Evolutionary studies in South American marsh rats (Rodentia: Holochilus)

Detalhes bibliográficos
Autor(a) principal: Prado, Joyce Rodrigues do
Data de Publicação: 2017
Tipo de documento: Tese
Idioma: eng
Título da fonte: Biblioteca Digital de Teses e Dissertações da USP
Texto Completo: http://www.teses.usp.br/teses/disponiveis/91/91131/tde-14032018-110612/
Resumo: An interdisciplinary approach integrating micro and macroevolution, genomic, morphometric and morphological variation, systematics, quantitative genetics, and biogeography was employed to investigate the evolutionary history of the genus Holochilus (Rodentia: Sigmodontinae). Holochilus presents poorly defined species, with nomenclatural problems and phylogenetic relationships on species level unknown. The current species number possibly does not reflect its real diversity, and no work combining genetic and morphometric evidences from all its geographic range was performed. This genus belongs to the tribe Oryzomyini, and along with other 14 genera constitute the Oryzomyini clade D, the most comprehensive generic diversity of the tribe, occupying distinct environments. The internal phylogenetic relationship within this clade is still unclear and variable. Due to its broad geographic distribution, Holochilus also represents a key piece on the study of the evolution of oryzomines of open formations of South America. Based on a comprehensive sampling, I analyzed patterns of morphometric and genomic variation within Holochilus, in order to delimit the species belonging to this genus, as well as access the phylogenetic relationship between these lineages. I investigated the sexual and ontogenetic variation in this group, comparing natural and captive populations, seeking for understand the effect of the environmental differences in the pattern of variation and ontogenetic trajectories (Chapter 1). I also evaluated and compared the genomic variation among three species of Holochilus to verify the influence of the biomes and the climatic changes in the genomic signatures (Chapter 2). I applied a model-based approach to delimit species (Chapter 3). And finally, additional investigations were made to propose the phylogenetic relationship between members of clade D, and provide date intervals for the main diversifications events, as well as the possible process responsible for the biogeographic pattern current observed related with the forest and open areas occupation (Chapter 4). Sexual dimorphism exhibited small degree of variation among populations. The greater ontogenetic variation is found in the younger age classes, but oldest individuals also show larger degree of differentiation. There are also great differences in the ontogenetic trajectories among samples, where individuals from the captive population exhibited the lower degree of variation between all age classes. The quantitative genetic analysis showed that genomic differences are observed across the taxa, and it was associated with geography. Ecological niche models revealed that biomes with larger areas of stability also presented more genomic structure, suggesting that historical dimension impacted population isolation/connectivity. Results also shows that biomes not only differ geographically and environmentally (based on past climatic conditions), but also show significant association between the environmental space and the genetic variation that is not related with geography. Eight independent lineages within Holochilus were recovered, and the phylogenetic arrangement partially corroborates previous studies. Finally, the phylogeny proposed for the clade D presented some differences in comparisons with other previously reported, and suggest that most of the cladogenetic events happened during the Pleistocene, being the expansion of open environments an important driver of diversification in this group.
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spelling Evolutionary studies in South American marsh rats (Rodentia: Holochilus)Estudos evolutivos dos ratos do brejo da América do Sul (Rodentia: Holochilus)BiogeografiaBiogeographyClade DClado DGenômicaGenomicsMorfometriaMorphometricsNext generation sequencingOryzomyiniOryzomyiniRodentsRoedoresSequenciamento de nova geraçãoAn interdisciplinary approach integrating micro and macroevolution, genomic, morphometric and morphological variation, systematics, quantitative genetics, and biogeography was employed to investigate the evolutionary history of the genus Holochilus (Rodentia: Sigmodontinae). Holochilus presents poorly defined species, with nomenclatural problems and phylogenetic relationships on species level unknown. The current species number possibly does not reflect its real diversity, and no work combining genetic and morphometric evidences from all its geographic range was performed. This genus belongs to the tribe Oryzomyini, and along with other 14 genera constitute the Oryzomyini clade D, the most comprehensive generic diversity of the tribe, occupying distinct environments. The internal phylogenetic relationship within this clade is still unclear and variable. Due to its broad geographic distribution, Holochilus also represents a key piece on the study of the evolution of oryzomines of open formations of South America. Based on a comprehensive sampling, I analyzed patterns of morphometric and genomic variation within Holochilus, in order to delimit the species belonging to this genus, as well as access the phylogenetic relationship between these lineages. I investigated the sexual and ontogenetic variation in this group, comparing natural and captive populations, seeking for understand the effect of the environmental differences in the pattern of variation and ontogenetic trajectories (Chapter 1). I also evaluated and compared the genomic variation among three species of Holochilus to verify the influence of the biomes and the climatic changes in the genomic signatures (Chapter 2). I applied a model-based approach to delimit species (Chapter 3). And finally, additional investigations were made to propose the phylogenetic relationship between members of clade D, and provide date intervals for the main diversifications events, as well as the possible process responsible for the biogeographic pattern current observed related with the forest and open areas occupation (Chapter 4). Sexual dimorphism exhibited small degree of variation among populations. The greater ontogenetic variation is found in the younger age classes, but oldest individuals also show larger degree of differentiation. There are also great differences in the ontogenetic trajectories among samples, where individuals from the captive population exhibited the lower degree of variation between all age classes. The quantitative genetic analysis showed that genomic differences are observed across the taxa, and it was associated with geography. Ecological niche models revealed that biomes with larger areas of stability also presented more genomic structure, suggesting that historical dimension impacted population isolation/connectivity. Results also shows that biomes not only differ geographically and environmentally (based on past climatic conditions), but also show significant association between the environmental space and the genetic variation that is not related with geography. Eight independent lineages within Holochilus were recovered, and the phylogenetic arrangement partially corroborates previous studies. Finally, the phylogeny proposed for the clade D presented some differences in comparisons with other previously reported, and suggest that most of the cladogenetic events happened during the Pleistocene, being the expansion of open environments an important driver of diversification in this group.Uma abordagem interdisciplinar integrando micro e macroevolução, variação genômica, morfométrica e morfológica, sistemática, genética quantitativa e biogeografia foi empregada para investigar a história evolutiva do gênero Holochilus (Rodentia: Sigmodontinae). O gênero Holochilus apresenta espécies mal definidas, com problemas nomenclaturais e relações desconhecida. O número atual de espécies possivelmente não reflete a sua diversidade real e, até o momento, não foi realizado nenhum trabalho combinando evidências genéticas e morfométricas englobando toda a distribuição geográfica desse grupo. Este gênero pertence à tribo Oryzomyini, e juntamente com outros 14 gêneros (a diversidade genérica mais abrangente da tribo) formam o clado D. A relação filogenética interna dentro deste clado ainda é variável. Devido à sua ampla distribuição geográfica, Holochilus também representa uma peça chave no estudo da evolução dos oryzomíneos de formações abertas da América do Sul. Com base em uma amostragem abrangente, analisei padrões de variação morfométrica e genômica dentro de Holochilus, a fim de delimitar as espécies pertencentes a este gênero, bem como acessar a relação filogenética entre essas linhagens. Investiguei a variação sexual e ontogenética deste grupo, comparando populações naturais e de cativeiro, buscando entender o efeito das diferenças ambientais no padrão de variação e nas trajetórias ontogenéticas (Capítulo 1). Eu também avaliei e comparei a variação genômica entre três espécies de Holochilus a fim de verificar a influência dos biomas e das mudanças climáticas nas assinaturas genômicas das espécies (Capítulo 2). Em seguida eu apliquei uma abordagem baseada em modelos para delimitar as espécies (Capítulo 3). Finalmente, investigações adicionais foram realizadas para propor as relações filogenéticas entre os membros do clade D, fornecendo datas para os principais eventos de diversificação, e inferências sobre possíveis processos responsáveis pelo padrão biogeográfico atual, relacionado os mesmos com a ocupação florestal e áreas abertas (Capítulo 4). O dimorfismo sexual apresentou pequeno grau de variação entre as populações. A maior variação ontogenética é encontrada nas classes etárias mais jovens e mais velhas. Há também grandes diferenças nas trajetórias ontogenéticas entre as amostras, onde indivíduos da população cativeiro exibiram o menor grau de variação entre todas as classes etárias. A análise genética quantitativa mostrou que diferenças genômicas são observadas em todos os táxons e essa diferença está associada à geografia. Modelos de nichos ecológicos revelaram que os biomas com maiores áreas de estabilidade também apresentaram maior estruturação genômica, sugerindo que uma dimensão histórica impactou o isolamento/conectividade entre as populações. Os resultados também mostram que os biomas não só diferem geograficamente e ambientalmente (baseado em condições climáticas passadas), mas também mostram associação significativa entre o espaço ambiental e a variação genética que não está relacionada com a geografia. Adicionalmente, foi recuperado oito linhagens independentes dentro de Holochilus, e o arranjo filogenético parcialmente corrobora estudos anteriores. Finalmente, a filogenia proposta para o clado D apresentou algumas diferenças em comparação com outros estudos, e sugeriu que a maioria dos eventos cladogenéticos ocorreram durante o Pleistoceno, sendo a expansão dos ambientes abertos um importante motor de diversificação neste grupo.Biblioteca Digitais de Teses e Dissertações da USPPercequillo, Alexandre ReisPrado, Joyce Rodrigues do2017-09-05info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/doctoralThesisapplication/pdfhttp://www.teses.usp.br/teses/disponiveis/91/91131/tde-14032018-110612/reponame:Biblioteca Digital de Teses e Dissertações da USPinstname:Universidade de São Paulo (USP)instacron:USPLiberar o conteúdo para acesso público.info:eu-repo/semantics/openAccesseng2018-07-19T20:50:39Zoai:teses.usp.br:tde-14032018-110612Biblioteca Digital de Teses e Dissertaçõeshttp://www.teses.usp.br/PUBhttp://www.teses.usp.br/cgi-bin/mtd2br.plvirginia@if.usp.br|| atendimento@aguia.usp.br||virginia@if.usp.bropendoar:27212018-07-19T20:50:39Biblioteca Digital de Teses e Dissertações da USP - Universidade de São Paulo (USP)false
dc.title.none.fl_str_mv Evolutionary studies in South American marsh rats (Rodentia: Holochilus)
Estudos evolutivos dos ratos do brejo da América do Sul (Rodentia: Holochilus)
title Evolutionary studies in South American marsh rats (Rodentia: Holochilus)
spellingShingle Evolutionary studies in South American marsh rats (Rodentia: Holochilus)
Prado, Joyce Rodrigues do
Biogeografia
Biogeography
Clade D
Clado D
Genômica
Genomics
Morfometria
Morphometrics
Next generation sequencing
Oryzomyini
Oryzomyini
Rodents
Roedores
Sequenciamento de nova geração
title_short Evolutionary studies in South American marsh rats (Rodentia: Holochilus)
title_full Evolutionary studies in South American marsh rats (Rodentia: Holochilus)
title_fullStr Evolutionary studies in South American marsh rats (Rodentia: Holochilus)
title_full_unstemmed Evolutionary studies in South American marsh rats (Rodentia: Holochilus)
title_sort Evolutionary studies in South American marsh rats (Rodentia: Holochilus)
author Prado, Joyce Rodrigues do
author_facet Prado, Joyce Rodrigues do
author_role author
dc.contributor.none.fl_str_mv Percequillo, Alexandre Reis
dc.contributor.author.fl_str_mv Prado, Joyce Rodrigues do
dc.subject.por.fl_str_mv Biogeografia
Biogeography
Clade D
Clado D
Genômica
Genomics
Morfometria
Morphometrics
Next generation sequencing
Oryzomyini
Oryzomyini
Rodents
Roedores
Sequenciamento de nova geração
topic Biogeografia
Biogeography
Clade D
Clado D
Genômica
Genomics
Morfometria
Morphometrics
Next generation sequencing
Oryzomyini
Oryzomyini
Rodents
Roedores
Sequenciamento de nova geração
description An interdisciplinary approach integrating micro and macroevolution, genomic, morphometric and morphological variation, systematics, quantitative genetics, and biogeography was employed to investigate the evolutionary history of the genus Holochilus (Rodentia: Sigmodontinae). Holochilus presents poorly defined species, with nomenclatural problems and phylogenetic relationships on species level unknown. The current species number possibly does not reflect its real diversity, and no work combining genetic and morphometric evidences from all its geographic range was performed. This genus belongs to the tribe Oryzomyini, and along with other 14 genera constitute the Oryzomyini clade D, the most comprehensive generic diversity of the tribe, occupying distinct environments. The internal phylogenetic relationship within this clade is still unclear and variable. Due to its broad geographic distribution, Holochilus also represents a key piece on the study of the evolution of oryzomines of open formations of South America. Based on a comprehensive sampling, I analyzed patterns of morphometric and genomic variation within Holochilus, in order to delimit the species belonging to this genus, as well as access the phylogenetic relationship between these lineages. I investigated the sexual and ontogenetic variation in this group, comparing natural and captive populations, seeking for understand the effect of the environmental differences in the pattern of variation and ontogenetic trajectories (Chapter 1). I also evaluated and compared the genomic variation among three species of Holochilus to verify the influence of the biomes and the climatic changes in the genomic signatures (Chapter 2). I applied a model-based approach to delimit species (Chapter 3). And finally, additional investigations were made to propose the phylogenetic relationship between members of clade D, and provide date intervals for the main diversifications events, as well as the possible process responsible for the biogeographic pattern current observed related with the forest and open areas occupation (Chapter 4). Sexual dimorphism exhibited small degree of variation among populations. The greater ontogenetic variation is found in the younger age classes, but oldest individuals also show larger degree of differentiation. There are also great differences in the ontogenetic trajectories among samples, where individuals from the captive population exhibited the lower degree of variation between all age classes. The quantitative genetic analysis showed that genomic differences are observed across the taxa, and it was associated with geography. Ecological niche models revealed that biomes with larger areas of stability also presented more genomic structure, suggesting that historical dimension impacted population isolation/connectivity. Results also shows that biomes not only differ geographically and environmentally (based on past climatic conditions), but also show significant association between the environmental space and the genetic variation that is not related with geography. Eight independent lineages within Holochilus were recovered, and the phylogenetic arrangement partially corroborates previous studies. Finally, the phylogeny proposed for the clade D presented some differences in comparisons with other previously reported, and suggest that most of the cladogenetic events happened during the Pleistocene, being the expansion of open environments an important driver of diversification in this group.
publishDate 2017
dc.date.none.fl_str_mv 2017-09-05
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/doctoralThesis
format doctoralThesis
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dc.identifier.uri.fl_str_mv http://www.teses.usp.br/teses/disponiveis/91/91131/tde-14032018-110612/
url http://www.teses.usp.br/teses/disponiveis/91/91131/tde-14032018-110612/
dc.language.iso.fl_str_mv eng
language eng
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dc.rights.driver.fl_str_mv Liberar o conteúdo para acesso público.
info:eu-repo/semantics/openAccess
rights_invalid_str_mv Liberar o conteúdo para acesso público.
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
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dc.publisher.none.fl_str_mv Biblioteca Digitais de Teses e Dissertações da USP
publisher.none.fl_str_mv Biblioteca Digitais de Teses e Dissertações da USP
dc.source.none.fl_str_mv
reponame:Biblioteca Digital de Teses e Dissertações da USP
instname:Universidade de São Paulo (USP)
instacron:USP
instname_str Universidade de São Paulo (USP)
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institution USP
reponame_str Biblioteca Digital de Teses e Dissertações da USP
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repository.name.fl_str_mv Biblioteca Digital de Teses e Dissertações da USP - Universidade de São Paulo (USP)
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