Classified in the Lissamphibia, modern amphibians are the only non-amniote tetrapods living today. They consist of three morphologically distinct groups: the tailless frogs and toads (Anura), the limbless caecilians (Gymnophiona), and the tailed salamanders and newts (Urodela). With 205 species, the caecilians are highly specialized worm-like forms that live a fossorial lifestyle, with a relatively narrow distribution in the tropic rainforests of South America, Africa and Asia (Duellman and Trueb, 1994; Amphibiaweb, 2015). Salamanders, with 683 species, are widely distributed in the North America, Asia and Europe, with a few plethodontids extending to Central and South America (Duellman and Trueb, 1994; Amphibiaweb, 2015). Frogs are the most diverse amphibian groups, with 6644 species distributed over all continents except Antarctica (Duellman and Trueb, 1994; Amphibiaweb, 2015). Both frogs and salamanders develop a wide array of lifestyles, ranging from terrestrial, aquatic, fossorial to aboreal lifestyles (Duellman and Trueb, 1994). During ontogeny, amphibian larvae usually undergo a drastic post-embryonic shift into an adult form, a term known as metamorphosis. In salamanders, another developmental pathway – neoteny – also occurs, in which the larval morphology is retained in sexually mature adults (Duellman and Trueb, 1994; Rose, 2003). Because of the diverse lifestyles and developmental pathways, frogs and salamanders are often used as model systems in many fields of biology (e.g., evo-devo). Over a century, but especially in the past two decades, a wealth of frog and salamander fossils has been discovered from the Mesozoic and Cenozoic of East Asia (e.g., Noble, 1924; Young, 1936; Borsuk-Bialynicka, 1978; Gao, 1986; Dong and Wang, 1998; Gao and Shubin, 2001, 2003, 2012; Gao and Wang, 2001; Gao and Chen, 2004; Wang and Rose, 2005; Wang and Evans, 2006b; Zhang et al., 2009; Chen et al., 2016; this study). Some of these fossils represent the earliest members of many crown clades, including the earliest crown salamanders from the Middle Jurassic (~165 Ma, Gao and Shubin, 2003), the earliest salamandroid from the Late Jurassic, the earliest sirenid from the Late Jurassic (this study), and the earliest spadefoot toads from the late Paleocence (Chen et al., 2016). Other fossils also bear important anatomical, temporal and geographical information in understanding their evolution. Unfortunately, the importance of many of these fossils remains obscure in a phylogenetic context. For example, an early-middle Oligocene Mongolian spadefoot toad Macropelobates osborni (Noble, 1924) was discovered outside the current distribution of spadefoot toads, yet its phylogenetic position and its implication on spadefoot toad biogeography remain not well understood. A major reason for the poor understanding of these fossils can be attributed to a trend of dichotomy between morphological and molecular phylogenies on amphibians. Whereas morphologists and paleontologists sometimes use a relatively small morphological dataset to reconstruct relationships (e.g., Gao and Shubin, 2012; Henrici, 2013), large-scale phylogenies are almost always conducted with molecular data with only living taxa (e.g., Roelants and Bossuyt, 2005; Pyron and Wiens, 2011). Very few studies on amphibian phylogeny have combined morphological and molecular data together, and even fewer also combined fossils. Because of this, the positions of many important fossils remains unclear, and the evolutionary scenarios inferred from only living species can sometimes be inconsistent with fossil evidence. In this thesis, I adopt a total-evidence approach to understand the evolution of amphibians, especially frogs and salamanders. I will incorporate information from fossils, morphology and molecules together to reconstruct the relationships. Compared with studies with each individual datasets, this approach incorporates all available data in a single analysis, with a goal to reach robust and congruent results that allow further discussions on character evolution and biogeographic reconstruction. The inclusion of fossils directly into the combined analysis provides the time dimension that is independent from molecular data (Norell, 1992). The anatomical combination of fossils can represent intermediate forms that help to solve the “long branch” problems caused by highly specialized modern taxa. The morphological dataset, despite its much smaller size with molecular data, is the only link between fossils and modern taxa. The inclusion of key morphological characters in both reconstructing phylogenetic hypotheses and examining character evolution provide consistent results that allow discussion on the homology/homoplasy of a certain character without ambiguity. The molecular sequence data provides overwhelmingly large data on modern taxa for phylogenetic reconstructions compared with morphological data, which helps to reach a robust hypothesis. Although fossils contain no molecular data, the inclusion of molecular sequence data into the combined analysis does have an effect on the positions of fossil taxa. By altering the relationship “framework” of modern taxa, the character optimization of fossils and other taxa of a combined analysis also varies compared with results of morphology-only analysis, thus changing the positions of fossils. In the following five chapters, I will describe a number of fossil amphibian species, reconstruct three combined phylogenies, and use the results for discussions on character evolution and biogeography. In Chapter 1 and Chapter 2, I focus on a frog clade called spadefoot toads (Anura: Pelobatoidea). In Chapter 1, I provide descriptions on three important fossil spadefoot toads from the Cenozoic of East Asia and North America: Macropelobates osborni from the early-middle Oligocene of Mongolia, Prospea holoserisca from the latest Paleocene of Mongolia, and Scaphiopus skinneri from the middle Oligocene of the United States. In Chapter 2, I conduct a combined phylogenetic analysis of archaeobatrachian frogs, and discuss the evolution of the bony spade and the historical biogeography of spadefoot toads based on the results of the phylogeny. In Chapter 3, I describe a new fossil frog from the Early Cretaceous of Inner Mongolia, China. The unique morphology of the new fossil is distinct from previous Early Cretaceous frogs from the Jehol Biota of China. Results of the combined analysis show that the new frog represents a basal member of the Pipanura. Comparisons between the Early Cretaceous frogs from China, Spain and Brazil show a high diversity of species coupled with a high degree of endemism during the Early Cretaceous. I discuss in the phylogenetic context how early frogs gradually reach their postcranial body plan with a shortened vertebral column, loss of ribs, and specialized pelvic regions. In Chapter 4, I provide a brief review of Mesozoic fossil salamanders from northern China, and describe a new fossil from the Late Jurassic of Liaoning Province, China. I conduct a combined phylogeny of higher-level relationships of salamanders. The new fossil, despite its general-looking appearance, represents a basal member of the highly specialized eel-like neotenic family Sirenidae on the cladogram. I discuss character evolutions in the Sirenidae, and how the neotenic developmental pathway evolved in early salamanders. In Chapter 5, I conduct a combined phylogenetic analysis of the salamander suborder Cryptobranchoidea, consisting of the neotenic giant salamanders (Cryptobranchidae) and the metamorphic Asiatic salamanders (Hynobiidae). The new morphological matrix includes new characters that were previously less sampled in the hynobranchial region. The monophyly of the Hynobiidae are confirmed by the new analysis, and four unequivocal synapomorphies are found for the clade. An S-DIVA biogeographic reconstruction is conducted to disscuss the distributional patterns of the Hynobiidae.

[Truncated abstract] Despite the costs associated with mating, females of many taxa solicit multiple mates during a single reproductive event (polyandry). Polyandry is clearly adaptive when females gain direct benefits from males at mating. However, polyandry has also been shown to increase female fitness in the absence of direct benefits. Thus, a number of genetic benefit hypotheses have been developed to account for the origin of this behaviour. Although not mutually exclusive, a distinction lays between genetic benefits that propose defense against reproductive failure (nonadditive genetic effects), and those that propose benefits from intrinsic sire effects (additive genetic effects). Nonadditive genetic benefits of polyandry have been documented in a number of species; by soliciting multiple mates females can avoid inbreeding and other forms of incompatibility between parental genotypes. Polyandry may also increase female reproductive success when genetically superior males have greater success in sperm competition, and produce better quality offspring. An inevitable consequence of polyandry is that sperm from rival males will overlap in the female reproductive tract and compete to fertilise the ova. The outcome of sperm competition is typically determined by bias in sperm use by the females, interactions between parental genotypes, and ejaculate characteristics that provide a fertilisation advantage. Thus, sperm competition is recognised as a persuasive force in the evolution of male reproductive traits. Comparative analyses across species, and competitive mating trials within species have suggested that sperm competition can influence the evolution of testis size and sperm production, and both sperm form and sperm function. ... After six generations of selection I observed phenotypic divergence in litter size - litter size increased in the polyandrous lines but not in the monandrous lines. This result was not attributable to inbreeding depression, or environmental/maternal effects associated with mating regime. Genetic benefits associated with polyandry could account for this result if increased litter size were attributable to increased embryo survival. However, males from the polyandrous lineages were subject to sperm competition, and evolved ejaculates with more sperm, suggesting that evolutionary increases in litter size may in part be due to improved male fertility. Finally, Chapter Five is an investigation of the natural variation in levels of polyandry in the wild, and the potential for sperm competition to drive macroevolutionary changes in male reproductive traits among geographically isolated island populations of house mice. I sampled seven island populations of house mice along the coast of Western Australia and, by genotyping pregnant females and their offspring, determined the frequency of multiply sired litters within each population. I applied the frequency of multiple paternity as an index of the risk of sperm competition, and looked for selective responses in testis size and ejaculate traits. I found that the risk of sperm competition predicted testis size across the seven island populations. However, variation in sperm traits was not explained by the risk of sperm competition. I discuss these results in relation to sperm competition theory, and extrinsic factors that influence ejaculate quality.

Computational evolutionary analyses, particularly phylogenetics and ancestral reconstruction, have been extensively exploited under different algorithms and evolutionary models to better understand genome evolution from both small- and large-scale perspectives in order to assign genotypes based on assortment, resolve species relationships and gene annotation issues, further understand gene gain/loss within individual gene families, measure functional divergence among homologs, and infer ancestral character states. These evolutionary studies provide us with insights into biologically relevant issues including paleoenvironments inferred from resurrected proteins, developmental physiology associated with functional divergence of duplicated genes, viral epidemics and modes of transmission in attempt to better prepare, prevent and control diseases, evolution of lineage-specific pathogenicity, and attempts to create a synthetic ancient organism that would benefit the field of synthetic biology. Our work also provides us with greater insights into the accuracies and limitations of ancestral sequence reconstruction methods. In total, our work highlights the diverse questions that evolutionary studies attempt to address and the different biological levels that can be studied to answer these questions.

The field of molecular evolution has benefited greatly from the use of ancestral sequence reconstruction as a methodology to better understand the molecular mechanisms associated with functional divergence. The method of ancestral sequence reconstruction has never been experimentally validated despite the method being exploited to generate high profile publications and gaining wider use in many laboratories. The failure to validate such a method is a consequence of 1) our inability to travel back in time to document evolutionary transitions and 2) the slow pace of natural evolutionary processes that prevent biologists from ‘witnessing’ evolution in action (pace viruses). In this thesis research, we have generated an experimentally known phylogeny of fluorescent proteins in order to benchmark ancestral sequence reconstruction methods. The tips/leaves of the fluorescent protein experimental phylogeny are used to determine the performances of various ASR methods. This is the first example of combining experimental phylogenetics and ancestral sequence reconstruction.

Thesis (Ph. D.)--University of Texas at Austin, 2008. / Vita. Includes bibliographical references.

Thesis (Ph. D.)--University of Washington, 1996. / Vita. Includes bibliographical references (leaves [269]-287).

Darwin's (1859) theory of evolution by natural selection accounts for the adaptations of organisms, but, as Fisher (1930) famously said, 'natural selection is not evolution.' Evolutionary theory has two major components: i) natural selection, which involves the underlying dynamics of populations; and ii) adaptive evolutionary change, which involves the optimisation of phenotypes for fitness maximisation. Many of the traditional theoretical frameworks in evolutionary theory have focussed on studying optimisation processes that generate biological adaptations. In recent years, however, a number of evolutionary theorists have turned to using frameworks such as the 'replicator dynamics' or 'eco-evolutionary dynamics', to explore the dynamics of natural selection. There has, however, been little attempt to explore how these dynamical systems frameworks relate to more traditional frameworks in evolutionary theory or how they incorporate the principles that embody the process of evolution by natural selection, namely, phenotypic variation, differential reproductive success, and heritability. In this thesis, I use these principles to provide the formal foundations of a general framework - a mathematical synthesis - in which the future state of an evolutionary system can be predicted from its present state; what I will call a 'dynamical systems theory of natural selection.' Given the state of an existing biological system, and a set of assumptions about how individuals within the system interact, the job of the dynamical systems theory of natural selection is no less than to predict the future in its entirety.

Orientador: Otavio Augusto Vuolo Marques / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-06T10:14:24Z (GMT). No. of bitstreams: 1 Prado_LigiaPizzattodo_D.pdf: 3835515 bytes, checksum: 7b2944c265d7bc36173b6191c53632b0 (MD5) Previous issue date: 2006 / Resumo: Síndromes morfológicas relacionadas ao uso do ambiente têm sido observadas em diversas serpentes. Entretanto, a morfologia corporal pode estar associada à linhagem filogenética dos organismos. Portanto, estudos eco-morfológicos podem ser melhor realizados utilizando-se métodos comparativos. Utilizando-se espécimes depositados em coleções, os Boidae (subfamílias Boinae e Pythoninae) foram comparados quanto à morfologia corporal e sua relação com o uso do ambiente. Espécies arborícolas apresentam maior compressão lateral do corpo e cauda relativamente maior quando comparadas àquelas terrícolas e aquáticas, mesmo quando removido o efeito filogenético. O dimorfismo sexual ocorreu em relação ao comprimento rostro-cloacal (CRC), tamanho relativo da cabeça, da cauda, circunferência corporal, compressão lateral do corpo e tamanho do esporão. Entretanto, dentre os Boinae, o dimorfismo de CRC não foi observado na maioria das espécies que apresentam combate (Epicrates spp.) e o de cauda não foi observado nas arborícolas. Na maioria dos casos o dimorfismo resulta de crescimento diferencial entre os sexos já que não estão presentes em recém-nascidos. A otimização dos caracteres morfológicos e de uso do ambiente nas hipóteses filogenéticas disponíveis sugere que os Boidae sofreram poucas modificações ao longo da evolução, muitas das quais representam autapomorfias das espécies ou subespécies. Duas hipóteses filogenéticas concordam que o ancestral dos Boinae possuía cauda curta, circunferência corporal moderada, cabeça pequena, baixo índice de dimorfismo sexual de CRC (SSD) e era semi-arborícola. Mas, não concordam em como seria o ancestral quanto ao tamanho corporal e compressão lateral do corpo. Informações sobre a biologia reprodutiva dos Boinae Neotropicais são restritas e referem-se basicamente a espécimes em cativeiro. Este trabalho apresenta informações sobre a ecologia reprodutiva dessas serpentes, a partir de exemplares preservados em coleções, e compara com as informações disponíveis na literatura para os Erycinae e Pythoninae. Com exceção de Corallus hortulanus e Eunectes murinus, todas as espécies apresentaram vitelogênese concentrada no outono-inverno, gestação do final do inverno até a primavera e nascimentos no final da primavera até o verão. Cópula foi observada em poucas espécies (Boa constrictor ssp. e Epicrates cenchria crassus) e ocorreu do outono até início do inverno. As espécies do gênero Corallus apresentaram vitelogênese mais prolongada. A gestação em C. hortulanus ocorreu desde o final do verão até início do inverno e os nascimentos no outono-inverno. Eunectes murinus apresentou vitelogênese na primavera, a gestação durante o verão e os nascimentos no outono-inverno. O ciclo testicular foi sazonal em B. c. constrictor (pico de espermatogênese no verão) e em E. c. crassus (pico de espermatogênese no verão-outono) e contínuo nas demais espécies analisadas (C. hotulanus, E. c. assisi e E. c. cenchria). O tamanho da ninhada variou de acordo com o tamanho das espécies. O padrão reprodutivo da maioria dos Boinae analisados parece diferir dos Boinae de Madagascar e dos Erycinae, assemelhando-se ao padrão da maioria dos Pythoninae. O tamanho da ninhada e dos recém-nascidos é semelhante nas sub-famílias Boinae e Pythoninae / Abstract: Morphological syndromes related to macrohabitat use have been detected in many snakes. However, body morphology can be also related to phylogenetic lineage and for this reason ecomorphological studies are better when using comparative methods. Body morphology and its relationship with macrohabitat use was compared among the Boidae snakes, using preserved specimens deposited in museum collections. Arboreal species are more flattened laterally and have relative longer tails, than terrestrial or aquatic species, even after removing phylogenetic effects. Sexual dimorphisms occurs in SVL, relative head size, tail length, body circumference, lateral flatness of the body and spur size. However, SVL dimorphism are absent in some species with ritual combat (Epicrates ssp.) and tail dimorphism is absent in arboreal species. In most cases sexual dimorphism results of diferential growth in sexes because it does not occur in newborn. Optimizations of morphological characters and microhabitat use on two phylogenetic hypotheses suggest that Boinae had little modifications during the evolution, and most of that represent autapomorphies in species or subspecies level. Both hypotheses agree that the ancestor of Boinae was a short-tailed snake, with medium-size body circumference, small head, low SSD and semi-arboreal, but they disagree how would be the ancestor in terms of body size and lateral flatness of the body. Data on the reproductive biology of Neotropical Boinae are mostly restricted to captive snakes. This work presents information on reproduction of these snakes, using preserved specimens from collections, and compares the results to those available in literature to the subfamilies Pythoninae and Erycinae. The Neotropical Boinae presented vitelogenesis mostly during the autumn and winter (except for Corallus hortulanus and Eunectes murinus), pregnancy from late winter to spring and birth from late spring to summer. Mating was only recorded to Boa constrictor spp. and Epicrates cenchria crassus, from autumn to early winter. Vitellogenis timing was more extended in Corallus hortulanus, the pregnancy was recorded from late summer to early winter, and birth from autumn to winter. In Eunectes murinus vitellogenesis occurred in the spring, pregnancy in the summer and birth from autumn to winter. Testicular cycles were seasonal in Boa c. constrictor (peak occurring in the summer) and in Epicrates c. crassus (peak occurring in the summer-autumn), but continuous in the other species (C. hotulanus, E. c. assisi e E. c. cenchria). Clutch size differs among species but it was related to SVL. The reproductive pattern in most Boinae species apparently differed from the Madagascan boas and Erycinae species but was very similar to the pattern recorded to most Pythoninae snakes. Clutch size and offspring size is similar among Boinae and Pythoninae snakes / Doutorado / Ecologia / Doutor em Ecologia

Orientador: Wilson Castro Ferreira Junior / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Matemática, Estatística e Computação Científica / Made available in DSpace on 2018-08-20T05:05:37Z (GMT). No. of bitstreams: 1 Assis_RaulAbreude_D.pdf: 6617583 bytes, checksum: 80b80410952f2ac47edc7cf71466fb07 (MD5) Previous issue date: 2012 / Resumo: Neste trabalho apresentamos modelos matemáticos de processos evolutivos, utilizando como abordagem principal a descrição da frequência de fenótipos em populações. São propostos diversos modelos baseados em equações diferenciais parciais, ordinárias e equações de recorrência. São apresentados resultados de suas análises, bem como comparações com modelos genéticos aditivos. Como uma ilustração do tipo de abordagem proposto, criamos um modelo de um sistema do tipo parasita-hospedeiro (Maculinea-Myrmica) utilizando-o com o objetivo de analisar comportamento de especificidade de hospedeiro. Finalmente, apresentamos generalizações dos modelos em espaços de fenótipos e indicamos direções para aprofundamento de pesquisa / Abstract: In this thesis we present models of evolutionary dynamics that describe the changes in frequencies of phenotypes in populations. The models proposed are based on ordinary and partial differential equations and difference equations. Results from the analysis of the models and comparisons with the behavior of additive genetic models are presented. We develop a model for a host-parasite system (Maculinea-Myrmica) using the phenotypic space aprroach with the objective of analysing the hostspecificity behavior of the species. Finally, we present generalizations of the models of phenotypic spaces and indicate directions for further research in the area / Doutorado / Matematica Aplicada / Doutor em Matemática Aplicada

Les systèmes toxine-antitoxine (TA) sont composés de deux gènes organisés en opéron retrouvés chez la quasi-totalité des bactéries ainsi que chez les archées. Ils ont été découverts sur des plasmides, où ils induisent une tuerie post-segregationnelle (PSK). En effet, l’antitoxine est instable car elle est dégradée par une protéase ATP dépendante. Lors de la réplication, si un plasmide portant un système TA n’est pas transmis à la cellule fille, celle-ci recevra tout de même une partie du cytoplasme de la cellule mère qui contenait des protéines de toxine et d’antitoxine. Cette dernière étant instable, et sans synthèse de novo, la toxine va se retrouver libre d’affecter sa cible cellulaire. Un système TA crée donc une addiction au plasmide qui le porte, stabilisant celui-ci.<p>Les systèmes TA se retrouvent également, dans un nombre de copies variable, au sein du chromosome. Dans ce cas, plusieurs hypothèses existent quant à leur fonction, comme la mort cellulaire programmée, la réponse au stress, la stabilisation de régions génomiques non essentielles, ou l’anti-addiction au plasmide.<p>L’origine et l’évolution des systèmes TA restent inconnues, alors qu’ils présentent des aspects intrigants. En effet, les toxines CcdB et MazF ont des séquences et des activités toxiques très différentes, malgré une structure proche ;les toxines RelE et ParE présentent des séquences proches, mais des fonctions différentes. À l’heure actuelle, les deux hypothèses concernant l’origine évolutive des systèmes TA sont soit qu’ils seraient tous issus d’un ancêtre commun, soit qu’ils auraient été réinventés plusieurs fois au cours de l’évolution, à partir d’un nombre limité de gènes.<p>Au cours de cette thèse, nous avons abordé la question de l’origine et l’évolution des systèmes TA de plusieurs manières :par la reconstruction de phylogénies et de séquences ancestrales, et par l’étude d’un système chromosomique particulier au sein de nombreuses souches d’Escherichia coli. Enfin, nous nous avons décidé d’analyser le contexte génomique des systèmes TA chromosomiques. Ces travaux ont notamment permis de mieux comprendre l’évolution des systèmes TA, et de conforter l’hypothèse selon laquelle ils seraient des éléments égoïstes, évoluant au sein des génomes sans gain d’aptitude pour l’hôte.<p> / Doctorat en Sciences / info:eu-repo/semantics/nonPublished