<p>Reconstructing the evolutionary history of a set of species is a fundamental problem in biology. This thesis concerns computational problems that arise in different settings and stages of phylogenetic tree reconstruction, but also in other contexts. The contributions include:</p><p>• A new distance-based tree reconstruction method with optimal reconstruction radius and optimal runtime complexity. Included in the result is a greatly simplified proof that the NJ algorithm also has optimal reconstruction radius. (co-author Jens Lagergren)</p><p>• NP-hardness results for the most common variations of Multiple Alignment. In particular, it is shown that SP-score, Star Alignment, and Tree Alignment, are NP hard for all metric symbol distances over all binary or larger alphabets.</p><p>• A 1.375-approximation algorithm for Sorting By Transpositions (SBT). SBT is the problem of sorting a permutation using as few block-transpositions as possible. The complexity of this problem is still open and it was a ten-year-old open problem to improve the best known 1.5-approximation ratio. The 1.375-approximation algorithm is based on a new upper bound on the diameter of 3-permutations. Moreover, a new lower bound on the transposition diameter of the symmetric group is presented and the exact transposition diameter of simple permutations is determined. (co-author Tzvika Hartman)</p><p>• Approximation, fixed-parameter tractable, and fast heuristic algorithms for two variants of the Ancestral Maximum Likelihood (AML) problem: when the phylogenetic tree is known and when it is unknown. AML is the problem of reconstructing the most likely genetic sequences of extinct ancestors along with the most likely mutation probabilities on the edges, given the phylogenetic tree and sequences at the leafs. (co-author Tamir Tuller)</p><p>• An algorithm for computing the number of mutational events between aligned DNA sequences which is several hundred times faster than the famous Phylip packages. Since pairwise distance estimation is a bottleneck in distance-based phylogeny reconstruction, the new algorithm improves the overall running time of many distancebased methods by a factor of several hundred. (co-author Jens Lagergren)</p>

This dissertation contributes an interpretation of the ancestral altar tradition among Vietnamese American first and second generation practitioners. It traces the contours of the shifting transformations in domestic religious practice, specifically the transnational and diasporic dimensions in people's lives. I address how and toward what ends the "spiritual" is accessed, experienced and/or transformed in the materiality of everyday life, in the context of a complex relationship to a diasporic homeland and an emerging second generation. The research was conducted in Houston, Dallas, Austin, San Antonio (Texas), Carthage (Missouri), Sài Gòn (Viet Nam) and Pulau Galang (Indonesia). I make two main assertions. The first is that domestic religious practices matter in exploring issues of cultural citizenship and belonging. As a collection of things, I explain how altar assemblages are constituted through the purposeful and chance encounters of the practitioner(s), which is a way to talk about the global (such as transnational mobilities or the discourses about diasporic citizenship) through the intimately local. My second claim is that ideas of cultural citizenship can intersect with religious motivations and practices, and that they happen (are performed, imagined and circulated) transnationally, or more precisely, translocatively. I document how practitioners' and groups of practitioners' struggle to combat the (current Vietnamese) state's interventions in re-narrating the circumstances of their exile and also the relative invisibility they face as historical subjects in the United States. By carefully examining ancestral altars as a constitution of "things" and as situated "spaces," I address various facets of what they are and how they work -- as ways to express a familial or diasporic imaginary; or as assemblages of things that are both intimately meaningful and private, yet situated at the intersections of geopolitical engagements and cultural politics. / text

Using dendroecological and archaeological methods and data we investigated the temporal dynamics of forest regeneration and fire history following depopulation of four large Pueblo IV period (1300-1600) villages on the Jemez Plateau, New Mexico. With tree rings we reconstructed the timing of reforestation on village footprints after depopulation–a novel approach to terminus ante quem dating of site occupation. Our tree-ring based forest age structure and fire history chronologies enabled us to reduce by 51 to 70 years the range of previous estimates of village depopulation dates derived primarily from terminal ceramic assemblages. One of the four village sites we investigated was depopulated in 1696, two were depopulated between 1625 and 1700 CE, while the fourth village was depopulated earlier (pre 1500), but the area was likely in continued use for agriculture or other seasonal purposes until the mid-1600s. Our results indicate that the Jemez were highly influential ecological agents. Forest structure and fire regime dynamics changed greatly after the departure of most people from these landscapes after circa 1650 CE. The terminus ante quem methods that we demonstrate in the Jemez Mountains have strong potential to constrain and refine low temporal resolution chronologies of human occupation at archaeological sites within other forested ecosystems of the Southwest and elsewhere.

No description available.

Thèse diffusée initialement dans le cadre d'un projet pilote des Presses de l'Université de Montréal/Centre d'édition numérique UdeM (1997-2008) avec l'autorisation de l'auteur.

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.

Doutor -- Universidade Estadual Paulista, Araraquara, 2002.

En los últimos veinte años el número de genomas completos que han sido secuenciados y depositados en bancos de datos  ha crecido dramáticamente. Esta abundancia de información de secuencias ha servido de base para la creación de una disciplina llamada paleogenética. En este artículo, sin ahondar en algoritmos complejos, presentamos algunos conceptos clave para comprender cómo las proteínas han evolucionado con el tiempo. Luego ilustraremos como la paleogenética es utilizada en biotecnología. Estos ejemplos resaltan la conexión entre la química y la biología, dos disciplinas que quizás veinte años atrás parecían ser mucho más distintas que lo que parecen ser hoy. / In the last twenty years, the number of complete genomes that have been sequenced and deposited in data banks has grown dramatically. This abundance in sequence information has supported the creation of the discipline known as  paleogenetics. In this article, without going into complex algorithms, we present some key concepts for understanding how proteins have evolved in time. We then illustrate how paleogenetic analysis can be used in biotechnology. These examples highlight the connection between chemistry and biology, two disciplines that twenty years ago seemed to be more different than what they seem to be today.

xvii, 167 p. : ill. (some col.) / The vacuolar proton-translocating ATPase (V-ATPase) is a multisubunit enzyme complex responsible for acidification of cellular organelles. The V-ATPase hydrolyzes ATP to pump protons across membranes to create an electrochemical gradient. Acidification of vesicular compartments is critical in numerous biological processes including protein trafficking, endocytosis, and ion homeostasis; defects in V-ATPase function can also lead to human diseases. While the function of the V-ATPase enzyme is highly conserved across eukaryotes, the molecular architecture of this protein complex has undergone unique structural changes through evolutionary time. The goal of this work is to investigate the assembly, transport, and evolution of this critical molecular machine in the model organism <italic>Saccharomyces cerevisiae</italic>. A series of genetic screens was performed in budding yeast to identify factors and pathways that are involved in promoting full V-ATPase function. I utilized several "assembly factor" alleles to serve as sensitized genetic backgrounds to partially reduce enzyme function; this work implicated sphingolipid composition in promoting full vacuolar ATPase enzyme function. I also used ancestral gene reconstruction to analyze the two isoforms of subunit a of the V₀ subdomain (Vph1p and Stv1p) by recreating the most recent common ancestral subunit (Anc.a). Characterization of Anc.a demonstrated that this ancient subunit was able to properly assemble and function within a hybrid V-ATPase complex. While the Vph1p-containing complex localized to the vacuole membrane and the Stv1p-containing complex was present on the Golgi/endosome, incorporation of Anc.a caused the V-ATPase to localize to both types of cellular compartments. Finally, I used ancestral reconstruction to investigate the lineage-specific gene duplication of one of the proteolipid subunits of the V₀ subcomplex that occurred within the fungal clade. I demonstrate that inclusion of a third proteolipid subunit within fungi (as compared to two subunits within metazoans) could have occurred via neutral processes by asymmetric degeneration of subunit-subunit interfaces that "ratcheted" the duplicated subunit with the V₀ ring. These results present a model that describes how macromolecular machines can increase in complexity through evolutionary time. This dissertation includes previously published co-authored material and unpublished co-authored material. / Committee in charge: George Sprague, Chairperson; Tom H. Stevens, Advisor; Victoria Herman, Member; Bruce Bowerman, Member; Ken Prehoda, Outside Member

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.