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The effects of external ownership a study of linkages and branch plant location /Malmberg, Bo, January 1990 (has links)
Thesis (doctoral)--Uppsala University, 1990. / Includes bibliographical references (p. 146-153).
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The effects of external ownership a study of linkages and branch plant location /Malmberg, Bo, January 1990 (has links)
Thesis (doctoral)--Uppsala University, 1990. / Includes bibliographical references (p. 146-153).
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Relação temporal de componentes morfológicos e composição química em plantas da caatinga, Serra Talhada – PESILVA, Crissanny Inês de Oliveira 18 October 2012 (has links)
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Previous issue date: 2012-10-18 / Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq / This study aimed to characterize bromatological and morphological components (leaves and stems) of some native plants during different periods of the year. Samples were collected at the farm located in San Miguel Serra Talhada PE. In Caatinga area grazed by sheep throughout the year. The samples were collected at intervals of approximately 45 days, from January to August 2011, totaling five evaluation. The evaluated the following species were: Catingueira (Caesalpinia pyramidalis Tui.), Jurema preta (Mimosa hostilis Benth.), Mororó (Bauhinia cheilantha), Marmeleiro (Cydonia oblonga), Malva branca (Sida cordifolia), Orelha de onça (Macroptilium martii), Capa bode (Ipomeae carnea Jacq.) e Pereiro (Aspidosperma pyrifolium). Sampling was conducted simulating grazing animals, collecting leaves and branches separately, three random samples from each species were collected, consisting of plant material with approximately 2 mm thick and picked up to 1.5 m tall. Average CP observed for the evaluated species were above the critical limits described by the literature for leaf fraction (10.5%) however, CP for the branch fraction was 4.4%. Ashes presented higher overall average of species for leaf fraction (7.7%) compared with the branch fraction (5.6%). There was an increase in the fraction of NDF throughout the research, which showed overall average among species ranged from 46.2 and to 67.1% from January and to August 2011, respectively. In variable tannin there was also an increase during the search among the plants studied. During the year, the chemical composition and tannin content of these forages undergo variations, which can interfere with the quality of these plants and consequently in animal feed. / Objetivou-se caracterizar bromatologicamente componentes morfológicos (folhas e ramos) de algumas plantas nativas durante diferentes períodos do ano. As coletas foram realizadas na fazenda São Miguel situada em Serra Talhada - PE, em área de Caatinga pastejada por ovinos durante todo ano. As coletas das amostras foram realizadas em intervalos de aproximadamente 45 dias no período de janeiro a agosto de 2011, totalizando cinco períodos de avaliações. Foram avaliadas as seguintes espécies: Catingueira (Caesalpinia pyramidalis Tui.), Jurema preta (Mimosa hostilis Benth.), Mororó (Bauhinia cheilantha), Marmeleiro (Cydonia oblonga), Malva branca (Sida cordifolia), Orelha de onça (Macroptilium martii), Capa bode (Ipomeae carnea Jacq.) e Pereiro (Aspidosperma pyrifolium). A amostragem foi realizada simulando pastejo dos animais, coletando as folhas e ramos separadamente, sendo colhidas três amostras aleatórias de cada espécie vegetal, constituídas de material com aproximadamente 2 mm de espessura e colhidos até 1,5 m de altura. Para a variável PB a média geral obtida entre as espécies, foi superior aos limites críticos descritos pela literatura consultada para fração folha 10,5% diferentemente da média geral entre espécies na fração ramos, que foi de 4,4%. A MM apresentou média geral das espécies maior para fração folha 7,7% quando comparado com fração ramos 5,6%. Observou-se aumento de FDN na fração folha ao longo da pesquisa onde apresentou média geral entre espécies de 46,2 e 67,1 % no mês de janeiro e mês de agosto de 2011. Na variável tanino também houve um aumento durante a pesquisa entre as plantas estudadas. Durante o ano, a composição química e teores de taninos destas forrageiras sofrem variações, que podem interferir na qualidade destas plantas e consequentemente no consumo animal.
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Medidas provisórias: os efeitos não antecipados da EC 32 nas relações entre Executivo e Legislativo / Provisional measures: the unanticipated effects of EC 32 in the relations between the Executive and LegislativeFernanda Machiaveli Morão de Oliveira 16 December 2009 (has links)
A presente dissertação tem como objeto a emenda constitucional 32 de 2001, a qual regulamentou o uso das medidas provisórias, estabelecendo limites materiais para o seu conteúdo e um rito mais rigoroso de tramitação. Entre as principais regras estabelecidas, estavam o fim das reedições e o estabelecimento de um prazo de 45 dias para a apreciação das MPs pelo Congresso, sob pena de trancamento da pauta legislativa. A dissertação analisa, em primeiro lugar, as razões que levaram os parlamentares a aprovarem as novas regras. O argumento defendido é que não se tratou de uma reação do Congresso contra a usurpação da função legislativa pelo Presidente, como fora justificado na época. O avanço da PEC das MPs se deveu sobretudo à divisão interna na coalizão de governo, que abriu espaço para a atuação estratégica da oposição. Além disso, a mudança no posicionamento dos ministros do Supremo Tribunal Federal e a campanha da OAB pela limitação do instrumento aumentaram os custos da protelação na apreciação da proposta. Os jogos que ocorriam em outras arenas alteraram os payoffs dos atores na arena parlamentar, criando incentivos para a cooperação entre governo e oposição. Finalmente, a aproximação das eleições presidenciais e a incerteza sobre os papeis que cada partido desempenharia no próximo governo propiciaram um contexto favorável ao acordo. Em seguida, são investigados os efeitos das novas regras sobre a relação entre Executivo e Legislativo. Ao contrário do esperado, o novo rito de tramitação não foi efetivo na redução das medidas provisórias. O uso do instrumento foi intensificado nos anos seguintes à aprovação da emenda constitucional. A principal razão foi o mecanismo de trancamento de pauta estabelecido pela EC 32, o qual conferiu ao Presidente amplo controle sobre a pauta legislativa. As MPs passaram a ser apreciadas em 120 dias, com alto percentual de aprovação. O efeito inesperado da emenda constitucional é explicado pelos pressupostos equivocados que motivaram a campanha pela limitação das MPs. A usurpação dos poderes legislativos era justificada pela paralisia do Congresso, que não apreciava as medidas provisórias deixando espaço para o Executivo legislar unilateralmente. A intensificação do uso do instrumento no período seguinte à EC 32 confirma que as medidas provisórias não são usadas contra as preferências da maioria. Ao contrário, mesmo com a obrigatoriedade de votação em Plenário e o uso frequente de mecanismos legislativos de negação de quórum pela oposição, o governo sai vitorioso em grande parte das votações. Assim, o controle da agenda é útil para coordenar as preferências da maioria e reforçar o seu poder. / This dissertation focuses on the Constitutional Amendment n.32 of 2001, which regulates the use of provisional measures (the Brazilian president´s executive decrees) and sets material limits on its content and more rigorous proceedings. Among its main rules were the prohibition of decree re-issuances and the establishment of a 45-day period for provisional measures to be appreciated by the Congress, under penalty of limiting the legislative agenda. First, the dissertation examines the reasons that led lawmakers to adopt the new rules. The argument is that such adoption was not the congressmen´s reaction against the president´s usurpation of the legislative function, as had been then justified. The advance in the constitutional amendment of the provisional measures results mainly from an internal division in the government coalition, which paved the way for the strategic behavior of the opposition. Moreover, changes in the opinion of the Justices of Brazilian Supreme Court and the Brazilian Bar Association´s campaign for the limitation of the instrument increased the costs of delaying the assessment of the proposal. Events taking place in other arenas have changed the payoffs of the players in the parliamentary arena, creating incentives for cooperation between government and the opposition. Finally, the upcoming presidential elections and the uncertainty about each party´s roles in the next government provided an environment conducive to agreement. Next, we investigated the effects of the new rules in the relationship between executive and legislative branches. Contrary to expectations, the new proceedings failed to reduce the number of presidential decrees. The use of the instrument increased in the years following the approval of the constitutional amendment. The main reason was the mechanism to limit the agenda under Constitutional Amendment n.32, which secured the president wide control over the legislative agenda. The provisional measures started to be assessed within 120 days, with a high percentage of approval. The unexpected effect of the constitutional amendment is explained through the flawed assumptions that led the campaign for the limitation of provisional measures. The \"usurpation of legislative powers\" was justified by the paralysis of Congressmen, who refrained from voting the provisional measures and left room for the Executive to legislate unilaterally. Broader use of the instrument in the period following the Constitutional Amendment n.32 confirms that the provisional measures are not used against the preferences of the majority. Instead, even with mandatory voting in the floor and the frequent use of legislative quorum denial mechanisms by the opposition, the government emerges victorious in most of the votes. Thus, control of the agenda is useful to coordinate the preferences of the majority and strengthen its power.
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Dinâmica da água e carboidratos durante período de repouso hibernal em pereira e pessegueiro nas condições de inverno ameno / Dinâmica da água e carboidratos durante período de repouso hibernal em pereira e pessegueiro nas condições de inverno ameno / Dynamics of water and carbohydrates during rest period in winter pear and peach trees in the mild winter / Dynamics of water and carbohydrates during rest period in winter pear and peach trees in the mild winterRICKES, Letícia Neutzling 28 February 2012 (has links)
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Previous issue date: 2012-02-28 / The translocation of water and carbohydrates in plant tissues temperate fruit still
creates doubts in the scientific field and knows that it is a factor to overcome
dormancy, because to be budburst is needed imports of soluble sugars, the which
are derived from starch conversion adjacent tissues. This work aimed to evaluate
biweekly water content (WC), content of total soluble sugars (TSS), sucrose content
and starch during the winter period (June to September) in tissues of pear cvs.
Housui and Packham's and peach cvs. Eldorado and Jubileu of the orchards
belonging to the Agricultural Center of Palma UFPel. During data collection, four
branches were collected from each cultivar were divided into three positions (basal,
median, apical) to assess where the WC, they were divided in two tissues: bark and
wood. It was found in pear cultivars in both tissue and skin tissue in the wood, do not
show large differences in the dynamics of WC in the three positions studied during
the winter period. However, peach WC on the wood was examined in more than one
shell in the three positions of the branch. The observed increase in WC can be a
physiological marker to break dormancy. This different behavior can be attributed to
the accumulation of cold. Regarding the dynamics of carbohydrate species in the
study behaved differently. In peach there was a significant increase in carbohydrate
content in the apical position around the time of shooting, not unlike what was
observed in the case of the pear. The lack of cold and thermal fluctuations directly
affect the activity of hydrolytic enzymes, which explains the lack of starch
degradation in the tissues of the pear. The two species have different requirements in
relation to the accumulation of cold, explaining the different behavior in the dynamics
of water and carbohydrates in the winter rest period. / A translocação de água e carboidratos nos tecidos de plantas frutíferas de clima
temperado ainda gera dúvidas no campo científico e sabe-se que é um fator
determinante para superação da dormência, pois para haver brotação das gemas é
necessário que haja importação de açúcares solúveis, aos quais são provenientes
da conversão do amido nos tecidos adjacentes. Este trabalho teve como objetivo
avaliar quinzenalmente o conteúdo de água (CA), conteúdo de açúcares solúveis
totais (AST), conteúdo de sacarose e amido, durante o período hibernal (junho à
setembro) em tecidos de pereira cvs. Housui e Packham´s e pessegueiro cvs.
Jubileu e Eldorado dos pomares pertencentes ao Centro Agropecuário da Palma da
UFPel. A cada coleta foram coletados quatro ramos de cada cultivar e divididos em
três posições (basal, mediana, apical) onde para avaliação do CA, estes foram
divididos em dois tecidos: casca e lenho. Foi verificado nas cultivares de pereira
tanto no tecido da casca quanto no tecido do lenho, não apresentar grandes
diferenças na dinâmica do CA nas três posições avaliadas durante o período
hibernal. No entanto, no pessegueiro o CA no lenho foi superior a aquele analisado
na casca nas três posições do ramo. O aumento do CA verificado pode ser um
marcador fisiológico para superação da dormência. Este comportamento
diferenciado pode ser atribuído ao acúmulo de frio. Em relação à dinâmica dos
carboidratos, as espécies do estudo comportaram-se de maneira diferenciada. No
pessegueiro houve um aumento significativo no conteúdo de carboidratos na
posição apical próximo ao período de brotação, o que contrariamente não foi
verificado no caso da pereira. A falta de frio e as oscilações térmicas afetam
diretamente a atividade das enzimas hidrolíticas, ao qual explica a falta de
degradação do amido nos tecidos da pereira. As duas espécies apresentam
exigências diferenciadas em relação ao acúmulo de frio, justificando o
comportamento diferenciado na dinâmica da água e carboidratos no período de
repouso hibernal.
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Comparison of Variable Rate Prescriptions and Optimum Seeding Rate in Soybean [Glycine max (L.) Merr] and the Impact of Soybean Seeding Rate on Combine Fuel Use and Grain Loss at HarvestHamman, William Patrick 26 August 2019 (has links)
No description available.
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Establishing Effective Techniques for Increasing Deep Neural Networks Inference Speed / Etablering av effektiva tekniker för att öka inferenshastigheten i djupa neurala nätverkSunesson, Albin January 2017 (has links)
Recent trend in deep learning research is to build ever more deep networks (i.e. increase the number of layers) to solve real world classification/optimization problems. This introduces challenges for applications with a latency dependence. The problem arises from the amount of computations that needs to be performed for each evaluation. This is addressed by reducing inference speed. In this study we analyze two different methods for speeding up the evaluation of deep neural networks. The first method reduces the number of weights in a convolutional layer by decomposing its convolutional kernel. The second method lets samples exit a network through early exit branches when classifications are certain. Both methods were evaluated on several network architectures with consistent results. Convolutional kernel decomposition shows 20-70% speed up with no more than 1% loss in classification accuracy in setups evaluated. Early exit branches show up to 300% speed up with no loss in classification accuracy when evaluated on CPUs. / De senaste årens trend inom deep learning har varit att addera fler och fler lager till neurala nätverk. Det här introducerar nya utmaningar i applikationer med latensberoende. Problemet uppstår från mängden beräkningar som måste utföras vid varje evaluering. Detta adresseras med en reducering av inferenshastigheten. Jag analyserar två olika metoder för att snabba upp evalueringen av djupa neurala näverk. Den första metoden reducerar antalet vikter i ett faltningslager via en tensordekomposition på dess kärna. Den andra metoden låter samples lämna nätverket via tidiga förgreningar när en klassificering är säker. Båda metoderna utvärderas på flertalet nätverksarkitekturer med konsistenta resultat. Dekomposition på fältningskärnan visar 20-70% hastighetsökning med mindre än 1% försämring av klassifikationssäkerhet i evaluerade konfigurationer. Tidiga förgreningar visar upp till 300% hastighetsökning utan någon försämring av klassifikationssäkerhet när de evalueras på CPU.
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Banken och kunderna : En studie om bankmedarbetares och företagskunders upplevda behov av kontakt i det fysiska rummet / The future of Swedish bank branches : A customer relationship studyHuttunen, Kristina, Schedvins, Johan January 2018 (has links)
99,9% av Sveriges företag är SMEs (små och medelstora företag), och de små företagen är viktiga bland annat för att hålla arbetslösheten nere. Trots det minskar antalet krediter till dessa företag. De fysiska bankkontoren försvinner, framför allt i mindre städer och orter, samtidigt som användningen av digitala tjänster ökar. I medierna riktas kritik mot bankerna och många menar att bankerna bara bryr sig om storstadsregionerna. Problemet är alltså att antalet bankkontor minskar, och detta gör att bankpersonal och kunder får minskade möjligheter att mötas i det fysiska rummet. Syftet med uppsatsen är att ta reda på hur relationen mellan banker och kunder i segmentet SMEs i mindre städer kan påverkas av möjligheten till kontakt i det fysiska rummet.Tidigare studier visar att det är fördelaktigt för företagskunder, särskilt SMEs, att ha en god relation till sin bank. Då ökar sannolikheten att få krediter beviljade samt att få bättre anpassade tjänster och finansiella produkter. En tidigare studie om bankkunder i Hong Kong visade att de är illojala mot sina banker, och att kostnaden att byta bank är liten jämfört med att “stå ut” med dålig service.För att nå syftet upprättades sju semistrukturerade intervjuer med personal från banker i mindre städer och orter, samt tre av deras företagskunder i SME-segmentet. Dessa intervjuer analyserades med hjälp av teorier om relationer och vad som gör kunder nöjda och i förlängningen lojala. Vi kom då fram till, i enlighet med teorin, att personlig kontakt verkar göra att kundnöjdheten och därmed också kundlojaliteten ökar. Personlig kontakt är viktig både för relationsbyggande och vid kreditbedömning, särskilt i segmentet SMEs eftersom det ofta saknas underlag för att göra en säker kvantitativ bedömning. Intervjusvaren tyder på att de företagskunder som intervjuats generellt, i motsats till den tidigare studien om lojalitet, är mycket lojala, särskilt i mer glesbefolkade områden där det finns få banker med kontor i närheten. I områden med fler alternativ ser bankpersonalen något oftare att kunder byter bank. Några av bankerna där vi intervjuat personal är just nu mitt i en förändring då bankkontor ska eller har stängts ner, vilket tyder på att antalet bankkontor fortsätter att minska. Detta trots att både bankpersonalen och de företagskunder vi intervjuat anser att bankkontoren är viktiga och att lokal närvaro och lokalkännedom bidrar till positiva synergieffekter för företagskunderna.I framtiden skulle vi gärna se en bredare studie av relationen ur företagens synvinkel. Det vore intressant med en studie som mer ingående ser på hur stort behov företag har generellt av bankkontor och kontakt med bankpersonal i det fysiska rummet. / 99,9% of all companies in Sweden are SMEs (small and medium sized enterprises), and these smaller companies are important for the employment rate. Despite this the number of credits for SMEs is decreasing. The bank branches are being closed down, especially in smaller cities, and meanwhile the usage of digital banking services is increasing. There have been several media articles discussing this matter and many believe that the banks only care about the more densely populated urban regions. The problem is that the number of bank branches is decreasing, and this means that the bank personnel and its customers have smaller chances of meeting in person. In this thesis we have studied the relationship between banks and their customers in the SME segment and how it can be affected by the opportunity for contact in person.Earlier studies show that it is beneficial for bank customers, especially SMEs, to have a good relationship with their bank. It increases the possibility for bank credits and for better service. An earlier study regarding bank customers in Hong Kong shows that they are generally illoyal to their banks, and that the cost of changing banks is small compared to receiving bad service.We performed seven semi-structured interviews with bank personnel from smaller cities, and three interviews with their SME customers. These interviews were analyzed with theories regarding relationships, customer satisfaction and customer loyalty. We found that, just like in the theories, personal contact seems to increase customer satisfaction, which also means that the customer loyalty increases. Personal contact is important both for building a relationship and increases the possibility to yield bank credits, especially in the SME segment, because it is difficult to find enough financial information to calculate a good credit score for companies in the segment. The answers from the interviews show that SMEs are generally very loyal to their banks, especially in more rural areas, where there are few banks with local bank branches. In areas with more alternatives the bank personnel can see that customers change banks more often. Some of the banks where we have interviewed personnel are currently closing down or have recently closed down bank branches. This suggests that the number of branches is still decreasing, despite the fact that both the bank personnel and the SMEs we have interviewed believe that the bank branches are important and that local presence and local knowledge create synergy effects for businesses.In the future we would like to see a broader study of the relationship from the businesses’ viewpoint. It would be interesting to study more in detail how important the bank branches, and contact with bank personnel in person, is to businesses in general.
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Postavení správce daně při zabezpečení státních příjmů / The position of tax administrator in providing the national incomeLodek, Jan January 2012 (has links)
The focus of this dissertation is in the area of theoretical knowledge in customs law and tax law connected with practical knowledge implemented throughout legal relations, its subjects and objects, the rights and obligations of parties in the Act on Taxes and Charges Administration and the new Tax Code as a complex concept of legal proceeding within individual branch of financial law while fulfilling the determining criterion in the system of law. I understand the term "system of law" has more meanings. The system of law is a variously formatted summary of relations between the branches of objective law and legal rules. I also take the term as a set of basic legal systems. Usually it can also be described as a system based on a set of elements connected to each other by a certain structure of relations. On the other hand the system of law symbolizes the indication of the structure of law as a normative legal framework. It then represents a greater unity but also the inner differential in law. The differential sign of dividing law into branches or sub-branches is the nature of the group of social relations which are subject to legislation. The legal system (objective law) is in every country (national law) always somehow structured. The way of matching and organizing the legal institutes into branches is...
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A phylogenomics approach to resolving fungal evolution, and phylogenetic method developmentLiu, Yu 12 1900 (has links)
Bien que les champignons soient régulièrement utilisés comme modèle d'étude des systèmes eucaryotes, leurs relations phylogénétiques soulèvent encore des questions controversées. Parmi celles-ci, la classification des zygomycètes reste inconsistante. Ils sont potentiellement paraphylétiques, i.e. regroupent de lignées fongiques non directement affiliées. La position phylogénétique du genre Schizosaccharomyces est aussi controversée: appartient-il aux Taphrinomycotina (précédemment connus comme archiascomycetes) comme prédit par l'analyse de gènes nucléaires, ou est-il plutôt relié aux Saccharomycotina (levures bourgeonnantes) tel que le suggère la phylogénie mitochondriale? Une autre question concerne la position phylogénétique des nucléariides, un groupe d'eucaryotes amiboïdes que l'on suppose étroitement relié aux champignons. Des analyses multi-gènes réalisées antérieurement n'ont pu conclure, étant donné le choix d'un nombre réduit de taxons et l'utilisation de six gènes nucléaires seulement.
Nous avons abordé ces questions par le biais d'inférences phylogénétiques et tests statistiques appliqués à des assemblages de données phylogénomiques nucléaires et mitochondriales. D'après nos résultats, les zygomycètes sont paraphylétiques (Chapitre 2) bien que le signal phylogénétique issu du jeu de données mitochondriales disponibles est insuffisant pour résoudre l'ordre de cet embranchement avec une confiance statistique significative. Dans le Chapitre 3, nous montrons à l'aide d'un jeu de données nucléaires important (plus de cent protéines) et avec supports statistiques concluants, que le genre Schizosaccharomyces appartient aux Taphrinomycotina. De plus, nous démontrons que le regroupement conflictuel des Schizosaccharomyces avec les Saccharomycotina, venant des données mitochondriales, est le résultat d'un type d'erreur phylogénétique connu: l'attraction des longues branches (ALB), un artéfact menant au regroupement
d'espèces dont le taux d'évolution rapide n'est pas représentatif de leur véritable position dans l'arbre phylogénétique. Dans le Chapitre 4, en utilisant encore un important jeu de données nucléaires, nous démontrons avec support statistique significatif que les nucleariides constituent le groupe lié de plus près aux champignons. Nous confirmons aussi la paraphylie des zygomycètes traditionnels tel que suggéré précédemment, avec support statistique significatif, bien que ne pouvant placer tous les membres du groupe avec confiance. Nos résultats remettent en cause des aspects d'une récente reclassification taxonomique des zygomycètes et de leurs voisins, les chytridiomycètes.
Contrer ou minimiser les artéfacts phylogénétiques telle l'attraction des longues branches (ALB) constitue une question récurrente majeure. Dans ce sens, nous avons développé une nouvelle méthode (Chapitre 5) qui identifie et élimine dans une séquence les sites présentant une grande variation du taux d'évolution (sites fortement hétérotaches - sites HH); ces sites sont connus comme contribuant significativement au phénomène d'ALB. Notre méthode est basée sur un test de rapport de vraisemblance (likelihood ratio test, LRT). Deux jeux de données publiés précédemment sont utilisés pour démontrer que le retrait graduel des sites HH chez les espèces à évolution accélérée (sensibles à l'ALB) augmente significativement le support pour la topologie « vraie » attendue, et ce, de façon plus efficace comparée à d'autres méthodes publiées de retrait de sites de séquences. Néanmoins, et de façon générale, la manipulation de
données préalable à l'analyse est loin d’être idéale. Les développements futurs devront viser l'intégration de l'identification et la pondération des sites HH au processus d'inférence phylogénétique lui-même. / Despite the popularity of fungi as eukaryotic model systems, several questions on their phylogenetic relationships continue to be controversial. These include the classification of zygomycetes that are potentially paraphyletic, i.e. a combination of several not directly related fungal lineages. The phylogenetic position of Schizosaccharomyces species has also been controversial: do they belong to Taphrinomycotina (previously known as archiascomycetes) as predicted by analyses with nuclear genes, or are they instead related to Saccharomycotina (budding yeast) as in mitochondrial phylogenies? Another question concerns the precise phylogenetic position of nucleariids, a group of amoeboid eukaryotes that are believed to be close relatives of Fungi. Previously conducted multi-gene analyses have been inconclusive, because of limited taxon sampling and the use of only six nuclear genes.
We have addressed these issues by assembling phylogenomic nuclear and mitochondrial datasets for phylogenetic inference and statistical testing. According to our results zygomycetes appear to be paraphyletic (Chapter 2), but the phylogenetic signal in the available mitochondrial dataset is insufficient for resolving their branching order with statistical confidence. In Chapter 3 we show with a large nuclear dataset (more than 100 proteins) and conclusive supports that Schizosaccharomyces species are part of Taphrinomycotina. We further demonstrate that the conflicting grouping of Schizosaccharomyces with budding yeasts, obtained with mitochondrial sequences, results from a phylogenetic error known as long-branch attraction (LBA, a common artifact that leads to the regrouping of species with high evolutionary rates irrespective of their true phylogenetic positions). In Chapter 4, using again a large nuclear dataset we demonstrate with significant
statistical support that nucleariids are the closest known relatives of Fungi. We also confirm paraphyly of traditional zygomycetes as previously suggested, with significant support, but without placing all members of this group with confidence. Our results question aspects of a recent taxonomical reclassification of zygomycetes and their chytridiomycete neighbors (a group of zoospore-producing Fungi).
Overcoming or minimizing phylogenetic artifacts such as LBA has been among our most recurring questions. We have therefore developed a new method (Chapter 5) that identifies and eliminates sequence sites with highly uneven evolutionary rates (highly heterotachous sites, or HH sites) that are known to contribute significantly to LBA. Our method is based on a likelihood ratio test (LRT). Two previously published datasets are used to demonstrate that gradual removal of HH sites in fast-evolving species (suspected for LBA) significantly increases the support for the expected ‘true’ topology, in a more effective way than comparable, published methods of sequence site removal. Yet in general, data manipulation prior to analysis is far from ideal. Future development should aim at integration of HH site identification and weighting into the phylogenetic inference process itself.
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