With the transition from water to land in early tetrapods, and with transitions to secondarily aquatic habits in numerous tetrapod lineages, the functions of the vertebral column were transformed. Morphological changes in the vertebral column are a major mechanism by which vertebrates accommodate changes in locomotor forces. Although morphometric measurements from vertebrae have been correlated with axial mechanics and locomotor behaviour in numerous extant taxa, few studies have sought to test or apply these principles in non-mammalian tetrapods. In my thesis, I reconstructed the vertebral mechanics of fossil taxa that represent intermediate stages in water/land transitions of their lineages. Study taxa were the basal tetrapod Pederpes finneyae, which is one of the earliest known tetrapods to show indications of terrestrial adaptation, and three extinct crocodylomorphs, Terrestrisuchus, Protosuchus, and Pelagosaurus, which span the spectrum from fully terrestrial to primarily aquatic. I used a combination of morphometric measurements and 3D virtual models of bone morphology to estimate intervertebral joint stiffness and range of motion. For comparison, I also reconstructed the vertebral mechanics of four related extant taxa. Correlations between vertebral morphometrics and axial stiffness were statistically tested in (cadaveric) modem crocodylians, and I validated my methodology by comparing my results with data from extant taxa. My results reveal similarities and differences between the two lineages. Intervertebral joint compliance and range of motion tended to decrease with adaptation for terrestrial locomotion, as expected, but this trend seems to have reversed in later forms. Additionally, vertebral mechanics may have been largely controlled by different structural mechanisms in different lineages. The relationship between biomechanics of vertebrae and environment appears to be more complex than previously supposed. However, approaches that combine experimental measurements from extant animals, thorough analysis of fossil morphology, and explicit phylogenetic considerations have the potential to greatly improve locomotor reconstructions of extinct taxa.

Laboratory bacterial populations provide ideal opportunities to experimentally test theories in ecology and evolutionary biology. I used a model laboratory microbial system, Pseudomonas fluorescens SBW25, to address an array of questions on the origin, maintenance, and functional role of biodiversity, and the evolution of biotic interactions. My thesis reports experiments with the following conclusions. (1) The extent of diversification in P. fluorescens populations is not affected by the presence of an interspecific competitor P. putida, although the early stage of the diversification in one environment (spatially homogeneous environment) could be speeded up by the competitor. (2) Niche and neutral mechanisms simultaneously contribute to the maintenance of phenotypic diversity in P. fluorescens populations; but the operation of niche processes does not lead to a positive effect of biodiversity on ecosystem functioning. (3) The competitive interactions among bacterial phenotypes are generally transitive, and competitive hierarchies inferred from pair-wise competition are fairly consistent to those from multi-species competition. (4) The niche complementarity and selection effects evaluated by random assembly biodiversity experiments can be used to predict the functional consequences of particular non-random species extinction scenarios. (5) P. fluorescens does not show an evolutionary trade-off in using several carbon substrates (glucose, galactose and trehalose), and evolution in environments containing these resources results in imperfect generalists; migration among populations may speed up fitness evolution of some generalists. (6) Biofilm formation at the air-broth interface by wrinkly spreader phenotypes in P. fluorescens is a cooperative behaviour which is costly to individuals but benefits the group; this behaviour could be exploited by smooth morph phenotypes. The cooperators and cheats in this system show reciprocal antagonistic coevolution in resistance and cheating performance.

A satisfactory account of human cognitive evolution will explain not only the psychological mechanisms that make our species unique, but also how, when, and why these traits evolved. To date, researchers have made substantial progress toward defining uniquely human aspects of cognition, but considerably less effort has been devoted to questions about the evolutionary processes through which these traits have arisen. In this article, I aim to link these complementary aims by synthesizing recent advances in our understanding of what makes human cognition unique, with theory and data regarding the processes of cognitive evolution. I review evidence that uniquely human cognition depends on synergism between both representational and motivational factors and is unlikely to be accounted for by changes to any singular cognitive system. I argue that, whereas no nonhuman animal possesses the full constellation of traits that define the human mind, homologies and analogies of critical aspects of human psychology can be found in diverse nonhuman taxa. I suggest that phylogenetic approaches to the study of animal cognition-which can address questions about the selective pressures and proximate mechanisms driving cognitive change-have the potential to yield important insights regarding the processes through which the human cognitive phenotype evolved.

Pterotermes is a very primitive genus of the lower termite family Kalotermitidae. Entire colonies were collected from standing dead Cercidium (palo verde) near Tucson, AZ. Most were maintained and recensused. Some were partitioned into groups by caste and instar, and the groups followed to determine developmental fates. Sorted material was preserved for morphometrics. Alate pairs were sealed in chambers in two sizes of palo verde and colonies allowed to grow. New colonies grow for several years, producing only "larvae" which develop into large workers, with occasional maturation to soldier form. Then most fifth or sixth instar larvae of upcoming cohorts undergo three nymphal instars before maturing to alates which leave to found new colonies. Workers do not seem to mature to alates, but may become soldiers or neotenic reproductives. Colonies are headed by a single royal pair, usually the founders, especially the founding queen (84%). Workers can be recruited by biting the wing bud region of larvae or nymphs. Bitten termites develop toward worker form. Workers may be biting siblings to recruit helpers, perhaps improving their own indirect fitness. In the two sizes of wood, no colony consumed more than a fraction of the wood volume, yet colonies in small branches restricted egg crop, hence colony, growth. In the field, branch size was a good predictor of colony size (r-squared 0.80). A theory is proposed based on spreading reproductive output over the expected lifespan of the royal pair. The data are interpreted to support a view of colonies as largely under royal pair control. Pterotermes seems to exhibit the worker-nymph developmental dimorphism proposed by Watson and Sewell (1981) to be an ancestral feature of termite biology. A scheme of origin is proposed, in which the parents suppressed facultative neotenic maturation, then all sexual maturation of earliest offspring. Workers were the result of arrested maturation (see also Myles, 1983). It is argued that once eusociality evolves, close genetic relatedness of colony members is not required for maintenance of the system, as long as some minimal degree of family structure remains.

Flowering time is a carefully regulated trait that integrates cues from temperature and photoperiod to coordinate flowering at favorable times of the year. This dissertation aims to understand the evolution of genetic architecture that facilitated the transition of Pooideae, a subfamily of grass, from the tropics to the temperate northern hemisphere approximately 50 million years ago. Two traits hypothesized to have facilitated this evolutionary shift are the use of long-term low-temperature (vernalization) to ready plants for flowering, and long-day photoperiods to induce flowering. In chapter one I review literature on the regulation of grass flowering by vernalization and photoperiod, and in chapters two and three I determine the role of VERNALIZATION 1 (VRN1) and VRN2, known to confer vernalization responsiveness in core Pooideae crop species, in flowering time across Pooideae. In chapter four, I then test predictions of the hypothesis that the Brachypodium distachyon miR5200 ortholog in the ancestor of Pooideae was important for suppressing short day flowering through its negative regulation of flowering time integrator FLOWERING LOCUS T (FT)/VERNALIZATION3 (VRN3). In combination with other studies, my data demonstrate that VRN1-mediated vernalization responsiveness evolved early in the Pooideae, while VRN2-mediated vernalization responsiveness appears to have evolved much later in the diversification of Pooideae. Although miR5200 likely evolved early in the Pooideae, its transcriptional regulation by short day photoperiod appears derived within Brachypodium distachyon. This work answers important questions about the evolutionary origin of temperature- and photoperiod-mediated flowering in an economically important clade that contains crop species such as wheat (Triticum aestivum) and barley (Hordeum vulgare). Directions for future work on this topic are discussed in chapter 5.

In this thesis, I present the results of a new search for, and study of, luminous galaxies in the first billion years of cosmic time. This work is primarily based on a new selection of bright (L≫L*) Lyman-break galaxies (LBGs) at z ≅6 and z≅7 in the UltraVISTA first and second data releases (DR1, DR2) and the UKIDSS (UKIRT Infrared Deep Survey) UDS DR10 (Ultra Deep Survey). The UltraVISTA survey provides deep Y, J,H andKs near-imaging over 1.5 deg² of the Cosmic Evolution Survey (COSMOS) field and the UKIDSS UDS provides J,H and K band data overlapping with the Subaru XMM-Newton Deep Survey (SXDS), with both fields also containing deep optical and mid-infrared imaging essential for the clean detection of z > 5 galaxies. The fields combined provide an unprecedented 1.65 deg² of deep multiwavelength data with which to securely select LBGs using a photometric redshift fitting technique, which can additionally remove probable low-redshift galaxy interlopers and galactic dwarf stars that can contaminate ground-based samples. At z ≅7, the DR1 of the UltraVISTA survey was used to select a sample of ten high-redshift galaxy candidates, which extended to a 5σ limiting magnitude of Y + J ~ 25 (AB magnitude, 2-arcsec diameter circular aperture) over 1 deg². A stack of the four most robust objects from the sample indicated that they were massive (M*≅5 × 109M ʘ), had blue rest-frame UV slopes (β ≅−2.0±0.2) and were highly star-forming (SFR ≅25–50Mʘ yr−1) when compared to previous, fainter, samples of galaxies at z = 7. The number counts of z≅7 galaxies selected within the UltraVISTA DR1 survey was higher than that expected from extrapolations of the rest-frame UltraViolet (UV) luminosity function (LF) from fainter data, a result that was strongly confirmed with an improved search for z ≅7 galaxies using the UltraVISTA DR2 imaging and the UDS field. A total of 34 galaxies at 6.5 < z < 7.5 were found in the combined fields, which included the previously identified robust galaxies from the DR1 imaging. This expanded sample allowed the first determination of the rest-frame UV LF in the range −23.0 < MUV < −21.5 at z ≅7, and the results reveal a power-law decline to bright magnitudes in contrast to the commonly assumed exponentially declining Schechter function extrapolated from fainter data. The excess of galaxies observed at bright magnitudes cannot be accounted for by gravitational lensing or by significant contamination of the sample by Active Galactic Nuclei (AGN) . The observed LF is well described by a double power law, which at the bright end follows the form of the underlying dark matter halo mass function, suggesting that the physical mechanism that inhibits star formation activity in massive galaxies (e.g. AGN feedback or some other form of ‘mass quenching’) has yet become efficient at z ≅7. The deeper imaging data confirm that the z ≅7 LBGs show blue rest-frame UV slopes (median β = −2.0) and are massive (up to M*≅1010M ʘ). Furthermore, an analysis of the ground-based imaging shows that the majority are resolved consistent with larger sizes (r1/2 ≅1–1.5 kpc) than displayed by less massive galaxies. Finally, a new search for z ≅6 galaxies within the UltraVISTA and UDS datasets was undertaken, resulting in a sample of 266 LBGs (−22.7 < MUV < −20.5) galaxies with which to investigate the rest-frame UV LF. The potential contamination by galactic brown dwarfs was investigated quantitatively using a simple model of the Galaxy, showing that the expected contamination rate of the sample was < 3 per cent, and that the stars can be effectively removed by fitting standard stellar spectra to the observed photometry. The galaxy surface density in the UltraVISTA/COSMOS field exceeds that in the UDS/SXDS by a factor of ≅1.4, indicating strong cosmic variance between the two fields. The number counts of galaxies we find are a factor of 2 lower than predicted by the recent LF determination by Bouwens et al., and the derived rest-frame UV LF at z ≅6 revealed that an under dense UDS field can account for some of the observed differences between previous analyses. An evolution in the characteristic magnitude between z ≅5 and z≅7 of ∆M*~ 0.5 was found in contrast to other smaller area surveys, and a double power law was shown to equally well describe the LF at z = 6 as compared to the commonly assumed Schechter function. The bright-end of the LF at z ≅6 tentatively shows a steeper decline than found at z ≅7, which could indicate the onset of mass quenching of the most massive galaxies or the rise of dust obscuration. Comparison with the predictions of the latest theoretical models and simulations of galaxies reveals that most models require substantial (A1500 ~ 1.5–2) average dust extinction at the bright end to reproduce the shape of the galaxy UV LF at z ≅7.

O gênero Astyanax é um dos mais especiosos da ordem Characiformes. Suas mais de 100 espécies distribuemse por praticamente toda a região Neotropical e habitam os mais diversos ambientes, como regiões montanhosas, trechos lóticos e leitos de rios, porções lênticas ou lagunares e nascentes. Durante cerca de trinta anos estes peixes têm sido alvo de estudos cromossômicos, que os caracterizaram como um grupo com grande diversidade citogenética. Recentemente, o advento de técnicas de citogenética molecular e de estudos empregando marcadores de DNA tem produzido novos dados sobre a biologia evolutiva do grupo, e possibilitado a revisitação de antigos problemas do gênero, como sua difícil classificação taxonômica. No presente trabalho buscouse a caracterização citogenética e a análise de segmentos do mtDNA (seqüências parciais das regiões dos genes ND2 e ATPase6/8) de diferentes espécies e populações de Astyanax, com a finalidade de contribuir para o reconhecimento de padrões e processos evolutivos no gênero. Foram analisados exemplares provenientes das bacias hidrográficas dos rios São Francisco, Tietê, Paranapanema, MogiGuaçu, Iguaçu, Paraíba do Sul, Ribeira de Iguape e Guapimirim. Os resultados forneceram panoramas filogeográficos e estabeleceram relações evolutivas entre as espécies analisadas, utilizando dados associados de duas classes diferentes de marcadores genéticos. Através da aplicação de técnicas citogenéticas clássicas e moleculares são apresentados dados cariotípicos de A. altiparanae, A. aff. bimaculatus, A. bockmanni, A. aff. fasciatus, A. hastatus, A. mexicanus e A. ribeirae. Nos estudos filogenéticos foram utilizadas, adicionalmente às seqüências das espécies acima citadas, dados provenientes de Astyanax sp.B, A. giton, A. intermedius, A. lacustris, A. aff. scabripinnis, Bryconamericus iheringii, Mimagoniatis microlepis e Roeboides occidentalis. Foram ainda incluídas nas análises seqüências do mtDNA de haplótipos diferentes de A. mexicanus e A. bimaculatus retirados da literatura. Para as diferentes populações amostradas dos grupos A. altiparanae, A. aff. bimaculatus e A. aff. fasciatus, foram efetuadas análises filogeográficas associadas a dados cromossômicos. As análises cromossômicas e moleculares do sistema de drenagem do Leste e de bacias circunvizinhas apresentadas no presente trabalho forneceram dados adicionais para o entendimento da biologia evolutiva do gênero Astyanax. iv Outra contribuição do presente estudo foi a inferência das relações evolutivas de algumas das mais bem estudadas espécies do gênero Astyanax, que a despeito da sua importância ecológica e de constituírem um modelo para estudos cromossômicos e evolutivos, ainda não apresentam estudos filogenéticos amplos. Ainda, a associação de dados cromossômicos e moleculares forneceu um panorama interessante sobre as relações evolutivas em algumas espécies do gênero, bem como sobre os processos e padrões evolutivos presentes nos Astyanax. / Astyanax is one of the species-richest genera within the order Characiformes. More than 100 representatives are widespread throughout nearly all the Neotropical region, inhabiting an array of environments, such as mountain areas, lotic and lentic river portions, lake systems and headwaters. This fish group has been a target of chromosomal studies for over 30 years, showing a remarkable cytogenetic diversity. Recently, the advances in molecular cytogenetics and DNA marker studies have provided new data about the evolutionary biology in this group, allowing revisiting former issues in species of this genus, such as their problematic taxonomical classification. In the present work, we attempted to obtain a cytogenetic characterization and analyze mtDNA segments (partial sequences of the genes ND2 and ATPase6/8) of different species and populations of Astyanax, in order to identify the evolutionary patterns and processes within the genus. Specimens from São Francisco, Tietê, Paranapanema, Mogi-Guaçu, Iguaçu, Paraíba do Sul, Ribeira de Iguape and Guapimirim hydrographic basins were collected. The results revealed phylogeographic scenarios and enabled us to establish the evolutionary relationships among the analyzed species, by associating data from two distinct classes of genetic markers. Through classic and molecular cytogenetic techniques, we present karyotypic data in A. altiparanae, A. aff. bimaculatus, A. bockmanni, A. aff. fasciatus, A. hastatus, A. mexicanus and A. ribeirae. For the phylogenetic studies, we also used, besides those sequences of the species abovementioned, data from the species Astyanax sp.B, A. giton, A. intermedius, A. lacustris, A. aff. scabripinnis, Bryconamericus iheringii, Mimagoniatis microlepis e Roeboides occidentalis. In the mtDNA analyses, sequences from the mtDNA of A. aeneus, and different haplotypes of A. mexicanus and A. bimaculatus available in the literature were included as well. Phylogeographic analyses coupled with chromosomal data were performed for the distinct populational samples in the groups A. altiparanae, A. aff. bimaculatus and A. aff. fasciatus. Both molecular and chromosomal analyses along Eastern drainage systems and nearby basins carried out in the present work provided additional information to the understanding of the evolutionary biology in the genus Astyanax. Another contribution of the present work refers to the inference on the evolutionary vi relationships in some of the most intensively studied species in the genus Astyanax, that, despite of their ecological importance and their role as a model for chromosomal and evolutionary studies, still lack more complete phylogenetic approaches. Furthermore, the association between chromosomal and molecular data revealed an interesting panorama about the evolutionary relationships in some species of this genus, as well as the evolutionary processes and patterns identified within Astyanax.

Les plantes terrestres vivent en association avec des champignons du sol, formant ce que l’on appelle des symbioses mycorhiziennes. Elles échangent du carbone (photosynthétats) contre de l’eau et des minéraux. Ce mutualisme est toutefois troublé par certaines plantes, appelées mycohétérotrophes, capables de soutirer du carbone à leurs symbiontes fongiques. Le plus souvent non photosynthétiques, elles dépendent alors entièrement des champignons mycorhiziens. Certaines ont en revanche conservé la photosynthèse et obtiennent leur carbone par ces deux voies, on les appelle mixotrophes. Cette thèse est consacrée à l’étude des plantes mycohétérotrophes et mixotrophes chez les orchidées, avec des éléments de comparaison chez les éricacées. Les différents travaux qui la structurent précisent la phylogénie de certains groupes clés, s’intéressent aux évolutions génomiques, métaboliques et physiologiques accompagnant ces modes de nutrition originaux, et à leur sensibilité face aux conditions environnementales. / Terrestrial plants live in collaboration with soil fungi, forming associations called mycorrhizal symbioses. They exchange carbon (photosynthates) for water and nutrients. This mutualism is however disrupted by some plants, called mycoheterotrophs, which are able to obtain carbon from their fungal symbionts. Non-photosynthetic most of the time, then they entirely depend on mycorrhizal fungi. Some yet have retained photosynthesis and acquire carbon from these two ways, we called them mixotrophs. This PhD thesis is dedicated to the study of mycoheterotrophic and mixotrophic plants in orchids, with points of comparison in Ericaceae. This dissertation is structured around different kinds of work, which clarify the phylogeny of some key lineages, provide insights into the genomic, metabolic and physiologic evolution going along with these unusual nutrition types, and question how they respond to environmental parameters.

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.

The evolution of snakes (Squamata: Serpentes) represents a major transition in squamate reptiles and involves extensive modifications in the body plan. Functional morphology and phylogeny are integrated to discuss adaptive morphological traits in the origin of snakes and in the evolution of the venom-injecting apparatus among lizards, which is convergent with that in snakes. The focus of these analyses is to determine how to best optimize morphological traits on the phylogeny and to use character distribution in terminal taxa to estimate ecological adaptation in ancestral nodes. To study the locomotion transition from lizards to snakes, 45 virtual models of the squamate bony labyrinth in the inner ear were reconstructed. The results show morphological diversifications of the vestibular region among burrowers, generalists and marine swimmers. The vestibule is enlarged in fossorial species, and reduced in marine snakes and the marine lizard Platecarpus coryphaeus. To quantify the morphological differences and provide tractable methods to reconstruct locomotion in ancestral snakes, I performed three-dimensional geometric morphometric analysis of the 45 samples, using six landmarks and 22 semilandmarks. ANOVA tests on the Procrustes coordinates supported differences among fossorial, generalist, and aquatic locomotion categories. Phylogenetic signal was insignificant in the Procrustes coordinates. Using a phylogeny with the 44 extant samples as terminal taxa, I reconstructed shape coordinates of all internal nodes. Reconstructed shape of the vestibular region of key ancestral nodes in snakes preferred a terrestrial origin for crown-group snakes. Morphological proxies used in this study can be applied to stem snakes to estimate locomotion. Methodologically, this study provides a novel approach to resolve the question whether snakes become limbless on land or in the oceans. Evolution of the venom-injection apparatus in lizards is discussed, based on new material of Estesia mongoliensis. A total-evidence phylogenetic analysis of anguimorph lizards is performed with 86 anguimorph taxa coded to 435 morphological characters and four genes. The matrix includes eight new morphological characters. The total-evidence phylogeny suggests that Estesia Mongoliensis is a basal monstersaur whose crown groups are Heloderma, the only living venomous lizards. Presence of tooth flanges with venom grooves is recognized as a new monstersaurian synapomorphy in this study. Estesia mongoliensis has venom grooves comparable to extant Heloderma, but has a deeper root-to-tip groove in the caudal tooth carina, revealing morphological variations of lizard venom delivery apparatus that are not recorded in extant species.