A delimitação de espécies é essencial para a caracterização e conservação da biodiversidade. No entanto, representa um desafio para grupos onde há pouca variação em morfologia, como no caso dos lagartos Iphisini. São conhecidas oito espécies pertencentes a seis gêneros na tribo, com base em análises moleculares e de anatomia hemipeniana foram detectadas quatro espécies candidatas para Iphisa. A tribo filogeneticamente aparentada Gymnophthalmini apresenta maior riqueza de espécies e diversidade morfológica, principalmente em espécies com adaptações para a vida fossorial. No entanto, ainda se conhece pouco sobre os mecanismos históricos e ecológicos que causam distintos padrões de especiação, apesar de historicamente o papel de isolamento geográfico ter sido enfatizado para a biota Neotropical. Em tempos recentes, foram desenvolvidos métodos quantitativos para abordar questões evolutivas como probabilidades de especiação, variações em taxas de diversificação e reconstrução de demografia histórica de populações e migração. Implementei neste estudo uma combinação de métodos quantitativos com uso de dados moleculares, morfológicos e ambientais para testar as hipóteses que: há diversidade não reconhecida em Iphisini; as diferenças em riqueza e disparidade morfológica entre Iphisini e outras tribos de Gymnophthalminae se deve a diferenças em tempo e modo de diversificação, e que a diversificação em Acratosaura ocorreu por isolamento geográfico causado por flutuações paleoclimáticas. Com base em análises moleculares, foram delimitadas quatro espécies candidatas para Iphisini, aumentando em 33% a diversidade conhecida para a tribo. Não houve variação entre as espécies candidatas de Acratosaura em morfometria. A filogenia estimada para Gymnophthalminae apresentou alto suporte para a relação entre Iphisini e Heterodactylini, e demonstra um tempo de diversificação e riqueza neste clado similar a Gymnophthalmini. As tribos apresentaram padrões de diversificação semelhantes, mas taxas distintas. Os padrões de evolução morfológica foram congruentes com a diversificação em Gymnophthalmini, porém distintas em Heterodactylini sensu lato, indicando que disparidade independe de diversificação. As análises filogeográficas indicam que as populações de Acratosaura apresentaram estabilidade demográfica e espacial ao longo do tempo, com evidências de fluxo gênico entre linhagens diferenciadas. Desta forma, os resultados sugerem que Acratosaura diversificou sem influência de variações históricas no clima, e provavelmente sem isolamento reprodutivo completo / Species delimitation is essential for characterization and conservation of biodiversity. Nevertheless, it represents a challenge for groups in which morphological variation is subtle, such as the microteiid lizards of the tribe Iphisini. Eight species from six genera are currently recognized in the tribe but recently, based on molecular analysis and hemipenial anatomy, four candidate species were inferred for Iphisa. The phylogenetically related tribe Gymnophthalmini presents higher species richness and morphological diversity, specially in forms with adaptations to fossoriality. Nevertheless, the historical and ecological mechanisms involved in the distinct speciation patterns are poorly known, although geographical isolation have been historically emphasized for neotropical biota. In recent times, quantitative methods were developed to address evolutionary questions such as speciation probabilities, variation in diversification rates and reconstruction of historical demography of populations and migration. In this study I used a combination of quantitative methods based on molecular, morphological and environmental data for testing the hypothesis that: there is unrecognized diversity within Iphisini; differences in species richness and disparity among Iphisini and related tribes are congruent with differences in time and mode of diversification; and that diversification in Acratosaura occurred with geographical isolation caused by paleoclimatic fluctuations. Based on the results of molecular analyses, four candidate species were delimited for Iphisini, rising in 33% the tribe diversity. There was no significant variation in morphometry between candidate species of Acratosaura. The phylogeny of Gymnophthalminae presented high support for the relationship between Iphisini and Heterodactylini, and showed diversification timming and species richness comparable between this clade and Gymnophthalmini. The tribes presented similar diversification patterns but distinct rates. The patterns of morphological evolution were congruent with diversification patterns in Gymnophthalmini but distinct in Heterodactylini sensu lato, indicating that disparity is independent from diversification in the group. The phylogeographic analyses indicate that populations of Acratosaura presented demographic and spatial stability through time, with evidences of gene flow among lineages after differentiation. Thus, the results suggest that diversification of Acratosaura was not influenced by variations in historical climate, and probably occurred without complete reproductive isolation

Métodos filogenéticos comparativos utilizam informações sobre as relações de ancestralidade entre as espécies para testar hipóteses evolutivas. Neste contexto, a Reconstrução de Caracteres Ancestrais (RCA) pode nos esclarecer muito a respeito dos organismos já extintos. A família Canidae apresenta variada gama de comportamentos, distribuída por quase todo o planeta. Sua rica história fóssil demonstra processos que nos dão pistas sobre a evolução e diversificação destes comportamentos ao longo de 46 Ma. Entender a importância de fatores bióticos e abióticos na evolução de carnívoros tem sido um dos grandes desafios em estudos macroevolutivos nos últimos anos. Aqui foram abordados aspectos evolutivos de Canidae com o intuito de demonstrar o papel de fatores ambientais e comportamentais, além de interações, na diversificação do grupo. Para isso, construiu-se a filogenia para todas as espécies vivas de canídeos e uma espécie recentemente extinta. No total, 37 espécies foram incluídas na árvore filogenética. Foram obtidos 23 marcadores moleculares usados na construção da filogenia. Utilizou-se também 68 caracteres morfológicos. A construção da filogenia foi feita utilizando inferência Bayesiana. O modelo evolutivo escolhido nessa etapa foi GTR + G + I. Também foi utilizado o algoritmo de Monte Carlo Markov Chain (MCMC) para obter a distribuição a posteriori, com 50 x 106 iterações. A datação da árvore filogenética foi feita através do método de Penalized Likelihood, onde foram utilizados 11 registros fósseis de nós conhecidos da filogenia. Após a filogenia feita, obteve-se os dados comportamentais para realização da RCA a respeito dos quatro atributos avaliados. As quatro reconstruções foram criadas com inferência em 1000 árvores cada. Todas análises de RCA foram realizadas com o método de parcimônia. Com o intuito de entender de que maneira os atributos se correlacionam ao longo da filogenia, foi calculada a correlação de Pagel além de Phylogenetic Generalized Least Squares (PGLS). A topologia obtida aqui foi diferente das demais árvores filogenéticas já criadas para Canidae. Além disso, a calibração temporal indica que o split entre Canini e Vulpini se deu há 12.6 Ma, diferente do que é apontado na literatura. A respeito das reconstruções, as linhagens ancestrais dos lobos e das raposas desenvolveram o hábito de viver em áreas abertas. Já os canídeos sulamericanos desenvolveram preferência por áreas florestais. Em relação à dieta, o ancestral de Caninae, assim como os ancestrais diretos das tribos Canini e Vulpini, apresentavam comportamento alimentar hipocarnívoro. O ancestral de todos os canídeos existentes hoje apresentou baixa organização social, enquanto que os lobos desenvolveram alto comportamento social, coincidindo com o surgimento do hábito hipercarnívoro. A respeito do tamanho corporal, o nó ancestral a todos os canídeos possuía tamanho médio, e as duas tribos que surgiram a partir desta linhagem divergiram seus tamanhos. O teste de Pagel demonstrou que há correlação entre dieta e socialidade, mostrando que a alimentação levou a modificações no comportamento Social. Os PGLSs mostram que três tipos de modelos evolutivos explicam as mudanças nos atributos ao longo do tempo. As mudanças no uso de habitat dos canídeos acompanharam as mudanças climáticas no planeta ao longo dos últimos 13 Ma. Já a alimentação meso e hipocarnívora dos sulamericanos se deve ao cenário encontrado na América do Sul ao chegarem, e como reflexo, não desenvolveram alto grau de socialidade. Os resultados sugerem que raposas tentaram evitar a competição com os lobos para não sobreporem seus nichos, sendo o fator fundamental para sua diversificação. / Phylogenetic comparative methods use information on ancestral relationships between species to test evolutionary hypotheses. In this context, the Ancestral Characters Reconstruction (ACR) can shed light on the already extinct organisms. The Canidae family has a wide range of behaviors, distributed throughout most of the planet. Its rich fossil history demonstrates processes that give us clues about the evolution and diversification of these behaviors over 46 Ma. Understanding the importance of biotic and abiotic factors in the evolution of carnivores has been one of the major challenges in macroevolutionary studies in recent years. Here we discuss the evolutionary aspects of Canidae with the purpose of demonstrating the role of environmental and behavioral factors, as well as interactions, in the diversification of the group. For this, the phylogeny was constructed for all living species of canids and a recently extinct species. In total, 37 species were included in the phylogenetic tree. A total of 23 molecular markers were used to construct the phylogeny. We also used 68 morphological characters. The construction of the phylogeny was done using Bayesian inference. The evolutionary model chosen in this step was GTR + G + I. The Monte Carlo Markov Chain algorithm (MCMC) was also used to obtain the posterior distribution, with 50 x 106 iterations. The phylogenetic tree was dated using the Penalized Likelihood method, where eleven fossil records of nodes known from the phylogeny were used. After the phylogeny, the behavioral data were obtained to perform the ACR in relation to the four attributes evaluated. The four reconstructions were created with inference in 1000 trees each. All ACR analyzes were performed using the parsimony method. In order to understand how the attributes correlate throughout the phylogeny, the Pagel correlation was calculated in addition to Phylogenetic Generalized Least Squares (PGLS). The topology obtained here was different from the other phylogenetic trees already created for Canidae. In addition, the time calibration indicates that the split between Canini and Vulpini occurred 12.6 Ma ago, different from what is pointed out in the literature. Concerning reconstructions, the ancestral lineages of wolves and foxes have developed the habit of living in open areas. South American canids have developed preference for forest areas. Regarding diet, Caninae's ancestor, as well as the direct ancestors of the Canini and Vulpini tribes, presented hypocampivorous feeding behavior. The ancestor of all canids present today had a low social organization, while the wolves developed a high social behavior, coinciding with the emergence of the hypercarnivore habit. Regarding the body size, the ancestral node to all canids had medium size, and the two tribes that have emerged from this lineage diverged their sizes. The Pagel test demonstrated that there is a correlation between diet and sociality, showing that diet led to changes in social behavior. The PGLSs show that three types of evolutionary models explain changes in attributes over time. The changes in the habitat use of the canids have accompanied the climatic changes in the planet during the last 13 Ma. The meso and hypocarnivorous feeding of the South Americans is due to the scenario found in South America when they arrived, and as a reflex, they did not develop high degree of Sociality. The results suggest that foxes tried to avoid competition with the wolves to avoid overlapping their niches, being the fundamental factor for their diversification.

Whether microevolutionary processes can explain macroevolutionary patterns has long been a matter of contentious debate. The debate has persisted largely because of the challenging task of connecting microevolutionary theory, which examines population-level phenomena on the generation scale, to data collected across larger spatial and temporal scales. My dissertation research broadly examines phenotypic evolution across multiple scales by connecting microevolutionary theory to macroevolutionary phenomena such as speciation and large-scale phenotypic change. In particular, I focus on the so-called "paradox of stasis"; which wrestles with the apparent conflict between frequently-observed cases of rapid evolution on short timescales and the frequent appearance of stasis in the fossil record. I attempt to link micro and macroevolution by using the theoretical framework of evolutionary quantitative genetics for modeling the effects of drift and selection. My four dissertation chapters examine four different systems (1) connecting quantitative genetic models of sexual selection to speciation (2) connecting microevolutionary and macroevolutionary body size data across scales of time (3) using phylogenetic comparative methods and quantitative genetic models to examine the evolution of a classic example of stasis, mammalian body temperature and (4) finally, using multi-locus phylogeography to understand the evolutionary processes that contribute to the diversification of a widespread snake across broad spatial scales. In chapter 2, I demonstrate that genetic drift combined with sexual selection can promotes speciation and diversification of male ornaments. Furthermore, I demonstrate that drift promotes the evolution of elaborate ornaments even when preferences are costly. In chapter 3, I combine data from microevolutionary field studies, the fossil record, and phylogenetic comparative data into a single analytical framework to resolve apparent conflicts between micro and macroevolutionary patterns. To do so, I compiled and analyzed the largest database of phenotypic divergence data in existence. I demonstrate that patterns of stasis persist until a million-year threshold, after which divergence begins to accumulate in a time-dependent manner. This pattern is best fit with a hierarchical model that describes evolution as occurring in bursts on the million-year timescale, but that allows for rapid, but bounded, evolution on short timescales. In chapter 4, I demonstrate that mammalian body temperature -- which has been previously presented as a classic example of stasis -- does in fact evolve extensively across the mammalian radiation (albeit slowly). Furthermore, I show that mammalian body temperature evolves in response to changing environmental conditions. Finally, I evaluate the role that genetic constraints play in the apparent slowness of body temperature evolution. In chapter 5, I examine a well-studied empirical system of garter snakes in which a strong signature of stabilizing selection has been found for phenotypic traits. Using multiple mitochondrial and nuclear loci, I show that introgression is rampant between species, and dynamic patterns of range expansion, contraction, and introgression among clades have led to a complex pattern of genetic variation. This structure of genetic variation underscores the need to examine range-wide processes for generating phenotypic divergence across clades. Overall, these chapters suggest that apparent disconnects between microevolutionary processes and macroevolutionary patterns could be explained by the scaling of population-level theory over large spatial and temporal scales. / Graduation date: 2013 / Access restricted to the OSU Community at author's request from Oct. 25, 2012 - Oct. 25, 2013

<p>This dissertation explores philosophical problems in biology, particularly those relating to macroevolutionary theory. It is comprised of a series of three papers drawn from work that is currently at the publication, re-submission, and review stage of the journal refereeing process, respectively. The first two chapters concern the overarching contours of complex life, while the third zeroes in on the short and long-term prospects of human evolution.</p><p>The rhetorical journey begins with a thought experiment proposed by the late paleontologist Stephen Jay Gould. Gould hypothesized that replaying the "tape of life" would result in radically different evolutionary outcomes, both with respect to animal life in general and the human species in particular. Increasingly, however, biologists and philosophers are pointing to convergent evolution as evidence for replicability and predictability in macroevolution. Chapters 1 and 2 are dedicated to fleshing out the Gouldian view of life and its antithesis, clarifying core concepts of the debate (including contingency, convergence, constraint and causation), and interpreting the empirical data in light of these conceptual clarifications. Chapter 3 examines the evolutionary biological future of the human species, and the ways in which powerful new biotechnologies can shape it, for better and for worse. More detailed chapter summaries are provided below.</p><p>In Chapter 1, I critique a book-length excoriation of Gould's contingency theory written by the paleobiologist Simon Conway Morris, in which he amasses and marshals a good bulk of the homoplasy literature in the service of promoting a more robust, counter-factually stable account of macroevolution. I show that there are serious conceptual and empirical difficulties that arise in broadly appealing to the frequency of homoplasy as evidence for robustness in the history of life. Most important is Conway Morris's failure to distinguish between convergent (`externally' constrained) and parallel (`internally' constrained) evolution, and to consider the respective implications of these significantly different sources of homoplasy for a strong adaptationist view of life.</p><p>In so doing, I propose a new definition of parallel evolution, one intended to rebut the common charge that parallelism differs from convergence merely in degree and not in kind. I argue that although organisms sharing a homoplastic trait will also share varying degrees of homology (given common decent), it is the underlying developmental homology with respect to the generators directly causally responsible for the homoplastic event that defines parallel evolution and non-arbitrarily distinguishes it from convergence. I make use of the philosophical concept of `screening-off' in order to distinguish the proximate generators of a homoplastic trait from its more distal genetic causes (such as conserved master control genes).</p><p>In Chapter 2, I critically examine a recent assessment of the contingency debate by the philosopher John Beatty, in which he offers an interpretation of Gould's thesis and argues that it is undermined by iterative ecomorphological evolution. I develop and defend alternative concepts of contingency and convergence, and show how much of the evidence generally held to negate the contingency thesis not only fails to do so, but in fact militates in favor of the Gouldian view of life. My argument once again rests heavily on the distinction between parallelism and convergence, which I elaborate on and defend against a recent assault by developmental biologists, in part by recourse to philosophical work on the ontological prioritization of biological causes.</p><p>In Chapter 3, I explore the probable (and improbable) evolutionary biological consequences of intentional germ-line modification, particularly in relation to human beings. A common worry about genetic engineering is that it will reduce the pool of genetic diversity, creating a biological monoculture that could not only increase our susceptibility to disease, but even hasten the extinction of our species. Thus far, however, the evolutionary implications of human genetic modification have remained largely unexplored. In this Chapter, I consider whether the widespread use of genetic engineering technology is likely to narrow the present range of genetic variation, and if so, whether this would in fact lead to the evolutionary harms that some authors envision. By examining the nature of biological variation and its relation to population immunity and evolvability, I show that not only will genetic engineering have a negligible impact on human genetic diversity, but that it will be more likely to ensure rather than undermine the health and longevity of the human species. To this end, I analyze the relationship between genotypic and phenotypic variation, consider process asymmetries between micro and macroevolution, and investigate the relevance of evolvability to clade-level persistence and extinction.</p> / Dissertation

The results of evolution can be inferred from comparative studies of related organisms. In this doctoral thesis, I use phylogenetic comparative methods along side geometric morphometrics to analyse shape variation in order to infer evolution of the caecilian skull. Caecilians are elongate, limbless amphibians that superficially resemble snakes or earthworms, and use their head as a locomotory organ. I characterise large-scale patterns of cranial morphological diversity and quantify variation across the main family-level clades by describing patterns relating to phylogeny, disparity and ecology. Then I examine the origins and evolution of morphological variation in the skull by describing patterns relating to morphological integration and modularity. This thesis demonstrates a variety of existing statistical techniques that can be used to infer processes from large-scale evolutionary patterns in morphological data using non model organisms. Throughout the thesis, I show that the evolution of the caecilian skull to be multifaceted. On the patterns of diversity, the most striking is a "starburst" arrangement in shape space, which suggests that early in caecilian evolution ancestral lineages traversed greater expanses of the shape space, while subsequent phylogenetic divergence within the main clades entailed less morphological diversification. This may be related to early diversification into different ecological-niches, yet more data are needed to test this. The clades differ considerably in their cranial disparity, but there appears to be no unified pattern across the whole order that indicates disparity is coupled with clade age or speciation events. I show that aquatic species are more diverse than their terrestrial relatives, and that there is convergence of cranial shape among dedicated burrowers with eyes covered by bone. On the patterns of morphological integration and modularity, another remarkable finding is the caecilian cranium is modular with respect to two functional regions, the snout and the back of the cranium. Modularity is important for understanding the evolution of this structure. The main elements of the caecilian anterior skeleton, the cranium, mandible and atlas vertebra, reveal different patterns of morphological integration, suggesting different developmental and evolutionary processes are involved in sorting and maintaining new variation of each structure. Allometry is an important component of integration in each of the structures. Covariation of the cranium-mandible after size correction is significant and follows the same direction of shape change across all levels and as shown for allometry. In contrast, covariation of the cranium-atlas follows different directions at each level. These results suggest the two main joint of the caecilian skull differ substantially in their origin and evolution. I discuss the contribution made in this thesis to caecilian and evolutionary biology and offer an outlook of how theses findings can be used to initiate future studies to better understand of the evolution of the caecilian skull.

Métodos filogenéticos comparativos utilizam informações sobre as relações de ancestralidade entre as espécies para testar hipóteses evolutivas. Neste contexto, a Reconstrução de Caracteres Ancestrais (RCA) pode nos esclarecer muito a respeito dos organismos já extintos. A família Canidae apresenta variada gama de comportamentos, distribuída por quase todo o planeta. Sua rica história fóssil demonstra processos que nos dão pistas sobre a evolução e diversificação destes comportamentos ao longo de 46 Ma. Entender a importância de fatores bióticos e abióticos na evolução de carnívoros tem sido um dos grandes desafios em estudos macroevolutivos nos últimos anos. Aqui foram abordados aspectos evolutivos de Canidae com o intuito de demonstrar o papel de fatores ambientais e comportamentais, além de interações, na diversificação do grupo. Para isso, construiu-se a filogenia para todas as espécies vivas de canídeos e uma espécie recentemente extinta. No total, 37 espécies foram incluídas na árvore filogenética. Foram obtidos 23 marcadores moleculares usados na construção da filogenia. Utilizou-se também 68 caracteres morfológicos. A construção da filogenia foi feita utilizando inferência Bayesiana. O modelo evolutivo escolhido nessa etapa foi GTR + G + I. Também foi utilizado o algoritmo de Monte Carlo Markov Chain (MCMC) para obter a distribuição a posteriori, com 50 x 106 iterações. A datação da árvore filogenética foi feita através do método de Penalized Likelihood, onde foram utilizados 11 registros fósseis de nós conhecidos da filogenia. Após a filogenia feita, obteve-se os dados comportamentais para realização da RCA a respeito dos quatro atributos avaliados. As quatro reconstruções foram criadas com inferência em 1000 árvores cada. Todas análises de RCA foram realizadas com o método de parcimônia. Com o intuito de entender de que maneira os atributos se correlacionam ao longo da filogenia, foi calculada a correlação de Pagel além de Phylogenetic Generalized Least Squares (PGLS). A topologia obtida aqui foi diferente das demais árvores filogenéticas já criadas para Canidae. Além disso, a calibração temporal indica que o split entre Canini e Vulpini se deu há 12.6 Ma, diferente do que é apontado na literatura. A respeito das reconstruções, as linhagens ancestrais dos lobos e das raposas desenvolveram o hábito de viver em áreas abertas. Já os canídeos sulamericanos desenvolveram preferência por áreas florestais. Em relação à dieta, o ancestral de Caninae, assim como os ancestrais diretos das tribos Canini e Vulpini, apresentavam comportamento alimentar hipocarnívoro. O ancestral de todos os canídeos existentes hoje apresentou baixa organização social, enquanto que os lobos desenvolveram alto comportamento social, coincidindo com o surgimento do hábito hipercarnívoro. A respeito do tamanho corporal, o nó ancestral a todos os canídeos possuía tamanho médio, e as duas tribos que surgiram a partir desta linhagem divergiram seus tamanhos. O teste de Pagel demonstrou que há correlação entre dieta e socialidade, mostrando que a alimentação levou a modificações no comportamento Social. Os PGLSs mostram que três tipos de modelos evolutivos explicam as mudanças nos atributos ao longo do tempo. As mudanças no uso de habitat dos canídeos acompanharam as mudanças climáticas no planeta ao longo dos últimos 13 Ma. Já a alimentação meso e hipocarnívora dos sulamericanos se deve ao cenário encontrado na América do Sul ao chegarem, e como reflexo, não desenvolveram alto grau de socialidade. Os resultados sugerem que raposas tentaram evitar a competição com os lobos para não sobreporem seus nichos, sendo o fator fundamental para sua diversificação. / Phylogenetic comparative methods use information on ancestral relationships between species to test evolutionary hypotheses. In this context, the Ancestral Characters Reconstruction (ACR) can shed light on the already extinct organisms. The Canidae family has a wide range of behaviors, distributed throughout most of the planet. Its rich fossil history demonstrates processes that give us clues about the evolution and diversification of these behaviors over 46 Ma. Understanding the importance of biotic and abiotic factors in the evolution of carnivores has been one of the major challenges in macroevolutionary studies in recent years. Here we discuss the evolutionary aspects of Canidae with the purpose of demonstrating the role of environmental and behavioral factors, as well as interactions, in the diversification of the group. For this, the phylogeny was constructed for all living species of canids and a recently extinct species. In total, 37 species were included in the phylogenetic tree. A total of 23 molecular markers were used to construct the phylogeny. We also used 68 morphological characters. The construction of the phylogeny was done using Bayesian inference. The evolutionary model chosen in this step was GTR + G + I. The Monte Carlo Markov Chain algorithm (MCMC) was also used to obtain the posterior distribution, with 50 x 106 iterations. The phylogenetic tree was dated using the Penalized Likelihood method, where eleven fossil records of nodes known from the phylogeny were used. After the phylogeny, the behavioral data were obtained to perform the ACR in relation to the four attributes evaluated. The four reconstructions were created with inference in 1000 trees each. All ACR analyzes were performed using the parsimony method. In order to understand how the attributes correlate throughout the phylogeny, the Pagel correlation was calculated in addition to Phylogenetic Generalized Least Squares (PGLS). The topology obtained here was different from the other phylogenetic trees already created for Canidae. In addition, the time calibration indicates that the split between Canini and Vulpini occurred 12.6 Ma ago, different from what is pointed out in the literature. Concerning reconstructions, the ancestral lineages of wolves and foxes have developed the habit of living in open areas. South American canids have developed preference for forest areas. Regarding diet, Caninae's ancestor, as well as the direct ancestors of the Canini and Vulpini tribes, presented hypocampivorous feeding behavior. The ancestor of all canids present today had a low social organization, while the wolves developed a high social behavior, coinciding with the emergence of the hypercarnivore habit. Regarding the body size, the ancestral node to all canids had medium size, and the two tribes that have emerged from this lineage diverged their sizes. The Pagel test demonstrated that there is a correlation between diet and sociality, showing that diet led to changes in social behavior. The PGLSs show that three types of evolutionary models explain changes in attributes over time. The changes in the habitat use of the canids have accompanied the climatic changes in the planet during the last 13 Ma. The meso and hypocarnivorous feeding of the South Americans is due to the scenario found in South America when they arrived, and as a reflex, they did not develop high degree of Sociality. The results suggest that foxes tried to avoid competition with the wolves to avoid overlapping their niches, being the fundamental factor for their diversification.

Métodos filogenéticos comparativos utilizam informações sobre as relações de ancestralidade entre as espécies para testar hipóteses evolutivas. Neste contexto, a Reconstrução de Caracteres Ancestrais (RCA) pode nos esclarecer muito a respeito dos organismos já extintos. A família Canidae apresenta variada gama de comportamentos, distribuída por quase todo o planeta. Sua rica história fóssil demonstra processos que nos dão pistas sobre a evolução e diversificação destes comportamentos ao longo de 46 Ma. Entender a importância de fatores bióticos e abióticos na evolução de carnívoros tem sido um dos grandes desafios em estudos macroevolutivos nos últimos anos. Aqui foram abordados aspectos evolutivos de Canidae com o intuito de demonstrar o papel de fatores ambientais e comportamentais, além de interações, na diversificação do grupo. Para isso, construiu-se a filogenia para todas as espécies vivas de canídeos e uma espécie recentemente extinta. No total, 37 espécies foram incluídas na árvore filogenética. Foram obtidos 23 marcadores moleculares usados na construção da filogenia. Utilizou-se também 68 caracteres morfológicos. A construção da filogenia foi feita utilizando inferência Bayesiana. O modelo evolutivo escolhido nessa etapa foi GTR + G + I. Também foi utilizado o algoritmo de Monte Carlo Markov Chain (MCMC) para obter a distribuição a posteriori, com 50 x 106 iterações. A datação da árvore filogenética foi feita através do método de Penalized Likelihood, onde foram utilizados 11 registros fósseis de nós conhecidos da filogenia. Após a filogenia feita, obteve-se os dados comportamentais para realização da RCA a respeito dos quatro atributos avaliados. As quatro reconstruções foram criadas com inferência em 1000 árvores cada. Todas análises de RCA foram realizadas com o método de parcimônia. Com o intuito de entender de que maneira os atributos se correlacionam ao longo da filogenia, foi calculada a correlação de Pagel além de Phylogenetic Generalized Least Squares (PGLS). A topologia obtida aqui foi diferente das demais árvores filogenéticas já criadas para Canidae. Além disso, a calibração temporal indica que o split entre Canini e Vulpini se deu há 12.6 Ma, diferente do que é apontado na literatura. A respeito das reconstruções, as linhagens ancestrais dos lobos e das raposas desenvolveram o hábito de viver em áreas abertas. Já os canídeos sulamericanos desenvolveram preferência por áreas florestais. Em relação à dieta, o ancestral de Caninae, assim como os ancestrais diretos das tribos Canini e Vulpini, apresentavam comportamento alimentar hipocarnívoro. O ancestral de todos os canídeos existentes hoje apresentou baixa organização social, enquanto que os lobos desenvolveram alto comportamento social, coincidindo com o surgimento do hábito hipercarnívoro. A respeito do tamanho corporal, o nó ancestral a todos os canídeos possuía tamanho médio, e as duas tribos que surgiram a partir desta linhagem divergiram seus tamanhos. O teste de Pagel demonstrou que há correlação entre dieta e socialidade, mostrando que a alimentação levou a modificações no comportamento Social. Os PGLSs mostram que três tipos de modelos evolutivos explicam as mudanças nos atributos ao longo do tempo. As mudanças no uso de habitat dos canídeos acompanharam as mudanças climáticas no planeta ao longo dos últimos 13 Ma. Já a alimentação meso e hipocarnívora dos sulamericanos se deve ao cenário encontrado na América do Sul ao chegarem, e como reflexo, não desenvolveram alto grau de socialidade. Os resultados sugerem que raposas tentaram evitar a competição com os lobos para não sobreporem seus nichos, sendo o fator fundamental para sua diversificação. / Phylogenetic comparative methods use information on ancestral relationships between species to test evolutionary hypotheses. In this context, the Ancestral Characters Reconstruction (ACR) can shed light on the already extinct organisms. The Canidae family has a wide range of behaviors, distributed throughout most of the planet. Its rich fossil history demonstrates processes that give us clues about the evolution and diversification of these behaviors over 46 Ma. Understanding the importance of biotic and abiotic factors in the evolution of carnivores has been one of the major challenges in macroevolutionary studies in recent years. Here we discuss the evolutionary aspects of Canidae with the purpose of demonstrating the role of environmental and behavioral factors, as well as interactions, in the diversification of the group. For this, the phylogeny was constructed for all living species of canids and a recently extinct species. In total, 37 species were included in the phylogenetic tree. A total of 23 molecular markers were used to construct the phylogeny. We also used 68 morphological characters. The construction of the phylogeny was done using Bayesian inference. The evolutionary model chosen in this step was GTR + G + I. The Monte Carlo Markov Chain algorithm (MCMC) was also used to obtain the posterior distribution, with 50 x 106 iterations. The phylogenetic tree was dated using the Penalized Likelihood method, where eleven fossil records of nodes known from the phylogeny were used. After the phylogeny, the behavioral data were obtained to perform the ACR in relation to the four attributes evaluated. The four reconstructions were created with inference in 1000 trees each. All ACR analyzes were performed using the parsimony method. In order to understand how the attributes correlate throughout the phylogeny, the Pagel correlation was calculated in addition to Phylogenetic Generalized Least Squares (PGLS). The topology obtained here was different from the other phylogenetic trees already created for Canidae. In addition, the time calibration indicates that the split between Canini and Vulpini occurred 12.6 Ma ago, different from what is pointed out in the literature. Concerning reconstructions, the ancestral lineages of wolves and foxes have developed the habit of living in open areas. South American canids have developed preference for forest areas. Regarding diet, Caninae's ancestor, as well as the direct ancestors of the Canini and Vulpini tribes, presented hypocampivorous feeding behavior. The ancestor of all canids present today had a low social organization, while the wolves developed a high social behavior, coinciding with the emergence of the hypercarnivore habit. Regarding the body size, the ancestral node to all canids had medium size, and the two tribes that have emerged from this lineage diverged their sizes. The Pagel test demonstrated that there is a correlation between diet and sociality, showing that diet led to changes in social behavior. The PGLSs show that three types of evolutionary models explain changes in attributes over time. The changes in the habitat use of the canids have accompanied the climatic changes in the planet during the last 13 Ma. The meso and hypocarnivorous feeding of the South Americans is due to the scenario found in South America when they arrived, and as a reflex, they did not develop high degree of Sociality. The results suggest that foxes tried to avoid competition with the wolves to avoid overlapping their niches, being the fundamental factor for their diversification.

Abstract There are more small-bodied species of birds than those having large bodies. Generally, and relative to occurrance in any one place, small-bodied species also contain more individuals than large-bodied species. The same patterns have been documented for several groups of higher organisms for example, snakes, flowering plants and mammals, which suggests that there exists a general reason "why", which applies to other groups of species as well as to birds. This thesis attempts to identify this reason. In the first place, it is possible that most species happened to become small-bodied by chance. Simulations of neutral body-size evolution indicate however that the observed bias towards small size is stronger than that accounted for by neutral evolution. Then, the most plausible explanation for why most species are small is that small-bodied species speciate faster. However, statistical analyses accounting for historical relatedness of present-day species indicate no relation between body size and the rate of speciation. Finally, instead of little by little, the dominance of small species may have arisen suddenly, when approximately 65 million years ago (presumably) a large meteorite hit the earth, causing mass extinctions. However, analysis of body sizes and genetic differences of extant species reveals that while avian species numbers were approximately halved, the catastrophe affected small and large species equally. Thus, the reason why most species are small does not seem to be due to differential rates of speciation or extinction. Instead, the cause appears to be in the tempo and mode of evolution. It was found by analysis of extant species' body size that probably most differences in body size between species arise at the moment of speciation. Differences between small-bodied species are smaller than between large-bodied species and probably this difference also has its origin at the moment of speciation. Consequently, groups of small species stay small whereas groups of large species are more variable in body size, so that in the end most species are small. / Tiivistelmä Maailman noin 10 000 lintulajin joukossa pienikokoisia lajeja on enemmän kuin suurikokoisia. Yleensä pienkokoiset lajit ovat myös yksilömääriltään suurempia kuin samalla paikalla esiintyvät suurikokoiset lajit. Koska sama ilmiö on havaittu monissa muissa suurissa eliöryhmissä (esim. nisäkkäät, käärmeet ja kukkakasvit), on ilmeistä, että on olemassa yhteinen syy, joka pätee niin linnuissa kuin muissakin eliöryhmissä. Tämän väitöskirjan tavoite on selvittää, mikä tämä yhteinen syy voisi olla. Ensinnäkin on mahdollista, että suurin osa lajeista on kehittynyt pienikokoisiksi aivan sattumalta. Ruumiin koon evoluution simulaatiot kuitenkin osoittavat, että on hyvin epätodennäköistä, että neutraali evoluutio olisi johtanut pienikokoisten lajien suuriin määrään havaitussa määrin. Toinen mahdollinen selitys ilmiölle on, että pienikokoiset lajit lajiutuvat nopeammin. Tilastolliset analyysit, jotka ottavat huomioon nykyisin elävien lajien sukulaisuussuhteet, osoittavat ettei ruumin koon ja lajiutumisen vauhdin välillä ole yhteyttä. Kolmas mahdollinen selitys pienikokoisten lajien suurelle määrällä on historiallinen. On mahdollista, että pienikokoisten lajien suhteellisen suuri määrä syntyi nopeasti noin 65 miljoonaa vuotta sitten tapahtuneen massasukupuuton seurauksena, joka fossiiliaineiston perusteella kohdistui erityisesti suurikokoisiin maaeläimiin (esimerkiksi dinosauruksiin). Vertaileva analyysi nykyään elävien lintulajien ruumiin koosta ja geneettisistä eroista osoittaa, että vaikka suuri osa lintulajeista hävisi massasukupuutossa, tämä katastrofi karsi lajeja riippumatta niiden ruumiin koosta. Näyttää siis siltä, etteivät erot lajiutumisen tai sukupuuttojen esiintymisessä selitä sitä, että suurin osa lajeista on pienikokoisia. Tämän tutkimuksen tulosten perusteella syy näyttäisi sen sijaan olevan ruumiin koon kehityksen vauhdissa ja siinä tavassa, jolla kehitys yleensä etenee. Analyysi nykyisten lajien ruumiin koosta paljasti, että suurin osa eroista lajien välillä syntyy (evolutiiviessa aikataulussa) suhteellisen nopeasti lajiutumistapahtuman yhteydessä (punktualismi) eikä vähitellen pitkien aikojen kuluessa (gradualismi), kuten yleensä oletetaan. Kehityslinjojen sisällä pienikokoisten lajien väliset erot ruumiin koossa olivat pienempiä kuin isokokoisten lajien väliset erot - ja todennäköisesti myöskin tämä ero syntyy lajiutumisen yhteydessä. Tämä johtaa evoluution kuluessa tilanteeseen, että alunperin pienikokoisista lajeista kehittyneet lajit ovat myös pienikokoisia, kun taas isokokoisten lajien kehityslinjoissa on nähtävissä huomattavasti paljon enemmän vaihtelua ruumiin koossa. Näiden seurauksena eliöstöissä suurin osa lajeista lopulta on pienikokoisia.

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Les rongeurs caviomorphes constituent l’un des groupes de mammifères placentaires les plus diversifiés d’Amérique du Sud. Malgré la grande diversité actuelle et néogène du groupe, les premières phases de l’histoire évolutive des caviomorphes n’étaient documentées que par quelques localités à l’échelle de tout le continent sud-américain. Les recherches paléontologiques récentes menées en Amazonie péruvienne ont permis la découverte de 18 localités éocènes et oligocènes, livrant de nombreux restes dentaires de caviomorphes inédits. L’étude de ces fossiles a conduit à la description et à la comparaison de 52 taxons distincts, dont 11 nouveaux genres et 17 nouvelles espèces. Ce travail révèle une riche diversité alpha-taxonomique des caviomorphes en Amazonie péruvienne à la fin de l’Éocène moyen, mais surtout à l’Oligocène inférieur et à l’Oligocène supérieur, trois fenêtres temporelles jusqu’alors très peu documentées dans les régions de basses latitudes du continent sud-américain. Les localités étudiées de la fin de l’Éocène moyen livrent les plus anciens caviomorphes connus à ce jour. Dans ces localités, la faible diversité taxinomique, associée à une faible disparité morphologique, incluant des taxons caractérisés par des traits dentaires plésiomorphes, rappelant les formes hystricognathes sub-contemporaines de l’Ancien Monde. Cela suggère un intervalle de temps court entre l’arrivée en Amérique du Sud des hystricognathes pionniers et l’émergence des espèces étudiées. Les assemblages de caviomorphes des localités plus récentes montrent une disparité plus importante et livrent des représentants des éréthizontoïdes, octodontoïdes et chinchilloïdes. L’analyse approfondie du matériel d’étude et sa comparaison avec des spécimens provenant d’autres gisements sud-américains ont permis une meilleure compréhension de l’homologie et de l’évolution des structures dentaires chez les caviomorphes. Une analyse cladistique de grande ampleur, incluant un grand nombre de familles des quatre super-familles (i.e., Cavioidea, Erethizontoidea, Chinchilloidea et Octodontoidea) a été réalisée. Elle a permis pour la première fois la reconnaissance de groupes basaux des caviomorphes. Les régions de basses latitudes du continent sud-américain paraissent être le centre d’origine des caviomorphes et le lieu d’une première diversification basale du groupe à la fin de l’Éocène moyen. Les quatre super-familles émergeraient au cours de l’Éocène supérieur–Oligocène inférieur, illustrant ainsi une deuxième radiation majeure du groupe au cours du Paléogène. Durant cette période, les caviomorphes se seraient dispersés aux moyennes et hautes latitudes. L’origine géographique des super-familles reste quelque peu ambiguë, excepté pour les chinchilloïdes qui émergeraient dans les régions de basses latitudes. Nos résultats mettent également en évidence l’existence d’une troisième radiation autour de la limite Oligocène–Miocène. Cette troisième phase correspondrait à la diversification des chinchilloïdes, octodontoïdes, et éréthizontinés basaux et à l’émergence du groupe couronne des caviidés, des octodontoïdes et très probablement des chinchilloïdes. Ces trois événements de diversifications majeures au cours du Paléogène sont concomitants avec des évènements climatiques globaux et des périodes intenses de surrection andine. / Caviomorph rodents represent one of the most successful groups of placental mammals from South America. Despite their high modern and Neogene diversity, their early evolutionary history has long remained obscure. Recent paleontological investigations in Peruvian Amazonia allowed for the discovery of 18 Eocene and Oligocene localities yielding many new fossils of caviomorphs (mainly isolated teeth). Fifty-two taxa, including 11 new genera and 17 new species, are described here. This study reveals a rich alpha-taxonomic diversity of caviomorphs in Peruvian Amazonia during the late Middle Eocene, Early Oligocene and Late Oligocene. These three periods were until now poorly documented in the low-latitudes of South America. The late Middle Eocene localities yield the earliest representatives of the group. In these localities, the low taxonomical diversity, associated with a low morphological disparity including taxa that harbor very primitive dental features, reminiscent to those observed in coeval Old World hystricognaths, suggest that a short time range of caviomorph evolutionary history had undergone in South America prior the emergence of these rodents. The most recent caviomorph assemblages show a higher disparity and yield representatives of erethizontoids, octodontoids and chinchilloids. The exhaustive analysis of the material and its comparison with specimens from other South American localities further our understanding regarding the homology and the evolution of dentary structures in caviomorphs. A cladistic assessment with a comprehensive taxonomic sampling including most families of the four superfamilies (i.e., Cavioidea, Erethizontoidea, Chinchilloidea, and Octodontoidea) was undertaken. For the first time, several stem Caviomorpha were recognized. Low latitudes of South America are thus viewed as the cradle and the first diversity hotspot of early caviomorphs. A second radiation would have occurred during the Late Eocene–Early Oligocene and would correspond to the emergence of the four superfamilies. At this time, caviomorphs would disperse towards the middle and high latitudes. The geographic origin of modern superfamilies remains somewhat ambiguous, except for chinchilloids which would emerge in low-latitude regions. A third radiation would have also occurred, around the Oligocene–Miocene transition, corresponding to the more recent diversification of stem Chinchilloidea, Octodontoidea, Erethizontoidea and the emergence of crown Erethizontinae, Caviidae, Octodontoidea, and probably Chinchilloidea. It is noteworthy that these three Paleogene diversification phases were contemporaneous with global climatic events and intense Andean uplift events.