To understand present patterns of biodiversity, knowledge of a lineage’s past – both evolutionary and geographic – is required. Here I present the first comprehensive phylogenomic study of an Amazonian poison frog genus, Ameerega, as well as the introduction of a new method for characterizing ancestral distributions via phylogenetic niche modeling, which I use to investigate Ameerega’s biogeographic past. I sequenced thousands of ultraconserved elements from over 100 tissue samples, representing almost every described Ameerega species, as well as undescribed cryptic diversity. My phylogenetic inference diverged strongly from those of previous studies. I also introduce a new phylogenetic niche modeling method, which accounts for issues of bias in other methods by incorporating knowledge of evolutionary relationships into niche models. Given modern-day and paleoclimatic data, species occurrence data, and a time-calibrated phylogeny, my method constructs niche models for each extant taxon, uses ancestral character estimation to reconstruct ancestral niche models, and projects these models into paleoclimate data to provide a historical estimate of the geographic range of a lineage. I demonstrate my method on the Ameerega bassleri group. I also use simulations to show that my method can reliably reconstruct the niche of a known ancestor in both geographic and environmental space.

Members of the Mylagaulidae have been known for over a century to bear nasal horns; the only rodents, extinct or extant, ever to have done so. This striking feature is known from five of the over 30 species of mylagaulid rodents discovered across North America and Eurasia, all relatively large animals that were likely less fossorial than their relatives. We describe herein a sixth new species of horned mylagaulid. This new taxon from Sioux County, Nebraska, offers the opportunity to reassess the phylogenetic relationships of Mylagaulidae and test several evolutionary hypotheses. Our analyses demonstrate that horns evolved only once in Mylagaulidae, in the common ancestor of Ceratogaulus, first as short horns exapted from the thickened nasals of fossorial ancestors, and later as taller horns. The horns evolved following a positive allometric scaling with body mass that suggests a response to predation pressure in these nearly blind animals. The evolution of tall horns also corresponds to a jump in body mass. The largest mylagaulids are not horn-bearing species, however. Additional analyses of the complex pattern of body mass evolution we reveal will be necessary to explain the evolution of the largest head-lift digging rodents in Earth history. https://zoobank.org/urn:lsid:zoobank.org:pub:81FE999A-F79E-4BD4-9A81-2C7D3D5D81CD.

Verrucariaceae are a family including mostly lichenized species (Verrucariales, Ascomycota). Its current generic classification, which mainly relies on three morphological characters (spore septation, thallus structure, and hymenial algae), has never been subjected to molecular data. Because these characters were suspected to be homoplastic, the monophyly of the genera as currently delimited based on morphology need to be assessed. A three-gene phylogenetic analysis was carried out using three methods (Maximum Parsimony, Maximum Likelihood, and a Bayesian approach) on 83 taxa, selected from 15 genera in Verrucariaceae. Ancestral state reconstructions were undertaken for four characters (spore septation, thallus structure, hymenial algae, and upper cortex structure). The results confirmed that most of the genera were not monophyletic, and that the most recent common ancestor of Verrucariaceae was most likely crustose, lacking hymenial algae, and with simple spores and a pseudocortex. The use of symplesiomorphic traits to define Verrucaria, the largest and type genus for the Verrucariaceae, as well as the non monophyly of the genera Polyblastia, Staurothele and Thelidium, explain most of the discrepancies between the current classification and a classification using monophyly as a grouping criterion. In order to accommodate newly inferred monophyletic groups, existing genera were re-delimited and three new genera were proposed. Recent broad-scale phylogenetic analyses have shown that Verrucariales was sister to Chaetothyriales, an order first known as including mostly saprophytes and opportunistic animal and human parasites. Investigations of fungal communities colonizing rocks in extreme environments have shown that some slow-growing melanized fungi inhabiting bare rock surfaces belonged to the Chaetothyriales. Multigene phylogenetic analyses were carried out using Maximum Likelihood and a Bayesian approach in order to confirm the affiliation of 25 of these rock isolates. Ancestral state reconstructions were then undertaken on two different datasets to look at the evolutionary history of lichenization within Pezizomycotina, and the rock-inhabiting habit within Eurotiomycetes. Results suggest that the ancestor of the lineage including Verrucariales and Chaetothyriales was likely to be an extremotolerant non-lichenized, rock-inhabiting fungus. Virulence factors of opportunistic parasites within Chaetothyriales, such as melanization and meristematic growth, might have primary been adaptations for life in extreme habitats. / Dissertation

The morphologies and behaviors of animals evolve and diversify, filling ecological niches in their environments. In this study I examine how a morphological trait, body mass, and three ecological traits, namely diel activity patterns, diving/non-diving locomotion, and diet, evolve in the Anseriformes (waterfowl). Through ancestral state reconstructions using a maximum likelihood approach the evolution of these traits was compared to see if any patterns of trait coevolution emerged. Body mass was compared to each ecological trait using a phylogenetic ANOVA to test if there were body size differences between ecological groups. The pattern of male and female body mass evolution across the clade was found to be remarkably similar, indicating that selection effected body mass in similar ways between the sexes. Diving locomotion appears to be the ancestral state for Anseriformes with non-diving independently evolving probably five times. The ancestral state of diet appears to be either herbivory or omnivory, with carnivory secondarily evolving twice independently. For diel activity patterns, the ancestral state reconstruction showed little resolution at the internal nodes, indicating the high degree of plasticity in this trait among the species studied. Body mass in both males and females was not significantly correlated with any particular diet, diving locomotion, or diel activity pattern.

xiv, 195 p. : ill. (some col.) A print copy of this thesis is available through the UO Libraries. Search the library catalog for the location and call number. / We explore the reconstruction of B-state vibrational wave packets in I 2 from simulated two-color nonlinear wave packet interferometry data. As a simplification of earlier proposals, we make use of different vibrational energy ranges in the B-state--rather than different electronic potential surfaces--for the short-pulse preparation and propagation of both target and reference wave packets. Numerical results from noisy interferograms indicate that experimental reconstruction should be possible with high fidelity (>0.99). Time-resolved coherent nonlinear optical experiments on small molecules in low-temperature host crystals are exposing valuable information on quantum mechanical dynamics in condensed media. We make use of generic features of these systems to frame two simple, comprehensive theories that will enable the efficient calculation of their ultrafast spectroscopic signals and support their interpretation in terms of the underlying chemical dynamics. Both treatments rely on the identification of normal coordinates to unambiguously partition the well-structured guest-host complex into a system and a bath and expand the overall wave function as a sum of product states between fully anharmonic vibrational basis states for the system and approximate Gaussian wave packets for the bath degrees of freedom. The theories exploit the fact that ultrafast experiments typically drive large-amplitude motion in a few intramolecular degrees of freedom of higher frequency than the crystal phonons, while these intramolecular vibrations indirectly induce smaller-amplitude--but still perhaps coherent--motion among the lattice modes. The equations of motion for the time-dependent parameters of the bath wave packets are fairly compact in a fixed vibrational basis/Gaussian bath (FVB/GB) approach. An alternative adiabatic vibrational basis/Gaussian bath (AVB/GB) treatment leads to more complicated equations of motion involving adiabatic and nonadiabatic vector potentials. Numerical tests of the FVB/GB are presented. We consider two bilinearly coupled harmonic oscillators with varying coupling strengths and initial conditions and show that the mixed quantum/semiclassical theory compares favorably with the exact results. Linear absorption spectra and wave-packet interferometry signals calculated using the theory are presented. This dissertation includes previously published coauthored material. / Committee in charge: David Herrick, Chairperson, Chemistry; Jeffrey Cina, Advisor, Chemistry; Thomas Dyke, Member, Chemistry Michael Kellman, Member, Chemistry; Hailin Wang, Outside Member, Physics

Orientador: Marcos César de Oliveira / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Fisica Gleb Wataghin. / Made available in DSpace on 2018-08-13T03:07:21Z (GMT). No. of bitstreams: 1 Steinhoff_FrankEduardodaSilva_M.pdf: 633661 bytes, checksum: 4c5305fba85a1d80713ed5dfe1f90f32 (MD5) Previous issue date: 2009 / Resumo: Propomos um método para obtenção de propriedades de sistemas quânticos compostos utilizando apenas medições estritamente locais e comunicação clássica. Isso difere dos esquemas usualmente utilizados em protocolos de informação quântica, que se utilizam em sua maioria de operações globais e/ou operações locais conjuntas. Nosso tratamento consiste em analisar o efeito de medições em um subsistema sobre as submatrizes da matriz densidade do sistema composto. Analisamos então como outros subsistemas podem ser expressos em termos dessas submatrizes, obtendo assim o efeito das medições feitas em um subsistema sobre os outros. Aplicamos esse resultado - válido para sistemas com espaços de Hilbert discretos de dimensão arbitrária - a dois problemas centrais em protocolos de informação quântica: a reconstrução de estados de sistemas compostos e a caracterização de emaranhamento. Para a tarefa de reconstrução, mostramos como determinar um estado de um sistema composto de dimensão finita arbitrária utilizando apenas medições locais e comunicação clássica de uma via. A vantagem de nossa proposta está em eliminar a necessidade de medições conjuntas, o que se traduz, no contexto de ótica linear, em eliminar medições de coincidência. Analisamos a caracterização de emaranhamento considerando classes especiais de estados. Para estados com alta simetria - estados isotrópicos, de Werner e de simetria rotacional constituídos por um qubit e um qudit - mostramos uma relação entre o grau de emaranhamento e a diferença de população medida por um subsistema condicionada a medições de paridade do outro subsistema, relação essa já evidenciada em estados gaussianos simétricos. Além disso, propomos uma nova família de estados cujo emaranhamento pode ser caracterizado com muito menos recursos do que os utilizados para a reconstrução, sendo esses recursos estritamente locais. / Abstract: We propose a method to obtain properties of composite quantum systems using strictly local measurements and classical communication only. This differs from schemes usually employed in quantum information protocols where global and/or joint local operations are commonly used. Our treatment consists of analysing the effect of measurements of a system over submatrices of the density matrix of the compound system. We analyse then how copies of a subsystem can be expressed in terms of these submatrices, obtaining thus the effect of the measurements done in a subsystem upon the others. We apply this result - valid for discrete Hilbert spaces of arbitrary dimension - to two central problems in quantum information protocols: the state reconstruction of composite systems and entanglement characterization. For the reconstruction task, we show how to determine a state of a arbitrary finite dimension composite system using local measurements and one-way classical communnication only. The advantage of our proposal lies in elimnating the need for joint measurements, which translates as eliminating coincidence measurements in linear optics context. We analyse entanglement characterization considering special classes of states. For high symmetry states -isotropic states, Werner states and rotationally symmetric states composed of a qubit and a qudit - we show a relation between entanglement degree and population difference measured by one subsystem conditioned to parity measurements of the other subsystem, this relation already present in gaussian symmetric states. Moreover, we propose a new family os states whose entanglement can be characterized with much fewer resources than that used for reconstruction, this resources being strictly local. / Mestrado / Física / Mestre em Física

Orientador: Maria das Graças Sajo / Resumo: Esta tese está organizada em dois Capítulos que tiveram como objetivos: a. descrever e revisar a anatomia radicular na subtribo Pleurothallidinae, b. apontar caracteres anatômicos radiculares que possam identificar táxons, c. reconstruir a história dos caracteres radiculares usando dados genéticos da região ITS disponíveis no GenBank, e por fim, d. mostrar a ontogenia dos tilossomos em Anathallis sclerophylla. No primeiro Capítulo foi analisada a anatomia radicular de 82 espécies distribuídas em 29 gêneros, abrangendo oito das nove Afinidades dentro da subtribo Pleurothallidinae. Concluímos que o velame biestratificado é comum na subtribo, ocorrendo nas oito Afinidades e em mais de 75% das espécies amostradas. Ainda ocorre velame uniestratificado em Lepanthes calodictyon, e velames com três, quatro e cinco camadas em espécies das Afinidades Restrepia e Masdevallia. Reafirmamos a importância taxonômica dos espessamentos parietais do velame apresentando-os de forma detalhada na organografia do complexo velame-exoderme, sendo os padrões morfológicos e sua distribuição entre as camadas do velame uma rica fonte de informação para o reconhecimento dos gêneros na subtribo. Mostramos os tilossomos de 39 espécies e notamos que morfologias mais simples ocorrem nas Afinidades mais basais e morfologias mais complexas ocorrem nas Afinidades mais derivadas. Na exoderme, espessamentos em “O” ou em “∩” ocorrem principalmente nos gêneros mais basais, a exoderme de paredes finas pode ser inter... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: This thesis is organized in two Chapters that aimed: a. describe and review the root anatomy in the Pleurothallidinae subtribe, b. point out radicular anatomical characters that can identify taxa, c. reconstruct the history of root characters using GenBank genetic data from ITS region, and finally d. to show the ontogeny of tilosomes in Anathallis sclerophylla. In the first Chapter we analyzed the root anatomy of 82 species distributed in 29 genera, covering eight of the nine Affinities within the Pleurothallidinae. We conclude that bistratified velamen is common, occurring in the eight Affinities and in more than 75% of the sampled species. Single layered velamen still occur in Lepanthes calodictyon, in the same way three, four, and five layer occurs in Restrepia and Masdevallia Affinities. We reinforce the taxonomic importance of the velamen parietal thickening, presenting them in detail such a velamen-exodermis complex organogram. The morphological patterns and their distribution between the velamen layers are a rich information source for the genera recognition in the subtribe. We show the tilosomes of 39 species and note that simpler morphologies occur at the early divergent Affinities, and more complex morphologies occur in late divergent ones. In exodermis, “O” or “∩” thickening occurs mainly in basal genera, thin-walled exodermis can be interpreted as a derived apomorphic feature, and “U” thickened exodermis in Barbosella is the only synapomorphy found in the subtribe... (Complete abstract click electronic access below) / Doutor

Liberal peacebuilding, the means by which transition societies can be reconfigured and reconstructed to bring about lasting peace, focussed on chieftaincy reform and decentralization as part of the peacebuilding package in Sierra Leone. The main focus of this research is to explore the efficacy of these structures as durable peacebuilding mechanisms in a transition society like Sierra Leone. The core argument is that liberal peacebuilding based on the reform of chieftaincy and decentralisation has failed to deliver effective peacebuilding mechanisms in Sierra Leone. Chieftaincy reform should have taken into consideration the specific context of the nature of chieftaincy in the country which in most cases transcends issues of leadership to one of collective identity. The decentralisation process is also fraught with a host of problems ranging from tension between the councils and the chiefs on the one hand, to the unwillingness on the part of central government to cede some of its powers to the local government. The control of central government over the councils and the decentralisation process is still very visible. The relevance of this research is that it enhances our understanding of key debates and policy intervention practices on post-war peacebuilding and state reconstruction in transition societies. It also contributes to the existing literature on post-conflict peacebuilding by positing that there is a huge challenge to the Liberal Peace paradigm in bringing about peace in war-torn societies. / Commonwealth Commission

Current approaches to post-war state reconstruction are primarily dominated by the liberal peace thesis. These approaches tend to ignore the indigenous institutions, societal resources and cultural agencies of post-conflict societies, although such entities are rooted in the sociological, historical, political and environmental realities of these societies. Such universalised and 'best practice' approaches, more often than not, tend to reproduce artificial states. The Poro and Sande are the largest indigenous sodality institutions in the 'hinterlands' - a pejorative term attributed to rural Liberia and Sierra Leone. Both the Poro and Sande exercise spiritual, political, economic and social authority. In this thesis, I use critical realism and the case study approach to investigate: a) the extent to which the liberal peace practitioners who are leading state reconstruction in Liberia and Sierra Leone recognised the role and potential utility of the Poro and Sande institutions; b) the extent to which the Poro and Sande were engaged; and c) the implications for the quality and viability of the reconstructed states. This evidence-based research suggests that the liberal peace project sidelined indigenous institutions, including the Poro and Sande, in the post-war recovery and rebuilding exercises. The disregard for indigenous and emerging resources in the context of state reconstruction in Liberia and Sierra Leone has contributed to the resurgence of 19th century counter-hegemonic resistance from the sodality-governed interior of both countries. At the same time, the reconstructed states are drifting back towards their pre-war status quo. Authority structures remain fragmented, kleptocracy is being restored, webs of militarised patronage networks are being emboldened, and spaces for constructive dialogues are shrinking. This thesis underscores the need for indigenisation as a complementary strategy to help reverse the deterioration, and to maximise gains from massive investments in peacebuilding.

Current approaches to post-war state reconstruction are primarily dominated by the liberal peace thesis. These approaches tend to ignore the indigenous institutions, societal resources and cultural agencies of post-conflict societies, although such entities are rooted in the sociological, historical, political and environmental realities of these societies. Such universalised and `best practice¿ approaches, more often than not, tend to reproduce artificial states. The Poro and Sande are the largest indigenous sodality institutions in the `hinterlands¿¿a pejorative term attributed to rural Liberia and Sierra Leone. Both the Poro and Sande exercise spiritual, political, economic and social authority. In this thesis, I use critical realism and the case study approach to investigate: a) the extent to which the liberal peace practitioners who are leading state reconstruction in Liberia and Sierra Leone recognised the role and potential utility of the Poro and Sande institutions; b) the extent to which the Poro and Sande were engaged; and c) the implications for the quality and viability of the reconstructed states. This evidence-based research suggests that the liberal peace project sidelined indigenous institutions, including the Poro and Sande, in the post-war recovery and rebuilding exercises. The disregard for indigenous and emerging resources in the context of state reconstruction in Liberia and Sierra Leone has contributed to the resurgence of 19th century counter-hegemonic resistance from the sodality-governed interior of both countries. At the same time, the reconstructed states are drifting back towards their pre-war status quo. Authority structures remain fragmented, kleptocracy is being restored, webs of militarised patronage networks are being emboldened, and spaces for constructive dialogues are shrinking. This thesis underscores the need for indigenisation as a complementary strategy to help reverse the deterioration, and to maximise gains from massive investments in peacebuilding.