Evolução cromossômica e diversidade genética em espécies de peixes da família Arapaimidae (Teleostei: Osteoglossiformes)
Autor(a) principal: | |
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Data de Publicação: | 2019 |
Tipo de documento: | Tese |
Idioma: | por |
Título da fonte: | Repositório Institucional da UFSCAR |
Texto Completo: | https://repositorio.ufscar.br/handle/ufscar/11819 |
Resumo: | The Neotropical region exhibits the largest diversity of freshwater fishes in the world and the demographic history of several taxa is related to the geomorphological and climatic history of this region. Among the Osteoglossiformes, the Arapaimidae family is represented by only two genera, with a South American representative Arapaima and another African Heterotis, an important ichthyological group that still has lacked genetic and cytogenetic studies. Therefore, the present work with the use of advanced population genomics tools, selection of demographic models by machine learning, conventional and molecular cytogenetics analysis, aimed at developing a broad understanding of the chromosomal, molecular and phylogeographic diversity of these species. We aimed to better clarify the evolutionary events that shaped the demographic history of this fish group. For that, South American and African representatives of Arapaimidae, namely Arapaima (four natural populations of the Am basin, three of the To-Ar basin and three fish farms) and Heterotis niloticus (a population of the Oluwa River in Nigeria) were examined. The species differed significantly by means of diploid chromosome numbers, with 2n = 56 found in Arapaima and 2n = 40 exhibited by H. niloticus. However, these species presented some general tendencies shared by other Osteoglossiformes analyzed so far, regarding the presence of only one pair of chromosomes bearing 18S and 5S rDNA sites and karyotypes dominated by acrocentric-submetacentric chromosomes, thus corresponding to hypothetical karyotype patterns ancestral to teleosts. In addition, their genomes showed remarkable divergence in terms of repetitive DNA content and distribution as revealed by Comparative Genomic Hybridization (CGH). On the other hand, genomic diversity of single-copy sequences (SNPs), retrieved through principal component analysis (PCA), based on alleles obtained by the DArTseq procedure, demonstrated a very low genetic distance between these genera. These data provided a clear view of the genetic diversity between African and South American Arapaimidae species and were highly consistent with the chromosomal, geographic and historical data, helping to understand its evolutionary diversification. Concerning the investigations of the genus Arapaima in South America, we observed a higher general level of genetic diversity in the Am populations when compared to the one observed in the To-Ar basin. In addition, a high genetic differentiation between the populations of the different basins was observed. By including samples of fish farming, the most likely ancestry of the used breeding herds was revealed, raising concerns about the use of broodstocks outside the distribution of their genetic grouping. No significant chromosome differentiations in the karyotypic structure and repetitive DNA compositions among the studied Arapaima populations was observed. Although the main routes for Arapaima colonization in South America are still unclear, the model selection from convolutional neural networks (CNN) applied to our empirical data indicated a scenario in which the Am basin was the first to be colonized, followed by the To-Ar one. Other studies should focus on a wider historical biogeographic reconstruction of the order Osteoglossiformes, which may potentially explain its relationship with the Gondwana break-up and the presence of this taxon in South America. |
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Oliveira, Ezequiel Aguiar deCioffi, Marcelo de Bellohttp://lattes.cnpq.br/0242034365085727http://lattes.cnpq.br/30355019061539085068a0f6-e0b7-4b11-95be-ee1f55903c362019-09-10T19:39:19Z2019-09-10T19:39:19Z2019-07-12OLIVEIRA, Ezequiel Aguiar de. Evolução cromossômica e diversidade genética em espécies de peixes da família Arapaimidae (Teleostei: Osteoglossiformes). 2019. Tese (Doutorado em Genética Evolutiva e Biologia Molecular) – Universidade Federal de São Carlos, São Carlos, 2019. Disponível em: https://repositorio.ufscar.br/handle/ufscar/11819.https://repositorio.ufscar.br/handle/ufscar/11819The Neotropical region exhibits the largest diversity of freshwater fishes in the world and the demographic history of several taxa is related to the geomorphological and climatic history of this region. Among the Osteoglossiformes, the Arapaimidae family is represented by only two genera, with a South American representative Arapaima and another African Heterotis, an important ichthyological group that still has lacked genetic and cytogenetic studies. Therefore, the present work with the use of advanced population genomics tools, selection of demographic models by machine learning, conventional and molecular cytogenetics analysis, aimed at developing a broad understanding of the chromosomal, molecular and phylogeographic diversity of these species. We aimed to better clarify the evolutionary events that shaped the demographic history of this fish group. For that, South American and African representatives of Arapaimidae, namely Arapaima (four natural populations of the Am basin, three of the To-Ar basin and three fish farms) and Heterotis niloticus (a population of the Oluwa River in Nigeria) were examined. The species differed significantly by means of diploid chromosome numbers, with 2n = 56 found in Arapaima and 2n = 40 exhibited by H. niloticus. However, these species presented some general tendencies shared by other Osteoglossiformes analyzed so far, regarding the presence of only one pair of chromosomes bearing 18S and 5S rDNA sites and karyotypes dominated by acrocentric-submetacentric chromosomes, thus corresponding to hypothetical karyotype patterns ancestral to teleosts. In addition, their genomes showed remarkable divergence in terms of repetitive DNA content and distribution as revealed by Comparative Genomic Hybridization (CGH). On the other hand, genomic diversity of single-copy sequences (SNPs), retrieved through principal component analysis (PCA), based on alleles obtained by the DArTseq procedure, demonstrated a very low genetic distance between these genera. These data provided a clear view of the genetic diversity between African and South American Arapaimidae species and were highly consistent with the chromosomal, geographic and historical data, helping to understand its evolutionary diversification. Concerning the investigations of the genus Arapaima in South America, we observed a higher general level of genetic diversity in the Am populations when compared to the one observed in the To-Ar basin. In addition, a high genetic differentiation between the populations of the different basins was observed. By including samples of fish farming, the most likely ancestry of the used breeding herds was revealed, raising concerns about the use of broodstocks outside the distribution of their genetic grouping. No significant chromosome differentiations in the karyotypic structure and repetitive DNA compositions among the studied Arapaima populations was observed. Although the main routes for Arapaima colonization in South America are still unclear, the model selection from convolutional neural networks (CNN) applied to our empirical data indicated a scenario in which the Am basin was the first to be colonized, followed by the To-Ar one. Other studies should focus on a wider historical biogeographic reconstruction of the order Osteoglossiformes, which may potentially explain its relationship with the Gondwana break-up and the presence of this taxon in South America.A região Neotropical exibe a maior diversidade de peixes de água doce do mundo e a história demográfica de vários táxons está relacionada com a história geomorfológica e climática desta região. Entre os Osteoglossiformes a família Arapaimidae é representada por apenas dois gêneros, com um representante Sul-Americano Arapaima e outro africano Heterotis, um importante grupo ictiológico que ainda apresenta escassez de dados genéticos. Portanto, as presentes investigações com o uso de ferramentas avançadas da genômica de populações, seleção de modelos demográficos por aprendizado de máquina, citogenética clássica, molecular e citogenômica, objetivaram desenvolver um entendimento amplo da diversidade cromossômica, molecular e filogeográfica destas espécies, com o intuito de esclarecer melhor os eventos evolutivos que moldaram a história demográfica deste grupo de peixes. Para tanto, foram examinados representantes sul-americanos e africanos de Arapaimidae, nomeadamente Arapaima (quatro populações naturais da bacia Am, três da bacia To-Ar e de três pisciculturas) e Heterotis niloticus (uma população do rio Oluwa na Nigéria). Nas abordagens comparativas intercontinentais e intraespecíficas, observou-se que as espécies diferiram significativamente por meio de números cromossômicos diploides, com 2n = 56 encontrado em Arapaima e 2n = 40 exibido por H. niloticus. Entretanto, estas espécies apresentaram algumas tendências gerais compartilhadas por outros osteoglossiformes analisados até o momento, como a presença de apenas um par de cromossomos portadores dos sítios de DNAr 18S e 5S e cariótipos dominados por cromossomos acrocêntricos-submetacêntrico, correspondendo assim aos padrões de cariótipo hipotético ancestral para os teleósteos. Além disso, seus genomas apresentam uma divergência notável em termos de conteúdo e distribuição de DNA repetitivos, como revelado por Hibridização Genômica Comparativa (CGH). Por outro lado, a diversidade genômica de sequências de cópia única (SNPs), estudadas através de análises de componentes principais (PCA), baseadas em alelos obtidos pelo procedimento DArTseq, demonstraram uma distância genética muito baixa entre estes gêneros. Estes dados forneceram uma visão clara da diversidade genética entre espécies africanas e sul-americanas de Arapaimidae e foram altamente consistentes com os dados cromossômicos, geográficos e históricos, auxiliando na compreensão de sua diversificação evolutiva. Já nas investigações do gênero Arapaima para a América do Sul, observamos um nível geral mais alto de diversidade genética nas populações do Am, quando comparado ao observado na bacia To-Ar. Adicionalmente, uma alta diferenciação genética entre as populações das diferentes bacias foi observada. Ao incluirmos amostras de piscicultura, também conseguimos evidenciar a ancestralidade mais provável dos reprodutores usados, levantando a discussão sobre o uso de reprodutores fora da distribuição de seu agrupamento genético. Não houve diferenciações cromossômicas significativas na estrutura cariotípica e nas composições de DNAs repetitivos mapeados entre as populações de Arapaima estudadas. Embora as principais vias para a colonização de Arapaima na América do Sul ainda não estejam claras, a seleção de modelo a partir de redes neurais convolucionais (CNN) aplicadas aos nossos dados empíricos indicam um cenário no qual a bacia do Am foi a primeira a ser colonizada, seguida da bacia To-Ar. Outros estudos devem se concentrar em uma reconstrução biogeográfica histórica mais ampla da ordem Osteoglossiformes, que pode potencialmente explicar sua relação com o rompimento do Gondwana e a presença deste táxon na América do Sul.Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)CAPES: Código de Financiamento 001porUniversidade Federal de São CarlosCâmpus São CarlosPrograma de Pós-Graduação em Genética Evolutiva e Biologia Molecular - PPGGEvUFSCarCromossomosSNPsGondwanaDNAs repetitivosPeixesCitogenética molecularChromosomesFishesRepetitive DNAsMolecular cytogeneticsCIENCIAS BIOLOGICAS::BIOQUIMICA::BIOLOGIA MOLECULARCIENCIAS BIOLOGICAS::GENETICA::GENETICA ANIMALEvolução cromossômica e diversidade genética em espécies de peixes da família Arapaimidae (Teleostei: Osteoglossiformes)Chromosomal evolution and genetic diversity in fish species of Arapaimidae family (Teleostei: Osteoglossiformes)Evolución cromosómica y diversidad genética en especies de Pez de la familia Arapaimidae (Teleostei: Osteoglossiformes)info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/doctoralThesisOnline600b27fbb2e-c4ae-4e52-8c47-a2a23d96a662info:eu-repo/semantics/openAccessreponame:Repositório Institucional da UFSCARinstname:Universidade Federal de São Carlos (UFSCAR)instacron:UFSCARORIGINALTese final pronta para depósito 19-08-2019.pdfTese final pronta para depósito 19-08-2019.pdfArtigo principalapplication/pdf15835390https://repositorio.ufscar.br/bitstream/ufscar/11819/1/Tese%20final%20pronta%20para%20dep%c3%b3sito%2019-08-2019.pdfaf539895edeef553ee0d4bc499b47f03MD51Carta comprovante.pdfCarta comprovante.pdfCarta comprovante orientadorapplication/pdf13945656https://repositorio.ufscar.br/bitstream/ufscar/11819/3/Carta%20comprovante.pdf85e65060ae262526151157a70c07844cMD53LICENSElicense.txtlicense.txttext/plain; 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dc.title.por.fl_str_mv |
Evolução cromossômica e diversidade genética em espécies de peixes da família Arapaimidae (Teleostei: Osteoglossiformes) |
dc.title.alternative.eng.fl_str_mv |
Chromosomal evolution and genetic diversity in fish species of Arapaimidae family (Teleostei: Osteoglossiformes) |
dc.title.alternative.spa.fl_str_mv |
Evolución cromosómica y diversidad genética en especies de Pez de la familia Arapaimidae (Teleostei: Osteoglossiformes) |
title |
Evolução cromossômica e diversidade genética em espécies de peixes da família Arapaimidae (Teleostei: Osteoglossiformes) |
spellingShingle |
Evolução cromossômica e diversidade genética em espécies de peixes da família Arapaimidae (Teleostei: Osteoglossiformes) Oliveira, Ezequiel Aguiar de Cromossomos SNPs Gondwana DNAs repetitivos Peixes Citogenética molecular Chromosomes Fishes Repetitive DNAs Molecular cytogenetics CIENCIAS BIOLOGICAS::BIOQUIMICA::BIOLOGIA MOLECULAR CIENCIAS BIOLOGICAS::GENETICA::GENETICA ANIMAL |
title_short |
Evolução cromossômica e diversidade genética em espécies de peixes da família Arapaimidae (Teleostei: Osteoglossiformes) |
title_full |
Evolução cromossômica e diversidade genética em espécies de peixes da família Arapaimidae (Teleostei: Osteoglossiformes) |
title_fullStr |
Evolução cromossômica e diversidade genética em espécies de peixes da família Arapaimidae (Teleostei: Osteoglossiformes) |
title_full_unstemmed |
Evolução cromossômica e diversidade genética em espécies de peixes da família Arapaimidae (Teleostei: Osteoglossiformes) |
title_sort |
Evolução cromossômica e diversidade genética em espécies de peixes da família Arapaimidae (Teleostei: Osteoglossiformes) |
author |
Oliveira, Ezequiel Aguiar de |
author_facet |
Oliveira, Ezequiel Aguiar de |
author_role |
author |
dc.contributor.authorlattes.por.fl_str_mv |
http://lattes.cnpq.br/3035501906153908 |
dc.contributor.author.fl_str_mv |
Oliveira, Ezequiel Aguiar de |
dc.contributor.advisor1.fl_str_mv |
Cioffi, Marcelo de Bello |
dc.contributor.advisor1Lattes.fl_str_mv |
http://lattes.cnpq.br/0242034365085727 |
dc.contributor.authorID.fl_str_mv |
5068a0f6-e0b7-4b11-95be-ee1f55903c36 |
contributor_str_mv |
Cioffi, Marcelo de Bello |
dc.subject.por.fl_str_mv |
Cromossomos SNPs Gondwana DNAs repetitivos Peixes Citogenética molecular |
topic |
Cromossomos SNPs Gondwana DNAs repetitivos Peixes Citogenética molecular Chromosomes Fishes Repetitive DNAs Molecular cytogenetics CIENCIAS BIOLOGICAS::BIOQUIMICA::BIOLOGIA MOLECULAR CIENCIAS BIOLOGICAS::GENETICA::GENETICA ANIMAL |
dc.subject.eng.fl_str_mv |
Chromosomes Fishes Repetitive DNAs Molecular cytogenetics |
dc.subject.cnpq.fl_str_mv |
CIENCIAS BIOLOGICAS::BIOQUIMICA::BIOLOGIA MOLECULAR CIENCIAS BIOLOGICAS::GENETICA::GENETICA ANIMAL |
description |
The Neotropical region exhibits the largest diversity of freshwater fishes in the world and the demographic history of several taxa is related to the geomorphological and climatic history of this region. Among the Osteoglossiformes, the Arapaimidae family is represented by only two genera, with a South American representative Arapaima and another African Heterotis, an important ichthyological group that still has lacked genetic and cytogenetic studies. Therefore, the present work with the use of advanced population genomics tools, selection of demographic models by machine learning, conventional and molecular cytogenetics analysis, aimed at developing a broad understanding of the chromosomal, molecular and phylogeographic diversity of these species. We aimed to better clarify the evolutionary events that shaped the demographic history of this fish group. For that, South American and African representatives of Arapaimidae, namely Arapaima (four natural populations of the Am basin, three of the To-Ar basin and three fish farms) and Heterotis niloticus (a population of the Oluwa River in Nigeria) were examined. The species differed significantly by means of diploid chromosome numbers, with 2n = 56 found in Arapaima and 2n = 40 exhibited by H. niloticus. However, these species presented some general tendencies shared by other Osteoglossiformes analyzed so far, regarding the presence of only one pair of chromosomes bearing 18S and 5S rDNA sites and karyotypes dominated by acrocentric-submetacentric chromosomes, thus corresponding to hypothetical karyotype patterns ancestral to teleosts. In addition, their genomes showed remarkable divergence in terms of repetitive DNA content and distribution as revealed by Comparative Genomic Hybridization (CGH). On the other hand, genomic diversity of single-copy sequences (SNPs), retrieved through principal component analysis (PCA), based on alleles obtained by the DArTseq procedure, demonstrated a very low genetic distance between these genera. These data provided a clear view of the genetic diversity between African and South American Arapaimidae species and were highly consistent with the chromosomal, geographic and historical data, helping to understand its evolutionary diversification. Concerning the investigations of the genus Arapaima in South America, we observed a higher general level of genetic diversity in the Am populations when compared to the one observed in the To-Ar basin. In addition, a high genetic differentiation between the populations of the different basins was observed. By including samples of fish farming, the most likely ancestry of the used breeding herds was revealed, raising concerns about the use of broodstocks outside the distribution of their genetic grouping. No significant chromosome differentiations in the karyotypic structure and repetitive DNA compositions among the studied Arapaima populations was observed. Although the main routes for Arapaima colonization in South America are still unclear, the model selection from convolutional neural networks (CNN) applied to our empirical data indicated a scenario in which the Am basin was the first to be colonized, followed by the To-Ar one. Other studies should focus on a wider historical biogeographic reconstruction of the order Osteoglossiformes, which may potentially explain its relationship with the Gondwana break-up and the presence of this taxon in South America. |
publishDate |
2019 |
dc.date.accessioned.fl_str_mv |
2019-09-10T19:39:19Z |
dc.date.available.fl_str_mv |
2019-09-10T19:39:19Z |
dc.date.issued.fl_str_mv |
2019-07-12 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/doctoralThesis |
format |
doctoralThesis |
status_str |
publishedVersion |
dc.identifier.citation.fl_str_mv |
OLIVEIRA, Ezequiel Aguiar de. Evolução cromossômica e diversidade genética em espécies de peixes da família Arapaimidae (Teleostei: Osteoglossiformes). 2019. Tese (Doutorado em Genética Evolutiva e Biologia Molecular) – Universidade Federal de São Carlos, São Carlos, 2019. Disponível em: https://repositorio.ufscar.br/handle/ufscar/11819. |
dc.identifier.uri.fl_str_mv |
https://repositorio.ufscar.br/handle/ufscar/11819 |
identifier_str_mv |
OLIVEIRA, Ezequiel Aguiar de. Evolução cromossômica e diversidade genética em espécies de peixes da família Arapaimidae (Teleostei: Osteoglossiformes). 2019. Tese (Doutorado em Genética Evolutiva e Biologia Molecular) – Universidade Federal de São Carlos, São Carlos, 2019. Disponível em: https://repositorio.ufscar.br/handle/ufscar/11819. |
url |
https://repositorio.ufscar.br/handle/ufscar/11819 |
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por |
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por |
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info:eu-repo/semantics/openAccess |
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openAccess |
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Universidade Federal de São Carlos Câmpus São Carlos |
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Programa de Pós-Graduação em Genética Evolutiva e Biologia Molecular - PPGGEv |
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UFSCar |
publisher.none.fl_str_mv |
Universidade Federal de São Carlos Câmpus São Carlos |
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UFSCAR |
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Repositório Institucional da UFSCAR |
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Repositório Institucional da UFSCAR |
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