Os roedores compõem a mais numerosa ordem dos mamíferos com, aproximadamente, 43 famílias, 354 gêneros e 1.700 espécies vivas. São membros importantes de quase todas as faunas, sendo cosmopolitas e nativos na maioria das áreas terrestres, exceto em algumas ilhas árticas e oceânicas, Nova Zelândia e Antártica. Possuem hábitos terrestres, fossorial, (semi) arborícola, semi-aquático ou palustre. Usualmente herbívoros, mas podem ser insetívoros, piscívoros ou carnívoros. A enorme variação na morfologia, nos hábitos de vida e alimentar são atributos que fizeram da ordem um dos grupos de mamíferos com maior sucesso evolutivo. Em nosso continente a ordem apresenta enorme importância na composição de sua fauna, pois perfaz, aproximadamente, 42% das espécies de mamíferos que aqui habitam. Entre os roedores sul-americanos, mais de 50% das espécies pertencem à família Cricetidae, distribuídos em apenas uma subfamília, Sigmodontinae, com aproximadamente 80 gêneros e 370 espécies. Oryzomyini é uma das sete tribos reconhecidas de Sigmodontinae, compreendendo cerca de 35% das espécies descritas para esta subfamília. Atualmente são descritos 27 gêneros e cerca de 120 espécies para esta tribo, incluindo propostas atuais que envolvem a descrição de novas espécies e, até mesmo, de novos gêneros.Os oryzomyinos habitam florestas, savanas, banhados, campos e ambientes semi-áridos, além de serem, na maioria das vezes, os mais abundantes pequenos mamíferos destes habitats. Seus hábitos alimentar vão de onívoros a insetívoros. A maioria possui hábito escansorial, mas alguns podem desenvolver hábitos arbóreos (Oecomys) ou até semiaquáticos (Nectomys), constituindo um dos mais claramente definidos grupos multigenéricos de muróides. A distribuição geográfica desta tribo é a mais ampla dentro dos Sigmodontinae, desde o extremo sul da América do Sul (Terra do Fogo) até o sudoeste dos Estados Unidos. Os objetivos desta tese, além de analisar as relações filogenéticas da tribo Oryzomyini com diferentes marcadores moleculares (citocromo b e IRBP), foi comprovar a validades das recentes mudanças propostas na classificação da tribo. Esta validação passa pela observação do caráter monofilético de cada um dos novos gêneros, bem como a comprovação da monofilia dos gêneros previamente reconhecidos. Também tivemos como objetivos estudar a filogenia e a filogeografia de um dos táxons da tribo, o gênero Oligoryzomys e traçar a rota de ocupação deste táxon nos ambientes sul-americanos. Além disto, foram examinadas a filogeografia e as estruturas genéticasdas populações de seis espécies da tribo Oryzomyini (Euryoryzomys russatus, Hylaeamys megacephalus, Oligoryzomys flavescens, O. moojeni, O. nigripes e Sooretamys angouya). Com relação à análise filogenética da tribo Oryzomyini, observamos que esta se comporta de forma monofilética tanto nos resultados com o gene citocromo b, como com o gene IRBP. Além disso, os resultados encontrados neste trabalho dão suporte às reformulações na classificação ocorrida na tribo Oryzomyini, com a proposição de 10 novos gêneros, onde a maioria dos gêneros da tribo Oryzomyini, tanto os antigos como os novos, são monofiléticos. A exceção foi o novo gênero Hylaeamys que se mostrou polifilético na análise com o gene citocromo b, em que cinco espécies se reuniram em um único agrupamento e a espécie H. yunganus se posicionou em um outro agrupamento. Todavia, Hylaeamys apresentou-se monofilético nas análises com o gene IRBP isolado e citocromo b e IRBP concatenados. As análises com o gênero Oligoryzomys mostraram que este táxon se apresenta de forma monofilética e com suas espécies distribuídas em dois grupos denominados, de acordo com suas origens geográficas, de grupo “Amazônico-Cerrado” e clado “Andino- Pampiano”. Estas espécies também apresentaram um gradiente geográfico no sentido norte-sul que fortemente suporta a hipótese de que o gênero iniciou sua ocupação no continente sul-americano a partir da Amazônia. Estudos filogeográficos e das estruturas genéticas das populações de seis espécies da tribo Oryzomyini observou-se a falta de diferenciação populacional, através da ausência de associação entre os haplótipos e suas distribuições geográficas, em duas das três espécies do gênero Oligoryzomys (O. flavescens e O. moojeni) analisadas. Estes resultados sugerem que a ausência intraespecíficas de populações pode ser um padrão geral do gênero. Já as outras três espécies analisadas apresentaram estruturação populacional e geográfica, além de estarem em equilíbrio demográfico. Nas análises filogenéticas realizadas, E. russatus e H. megacephalus mostraram seus espécimes agrupados em três clados distintos distribuídos em gradientes geográficos, sendo que o gradiente geográfico de H. megacephalus ocorre no sentido Norte-Sul. A divergência genética intraespecífica foi maior em H. megacephalus, seguida de E. russatus e sendo menor em S. angouya. Estes resultados podem fornecer subsídios para a elaboração de programas de conservação e manejo destas espécies e dos respectivos biomas que habitam, se necessário. / Rodents constitute the most numerous order of mammals with approximately 43 families, 354 genera and 1,700 living species. They are important members of almost all faunas, cosmopolitan and native to most terrestrial areas, except a few arctic and oceanic islands, New Zealand and Antarctica. They have terrestrial, fossorial, (semi) arboreal, semi-aquatic or palustrial habits. They are usually herbivore, but they may be insectivore, piscivore or carnivore. The huge variation in morphology, life and feeding habits are attributes that have made the order one of the mammal groups with the greatest success in evolution. On our continent, the order is very important as to fauna composition, because it makes up about 42% of the mammal species that inhabit here. Among the South American rodents, more than 50% of the species belong to the Cricetidae family, distributed into only a single subfamily, Sigmodontinae, with approximately 80 genera and 370 species. Oryzomyini is one of the seven acknowledged Sigmodontinae tribes, consisting of about 35% of the species described for this subfamily. Currently, 27 genera and about 120 species are described for this tribe, including current proposals that involve the description of new species and even new genera. The oryzomyines inhabit forests, savannahs, swamps, fields and semi-arid environments, besides often being the most abundant small mammals in these habitats. Their feeding habits range from omnivorous to insectivorous. Most of them have a scansorial habit, but some of them may develop arboreous habits (Oecomys) or even semi-aquatic habits (Nectomys), constituting one of the most clearly defined multigenera groups of muroids. The geographical distribution of this tribe is the broadest within the Sigmodontinae, from the far south of South American (Tierra del Fuego) to the southwest of the United States. The objective of this thesis, besides analyzing the phylogenetic relations of the tribe Oryzomyini with different molecular markers (cytochrome b and IRBP), was to prove the validities of the recent changes proposed in the classification of the tribe. This validation includes the observation of the monophyletic character of each of the new genera, as well as proving the monophyly of previously recognized genera. Our objectives were also to study the phylogeny and phylogeography of one of the taxa of the tribe, genus Oligoryzomys, and to trace the occupation route of this taxon in the South American environments. The phylogeography and genetic structures of the populations of six species of the tribeOryzomyini (Euryoryzomys russatus, Hylaeamys megacephalus, Oligoryzomys flavescens, O. moojeni, O. nigripes and Sooretamys angouya) were also examined. As to the phylogenetic analysis of the tribe Oryzomyini, we observed that the latter behaves in a monophyletic form, both in the results with the cytochrome b gene, and with gene IRBP. In addition the results found in this study support the reformulations in the classification that occurred for the tribe Oryzomyini, with the proposition of 10 new genera, where most of the genera of the tribe Oryzomyini both the old and the new, are monophyletic. The exception was the new genus Hylaeamys which proved be polyphyletic in the analysis with the cytochrome b gene, in which five species assembled in a single group and the species H. yunganus took a position in another group. However, Hylaeamys was monophyletic in the analyses with the isolated gene IRBP and cytochrome b and IRBP genes concatenated.The analyses of genus Oligoryzomys showed that this taxon was monophyletic and with its species distributed in two groups named, according to their geographic origins, the “Amazon-Cerrado” group and the “Pampa-Andean” clade. These species also presented a geographical gradient in the North-South direction which strongly supports the hypothesis that the genus began its occupation of the South American continent in the Amazon. Studies of phylogeography and of the genetic structures of the populations of six species of the tribe Oryzomyini showed a lack of population differentiation in two of the three species of genus Oligoryzomys (O. flavescens and O. moojeni) analyzed by the absence of association between the haplotypes and their geographic distributions. These results suggest that the intraspecific absence of populations may be a general pattern of the genus. On the other hand the three other species analyzed presented a population and geographic structuring, besides being in demographic equilibrium. In the phylogenetic analyses performed, E. russatus and H. megacephalus showed their specimens grouped in three distinct clades, distributed in geographic gradients, in which the geographic gradient of H. megacephalus occurs in the North-South direction. The intraspecific genetic divergence was greater in H. megacephalus, followed by E. russatus and smaller in S. angouya. These can aid to the elaboration of conservation and management programs of these species and biomes studied which they inhabit, if necessary.

Os roedores compõem a mais numerosa ordem dos mamíferos com, aproximadamente, 43 famílias, 354 gêneros e 1.700 espécies vivas. São membros importantes de quase todas as faunas, sendo cosmopolitas e nativos na maioria das áreas terrestres, exceto em algumas ilhas árticas e oceânicas, Nova Zelândia e Antártica. Possuem hábitos terrestres, fossorial, (semi) arborícola, semi-aquático ou palustre. Usualmente herbívoros, mas podem ser insetívoros, piscívoros ou carnívoros. A enorme variação na morfologia, nos hábitos de vida e alimentar são atributos que fizeram da ordem um dos grupos de mamíferos com maior sucesso evolutivo. Em nosso continente a ordem apresenta enorme importância na composição de sua fauna, pois perfaz, aproximadamente, 42% das espécies de mamíferos que aqui habitam. Entre os roedores sul-americanos, mais de 50% das espécies pertencem à família Cricetidae, distribuídos em apenas uma subfamília, Sigmodontinae, com aproximadamente 80 gêneros e 370 espécies. Oryzomyini é uma das sete tribos reconhecidas de Sigmodontinae, compreendendo cerca de 35% das espécies descritas para esta subfamília. Atualmente são descritos 27 gêneros e cerca de 120 espécies para esta tribo, incluindo propostas atuais que envolvem a descrição de novas espécies e, até mesmo, de novos gêneros.Os oryzomyinos habitam florestas, savanas, banhados, campos e ambientes semi-áridos, além de serem, na maioria das vezes, os mais abundantes pequenos mamíferos destes habitats. Seus hábitos alimentar vão de onívoros a insetívoros. A maioria possui hábito escansorial, mas alguns podem desenvolver hábitos arbóreos (Oecomys) ou até semiaquáticos (Nectomys), constituindo um dos mais claramente definidos grupos multigenéricos de muróides. A distribuição geográfica desta tribo é a mais ampla dentro dos Sigmodontinae, desde o extremo sul da América do Sul (Terra do Fogo) até o sudoeste dos Estados Unidos. Os objetivos desta tese, além de analisar as relações filogenéticas da tribo Oryzomyini com diferentes marcadores moleculares (citocromo b e IRBP), foi comprovar a validades das recentes mudanças propostas na classificação da tribo. Esta validação passa pela observação do caráter monofilético de cada um dos novos gêneros, bem como a comprovação da monofilia dos gêneros previamente reconhecidos. Também tivemos como objetivos estudar a filogenia e a filogeografia de um dos táxons da tribo, o gênero Oligoryzomys e traçar a rota de ocupação deste táxon nos ambientes sul-americanos. Além disto, foram examinadas a filogeografia e as estruturas genéticasdas populações de seis espécies da tribo Oryzomyini (Euryoryzomys russatus, Hylaeamys megacephalus, Oligoryzomys flavescens, O. moojeni, O. nigripes e Sooretamys angouya). Com relação à análise filogenética da tribo Oryzomyini, observamos que esta se comporta de forma monofilética tanto nos resultados com o gene citocromo b, como com o gene IRBP. Além disso, os resultados encontrados neste trabalho dão suporte às reformulações na classificação ocorrida na tribo Oryzomyini, com a proposição de 10 novos gêneros, onde a maioria dos gêneros da tribo Oryzomyini, tanto os antigos como os novos, são monofiléticos. A exceção foi o novo gênero Hylaeamys que se mostrou polifilético na análise com o gene citocromo b, em que cinco espécies se reuniram em um único agrupamento e a espécie H. yunganus se posicionou em um outro agrupamento. Todavia, Hylaeamys apresentou-se monofilético nas análises com o gene IRBP isolado e citocromo b e IRBP concatenados. As análises com o gênero Oligoryzomys mostraram que este táxon se apresenta de forma monofilética e com suas espécies distribuídas em dois grupos denominados, de acordo com suas origens geográficas, de grupo “Amazônico-Cerrado” e clado “Andino- Pampiano”. Estas espécies também apresentaram um gradiente geográfico no sentido norte-sul que fortemente suporta a hipótese de que o gênero iniciou sua ocupação no continente sul-americano a partir da Amazônia. Estudos filogeográficos e das estruturas genéticas das populações de seis espécies da tribo Oryzomyini observou-se a falta de diferenciação populacional, através da ausência de associação entre os haplótipos e suas distribuições geográficas, em duas das três espécies do gênero Oligoryzomys (O. flavescens e O. moojeni) analisadas. Estes resultados sugerem que a ausência intraespecíficas de populações pode ser um padrão geral do gênero. Já as outras três espécies analisadas apresentaram estruturação populacional e geográfica, além de estarem em equilíbrio demográfico. Nas análises filogenéticas realizadas, E. russatus e H. megacephalus mostraram seus espécimes agrupados em três clados distintos distribuídos em gradientes geográficos, sendo que o gradiente geográfico de H. megacephalus ocorre no sentido Norte-Sul. A divergência genética intraespecífica foi maior em H. megacephalus, seguida de E. russatus e sendo menor em S. angouya. Estes resultados podem fornecer subsídios para a elaboração de programas de conservação e manejo destas espécies e dos respectivos biomas que habitam, se necessário. / Rodents constitute the most numerous order of mammals with approximately 43 families, 354 genera and 1,700 living species. They are important members of almost all faunas, cosmopolitan and native to most terrestrial areas, except a few arctic and oceanic islands, New Zealand and Antarctica. They have terrestrial, fossorial, (semi) arboreal, semi-aquatic or palustrial habits. They are usually herbivore, but they may be insectivore, piscivore or carnivore. The huge variation in morphology, life and feeding habits are attributes that have made the order one of the mammal groups with the greatest success in evolution. On our continent, the order is very important as to fauna composition, because it makes up about 42% of the mammal species that inhabit here. Among the South American rodents, more than 50% of the species belong to the Cricetidae family, distributed into only a single subfamily, Sigmodontinae, with approximately 80 genera and 370 species. Oryzomyini is one of the seven acknowledged Sigmodontinae tribes, consisting of about 35% of the species described for this subfamily. Currently, 27 genera and about 120 species are described for this tribe, including current proposals that involve the description of new species and even new genera. The oryzomyines inhabit forests, savannahs, swamps, fields and semi-arid environments, besides often being the most abundant small mammals in these habitats. Their feeding habits range from omnivorous to insectivorous. Most of them have a scansorial habit, but some of them may develop arboreous habits (Oecomys) or even semi-aquatic habits (Nectomys), constituting one of the most clearly defined multigenera groups of muroids. The geographical distribution of this tribe is the broadest within the Sigmodontinae, from the far south of South American (Tierra del Fuego) to the southwest of the United States. The objective of this thesis, besides analyzing the phylogenetic relations of the tribe Oryzomyini with different molecular markers (cytochrome b and IRBP), was to prove the validities of the recent changes proposed in the classification of the tribe. This validation includes the observation of the monophyletic character of each of the new genera, as well as proving the monophyly of previously recognized genera. Our objectives were also to study the phylogeny and phylogeography of one of the taxa of the tribe, genus Oligoryzomys, and to trace the occupation route of this taxon in the South American environments. The phylogeography and genetic structures of the populations of six species of the tribeOryzomyini (Euryoryzomys russatus, Hylaeamys megacephalus, Oligoryzomys flavescens, O. moojeni, O. nigripes and Sooretamys angouya) were also examined. As to the phylogenetic analysis of the tribe Oryzomyini, we observed that the latter behaves in a monophyletic form, both in the results with the cytochrome b gene, and with gene IRBP. In addition the results found in this study support the reformulations in the classification that occurred for the tribe Oryzomyini, with the proposition of 10 new genera, where most of the genera of the tribe Oryzomyini both the old and the new, are monophyletic. The exception was the new genus Hylaeamys which proved be polyphyletic in the analysis with the cytochrome b gene, in which five species assembled in a single group and the species H. yunganus took a position in another group. However, Hylaeamys was monophyletic in the analyses with the isolated gene IRBP and cytochrome b and IRBP genes concatenated.The analyses of genus Oligoryzomys showed that this taxon was monophyletic and with its species distributed in two groups named, according to their geographic origins, the “Amazon-Cerrado” group and the “Pampa-Andean” clade. These species also presented a geographical gradient in the North-South direction which strongly supports the hypothesis that the genus began its occupation of the South American continent in the Amazon. Studies of phylogeography and of the genetic structures of the populations of six species of the tribe Oryzomyini showed a lack of population differentiation in two of the three species of genus Oligoryzomys (O. flavescens and O. moojeni) analyzed by the absence of association between the haplotypes and their geographic distributions. These results suggest that the intraspecific absence of populations may be a general pattern of the genus. On the other hand the three other species analyzed presented a population and geographic structuring, besides being in demographic equilibrium. In the phylogenetic analyses performed, E. russatus and H. megacephalus showed their specimens grouped in three distinct clades, distributed in geographic gradients, in which the geographic gradient of H. megacephalus occurs in the North-South direction. The intraspecific genetic divergence was greater in H. megacephalus, followed by E. russatus and smaller in S. angouya. These can aid to the elaboration of conservation and management programs of these species and biomes studied which they inhabit, if necessary.

Os roedores compõem a mais numerosa ordem dos mamíferos com, aproximadamente, 43 famílias, 354 gêneros e 1.700 espécies vivas. São membros importantes de quase todas as faunas, sendo cosmopolitas e nativos na maioria das áreas terrestres, exceto em algumas ilhas árticas e oceânicas, Nova Zelândia e Antártica. Possuem hábitos terrestres, fossorial, (semi) arborícola, semi-aquático ou palustre. Usualmente herbívoros, mas podem ser insetívoros, piscívoros ou carnívoros. A enorme variação na morfologia, nos hábitos de vida e alimentar são atributos que fizeram da ordem um dos grupos de mamíferos com maior sucesso evolutivo. Em nosso continente a ordem apresenta enorme importância na composição de sua fauna, pois perfaz, aproximadamente, 42% das espécies de mamíferos que aqui habitam. Entre os roedores sul-americanos, mais de 50% das espécies pertencem à família Cricetidae, distribuídos em apenas uma subfamília, Sigmodontinae, com aproximadamente 80 gêneros e 370 espécies. Oryzomyini é uma das sete tribos reconhecidas de Sigmodontinae, compreendendo cerca de 35% das espécies descritas para esta subfamília. Atualmente são descritos 27 gêneros e cerca de 120 espécies para esta tribo, incluindo propostas atuais que envolvem a descrição de novas espécies e, até mesmo, de novos gêneros.Os oryzomyinos habitam florestas, savanas, banhados, campos e ambientes semi-áridos, além de serem, na maioria das vezes, os mais abundantes pequenos mamíferos destes habitats. Seus hábitos alimentar vão de onívoros a insetívoros. A maioria possui hábito escansorial, mas alguns podem desenvolver hábitos arbóreos (Oecomys) ou até semiaquáticos (Nectomys), constituindo um dos mais claramente definidos grupos multigenéricos de muróides. A distribuição geográfica desta tribo é a mais ampla dentro dos Sigmodontinae, desde o extremo sul da América do Sul (Terra do Fogo) até o sudoeste dos Estados Unidos. Os objetivos desta tese, além de analisar as relações filogenéticas da tribo Oryzomyini com diferentes marcadores moleculares (citocromo b e IRBP), foi comprovar a validades das recentes mudanças propostas na classificação da tribo. Esta validação passa pela observação do caráter monofilético de cada um dos novos gêneros, bem como a comprovação da monofilia dos gêneros previamente reconhecidos. Também tivemos como objetivos estudar a filogenia e a filogeografia de um dos táxons da tribo, o gênero Oligoryzomys e traçar a rota de ocupação deste táxon nos ambientes sul-americanos. Além disto, foram examinadas a filogeografia e as estruturas genéticasdas populações de seis espécies da tribo Oryzomyini (Euryoryzomys russatus, Hylaeamys megacephalus, Oligoryzomys flavescens, O. moojeni, O. nigripes e Sooretamys angouya). Com relação à análise filogenética da tribo Oryzomyini, observamos que esta se comporta de forma monofilética tanto nos resultados com o gene citocromo b, como com o gene IRBP. Além disso, os resultados encontrados neste trabalho dão suporte às reformulações na classificação ocorrida na tribo Oryzomyini, com a proposição de 10 novos gêneros, onde a maioria dos gêneros da tribo Oryzomyini, tanto os antigos como os novos, são monofiléticos. A exceção foi o novo gênero Hylaeamys que se mostrou polifilético na análise com o gene citocromo b, em que cinco espécies se reuniram em um único agrupamento e a espécie H. yunganus se posicionou em um outro agrupamento. Todavia, Hylaeamys apresentou-se monofilético nas análises com o gene IRBP isolado e citocromo b e IRBP concatenados. As análises com o gênero Oligoryzomys mostraram que este táxon se apresenta de forma monofilética e com suas espécies distribuídas em dois grupos denominados, de acordo com suas origens geográficas, de grupo “Amazônico-Cerrado” e clado “Andino- Pampiano”. Estas espécies também apresentaram um gradiente geográfico no sentido norte-sul que fortemente suporta a hipótese de que o gênero iniciou sua ocupação no continente sul-americano a partir da Amazônia. Estudos filogeográficos e das estruturas genéticas das populações de seis espécies da tribo Oryzomyini observou-se a falta de diferenciação populacional, através da ausência de associação entre os haplótipos e suas distribuições geográficas, em duas das três espécies do gênero Oligoryzomys (O. flavescens e O. moojeni) analisadas. Estes resultados sugerem que a ausência intraespecíficas de populações pode ser um padrão geral do gênero. Já as outras três espécies analisadas apresentaram estruturação populacional e geográfica, além de estarem em equilíbrio demográfico. Nas análises filogenéticas realizadas, E. russatus e H. megacephalus mostraram seus espécimes agrupados em três clados distintos distribuídos em gradientes geográficos, sendo que o gradiente geográfico de H. megacephalus ocorre no sentido Norte-Sul. A divergência genética intraespecífica foi maior em H. megacephalus, seguida de E. russatus e sendo menor em S. angouya. Estes resultados podem fornecer subsídios para a elaboração de programas de conservação e manejo destas espécies e dos respectivos biomas que habitam, se necessário. / Rodents constitute the most numerous order of mammals with approximately 43 families, 354 genera and 1,700 living species. They are important members of almost all faunas, cosmopolitan and native to most terrestrial areas, except a few arctic and oceanic islands, New Zealand and Antarctica. They have terrestrial, fossorial, (semi) arboreal, semi-aquatic or palustrial habits. They are usually herbivore, but they may be insectivore, piscivore or carnivore. The huge variation in morphology, life and feeding habits are attributes that have made the order one of the mammal groups with the greatest success in evolution. On our continent, the order is very important as to fauna composition, because it makes up about 42% of the mammal species that inhabit here. Among the South American rodents, more than 50% of the species belong to the Cricetidae family, distributed into only a single subfamily, Sigmodontinae, with approximately 80 genera and 370 species. Oryzomyini is one of the seven acknowledged Sigmodontinae tribes, consisting of about 35% of the species described for this subfamily. Currently, 27 genera and about 120 species are described for this tribe, including current proposals that involve the description of new species and even new genera. The oryzomyines inhabit forests, savannahs, swamps, fields and semi-arid environments, besides often being the most abundant small mammals in these habitats. Their feeding habits range from omnivorous to insectivorous. Most of them have a scansorial habit, but some of them may develop arboreous habits (Oecomys) or even semi-aquatic habits (Nectomys), constituting one of the most clearly defined multigenera groups of muroids. The geographical distribution of this tribe is the broadest within the Sigmodontinae, from the far south of South American (Tierra del Fuego) to the southwest of the United States. The objective of this thesis, besides analyzing the phylogenetic relations of the tribe Oryzomyini with different molecular markers (cytochrome b and IRBP), was to prove the validities of the recent changes proposed in the classification of the tribe. This validation includes the observation of the monophyletic character of each of the new genera, as well as proving the monophyly of previously recognized genera. Our objectives were also to study the phylogeny and phylogeography of one of the taxa of the tribe, genus Oligoryzomys, and to trace the occupation route of this taxon in the South American environments. The phylogeography and genetic structures of the populations of six species of the tribeOryzomyini (Euryoryzomys russatus, Hylaeamys megacephalus, Oligoryzomys flavescens, O. moojeni, O. nigripes and Sooretamys angouya) were also examined. As to the phylogenetic analysis of the tribe Oryzomyini, we observed that the latter behaves in a monophyletic form, both in the results with the cytochrome b gene, and with gene IRBP. In addition the results found in this study support the reformulations in the classification that occurred for the tribe Oryzomyini, with the proposition of 10 new genera, where most of the genera of the tribe Oryzomyini both the old and the new, are monophyletic. The exception was the new genus Hylaeamys which proved be polyphyletic in the analysis with the cytochrome b gene, in which five species assembled in a single group and the species H. yunganus took a position in another group. However, Hylaeamys was monophyletic in the analyses with the isolated gene IRBP and cytochrome b and IRBP genes concatenated.The analyses of genus Oligoryzomys showed that this taxon was monophyletic and with its species distributed in two groups named, according to their geographic origins, the “Amazon-Cerrado” group and the “Pampa-Andean” clade. These species also presented a geographical gradient in the North-South direction which strongly supports the hypothesis that the genus began its occupation of the South American continent in the Amazon. Studies of phylogeography and of the genetic structures of the populations of six species of the tribe Oryzomyini showed a lack of population differentiation in two of the three species of genus Oligoryzomys (O. flavescens and O. moojeni) analyzed by the absence of association between the haplotypes and their geographic distributions. These results suggest that the intraspecific absence of populations may be a general pattern of the genus. On the other hand the three other species analyzed presented a population and geographic structuring, besides being in demographic equilibrium. In the phylogenetic analyses performed, E. russatus and H. megacephalus showed their specimens grouped in three distinct clades, distributed in geographic gradients, in which the geographic gradient of H. megacephalus occurs in the North-South direction. The intraspecific genetic divergence was greater in H. megacephalus, followed by E. russatus and smaller in S. angouya. These can aid to the elaboration of conservation and management programs of these species and biomes studied which they inhabit, if necessary.

Extensive development has destroyed and fragmented wildlife habitat in the Lower Florida Keys. The Lower Keys marsh rabbit (LKMR; Sylvilagus palustris hefneri) and the silver rice rat (SRR; Oryzomys argentatus) are listed by the United States Fish and Wildlife Service (USFWS) and the Florida Fish and Wildlife Conservation Commission (FFWCC) as endangered species. Both species depend on coastal prairies, freshwater marshes, and intertidal salt-marsh zones. The objective of this study was to meet specific, species-level recovery goals and to add reliable information that may modify or support current recovery plans. Specifically, I (1) evaluated the use of LKMR reintroduction to suitable habitat, (2) examined characteristics of habitat used by LKMR, and (3) surveyed the Lower Florida Keys for SRRs, documenting current range and examining survey results for the past decade. I reintroduced 7 rabbits (3 males, 4 females) to suitable habitat on Water Key, and monitored their survival and release-site fidelity. All reintroduced rabbits survived and some reproduced, suggesting these translocation techniques are a viable tool for recovery. On Boca Chica Key, I radio-collared 13 LKMRs and compared vegetation characteristics between core-use and avoided areas within home ranges. Binary logistic regression associated rabbit use with high vegetation heights (7–8 dm), low canopy coverage (<=10%), high bunchgrass densities (2.5–3.8/sq m), and forb presence (>5%), supporting the hypothesis that LKMRs may be detrimentally impacted by hardwood encroachment into salt-marsh habitats. For LKMR recovery, I recommend management to resist hardwood encroachment, together with active predator control. I surveyed 36 locations on 18 islands for SRRs, capturing rats on 12 islands, including 2 on which SRRs had not previously been found. Comparisons of my data with historic data suggest SRRs either have increased in abundance over the past decade or that previous trapping efforts were not effective. Abundance of SRRs does not appear to be significantly different from that of populations of rice rats on the mainland. The USFWS and FFWCC should consider revising the conservation status of the SRR; however, it still should be regarded as a unique evolutionary unit with a very limited potential range.

The Everglades, a wetland ecosystem unique to southern Florida has been degraded by the loss of nearly half of its area to urban and agricultural development as well as by alterations to Florida’s hydrology. Modifications to the flow of water to the Everglades have altered the remaining portion of the Everglades. Most prominent among these changes in the remaining Everglades is the loss of tree islands with a disproportionately greater loss of larger tree islands. Despite their significance as “keystone habitats”, our understanding of how changes to Everglades tree islands will affect fauna is poor. In the work presented, 16 study tree islands of Rock Reef Pass, Everglades National Park, Homestead, FL, were classified into three size classes (large, medium and small) and used animal capture histories collected between February 1994 and December 2005 to investigate the relationship between tree island size classes and indirect indicators of adult female hispid cotton rat (Sigmodon hispidus) and marsh rice rat (Oryzomys palustris) fitness and reproduction. Adult female S. hispidus and O. palustris body weights were used as an indicator of adult female fitness and compared among tree island size classes. The proportions of reproductively active females, the proportions of captures of individuals in the juvenile age class and the number of juveniles per female were used as indirect indicators of female reproduction and compared among island size classes. Animal capture histories were also used to perform multi-state mark-recapture analyses, where sates were defined as three island size classes, to draw inferences about state-specific rates of survival and state transition probabilities for Oryzomys palustris and Sigmodon hispidus as a function of the most salient features of the Everglades ecosystem, namely, its tree islands and its seasonal wet and dry periods. Specifically, Akaike’s, information criterion (AIC) was used to make inferences about factors influencing survival and transition probabilities by comparing the relative fit among models where survival and transition rates are described as functions of tree island size classes and as a function of environmental variables that distinguish seasonal periods (monthly water levels, total monthly rainfall, mean air temperature, days dry, days inundated). The probabilities of individuals remaining within the same island size class were interpreted as an indirect indicator of size-class specific tree island use. Results indicated that greater proportions of S. hispidus adult females were reproductively active and had higher fitness on larger islands than females on smaller islands. The body weights of S. hispidus adult females, the proportions of individuals in the juvenile age class and the number of juveniles per female, were positively correlated with tree island area while the proportions of reproductively active S. hispidus females were not. When compared among tree island size classes, S. hispidus females recaptured on the same large island weighed more than females recaptured on the same and medium or small island suggesting that females with greater fitness are found on larger tree islands. The proportions of reproductively active S. hispidus females and of individuals in the juvenile age class were greater on larger tree islands than on smaller islands, although the number of juveniles per females did not differ among tree islands. The results also indicated that differences in the fitness and reproductive condition of O. palustris females are not as distinct among females on different size tree islands. The body weights O. palustris adult females, the proportions of juveniles and the number of juveniles per female were not correlated with island area, while the proportions of reproductively active females were negatively correlated with tree island area. The body weights of O. palustris adult females recaptured on the same large tree island were higher than those of females on smaller islands while the proportions of females that were reproductively active and the proportions of captures of juveniles were higher on small islands than on large islands. Mark-recapture analysis provided evidence that overall, Sigmodon hispidus survival rates were higher on larger islands than on smaller islands. Evidence was not found that Oryzomys palustris survival rates differed among size classes, perhaps due to the limited spatial scale of this study relative to the spatial sale of O. palustris habitat use. Both species’ survival probabilities differed between seasons with Oryzomys palustris having higher survivorship during wet seasons and Sigmodon hispidus during the dry season. Both Oryzomys palustris and Sigmodon hispidus were more likely to remain on large island than on smaller islands.

Genetic analyses of two endangered species of mammals in the Lower Keys of Florida (Lower Keys marsh rabbit, LKMR, Sylvilagus palustris hefneri; silver rice rat, SRR, Oryzomys palustris natator) were performed to evaluate the genetic structure of their populations. Mitochondrial sequence data (control region; 763 base pairs (bp), LKMR; 788 bp, SRR) were used to explore patterns of genetic variation within and among island populations in both species. Analysis of the SRR also included 8 polymorphic nuclear microsatellite loci (9 to 16 alleles). Phylogenetic analyses of mitochondrial sequence data for both species revealed two main lineages corresponding to eastern and western localities, with high levels of genetic structuring (LKMR FST = 0.982, SRR ΦST = 0.916). The two species differed in the level of sequence divergence between eastern and western populations (LKMR, 19 bp; SRR 4 bp). In addition to an overall similar pattern of genetic subdivision, populations of both species possessed low levels of mtDNA variation (haplotypic diversity in the LKMR = 66.1%, SRR = 58.6%). Microsatellite analyses of the SRR revealed subdivision between eastern and western regions. Although less pronounced than the structure observed in mtDNA, the overall pattern was still apparent. Additional examination of divergence between mainland and Lower Keys rice rats revealed a genetic division that indicated a lack of recent gene exchange between the regions (i.e. no shared haplotypes, the presence of private alleles, and distinctive separation in numerous analyses). Although this degree of division does not warrant species designation, the levels and patterns of divergence, both morphological and genetic, do suggest genetic isolation of mainland and island forms. This fact, along with restricted gene flow between the Lower Keys and the Everglades, suggests that the SRR is on an evolutionary trajectory separate from its mainland counterparts and validates its identification as a separate subspecies, Oryzomys palustris natator. Finally, the genetic division between eastern and western populations of the SRR and LKMR suggests that populations of both species in these two regions of the Lower Keys should be treated as separate management units, especially when considering the enhancement of populations via translocations.

The marsh rice rat (Oryzomys sp.) is a semiaquatic rodent native to wetlands in the southeastern United States. The northwestern-most part of the rice rat’s range extends to Illinois where rice rats are found in wetlands across the southern part of the state. Recent studies have shown that rice rats in the United States can be divided into two species: O. palustris and O. texensis, but the taxonomic status of rice rats in Southern Illinois is unclear. To resolve this, I sequenced cytochrome-b and the control region, two regions of mitochondrial DNA, for 16 rice rats and constructed a phylogeny using these new sequences and previously obtained O. palustris and O. texensis sequences. In contrast to previous morphological assessments, I found that rice rats in Southern Illinois should be classified as O. texensis. This would extend the range of O. texensis north and west from its current extent. Further investigation using nuclear loci will be needed to confirm this classification.

Thesis--University of Michigan. / Bibliography: p. 121-124.

The marsh rice rat (Oryzomys palustris) is a semi-aquatic rodent classified as state-threatened in Illinois due to historical wetland loss coupled with being on the northern periphery of its range. The most recent survey for this species in Illinois occurred in 1988, and this study reassessed its status and distribution. From 2007 to 2009, I used live traps to sample for rice rats at previously occupied and random wetland-dominated sites in 5 southern Illinois watersheds. I captured 132 individual rice rats 192 times in 13,248 trap nights. Capture success was 15.10 captures/1,000 trap nights. I detected rice rats within 3 of 5 watersheds, 16 of 48 sites, and 5 new locations. Most rice rats were captured in permanent or semi-permanent emergent wetlands and rice rat occurrence was strongly related with coal mine-associated wetlands. I collected microhabitat measurements at 10% of trap locations and recorded landcover types within and around sites. I analyzed data using t-tests, logistic regression, and occupancy modeling. Percent herbaceous cover and percent visual obstruction (0.0-0.5m) positively influenced rice rat occurrence and were among the most important microhabitat models. The best model in the candidate set of landcover variables included proportion of upland grass in areas surrounding wetlands as a predictor of rice rat occurrence. I believe insufficient evidence exists to warrant removal of the threatened status of the marsh rice rat. However, current management practices, such as wetland restoration, grassland restoration, and mowing of roadside ditches, likely benefit rice rat populations. Slight modification of these management activities may facilitate the eventual delisting of marsh rice rats.

Island isolation can cause changes in body size, cranial characteristics, and genetic variation in mammals. We use geometric morphometrics to test skull and mandible shape and size change across three species of endemic Cozumel Island rodents in order to test the “island rule” of larger size in isolated rodents. We also sequenced the D-Loop and cytochrome b region of the mitochondrial genome and tested for differences in genetic variation between island and mainland groups, as well as population structure and gene flow in order to assess the effect of island isolation on these three rodents. We found that the three species of rodents showed varying degrees of size and shape differences from island to mainland with some species varying considerably and others not at all. The genetic results were similar with some species exhibiting potential founder effects, while others showed little differentiation between the island and mainland. We conclude that evolution on islands is highly conditional on the history, community composition, and biology of the colonizing species.