This thesis explores the far-reaching impacts of sexual conflict over care on a suite of traits in the penduline tit family (Remizidae), further confirming the intricate relationships between parental care, mating systems and sexual selection. The results reveal the first genetic phylogeny of this family and suggest that uniparental care evolved once in this group. The transition to uniparental care is associated with rapid evolution of male plumage ornaments most likely driven by increased sexual selection. The results also suggest a relationship between male care and the likelihood of paternity on an evolutionary time-scale, as the biparental species exhibit much lower levels of promiscuity than the uniparental European penduline tit. Increased promiscuity was also found to impact sperm morphology in the penduline tits and allies with greater sperm length uniformity in more promiscuous species. This sperm trait was also discovered to co-vary with a sexually selected plumage trait in the European penduline tit suggesting potential interactions between female mate choice and male fertility. An investigation into genetic diversity within the Sylvioidea super-family finds large variation but does not suggest any link between promiscuity and genetic diversity as predicted if promiscuity maintains a higher effective population size in these passerines. The work highlights the interlinked relationships between parental care, mating systems and sexually selected traits, which are increasingly studied in concert. The consequences of sexual conflict over care appear to be far-reaching in the penduline tits, however the degree to which they feedback upon each other and the effect that it has on speciation remains to be seen. The penduline tits further prove their ability to provide valuable insight into the evolution of sexual conflict.

Molecular ecology has already provided profound insights into behaviour, ecology and systematics of organisms improving our understanding of the relationship between genetic variation and biodiversity. The objectives of my PhD were to develop new genetic markers and use these markers to address fundamental issues in evolutionary biology using shorebirds as model organisms. Shorebirds are part of the ancient avian Charadriiformes order and are characterised by extraordinary ecological and behavioural diversity. However, due to the lack of appropriate genetic markers the molecular ecology of many shorebirds has not been investigated previously. Therefore, first, I developed polymorphic microsatellite markers from genomic libraries for a behaviourally diverse shorebird, the Kentish plover Charadrius alexandrinus (Chapter II). Second, using the genomic data-bases I expended this work to develop further markers that cannot only be used in the Kentish plover, but also a large number of other shorebird species (Chapter III). Third, I investigated population differentiation and genetic diversity of Eurasian and American Kentish plover populations using the newly developed microsatellite markers and further mitochondrial markers (Chapter IV). The genetic differences between Eurasian and American populations that are mirrored by phenotypic differences call for a reconsideration of the current taxonomic status of the species; Eurasian and American populations should be recognised as belonging to two separate species. Finally, I asked how genetic diversity influences the fitness of precocial Kentish plover young (Chapter V). I found that survival of chicks until fledging was associated with genetic diversity (measured as heterozygosity) at three of eleven marker loci. Genetic diversity at one marker locus had a positive effect on survival whilst it had negative effects at two loci. The results of my PhD have brought up many new questions and I propose promising lines that need to be explored in the future (Chapter VI).

In this thesis, I study a radiation of brood-parasitic finch species, the indigobirds and whydahs (genus Vidua), that occur across Africa. Host colonisation is tightly linked to speciation in Vidua because of their remarkable capacity to imprint on their hosts, with mating traits and host preferences being influenced by the parasite's early environment. The challenge of explaining why the radiation has diversified to the extent it has therefore simplifies to understanding why only certain potential host species have been successfully colonised. Following on from the introduction (Chapter 1), I begin by critically examining the logic with which mimicry in the natural world can be conceptually organized (Chapter 2). This creates a “mimicry landscape” in which to situate the mimetic adaptations of hosts exhibited by Vidua. The framework can be used to contrast and draw parallels between these and other mimetic adaptations present in the natural world. In Chapter 3, I review the literature on begging call mimicry and development across all avian brood parasite species. I outline the conditions under which we expect begging call mimicry to evolve, and when we expect it to develop primarily through genetic or environmental cues. This provides clear predictions for what we expect to occur in Vidua finches, which are tested in Chapters 4 and 5. In Chapter 4, I quantify the mimicry of host nestlings by Vidua in detail. I provide the first quantitative evidence that Vidua nestlings mimic the begging calls and show for the first time that Vidua are imperfect mimics of their hosts. In Chapter 5, I simulate the colonisation of a new host by transferring Vidua eggs into the nest of a new host species. I monitor Vidua survival in the foreign host environment and test several hypotheses about what explains differences in chick survival. I find that Vidua survive poorly in the new nest environment and that they do not show adaptive plasticity in begging calls or head movements. This poor survival occurs despite there being minimal differences in the diets each host species feeds their young. Finally, in Chapter 6, I carry out a comparative analysis on the evolution of estrildid mouth markings. Estrildid finches are the hosts of Vidua and so provide the landscape of potential ecological niches that Vidua may colonise and adapt to. I demonstrate that the host family shows strong phylogenetic signal in mouth marking traits, and find no evidence that ecological factors such as light environment or predation pressure has shaped estrildid mouth marking evolution. The work in this thesis highlights how difficult successfully colonising new hosts is for Vidua finches. Vidua must mimic hosts in multiple traits (mouth markings, begging calls, head movements) to obtain sufficient amounts of food from host parents. Overall, habitat filters, the complex and diverse begging displays of estrildid nestlings, the discriminatory behaviour of estrildid parents against mismatching chicks and the lack of adaptive plasticity in begging displays by Vidua together help explain why the Vidua radiation consists of only 19 species rather than many more or fewer.

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.

A diversidade de espécies e fenotípica pode variar consideravelmente entre grupos taxonômicos e ao longo do tempo em uma mesma linhagem. O estudo de tais variações tornou-se um dos principais objetivos da biologia evolutiva fornecendo informações importantes a respeito dos possíveis mecanismos que regulam a biodiversidade. Dessa forma, o objetivo geral da presente tese foi investigar os padrões da diversificação de espécies e da morfologia em um grupo cosmopolita de serpentes, a família Viperidae, e os potenciais processos subjacentes. Primeiramente, (1) reconstruímos as relações filogenéticas e estimamos os tempos de divergência entre as linhagens da família Viperidae utilizando uma abordagem Bayesiana. (2) Aplicando um método recentemente desenvolvido (BAMM), exploramos como as taxas de especiação e extinção variaram ao longo da radiação do grupo inferindo os possíveis processos reguladores. Por fim, (3) analisamos se a evolução do tamanho do corpo e as taxas de especiação variam nos diferentes habitats ocupados pelos viperídeos (terrestres vs arborícola). Nesta tese geramos a filogenia molecular de viperídeos mais completa até o momento utilizando sequências para 11 genes mitocondriais e nucleares abrangendo 79% das espécies viventes (264 terminais) e todos com exceção de um gênero. De maneira geral, foi possível obter relações filogenéticas robustas para o grupo com a maioria dos gêneros sendo monofilética. Os tempos de divergência obtidos indicam que os viperídeos começaram a diversificar em meados do Paleoceno tardio/meio do Eoceno inferindo idades um pouco mais tardias que o encontrado em estudos anteriores. Durante a radiação do grupo, um aumento nas taxas de especiação parece ter ocorrido durante a diversificação dos crotalíneos (pit vipers) em decorrência não só da evolução das fossetas loreais mas também como resultado de mudanças geológicas e climáticas na Ásia e da invasão do novo mundo. Após este rápido aumento inicial, as taxas de especiação desaceleraram em direção ao presente. Por fim, os resultados aqui apresentados indicam que apesar dos habitats arborícolas limitarem a evolução morfológica nos viperídeos, a evolução da arborealidade parece não afetar as taxas de especiação que permanecem similares entre linhagens arborícolas e terrestres. Isto sugere dois cenários: (1) a especiação acontece de forma independente das mudanças morfológicas nos viperídeos; ou (2) o isolamento geográfico seria um mecanismo importante na diversificação de linhagens arborícolas contrabalançando decréscimos nas oportunidades de especiação possivelmente relacionados às pressões seletivas impostas pelo ambiente arborícola. A presente tese contribui para entendermos mais sobre como evoluíram os viperídeos ao longo dos seus ∼50 milhões de anos. Além de propor cenários e hipóteses a serem futuramente explorados com os viperídeos, elaboramos uma discussão ampla e conceitual a respeito dos possíveis mecanismos por trás da diversificação de espécies e da morfologia que poderiam também ser contemplados para outros grupos de organismos. Portanto, a presente tese contribui não só para entendermos os mecanismos que geram e mantém a diversidade de serpentes, mas também para enriquecer a discussão dos mecanismos que geram e mantém a biodiversidade como um todo / Species and phenotypic diversity may vary considerably between taxonomic groups and through time for a given lineage. The study of such variation became one of the main goals of evolutionary biology and provides important information related to the possible mechanisms regulating biodiversity. The general goal of the present thesis was to investigate the patterns of species and morphological diversification in a cosmopolitan group of snakes, the family Viperidae, and the potential underlying processes. First, (1) we estimated the phylogenetic relationships and divergence times between lineages of the family Viperidae using a Bayesian approach; then we (2) applyed a recently developed method (BAMM) to explore how speciation and extinction rates varied during the radiation of the group suggesting possible underlying processes. Finally, (3) we analyzed if body size evolution and speciation rates showed distinct patterns among vipers occurring in different habitats (terrestrial vs arboreal). Herein we generated the most complete molecular phylogeny for vipers until this moment using sequences from 11 mitochondrial and nuclear genes comprising 79% of extant species (264 terminals) and all except one genus. In general, we were able to recover well supported phylogenetic relationships with most genera being monophyletic. Divergence time estimates suggested that vipers started to diversify around the late Paleocene/middle Eocene finding older ages than previous studies. During the group radiation, an increase in speciation rates seems to have occurred during the diversification of crotalines (pit vipers) not only due to the evolution of loreal pits but also as a result of climatic and geological changes in Asia and the invasion of the New World. After this rapid initial increase, speciation rates decelerated toward the present. Lastly, the results presented here suggest that although arboreal habitats constrain morphological evolution in vipers the evolution of arboreality does not seem to affect speciation rates, which remain similar among arboreal and terrestrial lineages. Our results suggest two distinct scenarios: (1) speciation could be independent of morphological evolution in vipers; or (2) geographic isolation would be an important mechanism underlying species diversification in arboreal lineages offsetting decreases in speciation opportunities potentially related to the selective pressures imposed by the arboreal environment. The present thesis contribute to increase our understanding about how vipers evolved during their ∼50 million years. In addition to providing scenarios and hypotheses to be further explored with vipers, we elaborated a broad and conceptual discussion about the possible mechanisms underlying species and morphological diversification that might apply to other groups of organisms. Therefore, this thesis comprises a contribution that goes beyond the understanding of mechanisms generating and maintaining the diversity of snakes, but will hopefuly enrich the discussion of mechanisms that generate and maintain biodiversity as a whole

Le comportement de certains radionucléides (RN) anthropiques (137Cs, 238,239+240Pu et 241Am) a été étudié dans des échantillons naturels de sol, d’eau et de sédiments prélevés dans le Massif du Boréon. Dans ce milieu non anthropisé, ces RN restent détectables et proviennent des essais nucléaires atmosphériques (238,239+240Pu et 241Am) et de l’accident de la centrale nucléaire de Tchernobyl (137Cs). Les pollutions radioactives restent en surface dans ces sols non perturbés. Dans les sédiments lacustres, l’apport direct des retombées radioactives est détectable en profondeur car sous l’effet de la sédimentation les RN ont quitté la surface. Les transferts entre ces 2 compartiments naturels ont montré l’importance de l’eau comme vecteur de transport et la prédominance du lessivage par rapport à la lixiviation. Le lessivage transporte les RN des pentes du bassin versant, vers la clairière puis vers les sédiments via la phase aqueuse. Dans les échantillons solides, les RN ont une faible mobilité, 241Am est l’isotope le plus mobile et 137Cs l’isotope le moins mobile. Les isotopes 238,239+240Pu ont un comportement intermédiaire. La mobilité est corrélée au contact de l’échantillon solide avec l’eau, ainsi la mobilité des RN est plus importante dans les sédiments que dans le sol. L’évolution temporelle de la radioactivité n’a pu être décrite malgré un essai basé sur les isotopes de Pb en raison de la complexité du milieu naturel. Deux approches (tests de sorption et analyse structurale de l’eau et du sédiment dopés par spectroscopie d’absorption X et spectroscopie laser résolue en temps) au laboratoire ont permis de mieux comprendre le comportement de Am à travers son analogue Eu. Dans l’eau dopée, la présence de 2 complexes, un inorganique Eu(OH)CO3(aq) et un organique avec les acides humiques, a été envisagée. Les sédiments lacustres ont une importante capacité de rétention avec une cinétique de sorption rapide présageant de la faible mobilité de Am dans ce milieu naturel. / The behavior of certain anthropogenic radionuclides (RNs) (137Cs, 238,239+240Pu, 241Am) was studied in samples of soil, water and sediment collected in the Boreon Massif. In this non-anthropized environment, these RNs are still measurable. They come from nuclear weapon tests (238,239+240Pu and 241Am) and from the Chernobyl nuclear power plant accident (137Cs). Radioactive pollutions stay near the surface in these undisturbed soils. In the lake sediments, direct deposits of the radioactive fallouts are detected in depth due to the effect of sedimentation causing RNs to leave the ground surface. The transference between those two natural compartments has shown the importance of water as a transport vehicle and the prevalence of leaching compared to lixiviation. Leaching carries RNs from the drainage basin slopes, to the clearing and then to the sediment through the aqueous phase. In solid samples, RNs have a low mobility, 241Am is the most movable isotope and 137Cs the less movable. 238,239+240Pu isotopes have an intermediate behavior. Mobility rate is correlated with the contact of the solid sample with water. Thus, RN mobility is more important in sediment than in soil. Temporal evolution has not been performed despite a tentative based on Pb isotopes due to the natural environment complexity. Two approaches (sorption tests and structural analysis of spiked water and sediment by X-ray absorption spectroscopy and time-resolved laser induced spectroscopy) in the laboratory have led to a better knowledge of Am behavior using Eu as an analog. In spiked water, the presence of two complexes, one inorganic Eu(OH)CO3(aq) and one organic with humic acids, has been considered. Lake sediment has an important retention capacity with a kinesis of rapid sorption predicting the low mobility of Am in this natural environment.

Les radiations évolutives sont des phénomènes de diversification rapide, et une source majeure de la diversité biologique sur Terre. J'explore ici l'hypothèse selon laquelle les mécanismes écologiques et génétiques à la base des radiations évolutives structurent les patrons macroécologiques et macroévolutifs de diversité. Pour ce faire, j'analyse les prédictions de plusieurs modèles de radiation émergeant des dynamiques spatio-temporelles à l'échelle individuelle. Ces analyses montrent d'abord que la structuration spatiale est un facteur majeur de diversité et d'endémisme au sein des archipels océaniques, en raison d'interactions entre dispersion et spéciation allopatrique. L'intégration de la dynamique des paysages et des processus d'interactions compétitives révèle ensuite comment ces facteurs se combinent pour structurer la forme des arbres phylogénétiques, et notamment générer des arbres déséquilibrés et une décélération du tempo de branchement, souvent observés dans les phylogénies moléculaires. J'explore alors les mécanismes responsables de cette décélération. Je montre qu'elle reflète une diversité-dépendance négative du taux de spéciation, liée à une réduction de la persistance et différentiation écologique des nouvelles populations. Le taux d'extinction n'est lui pas influencé par la diversité, les extinctions étant ici surtout causées par une combinaison d'exclusion compétitive et d'hybridation d'espèces incipientes. Enfin, je mets en évidence l'importance, lors d'une crise d'extinction, de la topologie rangée des arbres phylogénétiques et de la distribution des extinctions sur les pertes de diversité phylogénétique, et donc sur le potentiel d'évolution future. / Evolutionary radiations are phenomena of rapid diversification, and one of the major sources of biodiversity on Earth. Here, I explore the hypothesis that ecological and genetic mechanisms underpinning evolutionary radiations structure macroecological and macroevolutionary patterns of diversity. To this end, I analyse the predictions of several models in which radiations emerge from spatio-temporal dynamics at the scale of the individual. These analyses first show that spatial structure is a major driver of diversity and endemism on oceanic archipelagos due to interactions between dispersal and allopatric speciation. Second, by integrating landscape dynamics and the processes of competitive interactions, I reveal how these factors combine to shape phylogenetic trees, and in particular to beget trees that are unbalanced and exhibit a deceleration in branching tempo, which is often observed on molecular phylogenies. I then explore the mechanisms responsible for this deceleration. I show that it reflects a negative diversity-dependence of the speciation rate, itself linked to a reduction in the persistence and ecological differentiation of new populations. The extinction rate is, on the other hand, uninfluenced by species diversity, extinctions being here mainly caused by a combinaison of competitive exclusion and hybridization of incipient species. Finally, I show that during mass extinctions the ranked topology of phylogenetic trees and the distribution of extinctions among the tips have a strong impact on the loss of phylogenetic diversity, and hence on the potential for future evolution.

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.

Speciation – the process by which new species arise – is of fundamental importance in the biological sciences. The means by which new species arise, and the relationship among living species, has been a topic that has captivated both lay and scientific observers for centuries. In recent years, the study of speciation has enjoyed increased attention, resulting in significant advances in our understanding of how species form. Although our understanding of the processes that contribute to speciation has increased dramatically in recent years, our knowledge of how reproductive barriers accumulate as speciation proceeds is still limited. Thus, studies that evaluate trait divergence and its consequences at early verses late stages of divergence can provide valuable insight into the speciation process. Chapter 1 of my dissertation focuses on the role of animal personality in the speciation process. Animal personality – defined as consistent individual differences in behavioral tendencies – has been identified as a key player in several ecological and evolutionary processes, yet the role of personality in speciation remains unexplored. In this chapter I discuss the ways by which personality can contribute to a suite of reproductive barriers and drive the speciation process. Chapters 2 through 5 provide a case study evaluating how selection acts on traits at early and late stages of speciation, using the Neotropical Livebearing fish genus Brachyrhaphis as a model system. Brachyrhaphis is ideally suited for this research because several species pairs and population pairs within species occur in similarly divergent selective regimes. I first present results from a field demographic study that shows that the strength of divergent selection acting on life-history traits in populations from divergent predation environments diminishes as speciation proceeds. I then show that population pairs at different stages of divergence are evolving similar morphological patterns along parallel trajectories. At both early and late stages of divergence, populations from environments with dense predator populations have a body shape that appears to be optimized for burst-speed swimming, and important component of predator escape. In contrast, populations from environments lacking predators have a body shape optimized for endurance swimming ability, which is important in environments where competition for foods and mates is high. Next, I show that populations from divergent predation environments do indeed differ in their swimming abilities according to our predictions, reflecting a population level trade-off between burst and endurance swimming ability. Although population level trade-offs were strong, I found no evidence of within population level trade-offs, suggesting that populations have arrived at novel solutions to between population trade-offs that were not present within ancestral populations. Finally, I show that these specialized swimming modes are locally adaptive, and that divergent ecology selects against immigrants, effectively reducing gene flow between populations from divergent environments. Together, these studies provide a valuable glimpse into the repeatability and predictability of trait divergence at different stages of speciation.

The inference of species boundaries and phylogenetic relationships are fundamental for evolutionary, ecological, and conservation studies. The resolution of species boundaries and the inference of phylogenetic relationships among species are required to define the units of analysis and to find the most closely related units for evaluating alternative models of speciation. I highlight lizards as model organisms for ecological and evolutionary studies, emphasizing their contributions to advances in understanding linkages between phylogeography and speciation. In this dissertation, I focus on the phylogenetic relationships of the lizards in the Liolaemus darwinii group, and the species boundaries of a nested clade within the group, the L. darwinii complex, because of several advantages that make these taxa ideal for phylogeographic studies of speciation. I infer a phylogeny for the L. darwinii group based on DNA sequences of 20 loci (19 nuclear and 1 mitochondrial) using species trees methods that take into account the incongruence among gene trees. I found the minimum number of loci, number of sequences per species, and number of base pairs per locus that should be included in an analysis for an accurate and precise estimate of the species tree. The species tree based on all available data support a clade of closely related species (L. darwinii, L. grosseorum, and L. laurenti) known as the L. darwinii complex. A new method for species delimitation using Approximate Bayesian Computation is introduced and is shown to accurately delimit species given that limited or no gene flow has occurred after divergence and despite biased estimates of demographic parameters. ABC analyses supported the distinctness of two lineages within L. darwinii under a model of speciation with gene flow. Based on the species tree and the species limits obtained in this dissertation, phylogenetic comparative methods can be carried out to address the morphological and ecological evolution in the L. darwinii group and several sister species can be used for testing the alternative speciation models via correlation analyses of genetic, morphological, and ecological datasets. Future studies should assess the role speciation due to adaptive processes and its association the species' ecological niches and life histories.