Nesta Tese foram descritos padrões de diversificação de pássaros que ocorrem na Amazônia e na Mata Atlântica, os quais permitiram fazer inferências sobre os processos que podem ter influenciado a evolução das biotas residentes nestes biomas. Nós produzimos sequências de genes mitocondriais e nucleares para fazer inferências sobre a biogeografia histórica destes biomas. A Tese foi dividida em seis capítulos. Nos capítulos 1 a 4 os táxons Basileuterus leucoblepharus, Myrmotherula gularis e o complexo Synallaxis ruficapilla foram estudados para se entender a diversificação da Mata Atlântica. Estes estudos revelaram que os ciclos glaciais do fim do Pleistoceno tiveram importante papel na diversificação destes táxons. Ainda, atividades tectônicas ocorridas durante o Quaternário possivelmente contribuíram para a diversificação do complexo S. ruficapilla. No capítulo 5 o complexo Thamnomanes caesius/T. schistogynus foi analisado visando inferir a história evolutiva da Amazônia. Os resultados deste estudo mostraram que tanto a origem recente dos rios amazônicos (do Plioceno ao Pleistoceno) quanto os ciclos glaciais possivelmente foram responsáveis pela diversificação deste grupo. No capítulo 6 o grupo Suboscines foi estudado para compreender a dinâmica das conexões históricas entre as florestas Amazônica e Atlântica. Os resultados mostraram que os contatos históricos entre estes dois biomas correspondem a duas conexões espaço-temporais distintas: uma mais antiga durante o Mioceno através da porção sul da diagonal seca da América do sul, e uma mais recente durante o Plioceno e o Pleistoceno através da Caatinga e Cerrado no Nordeste do Brasil. Os dados desta Tese permitiram testar o papel de algumas hipóteses concorrentes na diversificação da Amazônia e da Mata Atlântica. A hipótese dos rios parece ter contribuído para a diversificação da Amazônia. A hipótese dos refúgios florestais possivelmente teve um papel crucial da diversificação da biota da Mata Atlântica. A hipótese dos refúgios também não pode ser rejeitada como um das forças que deu origem à biota da Amazônia que observamos atualmente. Eventos tectônicos e mudanças climáticas contribuíram para conexões históricas entre a Amazônia e Mata Atlântica / This PhD Dissertation describes patterns of diversification of species of passerines that occur in the Amazon and the Atlantic Forest and that allowed making inferences on the processes that may have influenced the evolution of the organisms that live in these forests. We generated sequences of mitochondrial and nuclear genes to study the historical biogeography of these biomes. This work includes six chapters. In chapters 1 to 4 we analyzed Basileuterus leucoblepharus, Myrmotherula gularis, and the Synallaxis ruficapilla complex in order to depict the diversification within the Atlantic Forest. These studies revealed that late Pleistocene glacial cycles played an important role on the diversification of these taxa. Furthermore, tectonic activities in the Quaternary may have contributed for the diversification of the S. ruficapilla complex. In chapter 5 we analyzed the Thamnomanes caesius/T. schistogynus complex in order to infer about the diversification in the Amazon. The results of this study showed that both the recent origin of Amazonian rivers (Pliocene to Pleistocene) as glacial cycles could be responsible for the diversification of these organisms. In chapter 6 we analyzed the New World suboscines in order to depict the historical connection dynamics between the Amazon and the Atlantic Forest. Our results pointed to two distinct spatiotemporal pathways connecting these forests in the past: (1) older connections during the Miocene through southern South America dry diagonal; (2) younger connections during the Pliocene to Pleistocene through Cerrado and Caatinga in northeastern Brazil. The results of this PhD Dissertation allowed us to test the role of concurrent hypotheses of diversification in the Amazon and the Atlantic Forest. The riverine hypothesis seems to have contributed to the evolution of the Amazonian biota. The refuge hypothesis seems to be the main force of diversification of organisms from the Atlantic Forest. Moreover, we could not reject the refuge hypothesis as a force of diversification of organisms that occur in the Amazon forest. Tectonic events and climate changes played important roles in the historical connection between the Amazon and the Atlantic Forest

Cynodontidae (sensu Lucena & Menezes, 1998) é uma família de Characiformes com 14 espécies válidas divididas em duas subfamílias (Cynodontinae e Roestinae). As espécies de Cynodontinae sempre foram classificadas em um mesmo grupo, enquanto que Roestinae já foi classificada junto com Characidae. Com o objetivo de testar o monofiletismo de Cynodontidae, realizamos uma análise de máxima parcimônia com o algoritmo TBR em 42 táxons representando 12 famílias de Characiformes. A análise foi realizada com três regiões nuclearas e três genes mitocondriais; entretanto, o íntron da RPS7 foi retirado da análise final por questões de homologia do alinhamento. A árvore consenso obtida com 9842 passos (IC = 0,351 e IR = 0,358) evidencia o não monofiletismo de Cynodontidae, com Cynodontinae relacionada a um clado composto por Serrasalmidae, Prochilodontidae, Hemiodontidae e Parodontidae, enquanto que Roestinae aparece dentro de Characidae relacionada à Heterocharacinae. Acestrorhynchidae foi recuperada na base do clado Roestinae/Heterocharacinae, o que condiz com outras filogenias moleculares e difere das filogenias morfológicas. As relações entre as espécies de Roestes e de Hydrolycus também foram recuperadas. As outras relações encontradas condizem com dados recentes da literatura, fortalecendo o conhecimento sobre a ictiofauna de água doce. A espécie Rhaphiodon vulpinus se destaca entre os Cynodontíneos por apresentar uma ampla distribuição geográfica, sendo encontrada em sistemas atualmente separados como as bacias do Paraná e do Amazonas. Por isso, uma análise da variabilidade e da estrutura populacional desta espécie foi realizada com o intuito de ampliar o conhecimento sobre a influência do passado geológico na distribuição da ictiofauna Neotropical, além de fornecer áreas prioritárias de conservação. Inicialmente, o estudo foi realizado com sequencias do gene da ATPase do mtDNA, e os resultados evidenciaram a existência de três grupos genéticos que foram considerados UES distintas (Bacia do Paraná, oeste da Amazônia e leste da Amazônia). Entretanto, a hipótese de contato secundário com mistura de fauna entre a Bacia do Paraná e o Rio Madeira foi postulada para explicar os resultados. Para testar tal hipótese, foi desenvolvida a biblioteca de microssatélites de R. vulpinus, já que este marcador é mais sensível para a detecção de estruturas populacionais. Foram obtidos 11 locos polimórficos, sendo que sete funcionaram em outros gêneros de Cynodontinae. A análise com microssatélites confirmou a conexão entre o oeste da Amazônia e a Bacia do Paraná, provavelmente devido à captura de riachos para a sub bacia do Rio Madeira. Uma grande diferença entre as análise é a subdivisão UES do leste da Amazônia (rios Araguaia e Xingu) devido à grande diferenciação do alto Xingu. Além disso, esta localidade parece ter contribuído no pool gênico do Araguaia após a estruturação, o que pode indicar outro evento de captura de cabeceiras. Estes eventos, no entanto, seriam relativamente recentes na história evolutiva de R. vulpinus, assim como é a barreira estabelecida pela Cachoeira do Teotônio no Rio Madeira, já que a mesma não foi detectada como barreira na análise do mtDNA. A história demográfica de Rhaphiodon vulpinus parece estar intimamente relacionada a eventos geológicos, já que a estruturação encontrada reflete o conhecimento atual sobre a formação das bacias hidrográficas. Além disso, R. vulpinus parece ser uma espécie bastante antiga, especialmente pela estruturação encontrada dentro da Bacia Amazônica. Por isso, tanto a diminuição do tamanho populacional (detectada no leste da Amazônia pelos microssatélites) quanto a expansão populacional (detectada no oeste da Amazônia pela ATPase) podem ter acontecido nesta espécie. R. vulpinus parece ser uma espécie com grande capacidade migratória, já que apresenta isolamento pela distância e estruturação relacionada à barreiras históricas. Em relação aos padrões de diversidade, ambos os marcadores evidenciaram uma diversidade moderadamente alta na Amazônia (com os maiores valores no oeste) e uma baixa diversidade na Bacia do Paraná, provavelmente devido à colonização da bacia aliado às alterações ambientais ocorridas na região. O conjunto de dados obtidos contribuirá para o esclarecimento das relações filogenéticas em Characiformes e também para a compreensão de aspectos da história evolutiva e da dinâmica de populações de R. vulpinus, uma espécie que parece ser mais antiga do que a formação atual dos sistemas de drenagem. / Cynodontidae (sensu Lucena & Menezes, 1998) is a Characiform family with 14 valid species which are divided in two subfamilies (Cynodontinae and Roestinae). Cynodontinae species were always classified in the same group meanwhile Roestinae has already been classified together with Characidae. In order to test the monophylestism of Cynodontidae, we have conducted a Maximum Parsimony Analysis using the algorithm TBR in 42 taxa, which represent 12 Characiform families. The analysis was performed with three nuclear regions and three mitochondrial genes; the first intron of RPS7 was removed from the final analysis due to problems related to alignment homology. The consensus tree obtained with 9842 steps (IC = 0,351 and IR = 0,358) does not support the monophylestism of Cynodontidae, which appears in a clade composed by Serrasalmidae, Prochilodontidae, Hemiodontidae, and Parodontidae; Roestinae appears within Characidae, close-related to Heterocharacinae. Acestrorhynchidae was recovered at the base of Roestinae/Heterocharacinae clade, which is in agreement with other molecular phylogenies and in disagreement with the morphological ones. The relationship between Roestes and Hydrolycus species was also recovered. Other relationships obtained are in agreement with recent data described elsewhere, which reinforces the knowledge on the freshwater fish fauna. The species Rhaphiodon vulpinus stands out from other Cynodontinae species due to its wide geographic distribution, occurring in basins that are currently separated as is the case of Paraná and Amazon. Within this context, population variability and structure analyses were conducted with the aim of expanding the knowledge related to the influence of geological history on the distribution of Neotropical fish fauna as well as to provide priority areas for conservation means. Initially, the study was carried out with ATPase gene sequences from mtDNA and the results evidenced the existence of three genetic groups which were considered as different ESUs (Evolutionary Significant Units; Paraná, Western Amazon, and Eastern Amazon). However, a secondary contact hypothesis with fauna mixture between Paraná and Madeira river basins was formulated in order to explain the results. In order to test such hypothesis, a microsatellite library was developed for R. vulpinus, once this marker is more sensitive for the detection of population structure. 11 polymorphic loci were obtained and among them, seven showed to be useful in other Cynodontinae genus. The microsatellite analysis confirmed the connection between the Western Amazon and the Paraná basin, which probably occurred as a result of headwaters capture by the Madeira river sub-basin. The major difference between the analyses comprises the ESU sub-division in Easter Amazon (Araguaia and Xingu rivers) due to the high differentiation of Upper Xingu. Moreover, this locality may have contributed on the Araguaia gene pool after its structuration process, which may be an indicative of another headwaters capture event. However, those events would be relatively recent in the R. vulpinus evolutive history, likewise the barrier formed by Teotônio Falls in Madeira river, once it was not detected as a barrier by mtDNA analysis. The demographic history of R. vulpinus seems to be tightly related to geologic events, once the structure obtained reflects the current knowledge on the formation of hydrographic basins. Furthermore, R. vulpinus seems to be a very old species, mainly due to the structure found within the Amazon basin. Thus, both the reduction of population size (detected in Eastern Amazon by microsatellite) and the population expansion (detected in Western Amazon by ATPase) may have occurred in this species. R. vulpinus seems to be a species with a high migration capacity, once it presents isolation by the distance and structuration related to historical barriers. Regarding the diversity patterns, both markers evidenced a slightly high diversity in the Amazon (high values on Western) and low diversity in the Paraná basin, possibly due to the occupation of the basin modulated by environmental changes that occurred in the region. Those data will contribute to resolve the phylogenetic relationships in Characiform and for the understanding of some aspects of the evolutive history and population dynamics of R. vulpinus, a species that seems to be older than the current drainage systems.

Visando contribuir para a compreensão dos processos que originaram e mantiveram a biodiversidade na Mata Atlântica (MA), o presente estudo teve como objetivo inferir a história evolutiva - bem como os processos biogeográficos envolvidos - de duas espécies de aves da MA, P. atra (120 indivíduols) e P. leucoptera (434 indivíduos). Realizamos uma análise filogeográfica envolvendo marcadores com diferentes tipos de herança: materna (gene mitocondrial da subunidade II da NADH desidrogenase), biparental (três marcadores anônimos VIDY, GK439 e 55J7) e ligada ao cromossomo Z (íntron 18 da helicase com cromo-domínio de ligação ao DNA, íntron 15 da helicase Brahma dependente de ATP e íntron 1 da fosfolipase A2). Duas questões principais foram abordadas: (i) Qual hipótese de diversificação é mais congruente com os resultados do presente estudo? (ii) Os resultados baseados em marcadores com diferentes tipos de herança são congruentes? Para responder a primeira questão, algumas das previsões de cada hipótese foram testadas. Foi encontrada evidência de que as mudanças climáticas no final do Pleistoceno parecem ter sido importantes na estrutura filogeográfica de Pyriglena atra e Pyriglena leucoptera na MA. Os resultados encontrados foram congruentes com a Hipótese dos Isolados de Montanha, mas aparentemente refutam outras hipóteses, tais como: a Hipótese dos Refúgios do Pleistoceno no contexto do modelo paleoclimático proposto por Carnaval & Moritz (2008), Hipótese de estruturas fisiográficas (rios ou montanhas) como barreiras, e a Hipótese de Gradientes Ecológicos. Além disso, os rios Doce e Contas parecem ser barreiras secundárias interrompendo parcialmente o gênico. Finalmente, os marcadores revelaram diferentes níveis de estrutura geográfica e sinais nem sempre totalmente congruentes. Assim, embora os marcadores mitocondriais sejam muito informativos em reconstruções filogeográficas, é importante usar vários tipos de marcadores para recuperar de forma mais completa a história dos processos evolutivos dos organismos e os possíveis fatores que geraram essa biodiversidade / To contribute to the understanding of the processes that originated and maintained biodiversity in the Atlantic Forest (AF), the present study aimed to infer the evolutionary history - as well as the biogeographic processes involved - of two AF bird species, P. atra (120 individuals) and P. leucoptera (434 individuals). We performed a phylogeographic analysis based on markers with different types of inheritance: maternal (mitochondrial gene of the NADH dehydrogenase subunit II), biparental (three annonymous markers: VIDY, GK439, 55J7) and Z-linked (intron 18 of the chromo-DNA-binding domain helicase, intron 15 of the ATP-dependent Brahma helicase and intron 1 of the Phospholipase A2). Two major questions were addressed: (i) Which diversification hypothesis best fits the results of the present study? (ii) Are the results based on markers with different types of inheritance congruent? In order to answer the first question, some of the predictions of each hypothesis were tested. We found evidence that climate changes in the late Pleistocene seem to have been important for shaping the phylogeographic structure of Pyriglena atra and Pyriglena leucoptera in the AF. The results are congruent with the Montane Isolation Hypothesis but apparently refute other hypotheses, such as: The Pleistocene Refuge Hypothesis in the context of the paleoclimatic model proposed by Carnaval & Moritz (2008), Hypothesis of physiographic structures (i.e. rivers or mountains) as barriers, and the Ecological Gradients Hypothesis. Additionaly, the Doce and Contas rivers seem to act as secondary barriers partially disrupting gene flow. Finally, the markers revealed varying levels of geographical structure that were not totally congruent. Thus, although mitochondrial markers are very informative for phylogeographic reconstructions, it is important to use several types of markers in order to recover the history of the evolutionary processes of organisms and the possible factors that generate this biodiversity

Na presente Tese foram usados métodos de inferência filogenética e de filogeografia buscando identificar os processos históricos de diversificação do gênero Conopophaga na América do Sul, em especial na Mata Atlântica. O monofiletismo do gênero e a estrutura filogeográfica das espécies distribuídas no sudeste da Mata Atlântica (Conopophaga lineata e C. melanops), foram testados utilizando seqüências de DNA mitocondrial. Para a filogenia foram utilizadas duas matrizes, sendo uma de 2270 pb (941 pb da subunidade 2 da NADH desidrogenase (ND2), 343 pb do ND3 e 986 pb do citocromo b) e outra de 878 pb (461 pb do ND2 e 417 pb do cit b). Nas análises de filogeografia de C. lineata e C. melanops foram utilizadas seqüências da região controladora de 472 pb e 439 pb, respectivamente. Os resultados demonstraram que o gênero Conopophaga é monofilético e que provavelmente uma rápida radiação ocorreu nesse gênero depois da especiação de C. melanogaster e de C. melanops. Dessa radiação, foram recuperados dois grupos: (1) Um grupo que se distribui somente na Amazônia e mantém a característica ancestral da coloração negra da mandíbula e (2) um grupo distribuindo-se na Amazônia e também na Mata Atlântica e que possui a mandíbula branca. Nesse último grupo, C. l. cearae não se agrupou com C. lineata, demonstrando que essa espécie não é uma espécie monofilética. A relação entre as espécies que apresentam a mandíbula branca parece indicar a ocorrência de uma conexão entre o leste da Amazônia e a Mata Atlântica no passado. O estudo filogeográfico de C. lineata revelou a existência de possíveis eventos de vicariância: (1) na região compreendida pelo Vale do Rio Paraíba do Sul e (2) à oeste de São Paulo e Paraná, separando as populações mais ao sul. Apesar de as inferências filogenéticas realizadas em C. melanops e C. lineata não serem totalmente concordantes, é possível que exista um padrão de vicariância nessa região. Concluindo, a ocorrência desses eventos vicariantes, tais como eventos geológicos e ciclos de alterações climáticas tenham influenciado na diversificação da família Conopophagidae. Além disso, eventos de dispersão e/ou seleção também podem auxiliar no entendimento da história biogeográfica do grupo, bem como de outros grupos na América do Sul. / In order to identify the historical processes of diversification of the gender textitConopophaga in South America, especially in the Atlantic forest, methods of phylogenetic and phylogeography inference were used in the present thesis. The genus phylogeny and the phylogeographic structure of two species ( textitConopophaga lineata and textitC. melanops) which occurs in the Southeast of the Atlantic forest were tested using sequences of mithocondrial DNA. Two matrixes were used to perform the phylogenetic analyses. The first one comprising 2270 bp (941 bp of ND2, 343 bp of ND3 and 986 bp of cytochrome b) and the second one comprising of 878 bp (461 bp of ND2 and 417 bp of cytochrome b). The phylogeography analyses of textitC. lineata and textitC. melanops were done using sequences from the control region consisting of 472 bp and 439 bp, respectively. The results demonstrated that the genus textitConopophaga is monophyletic and probably after textitC. melanogaster and textitC. melanops speciation, a rapid diversification had occurred in this genus. Following this event two distinct groups were recovered: (1) a group distributed in Amazonian, which maintains the ancestral characteristic of black jaw and (2) a group possessing white jaw occurring in the Amazonian and also in the Atlantic forest. In the last group, the subspecies C. l. cearae did not grouped with textitC. lineata demonstrating that this species is not monophyletic. Moreover, the distribution pattern of species presenting white jaw indicates a plausible a connection between the east of the Amazonian and the Atlantic forest in the past. The phylogeographic study of textitC. lineata revealed the existence of possible vicariant events: (1) in the area of Vale do Rio Paraíba do Sul and (2) in the west of São Paulo and Paraná, separating the southern south populations. Although the phylogeographic structure observed in textitC. melanops and in textitC. lineata are not in total agreement, the occurrence of vicariant events still remains as a possible explanation for the phylogeographic patterns in this region. Finally, the occurrence of these vicariant events like, geological events and climatic oscilations, may have influenced the diversification of the family Conopophagidae. Moreover, dispersion events and/or selection should also be considered for the understanding of biogeographic history of this group and also other ones in South America.

O gênero Oligoryzomys é um dos mais complexos e diversos da subfamília Sigmodontinae e da tribo Oryzomyini. Dentre os mamíferos destaca-se por apresentar notável incongruência taxonômica, já que o número de espécies não é consenso entre os autores. Esta tese tem a finalidade de esclarecer alguns pontos conflitantes da taxonomia deste grupo e fornecer mapas atualizados da distribuição das espécies do gênero. Espero que os dados coligidos e analisados aqui possam contribuir significativamente para qualquer tentativa de revisão sistemática do Gênero no futuro. Para tanto, foram feitas comparações utilizando dados cariotípicos (2n e NFa), morfológicos e sequências do gene mitocondrial citocromo b e do íntron 7 do beta fibrinogênio. O presente trabalho está estruturado em 5 capítulos. O primeiro capítulo apresenta uma breve história da diversificação dos sigmodontíneos, uma introdução sobre o nível atual de conhecimento do gênero Oligoryzomys e por fim traz uma explanação dos aspectos filosóficos envolvidos no reconhecimento de espécie. O segundo capítulo trata dos métodos utilizados na aquisição dos espécimes em trabalhos de campo, na obtenção do material para análises citogenéticas, da extração de DNA e subsequente sequenciamento do gene mitocondrial citocromo b e do íntron 7 do beta fibrinogênio. Descreve ainda as estimativas de relacionamento filogenético, a metodologia de análise da estrutura e história populacional e como foram exploradas a variação morfológica e delimitação taxonômica. O terceiro capítulo discorre sobre aspectos citogenéticos e moleculares das espécies da Bolívia, cuja amostra foi gentilmente cedida pelo Prof. Dr. Jorge Salazar-Bravo no intuito de preencher com tais informações a lacuna existente nesta fauna. As lâminas deste material boliviano foram analisadas por mim para obter os dados brutos de cariótipo assim como todo o sequenciamento do material e posterior análises. Dentro dessa abordagem foram documentadas a variação cariotípica de algumas populações e discutidas questões taxonômicas visando responder quem são e onde estão as espécies reconhecidas para a Bolívia. O quarto capítulo visa reconhecer as espécies válidas de Oligoryzomys e estabelecer as relações filogenéticas entre elas. Neste capítulo foram testadas as hipóteses dos grupos de espécies de acordo com as propostas de Carleton e Musser (1989) e Miranda et al. (2009). A partir dos resultados obtidos foram realizadas comparações entre as espécies dos grupos, as quais, permitiram fornecer dados qualitativos capazes de auxiliar na diagnose das espécies e da sua distribuição. O quinto capítulo apresenta hipóteses dos processos e eventos envolvidos na diversificação do gênero na região Neotropical e encerra a monografia apresentando uma cronologia de diversificação das espécies estudadas. / O gênero Oligoryzomys é um dos mais complexos e diversos da subfamília Sigmodontinae e da tribo Oryzomyini. Dentre os mamíferos destaca-se por apresentar notável incongruência taxonômica, já que o número de espécies não é consenso entre os autores. Esta tese tem a finalidade de esclarecer alguns pontos conflitantes da taxonomia deste grupo e fornecer mapas atualizados da distribuição das espécies do gênero. Espero que os dados coligidos e analisados aqui possam contribuir significativamente para qualquer tentativa de revisão sistemática do Gênero no futuro. Para tanto, foram feitas comparações utilizando dados cariotípicos (2n e NFa), morfológicos e sequências do gene mitocondrial citocromo b e do íntron 7 do beta fibrinogênio. O presente trabalho está estruturado em 5 capítulos. O primeiro capítulo apresenta uma breve história da diversificação dos sigmodontíneos, uma introdução sobre o nível atual de conhecimento do gênero Oligoryzomys e por fim traz uma explanação dos aspectos filosóficos envolvidos no reconhecimento de espécie. O segundo capítulo trata dos métodos utilizados na aquisição dos espécimes em trabalhos de campo, na obtenção do material para análises citogenéticas, da extração de DNA e subsequente sequenciamento do gene mitocondrial citocromo b e do íntron 7 do beta fibrinogênio. Descreve ainda as estimativas de relacionamento filogenético, a metodologia de análise da estrutura e história populacional e como foram exploradas a variação morfológica e delimitação taxonômica. O terceiro capítulo discorre sobre aspectos citogenéticos e moleculares das espécies da Bolívia, cuja amostra foi gentilmente cedida pelo Prof. Dr. Jorge Salazar-Bravo no intuito de preencher com tais informações a lacuna existente nesta fauna. As lâminas deste material boliviano foram analisadas por mim para obter os dados brutos de cariótipo assim como todo o sequenciamento do material e posterior análises. Dentro dessa abordagem foram documentadas a variação cariotípica de algumas populações e discutidas questões taxonômicas visando responder quem são e onde estão as espécies reconhecidas para a Bolívia. O quarto capítulo visa reconhecer as espécies válidas de Oligoryzomys e estabelecer as relações filogenéticas entre elas. Neste capítulo foram testadas as hipóteses dos grupos de espécies de acordo com as propostas de Carleton e Musser (1989) e Miranda et al. (2009). A partir dos resultados obtidos foram realizadas comparações entre as espécies dos grupos, as quais, permitiram fornecer dados qualitativos capazes de auxiliar na diagnose das espécies e da sua distribuição. O quinto capítulo apresenta hipóteses dos processos e eventos envolvidos na diversificação do gênero na região Neotropical e encerra a monografia apresentando uma cronologia de diversificação das espécies estudadas.

Freshwater sculpins (Cottus) are common throughout temperate regions of the Northern Hemisphere. Their broad distribution in the Western North America makes them a good model for understanding phylogeographic relationships among western fishes. Within much of the interior west three lineages, C. bairdii, C. confusus, and the C. beldingii complex, are most prevalent. The distribution of these three overlap in the Snake River Basin. All occur below Shoshone Falls on the Snake River. However, only two currently reside in the Upper Snake River above the falls. An exception are the Lost River streams of central Idaho. While these streams are technically part of the Upper Snake River Basin, they do not directly connect with the Snake River. Preliminary studies with a single mitochondrial DNA (mtDNA) gene suggested multiple pathways for Cottus introduction into the Lost River stream complex. Here, three mitochondrial and five nuclear genes were examined to investigate the phylogenetic relationships of these three lineages. Sequences were obtained from 71 different populations in the Lost River streams and surrounding basins. Maximum Likelihood (ML) phylogenies were constructed using these data. Our data indicate that relationships among populations within these species are complex and that no single invasion into the Lost River streams and surrounding regions can account for the phylogenetic signals detected. Instead, it appears that multiple invasions in an evolving landscape played a significant role in the modern distribution of species in this region.

Understanding the history of diversification in the North American deserts has long been a goal of biogeographers and evolutionary biologists. While it seems that a consensus is forming regarding the patterns of diversification in the Nearctic deserts in vertebrate taxa, little work has been done exploring the historical biogeography of widespread invertebrate taxa. Before a robust model of geobiotic change in the North American deserts can be proposed, it needs to be determined if the same historical events affected vertebrate and invertebrate taxa in the same way. I explored the phylogeographic patterns in four groups of widespread nocturnal velvet ants using two rDNA loci, the internal transcribed spacer regions 1 and 2 (ITS1 and ITS2). I used Bayesian phylogenetic analyses and haplotype network analyses to determine if a consistent geographic pattern exists among species and populations within each group. I also used molecular dating techniques to estimate divergence dates for each of the major phylogenetic clades. These analyses indicate that the species-level divergences in some groups occurred in the Neogene, and likely were driven by mountain building during Miocene-Pliocene times (~5 Ma) similar to the divergences in many vertebrate taxa, while species-level divergence in other groups occurred during the Pleistocene (1.8-0.1 Ma) and were likely driven by climatic oscillations and range contractions and expansion. Several recent studies have suggested that Neogene mountain-building events were more important to the development of a diverse desert-adapted biota. My research suggests, however, that both Neogene events and Pleistocene climatic changes were influential in the development of a species-rich nocturnal velvet ant fauna.

Climatic and geographic events such as glaciations, island formation, river formation, and urbanization strongly affect habitat specialist species. By contrast, it is traditionally assumed that these events have little effect on habitat generalists but few studies have tested this assumption. In this study I sought to identify the effects of historic and contemporary biogeographic events on the genetic structure of a habitat generalist, the cotton mouse (Peromyscus gossypinus). This species is distributed throughout the southeastern United States, a region that has experienced dramatic geographic changes associated with both historic Pleistocene glacial cycles, as well as contemporary anthropogenic forces. In analyzing the genetic structuring in this species I took a telescopic approach, beginning with the patterns of variation throughout the species range from a phylogenetic standpoint. Using mitochondrial sequence data I identified three reciprocally monophyletic clades of the cotton mouse, a southeastern, northeaster, and western clade. Among these clades I identified eight distinct subspecies, four of which had previously not been identified using morphological characters. Of the four previously identified subspecies, this study resulted in a restructuring of the range of all except the Key Largo cotton mouse, which is restricted to northern Key Largo Florida. Secondly, I employed phylogeographic methods to examine the genetic patterns of the cotton mouse in a geographic context. Phylogeographic breaks in the cotton mouse are largely consistent with those observed in other taxa distributed throughout the southeastern United States. Geographic structuring in this species shows deep patterns associated with glacial maxima and minima of the Pleistocene period. Many of these patterns are maintained by contemporary geographic barriers to gene flow. Thirdly, I identified geographic structuring of genetic variation at a regional and local level. This structuring is partially due to the cotton mouse’s limited dispersal ability but is strengthened and reinforced by naturally occurring contemporary barriers to gene flow and contemporary anthropogenic forces which serve to limit dispersal in this species. Finally, I determined that urbanization has a dramatic negative effect on gene flow and genetic variation in this species on a local scale. Over a twenty year period populations in urban areas experienced a marked decrease in genetic variation while populations in non-urban areas experienced an increase in variation. During this time period, gene flow was effectively cut off among populations that had previously been panmictic. This study demonstrates that small mammal habitat generalists can be affected by both historic and contemporary climatic and geographic events at multiple geographic scales. These effects range from large scale geographic structuring throughout the species’ range to fine scale structuring associated with contemporary anthropogenic forces.

Η γεωμορφολογία της Ελλάδας και η ποικιλία των βιοτόπων της την καθιστούν ιδιαίτερη περιοχή μελέτης ως προς την ερπετοπανίδα της. Σήμερα, εκτιμάται ότι στην Ελλάδα υπάρχουν 64 είδη ερπετών, με τα εννέα από αυτά να είναι ενδημικά. Το κεφαλονίτικο κονάκι Anguis cephallonica πρόκειται για μια περίπτωση άποδης σαύρας με κρυπτική οικολογία, που εντοπίζεται στην Πελοπόννησο και τα νησιά Κεφαλονιά, Ζάκυνθος και Ιθάκη του Ιονίου Πελάγους. Έως πρόσφατα, αναγνωρίζονταν δύο είδη στο γένος Anguis (Reptilla: Anguidae): το A. cephallonica Werner, 1894 και το A. fragilis Linnaeus, 1758 με το δεύτερο να θεωρείται ότι εξαπλώνεται σε ολόκληρη τη δυτική περιοχή της Παλαιαρκτικής. Σήμερα, οι εξελικτικές γραμμές του γένους έχουν μερικώς αποκαλυφθεί. Εκτός από τα δύο προαναφερόμενα, θεωρούνται αποδεκτά τα είδη A. colchica (Nordmann 1840) και A. graeca Bedriaga, 1881, ενώ πρόσφατα προτάθηκε και η ύπαρξη ενός νέου είδους, του A. veronensis Pollini, 1818. Από αυτά, εκτός του A. cephallonica, εντοπίζονται στην Ελλάδα το ευρωπαϊκό κονάκι A. fragilis, που απαντάται στη Βόρεια Ελλάδα και το ελληνικό κονάκι A. graeca, που απαντάται στην ηπειρωτική Ελλάδα δυτικά της κεντρικής Μακεδονίας, στην Εύβοια, στη Βόρεια Πελοπόννησο και στα νησιά Κέρκυρα και Λευκάδα. Στην παρούσα εργασία, σκοπός είναι η διερεύνηση των φυλογενετικών σχέσεων και η ταξινόμηση των γενεαλογικών γραμμών τόσο εντός του είδους A. cephallonica, όσο και σε σχέση με τα συγγενικά με αυτό είδη- ιδιαίτερα με το μερικώς συμπάτριο A. graeca, έτσι ώστε να προσεγγισθούν βασικά ερωτήματα που αφορούν στις διεργασίες που καθόρισαν ή επηρέασαν την εξελικτική και βιογεωγραφική ιστορία του είδους. Για τον σκοπό αυτό χρησιμοποιήθηκε ένα εκτεταμένο δίκτυο πληθυσμών από τοποθεσίες της Πελοποννήσου, της Κεφαλονιάς και της δυτικής ηπειρωτικής Ελλάδας. Η πειραματική πορεία που ακολουθήθηκε αρχίζει με την εξαγωγή ολικού γονιδιωματικού DNA από κάθε χρησιμοποιούμενο δείγμα και συνεχίζεται με την αλυσιδωτή αντίδραση πολυμεράσης για τον μοριακό δείκτη που χρησιμοποιήθηκε, τον καθαρισμό του προϊόντος της PCR και την αλληλούχηση. Ο μοριακός δείκτης που επιλέχθηκε για την προσέγγιση των φυλογενετικών σχέσεων και τη διερεύνηση των γενεαλογικών γραμμών τόσο εντός του A. cephallonica, όσο και μεταξύ αυτού και των συγγενών με αυτό ειδών, είναι το τμήμα του μιτοχονδριακού DNA που περιέχει το κωδικό γονίδιο ND2 και πέντε αλληλουχίες tRNA και επιλέχθηκε κυρίως γιατί έχει χρησιμοποιηθεί ευρύτατα και με επιτυχία σε άλλες φυλογενετικές αναλύσεις ερπετών και αμφιβίων, ενώ φέρει όλα τα πλεονεκτήματα του μιτοχονδριακού DNA. Μετά το πέρας της πειραματικής διαδικασίας είχαν προσδιορισθεί 22 νέες αλληλουχίες για τον μοριακό δείκτη, που αντιστοιχούν σε 14 απλοτύπους. Πιο συγκεκριμένα, για το A. cephallonica προσδιορίσθηκαν 17 αλληλουχίες που αντιστοιχούν σε εννέα απλοτύπους και για το είδος A. graeca προσδιορίσθηκαν πέντε αλληλουχίες που αντιστοιχούν σε πέντε διαφορετικούς απλοτύπους. Στην ανάλυση συμπεριελήφθησαν ακόμα 19 αλληλουχίες, που ανακτήθηκαν από τη βάση δεδομένων του Εθνικού Κέντρου Βιοτεχνολογικής Πληροφορίας των ΗΠΑ NCBI (National Center for Biotechnology Information), έτσι ώστε συνολικά, για το είδος A. cephallonica στην ανάλυση να έχουν συμπεριληφθεί 19 αλληλουχίες που ισοδυναμούν με εννέα απλοτύπους, για το είδος A. graeca 19 αλληλουχίες που αντιστοιχούν σε 16 διαφορετικούς απλοτύπους και για το είδος A. fragilis δύο αλληλουχίες που αντιστοιχούν σε δύο διαφορετικούς απλοτύπους. Μετά την ανάγνωση των αλληλουχιών σειρά είχε η εκτίμηση των γενετικών αποστάσεων με βάση τo μοντέλο Tamura–Nei και η φυλογενετική ανάλυση. Εφαρμόσθηκαν τρεις διαφορετικές μέθοδοι αναλύσεων: η μέθοδος Σύνδεσης Γειτόνων, Μέγιστης Πιθανοφάνειας και Μπεϋεσιανής Συμπερασματολογίας. Ως εξωομάδα, χρησιμοποιήθηκε σε όλες τις αναλύσεις ένας απλότυπος Pseudopus apodus. Η χρήση του κρίθηκε κατάλληλη εφόσον τα γένη Pseudopus και Anguis είναι αδελφά taxa, με το είδος Pseudopus apodus να εντοπίζεται στην Ελλάδα. Με βάση τα αποτελέσματα της παρούσας εργασίας, όσον αφορά τόσο στις γενετικές αποστάσεις όσο και στις φυλογενετικές αναλύσεις, τα διαθέσιμα δεδομένα για τον μοριακό δείκτη που επιλέχθηκε κατατάχθηκαν ευκρινώς σε τρία διαφορετικά taxa που αντιστοιχούν στα είδη A. cephallonica, A. graeca και A. fragilis. Στην τοπολογία των φυλογενετικών δέντρων διακρίνονται τρεις κλάδοι, με απόλυτη στατιστική υποστήριξη, που αντιστοιχούν σε κάθε ένα από τα τρία προαναφερόμενα είδη Anguis. Η τοπολογία των δέντρων δείχνει ότι το ελληνικό κονάκι A. graeca φαίνεται να ακολουθεί ένα γενικό γεωγραφικό πρότυπο με κατεύθυνση από τον βορρά προς τον νότο. Στην ανάλυση με τη μέθοδο της μέγιστης πιθανοφάνειας, το ελληνικό κονάκι A. graeca ομαδοποιείται εγγύτερα στο κεφαλλονίτικο κονάκι A. cephallonica, από ό, τι στο A. fragilis, ωστόσο με πολύ χαμηλή στατιστική υποστήριξη. Από άποψη γενετικής απόστασης, βρίσκεται εγγύτερα στο είδος A. fragilis, κάτι που συμφωνεί και με το γεωγραφικό πρότυπο εξέλιξης του κάθε είδους. Τα φυλογενετικά δέντρα συμφωνούν για το είδος A. cephallonica, όσον αφορά στη σχέση των κύριων κλάδων με τα γεωγραφικά δεδομένα. Το κεφαλλονίτικο κονάκι A. cephallonica φαίνεται να ακολουθεί ένα σαφές γενικό γεωγραφικό πρότυπο εξέλιξης στην Πελοπόννησο και το Ιόνιο, από τα νότια προς τα βόρεια ή τα βορειοδυτικά. Η ανάλυση με τις μεθόδους μπεϋεσιανής συμπερασματολογίας, μέγιστης πιθανοφάνειας και σύνδεσης γειτόνων συμφωνούν μεταξύ τους και αποκαλύπτουν διακριτές και γεωγραφικά εντοπισμένες επιμέρους γενεαλογικές γραμμές. Πλέον, μπορούμε να υποστηρίξουμε ότι το είδος A. fragilis, που θεωρείτο ότι καλύπτει την μεγαλύτερη περιοχή της ηπειρωτικής Ελλάδας, έχει το νότιο όριό του στην Βόρεια Ελλάδα. Επίσης, το είδος A. colchica δεν θεωρείται πλέον ότι εξαπλώνεται ως τα νότια Βαλκάνια. Η μορφή που συναντούμε νοτιότερα στην ηπειρωτική Ελλάδα, μέχρι και την Πελοπόννησο, χωρίς ωστόσο το όριο της εξάπλωσής της στην Πελοπόννησο να μπορεί να ορισθεί με βεβαιότητα, γνωρίζουμε, πλέον, ότι είναι διαφορετικό είδος, το ελληνικό κονάκι A. graeca. Τα διαφορετικά εξελικτικά πρότυπα, οι γενετικές αποστάσεις και τοπολογίες των ειδών A. graeca και A. cephallonica αποκλείουν μία κοινή γενεαλογική γραμμή στον ελλαδικό χώρο, που μπορεί να οδήγησε στην σημερινή εξάπλωση του γένους σε αυτόν. Σε συνδυασμό με το στοιχείο της μικρότερης γενετικής απόστασης που συνδέει το A. graeca με το A. fragilis, φαίνεται να επαληθεύεται η υπόθεση πως το κεφαλλονίτικο κονάκι ανήκει σε διαφορετικό εξελικτικό κλάδο από αυτόν που ανήκουν τα δύο άλλα είδη. Οι δύο εξελικτικές γραμμές φαίνεται ότι συναντήθηκαν γεωγραφικά, με αποτέλεσμα τη μερικώς συμπάτρια εξάπλωσή τους στη Βόρεια Πελοπόννησο. Η παρούσα εργασία επιχειρεί να διαλευκάνει τμήμα της εξελικτικής διαφοροποίησης εντός του γένους Anguis. Μπορεί να συμβάλει σε μελλοντικές προσπάθειες περαιτέρω διερεύνησής της, όπως και σε μελέτες που θα ασχοληθούν με τη διαχείριση των πληθυσμών του. / The geomorphology and the vast diversity of biotopes make Greece a special region as far as the reptile fauna is concerned. It is estimated that Greece is the home of 64 reptile species with nine of them being characterized as endemic. One of them is the slowworm of Cephalonia, Anguis cephallonica, which is a legless lizard of cryptic ecology, found in Peloponnesus and the islands of Cephalonia, Zakynthos and Ithaca of the Ionian Sea. Up until recently, only two species were recognized among the Anguis genus (Reptilla: Anguidae): A. cephallonica Werner, 1894 and A. fragilis Linnaeus, 1758. A. fragilis dispersal was supposed to cover a wide region of the whole western Palaiarctic. Today, it is believed that the evolutionary lineages of the genus complex has been partially revealed. Apart from the aforementioned species, A. colchica (Nordmann, 1840), A. graeca Bedriaga, 1818 and the recently proposed from the Italian peninsula A. veronensis Pollini, 1818 have also been referred as different species, with A. cephallonica, A. graeca and A. fragilis occurring in the Greek region. The European slowworm A. fragilis is supposed to be found in Northern and North-Eastern Greece, while the dispersal of the Greek slowworm, A. graeca corresponds to western continental Greece, towards Euboia and Northern Peloponnesus and also to the Ionian islands of Corfu and Lefkas. The aim of the present study focuses on the revealing of the phylogenetic relationships and the classification of the genealogical lineages both within A. cephallonica and also between A. cephallonica and the partially sympatric A. graeca, so that the basic questions, which relate to the processes which affected and determined the evolutionary and biogeographic history of the species, are approached. For this purpose, an extensive population net was used from locations from Peloponnesus, Cephalonia and western continental Greece. The experimental procedure followed begins with the whole genomic DNA extraction for each sample included in this study. The procedure continues with PCR amplification for the mitochondrial molecular marker selected, clean-up of the PCR product and sequencing. The molecular marker selected is a fragment of mitochondrial DNA, which includes ND2 gene and five smaller sequences which are transcripted to tRNAs. This particular marker was selected, mostly because of the successful application of which in former phylogenetic studies of reptiles and amphibians, while it also carries all the advantages that refer to mitochondrial DNA. After the laboratorian procedure was completed, 22 new sequences had been determined, corresponding to 14 different haplotypes. 17 sequences corresponding to nine haplotypes referring to A. cephallonica and five sequences each corresponding to a different haplotype referring to A. graeca. 19 more sequences retrieved from NCBI were included in the phylogenetic analysis, so as for A. cephallonica to sum up to nine haplotypes and for A. graeca to 16. Also, two sequences corresponding to two haplotypes were included for A. fragilis. After the sequences data set editing, the estimation of the genetic distences among them, using the Tamura Nei model, and also the phylogenetic analysis could proceed. Three different methods were used for the cladograms to be built: Neighbour Joining, Maximum likelihood and Bayesian Inference. A Pseudopus apodus haplotype was used as an outgroup for the genetic distances estimation and the phylogenetic analyses, as this species is found in Greece with the Pseudopus genus being quite relative to genus Anguis. The haplotype trees built, both based on genetic distances estimation and also on phylogenetic analysis, all agreed on a three clade motif, each corresponding to one of the three Anguis species included. The phylogenetic trees topology discriminates three clades each corresponding to one of the three Anguis species, with absolute statistical support. All trees topology shows that A. graeca follows a genetical degradation among a North to South axon. In ML analysis, A. graeca is more closely grouped with A. cephallonica rather than A. fragilis; however, the statistical support is extremely low while this doesn’t agree both with the genetic distance estimations and also with the geographical pattern of each species. Phylogenetic trees agree as far as the internal A. cephallonica clades are concerned, in accordance with geographical correspondence. A. cephallonica seems to follow a clear general geographical evolutionary pattern from the South to the North or Northwest. BI and ML analyses agree, showing discrete and geographically located genealogical lines. We can now support that A. fragilis, which was supposed to cover all continental Greece region has its south European border at Northern Greece. Also, A. colchica dispersal does not reach Southern Balkans, as it was formerly believed. The morphotype which corresponds to findings from continental Greece and north Peloponnesus is identified as A. graeca, the Greek slow worm. Different evolutionary patterns, genetic distances and tree topologies outrule a common genealogical line within the Greek region for the two species. it seems that the hypothesis of closer connection for the Greek and the European slowworm is confirmed, with the slowworm from Cephalonia belonging to a different evolutionary clade. Present study is intended on revealing a part of the evolutionary differentiation within Anguis genus in Greece. it can thus contribute to future attempts of further investigation and also should be taken under consideration for future conservation and protection management decisions.

The spatial scale at which populations are genetically structured is of immense interest for the understanding of a species’ ecology and evolutionary biology. This can have important implications for management of resources as well as predicting responses to future change. Rainbow smelt (Osmerus mordax) is an anadromous species with a relatively short freshwater residence time compared to other species with similar life-history strategies. Therefore, while they offer the opportunity to sample distinct spawning aggregations, they also offer an insight into the relative roles of contemporary and historical factors shaping connectivity among marine populations, an area of great interest, and for which further understanding is required. With the use of both mitochondrial DNA and nuclear microsatellite markers, I explored the historical and contemporary factors influencing population structure in smelt. While previous phylogeographic work on this species has resolved two mtDNA lineages dating back to previous glacial episodes, I document the discovery of a zone of contact between these lineages in Newfoundland. This is in addition to the established contact zone in the St. Lawrence estuary, and results in a longitudinal distribution of the races with one race predominating on opposite ends of the species distribution, while the other race is geographically intermediate. Patterns of nuclear genetic variation largely mirror the phylogeographic signals in Newfoundland and suggest a more recent colonization of the Avalon Peninsula as well as implicating a remnant historical signal of colonization of the west coast of Newfoundland from the mainland. In addition, contrasting patterns of genetic diversity and levels of differentiation were apparent between the mainland and Newfoundland and suggest differing scales of dispersal within this species. While the population structure within Newfoundland is most consistent with dispersal restricted to within bays, larger scale biogeographic regions were identified in the mainland range, suggesting dispersal is more common and widespread. In addition, sampling of different run times (i.e. ‘early’ vs. ‘late’) demonstrated the potential for isolation by time when spawning events are separated by a break in activity. Overall, these results shed light into the possible roles of both historical and contemporary factors shaping the dynamics and connectivity among populations.