammalia) and later made the unique member of the order Arrhinolemuroidea within the Mammalia, our analysis indicates that the specimen is rather a fish of the genus Leporinus, family Anostomidae (Characiformes). The species is redescribed, and the characters that support its new generic assignment are discussed. A especie fossil Arrhinolemur scalabrinii, descrita de depositos do Mioceno Superior de Entre Rios, Argentina, e reavaliada. Apesar da especie ter sido originalmente incluida em Primata (Mammalia), constituindo-se posteriormente no unico membro da ordem Arrhinolemuroidea dentro de Mammalia, nossa analise indica que o especime trata-se de um peixe do genero Leporinus, familia Anostomidae (Characiformes). A especie e redescrita, e os caracteres que fundamentam a nova posicao do genero sao discutidos.
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phylogenetic relationships within the speciose family characidae teleostei ostariophysi Characiformes based on multilocus analysis and extensive ingroup sampling
BMC Evolutionary Biology, 2011Co-Authors: Claudio Oliveira, Gleisy S. Avelino, Tatiane C Mariguela, Ricardo C. Benine, Richard P Vari, Guillermo Orti, Ricardo M. C. CastroAbstract:Background With nearly 1,100 species, the fish family Characidae represents more than half of the species of Characiformes, and is a key component of Neotropical freshwater ecosystems. The composition, phylogeny, and classification of Characidae is currently uncertain, despite significant efforts based on analysis of morphological and molecular data. No consensus about the monophyly of this group or its position within the order Characiformes has been reached, challenged by the fact that many key studies to date have non-overlapping taxonomic representation and focus only on subsets of this diversity.
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Phylogenetic relationships within the speciose family Characidae (Teleostei: Ostariophysi: Characiformes) based on multilocus analysis and extensive ingroup sampling
BMC evolutionary biology, 2011Co-Authors: Claudio Oliveira, Gleisy S. Avelino, Tatiane C Mariguela, Ricardo C. Benine, Richard P Vari, Guillermo Orti, Kelly T. Abe, Ricardo M. C. CastroAbstract:With nearly 1,100 species, the fish family Characidae represents more than half of the species of Characiformes, and is a key component of Neotropical freshwater ecosystems. The composition, phylogeny, and classification of Characidae is currently uncertain, despite significant efforts based on analysis of morphological and molecular data. No consensus about the monophyly of this group or its position within the order Characiformes has been reached, challenged by the fact that many key studies to date have non-overlapping taxonomic representation and focus only on subsets of this diversity. In the present study we propose a new definition of the family Characidae and a hypothesis of relationships for the Characiformes based on phylogenetic analysis of DNA sequences of two mitochondrial and three nuclear genes (4,680 base pairs). The sequences were obtained from 211 samples representing 166 genera distributed among all 18 recognized families in the order Characiformes, all 14 recognized subfamilies in the Characidae, plus 56 of the genera so far considered incertae sedis in the Characidae. The phylogeny obtained is robust, with most lineages significantly supported by posterior probabilities in Bayesian analysis, and high bootstrap values from maximum likelihood and parsimony analyses. A monophyletic assemblage strongly supported in all our phylogenetic analysis is herein defined as the Characidae and includes the characiform species lacking a supraorbital bone and with a derived position of the emergence of the hyoid artery from the anterior ceratohyal. To recognize this and several other monophyletic groups within characiforms we propose changes in the limits of several families to facilitate future studies in the Characiformes and particularly the Characidae. This work presents a new phylogenetic framework for a speciose and morphologically diverse group of freshwater fishes of significant ecological and evolutionary importance across the Neotropics and portions of Africa.
Michele E. R. Pierotti - One of the best experts on this subject based on the ideXlab platform.
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Visual pigment evolution in Characiformes: the dynamic interplay of teleost whole‐genome duplication, surviving opsins and spectral tuning
Molecular ecology, 2020Co-Authors: Daniel Escobar-camacho, Karen L. Carleton, Devika W. Narain, Michele E. R. PierottiAbstract:Vision represents an excellent model for studying adaptation, given the genotype-to-phenotype map that has been characterized in a number of taxa. Fish possess a diverse range of visual sensitivities and adaptations to underwater light, making them an excellent group to study visual system evolution. In particular, some speciose but understudied lineages can provide a unique opportunity to better understand aspects of visual system evolution such as opsin gene duplication and neofunctionalization. In this study, we showcase the visual system evolution of neotropical Characiformes and the spectral tuning mechanisms they exhibit to modulate their visual sensitivities. Such mechanisms include gene duplications and losses, gene conversion, opsin amino acid sequence and expression variation, and A1 /A2 -chromophore shifts. The Characiforms we studied utilize three cone opsin classes (SWS2, RH2, LWS) and a rod opsin (RH1). However, the characiform's entire opsin gene repertoire is a product of dynamic evolution by opsin gene loss (SWS1, RH2) and duplication (LWS, RH1). The LWS- and RH1-duplicates originated from a teleost specific whole-genome duplication as well as characiform-specific duplication events. Both LWS-opsins exhibit gene conversion and, through substitutions in key tuning sites, one of the LWS-paralogues has acquired spectral sensitivity to green light. These sequence changes suggest reversion and parallel evolution of key tuning sites. Furthermore, characiforms' colour vision is based on the expression of both LWS-paralogues and SWS2. Finally, we found interspecific and intraspecific variation in A1 /A2 -chromophores proportions, correlating with the light environment. These multiple mechanisms may be a result of the diverse visual environments where Characiformes have evolved.
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Visual pigment evolution in Characiformes: the dynamic interplay of teleost whole-genome duplication, surviving opsins and spectral tuning
2019Co-Authors: Daniel Escobar-camacho, Karen L. Carleton, Devika W. Narain, Michele E. R. PierottiAbstract:Vision represents an excellent model for studying adaptation, given the genotype-to-phenotype-map that has been characterized in a number of taxa. Fish possess a diverse range of visual sensitivities and adaptations to underwater light making them an excellent group to study visual system evolution. In particular, some speciose but understudied lineages can provide a unique opportunity to better understand aspects of visual system evolution such as opsin gene duplication and neofunctionalization. In this study, we characterized the visual system of Neotropical Characiformes, which is the result of several spectral tuning mechanisms acting in concert including gene duplications and losses, gene conversion, opsin amino acid sequence and expression variation, and A1/A2-chromophore shifts. The Characiforms we studied utilize three cone opsin classes (SWS2, RH2, LWS) and a rod opsin (RH1). However, the entire opsin gene repertoire of characiforms is a product of dynamic evolution by opsin gene loss (SWS1, RH2) and duplication (LWS, RH1). The LWS- and RH1-duplicates originated from a teleost specific whole-genome duplication as well as characiform-specific duplication events. Both LWS-opsins exhibit gene conversion and, through substitutions in key tuning sites, one of the LWS-paralogs has acquired spectral sensitivity to green light. These sequence changes suggest reversion and parallel evolution of key tuning sites. In addition, characiforms exhibited species-specific differences in opsin expression. Finally, we found interspecific and intraspecific variation in the use of A1/A2-chromophores correlating with the light environment. These multiple mechanisms may be a result of the highly diverse visual environments where Characiformes have evolved.
Ricardo Betancurr - One of the best experts on this subject based on the ideXlab platform.
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phylogenomic incongruence hypothesis testing and taxonomic sampling the monophyly of characiform fishes
Evolution, 2019Co-Authors: Claudio Oliveira, Richard P Vari, Ricardo Betancurr, Dahiana Arcila, Lily C Hughes, Mark H SabajAbstract:: Phylogenomic studies using genome-wide datasets are quickly becoming the state of the art for systematics and comparative studies, but in many cases, they result in strongly supported incongruent results. The extent to which this conflict is real depends on different sources of error potentially affecting big datasets (assembly, stochastic, and systematic error). Here, we apply a recently developed methodology (GGI or gene genealogy interrogation) and data curation to new and published datasets with more than 1000 exons, 500 ultraconserved element (UCE) loci, and transcriptomic sequences that support incongruent hypotheses. The contentious non-monophyly of the order Characiformes proposed by two studies is shown to be a spurious outcome induced by sample contamination in the transcriptomic dataset and an ambiguous result due to poor taxonomic sampling in the UCE dataset. By exploring the effects of number of taxa and loci used for analysis, we show that the power of GGI to discriminate among competing hypotheses is diminished by limited taxonomic sampling, but not equally sensitive to gene sampling. Taken together, our results reinforce the notion that merely increasing the number of genetic loci for a few representative taxa is not a robust strategy to advance phylogenetic knowledge of recalcitrant groups. We leverage the expanded exon capture dataset generated here for Characiformes (206 species in 23 out of 24 families) to produce a comprehensive phylogeny and a revised classification of the order.