A sistemática da família Rubiaceae passou por grandes mudanças nas últimas duas décadas. O uso de dados moleculares levou a revisões significativas na classificação intra-familiar, principalmente a nível genérico. As relações entre alguns dos gêneros neotropicais mais diversos de Rubiaceae (e.g. Psychotria, Palicourea e Rudgea) estão sendo investigadas. O gênero neotropical Rudgea possui c. 130 espécies, distribuídas do México ao nordeste da Argentina, com dois centros de diversidade, um no noroeste da América do Sul, e outro no sudeste do Brasil. As espécies são caracterizadas pelas estípulas inteiras ou fimbriadas, com apêndices glandulares, presença de domácias nas folhas, inflorescência terminal, lobos da corola corniculados e sementes profundamente sulcadas na face adaxial. Trabalhos filogenéticos anteriores incluíram uma amostragem limitada de espécies do gênero Rudgea. Nossas análises moleculares mostram Rudgea como um gênero monofilético com a exclusão de R. woronovii, uma espécie mais próxima de Palicourea sensu lato. Por outro lado, R. stipulacea emergiu como grupo-irmão das demais espécies de Rudgea, sendo o grupo formado por estas espécies altamente sustentado e denominado \"Rudgea sensu stricto\". Mudanças taxonômicas serão necessárias para acomodar Rudgea stipulacea, e uma classificação infragenérica de Rudgea será proposta, com suporte molecular e morfológico. Além da análises filogenéticas, também foi realizado um tratamento taxonômico para as espécies brasileiras de Rudgea, com 64 espécies aceitas e 26 sinônimos novos. Informações nomenclaturais completas foram fornecidas e 36 lectótipos foram designados. Chaves de identificação para as espécies e subespécies (quando apropriado) também foram apresentadas. Informações sobre distribuição geográfica, habitat, fenologia, discussões taxonômicas, material examinado e figuras também foram apresentadas. Este é o primeiro tratamento de Rudgea para o Brasil desde a monografia de Mueller Argoviensis em 1881 para a Flora Brasiliensis. Como parte dos estudos taxonômicos em Rudgea, o manuscrito que compreende as descrições de duas novas espécies da Bahia (Brasil) e o manuscrito com novas combinações em Rudgea e Palicourea sensu lato também foram incluídos nesta tese / Systematics of Rubiaceae has undergone major changes during the last two decades. The use of molecular data has lead to a profound revision in the intra-familiar classification, mainly at generic level. It has become clear that the relationships between some of the largest genera of Neotropical Rubiaceae (e.g. Psychotria, Palicourea and Rudgea) had to be investigated. The neotropical genus Rudgea encompasses c. 130 species distributed from Mexico to northeastern Argentina with two main centers of diversity, one in the western portion of South America and another in southeastern Brazil. The species are characterized by the entire to fimbriate stipules, with glandular appendages, presence of domatia in the leaves, terminal inflorescence, corniculate corolla-lobes and pyrenes deeply furrowed adaxially. Previous Rubiaceae phylogenies have included a limited sample of Rudgea species. Our molecular analyses have shown Rudgea as a monophyletic genus with the exclusion of R. woronovii, a species more closely related to Palicourea sensu lato. On the other hand, R. stipulacea appears as sister to all other Rudgea, this last group strongly supported and formed by the species of \"Rudgea sensu stricto\". Taxonomic changes will be necessary to accommodate R. stipulacea and an infrageneric classification of Rudgea will be proposed, with molecular and morphological support. Besides the phylogenetic analyses, it was also conducted a taxonomic study for the Brazilian species of Rudgea, with 64 species accepted species and 26 new synonyms proposed. Comprehensive nomenclatural information is supplied and 36 lectotypes are designated. Identification key for the species and subspecies (where appropriate) are provided and information on geographical distribution, habitat, phenology, taxonomic notes, examined material and illustrations are also provided. This is the first comprehensive treatment of Rudgea for Brazil since Mueller Argoviensis published the Flora Brasiliensis monograph in 1881. As part of the taxonomic studies with Rudgea, the manuscript comprising the descriptions of two new species from Bahia (Brazil) and the manuscript with new combinations in Rudgea and Palicourea sensu lato were also included in this thesis

Área de endemismo ou elemento biótico é uma região geográfica que apresenta congruência distribucional entre táxons. Não há um padrão aceito universalmente para delimitação de áreas de endemismo e, portanto, várias metodologias são usadas para sua identificação. Nesta dissertação, propomos uma comparação integrada de alguns métodos de análises de endemismo, com base em dados de distribuição hipotéticos e reais. Desta forma, este estudo tem como objetivos: (1) comparar a Análise de Parcimônia de endemicidade (PAE), a Análise de endemicidade (EA) e um novo método de codificação que propomos a Análise de Distribuições de Três-Itens (3ID), avaliando sua performance com base na capacidade de identificar padrões hipotéticos predefinidos de áreas de endemismo, representando áreas não conflitantes, aninhadas e sobrepostas; (2) analisar os padrões de distribuição de 214 espécies de hidrozoários bentônicos, pelágicos e benthopelágicos não-sifonóforos do Oceano Atlântico Sul Ocidental (OASO), usando três métodos biogeográficos para testar hipóteses anteriores de regionalização biogeográfica e avaliar o performance da PAE, a EA e a 3ID com conjuntos de dados reais. No capítulo 2, intitulado “Comparison of analysis of endemism procedures based on hypothetical distributions”, nós comparamos a PAE, EA e 3ID e encontramos que a 3ID tem o maior percentual de sucesso na recuperação de áreas de endemismo predefinidas. Adicionalmente, a EA é o único método capaz de recuperar padrões sobrepostos, porém também encontra padrões espúrios. Nós sugerimos, portanto, que a melhor opção para identificação de áreas de endemismo é o uso de 3ID e EA em conjunto. No capítulo 3, intitulado “Biogeographic patterns of benthic and planktonic hydrozoans from the southwestern Atlantic Ocean”, nós utilizamos dados distribucionais de 214 espécies de hidrozoários bentônicos, pelágicos e bentopelágicos não-sifonóforos do OASO (20°-60°S, 33°-75°W), os quais foram organizados em diferentes matrizes (concatenada, bentônica, pelágica, e bentopelágica) de acordo com as diferentes estratégias de ciclo de vida em Hydrozoa. Todas as matrizes foram analisadas por meio da PAE, EA e 3ID. Os resultados mostram três padrões biogeográficos gerais: (1) Tropical (2) Temperado-Quente, e (3) Temperado-Frio. Os padrões obtidos variam de acordo com o tipo de ciclo de vida em Hydrozoa, demonstrando a importância de analisar-se separadamente conjuntos de dados de espécies com diferentes estratégias de reprodução. Cada método teve um desempenho diferente e, portanto, concluímos que o uso de 3ID e EA em conjunto é a melhor opção para inferir padrões biogeográficos marinhos / Areas of endemism or biotic elements comprise regions delimited by more than one taxon with coincident patterns of distribution. There is not an accepted universal protocol for delimitation of areas of endemism, and therefore, they are identified by several different methods. In this study, we propose an integrative comparison of different methods for identification of areas of endemism based on data of hypothetical and real distributions. Therefore, the general aims of this study are: (1) to compare the Parsimony Analysis of Endemicity (PAE), the Endemicity Analysis (EA) and a new coding method that we propose, the Three-Item Analysis of Distributions (3ID) to contrast their performance based on their ability to identify hypothetical predefined areas of endemism representing non-conflicting, nested and overlapping patterns; (2) to analyze the patterns of distribution of benthic, pelagic and benthopelagic non-siphonophore hydrozoans of the Southwestern Atlantic Ocean (SWAO), to test previous biogeographic hypotheses of regionalization for the area and to evaluate the performance of the endemicity methods based on real datasets. In chapter 2, entitled “Comparison of analysis of endemism procedures based on hypothetical distributions”, we compared the performance of PAE, EA and 3ID, and we found that 3ID has the greatest percentage of success in retrieving predefined areas of endemism. EA is the only method that recovers overlapping patterns, but it can also find spurious patterns. We recommend the use of 3ID together with EA as the best available option for hypothesizing areas of endemism. In chapter 3, entitled “Biogeographic patterns of benthic and planktonic hydrozoans from the southwestern Atlantic Ocean”, we used the distribution 214 hydrozoan species from the SWAO (20°-60°S, 33°-75°W), which were organized in different data matrices (concatenated, benthic, pelagic, and benthopelagic) according to the different life cycle strategies in Hydrozoa. All matrices were analyzed through PAE, EA and 3ID. The resulting areas showed three broad biogeographic patterns: (1) Tropical, (2) Warm-Temperate and (3) Cold-Temperate. The output patterns varied according to the life cycle of hydrozoan species, demonstrating the importance in analyzing separately data of species with different strategies of life cycle. Each method performed differently, and we concluded that the use of 3ID and EA together is the best approach to infer strong biogeographic patterns for the marine realm

Parareptilien stellen ein artenreiches Monophylum paläozoischer und früh-mesozoischer Amnioten dar; sie bilden innerhalb der Reptilien die Schwestergruppe zu den Eureptilien. Pareiasaurier, eine Untergruppe der Parareptilien, sind eine bedeutende Komponente spät-permischer …kosysteme. Jüngst wurde ein Schwestergruppenverhältnis zu den Nycyeroletern entdeckt, mit welchen sie die "Pareiasauromorpha" bilden. Diese Arbeit befasst sich mit der Beschreibung einiger dieser bisher schlecht untersuchten Parareptilien und deren Verwandtschaftsverhältnisse.Der Pareiasaurier Deltavjatia vjatkensis und der Nycteroleter Emeroleter levis aus der russischen Lokalität Kotel''nich werden mithilfe neu entdeckten Materials im Detail beschrieben. Das gut erhaltene Deltavjatja Materials umfasst mehrere Grössenstadien und erlaubt eine Analyse der Wachstumsraten. Eine geometrisch-morphometrische Analyse des Schädeldachs lässt eine allometrische Zunahme von Schnauzenlänge und Postorbitalregion erkennen. Auch wird der historisch erste Pareiasaurier, Parasaurus geinitzi, aus dem oberpermischen Kupferschiefer von Deutschland neu beschrieben. Zudem ergibt eine Neuanalyse der russischen Nycteroleter eine Synonymie von Tokosaurus perforatus und Macroleter poezicus. Eine phylogenetische Analyse unter Verwendung von Parsimonie und bayesischen Methoden ergibt eine basale Stellung von Parasaurus und eine Monophylie der Nycteroleter; letztere wird aber nur durch die Parsimonie unterstützt. Alle phylogenetischen Methoden ergeben jedoch eine Monophylie der Pareiasauromorpha. Eine strato-kladistische Analyse zeigt zudem eine ähnliche Topologie. Eine biogeographische Analyse der Pareiasauromorpha ergibt mehrfache Verbreitungsereignisse nach Russland und China. Diese stimmen überein mit denen anderer oberpermischer Gruppen, jedoch werden nur wenige dieser Ereignisse komplett bei allen Taxa gefunden. / Parareptilia is a diverse, yet enigmatic clade of fossil amniotes, sister-group to Eureptilia within Reptilia. Pareiasauria, a widely distributed and speciose parareptile group, was a prominent part of Late Permian ecosystems, yet few taxa have been examined in detail. This work describes some poorly known parareptiles, using this data to assess interrelationships and evaluate evolutionary trends within the clade. A reassessment of a group of derived parareptiles, the Russian ''nycteroleters'', results in the synonymy of Tokosaurus perforatus with Macroleter poezicus. A phylogenetic analysis of parareptilian relationships recovers a ''nycteroleter'' monophyly in the parsimony analysis, but not with Bayesian, with the genus Bashkyroleter paraphyletic in both. A monophyletic clade consisting of the nycteroleters and pareiasaurs, termed Pareiasauromorpha, is supported by all methods. Parasaurus geinitzi von Mayer, 1857 is redescribed and confirmed to be a pareiasaur based on the anatomy of the type specimens and fragmentary material that has subsequently been assigned to the taxon. Well-preserved cranial and postcranial material of the pareiasaur Deltavjatia vjatkensis from Kotel''nich, Russia, is described in detail for the first time, including specimens of radically different size classes. The first geometric morphometric analysis of a parareptile reveals an allometric increase in snout length along with an increase in postorbital length. A reassessment of the relationships of Pareiasauromorpha using different methods of phylogenetic inference recovers similar results. The topologies are not well supported, but are relatively consistent with the stratigraphic record. Biogeographic analysis of pareiasauromorph taxa recovers complex and reticulated patterns of dispersal and vicariance, including multiple dispersal events into both Russia and China; patterns that are consistent with those seen in other Late Permian groups, though few events are shared by all clades.

A sistemática da família Rubiaceae passou por grandes mudanças nas últimas duas décadas. O uso de dados moleculares levou a revisões significativas na classificação intra-familiar, principalmente a nível genérico. As relações entre alguns dos gêneros neotropicais mais diversos de Rubiaceae (e.g. Psychotria, Palicourea e Rudgea) estão sendo investigadas. O gênero neotropical Rudgea possui c. 130 espécies, distribuídas do México ao nordeste da Argentina, com dois centros de diversidade, um no noroeste da América do Sul, e outro no sudeste do Brasil. As espécies são caracterizadas pelas estípulas inteiras ou fimbriadas, com apêndices glandulares, presença de domácias nas folhas, inflorescência terminal, lobos da corola corniculados e sementes profundamente sulcadas na face adaxial. Trabalhos filogenéticos anteriores incluíram uma amostragem limitada de espécies do gênero Rudgea. Nossas análises moleculares mostram Rudgea como um gênero monofilético com a exclusão de R. woronovii, uma espécie mais próxima de Palicourea sensu lato. Por outro lado, R. stipulacea emergiu como grupo-irmão das demais espécies de Rudgea, sendo o grupo formado por estas espécies altamente sustentado e denominado \"Rudgea sensu stricto\". Mudanças taxonômicas serão necessárias para acomodar Rudgea stipulacea, e uma classificação infragenérica de Rudgea será proposta, com suporte molecular e morfológico. Além da análises filogenéticas, também foi realizado um tratamento taxonômico para as espécies brasileiras de Rudgea, com 64 espécies aceitas e 26 sinônimos novos. Informações nomenclaturais completas foram fornecidas e 36 lectótipos foram designados. Chaves de identificação para as espécies e subespécies (quando apropriado) também foram apresentadas. Informações sobre distribuição geográfica, habitat, fenologia, discussões taxonômicas, material examinado e figuras também foram apresentadas. Este é o primeiro tratamento de Rudgea para o Brasil desde a monografia de Mueller Argoviensis em 1881 para a Flora Brasiliensis. Como parte dos estudos taxonômicos em Rudgea, o manuscrito que compreende as descrições de duas novas espécies da Bahia (Brasil) e o manuscrito com novas combinações em Rudgea e Palicourea sensu lato também foram incluídos nesta tese / Systematics of Rubiaceae has undergone major changes during the last two decades. The use of molecular data has lead to a profound revision in the intra-familiar classification, mainly at generic level. It has become clear that the relationships between some of the largest genera of Neotropical Rubiaceae (e.g. Psychotria, Palicourea and Rudgea) had to be investigated. The neotropical genus Rudgea encompasses c. 130 species distributed from Mexico to northeastern Argentina with two main centers of diversity, one in the western portion of South America and another in southeastern Brazil. The species are characterized by the entire to fimbriate stipules, with glandular appendages, presence of domatia in the leaves, terminal inflorescence, corniculate corolla-lobes and pyrenes deeply furrowed adaxially. Previous Rubiaceae phylogenies have included a limited sample of Rudgea species. Our molecular analyses have shown Rudgea as a monophyletic genus with the exclusion of R. woronovii, a species more closely related to Palicourea sensu lato. On the other hand, R. stipulacea appears as sister to all other Rudgea, this last group strongly supported and formed by the species of \"Rudgea sensu stricto\". Taxonomic changes will be necessary to accommodate R. stipulacea and an infrageneric classification of Rudgea will be proposed, with molecular and morphological support. Besides the phylogenetic analyses, it was also conducted a taxonomic study for the Brazilian species of Rudgea, with 64 species accepted species and 26 new synonyms proposed. Comprehensive nomenclatural information is supplied and 36 lectotypes are designated. Identification key for the species and subspecies (where appropriate) are provided and information on geographical distribution, habitat, phenology, taxonomic notes, examined material and illustrations are also provided. This is the first comprehensive treatment of Rudgea for Brazil since Mueller Argoviensis published the Flora Brasiliensis monograph in 1881. As part of the taxonomic studies with Rudgea, the manuscript comprising the descriptions of two new species from Bahia (Brazil) and the manuscript with new combinations in Rudgea and Palicourea sensu lato were also included in this thesis

<p>Sexual conflict can lead to antagonistic coevolution between the sexes, but empirical examples are few. In this thesis secondary sexual characters in diving beetles are interpreted in the light of sexual conflict theory. Whether the male tarsal suction cups and female dorsal modifications are involved in a coevolutionary arms race is tested in two ways. First eight populations of a species with dimorphic females that varied in frequency of the morphs were investigated and male tarsal characteristics quantified. The frequency of female morphs is shown to be significantly correlated to the average number and size of male tarsal suction cups in the population, a prediction of the arms race hypothesis. Second, the hypothesis is tested in a phylogenetic perspective by optimizing the secondary sexual characters on a phylogeny. A full taxonomic revision of the genus <i>Acilius</i> is presented, including new synonyms, lectotype designations, geographic distributions based on more than five thousand examined museum specimens and the description of a new species from northeastern USA. Specimens of all species (except one possibly extinct that failed to be found in Yunnan, China 2000), were field collected between 2000 and 2003 in Sardinia, Sweden, Russia, Honshu and Hokkaido in Japan, New York, Maryland, California and Alberta. Three genes (CO1, H3 and Wingless) were sequenced from the fresh material as well as scoring a morphological character matrix all of which was used to derive a robust and complete hypothesis of the phylogenetic relationship in the group. The phylogeny was derived using Bayesian phylogenetics with Markov Chain Monte Carlo techniques and received a posterior probability of 0.85. Changes in male and female characters turned out to be perfectly correlated across the phylogeny, providing one of the best empirical examples to date of an antagonistic arms race between the sexes in a group of organisms. Finally, a review of a pitfall to phylogenetic analysis known under the name long-branch attraction (LBA), is provided. The problem is well known theoretically but has been questioned to occur in real data, and LBA has been in the core center of the hard debate between parsimony and likelihood advocates since different inference methods vary in sensitivity to the phenomenon. Most important conclusions from the review are; LBA is very common in real data, and is most often introduced with the inclusion of outgroups that almost always provide long branches, pulling down long terminal ingroup branches towards the root. Therefore it is recommended to always run analyses with and without outgroups. Taxon sampling is very important to avoid the pitfall as well as including different kind of data, especially morphological data, i.e. many LBA-affected conclusions have recently been reached by analyses of few taxa with complete genomes. Long-branch extraction (incl. outgroup exclusion), methodological disconcordance (parsimony vs modelbased), separate partition analyses (morphology vs molecules, codon positions, genes, etc), parametric simulation (incl. random outgroups), and split graphs are available relevant methods for the detection of LBA that should be used in combinations, because none alone is enough to stipulate LBA.</p>

<p>This thesis deals with evolutionary relationships within the asterids, a group of plants comprising about one-third of all flowering plants.</p><p>Two new families are recognised: Pennantiaceae and Stemonuraceae. The woody <i>Pennantia</i> from New Zealand and Australia is the sole genus of Pennantiaceae. Stemonuraceae consist of a dozen woody genera with a pantropical distribution and a centre of diversity in South East Asia and the Malesian islands. They are characterised by long hairs on their stamens and/or fleshy appendages on their fruits. Both families were formerly included in Icacinaceae. While Pennantiaceae are unrelated to any of the former Icacinaceae and placed in the order Apiales, other former Icacinaceae genera are related to <i>Cardiopteris</i>, a twining herb from South East Asia and Malesia. The monogeneric family Cardiopteridaceae is enlarged as to include also these. Cardiopteridaceae and Stemonuraceae are sister groups and placed in Aquifoliales. The three other families of Aquifoliales are monogeneric and closely related. The Asian Helwingiaceae and the Central/South American Phyllonomaceae are suggested to be merged into Aquifoliaceae (hollies). The genera of Icacinaceae in the traditional sense not placed in any of the above families (all euasterids II) are members of early diverging lineages of the euasterids I and possibly included in the order Garryales.</p><p>The three woody Australasian families Alseuosmiaceae, Argophyllaceae, and Phellinaceae are confirmed as members of Asterales, despite traditional placements not close to that order. They are, moreover, supported as each other’s closest relatives.</p><p>The results are based mainly on parsimony analysis of DNA sequence data, but morphological studies have revealed characters in support for the molecularly based conclusions. The gene that has provided most new information is the chloroplast <i>ndh</i>F gene. The results are, however, drawn from combined analyses of sequences from one or several additional genes (<i>atp</i>B, <i>mat</i>K, <i>rbc</i>L, <i>18S</i> rDNA). The data have also been explored with Bayesian analysis, a statistical, model-based method that most recently has been developed for phylogeny reconstruction.</p>

This thesis deals with evolutionary relationships within the asterids, a group of plants comprising about one-third of all flowering plants. Two new families are recognised: Pennantiaceae and Stemonuraceae. The woody Pennantia from New Zealand and Australia is the sole genus of Pennantiaceae. Stemonuraceae consist of a dozen woody genera with a pantropical distribution and a centre of diversity in South East Asia and the Malesian islands. They are characterised by long hairs on their stamens and/or fleshy appendages on their fruits. Both families were formerly included in Icacinaceae. While Pennantiaceae are unrelated to any of the former Icacinaceae and placed in the order Apiales, other former Icacinaceae genera are related to Cardiopteris, a twining herb from South East Asia and Malesia. The monogeneric family Cardiopteridaceae is enlarged as to include also these. Cardiopteridaceae and Stemonuraceae are sister groups and placed in Aquifoliales. The three other families of Aquifoliales are monogeneric and closely related. The Asian Helwingiaceae and the Central/South American Phyllonomaceae are suggested to be merged into Aquifoliaceae (hollies). The genera of Icacinaceae in the traditional sense not placed in any of the above families (all euasterids II) are members of early diverging lineages of the euasterids I and possibly included in the order Garryales. The three woody Australasian families Alseuosmiaceae, Argophyllaceae, and Phellinaceae are confirmed as members of Asterales, despite traditional placements not close to that order. They are, moreover, supported as each other’s closest relatives. The results are based mainly on parsimony analysis of DNA sequence data, but morphological studies have revealed characters in support for the molecularly based conclusions. The gene that has provided most new information is the chloroplast ndhF gene. The results are, however, drawn from combined analyses of sequences from one or several additional genes (atpB, matK, rbcL, 18S rDNA). The data have also been explored with Bayesian analysis, a statistical, model-based method that most recently has been developed for phylogeny reconstruction.

Sexual conflict can lead to antagonistic coevolution between the sexes, but empirical examples are few. In this thesis secondary sexual characters in diving beetles are interpreted in the light of sexual conflict theory. Whether the male tarsal suction cups and female dorsal modifications are involved in a coevolutionary arms race is tested in two ways. First eight populations of a species with dimorphic females that varied in frequency of the morphs were investigated and male tarsal characteristics quantified. The frequency of female morphs is shown to be significantly correlated to the average number and size of male tarsal suction cups in the population, a prediction of the arms race hypothesis. Second, the hypothesis is tested in a phylogenetic perspective by optimizing the secondary sexual characters on a phylogeny. A full taxonomic revision of the genus Acilius is presented, including new synonyms, lectotype designations, geographic distributions based on more than five thousand examined museum specimens and the description of a new species from northeastern USA. Specimens of all species (except one possibly extinct that failed to be found in Yunnan, China 2000), were field collected between 2000 and 2003 in Sardinia, Sweden, Russia, Honshu and Hokkaido in Japan, New York, Maryland, California and Alberta. Three genes (CO1, H3 and Wingless) were sequenced from the fresh material as well as scoring a morphological character matrix all of which was used to derive a robust and complete hypothesis of the phylogenetic relationship in the group. The phylogeny was derived using Bayesian phylogenetics with Markov Chain Monte Carlo techniques and received a posterior probability of 0.85. Changes in male and female characters turned out to be perfectly correlated across the phylogeny, providing one of the best empirical examples to date of an antagonistic arms race between the sexes in a group of organisms. Finally, a review of a pitfall to phylogenetic analysis known under the name long-branch attraction (LBA), is provided. The problem is well known theoretically but has been questioned to occur in real data, and LBA has been in the core center of the hard debate between parsimony and likelihood advocates since different inference methods vary in sensitivity to the phenomenon. Most important conclusions from the review are; LBA is very common in real data, and is most often introduced with the inclusion of outgroups that almost always provide long branches, pulling down long terminal ingroup branches towards the root. Therefore it is recommended to always run analyses with and without outgroups. Taxon sampling is very important to avoid the pitfall as well as including different kind of data, especially morphological data, i.e. many LBA-affected conclusions have recently been reached by analyses of few taxa with complete genomes. Long-branch extraction (incl. outgroup exclusion), methodological disconcordance (parsimony vs modelbased), separate partition analyses (morphology vs molecules, codon positions, genes, etc), parametric simulation (incl. random outgroups), and split graphs are available relevant methods for the detection of LBA that should be used in combinations, because none alone is enough to stipulate LBA.

This thesis studies a neural network inspired by human neocortex. An extension of the recurrent and binary network proposed by Gripon and Berrou is given to store sparse messages. In this new version of the neural network, information is borne by graphical codewords (cliques) that use a fraction of the network available resources. These codewords can have different sizes that carry variable length information. We have examined this concept and computed the capacity limits on erasure correction as a function of error rate. These limits are compared with simulation results that are obtained from different experiment setups. We have finally studied the network under the formalism of information theory and established a connection between compressed sensing and the proposed network.

The advent of new technology enhance the speed and reduce the cost for sequencing biological data. Making biological sense of this genomic data is a big challenge to the algorithm design as well as the high performance computing society. There are many problems in Bioinformatics, such as how new functional genes arise, why genes are organized into chromosomes, how species are connected through the evolutionary tree of life, or why arrangements are subject to change. Phylogenetic analyses have become essential to research on the evolutionary tree of life. It can help us to track the history of species and the relationship between different genes or genomes through millions of years. One of the fundamentals for phylogenetic construction is the computation of distances between genomes. Since there are much more complicated combinatoric patterns in rearrangement events, the distance computation is still a hot topic as much belongs to mathematics as to biology. For the distance computation with input of two genomes containing unequal gene contents (with insertions/deletions and duplications) the problem is especially hard. In this thesis, we will discuss about our contributions to the distance estimation for unequal gene order data. The problem of finding the median of three genomes is the key process in building the most parsimonious phylogenetic trees from genome rearrangement data. For genomes with unequal contents, to the best of our knowledge, there is no algorithm that can help to find the median. In this thesis, we make our contributions to the median computation in two aspects. 1) Algorithm engineering aspect, we harness the power of streaming graph analytics methods to implement an exact DCJ median algorithm which run as fast as the heuristic algorithm and can help construct a better phylogenetic tree. 2) Algorithmic aspect, we theoretically formulate the problem of finding median with input of genomes having unequal gene content, which leads to the design and implementation of an efficient Lin-Kernighan heuristic based median algorithm. Inferring phylogenies (evolutionary history) of a set of given species is the ultimate goal when the distance and median model are chosen. For more than a decade, biologists and computer scientists have studied how to infer phylogenies by the measurement of genome rearrangement events using gene order data. While evolution is not an inherently parsimonious process, maximum parsimony (MP) phylogenetic analysis has been supported by widely applied to the phylogeny inference to study the evolutionary patterns of genome rearrangements. There are generally two problems with the MP phylogenetic arose by genome rearrangement: One is, given a set of modern genomes, how to compute the topologies of the according phylogenetic tree; Another is, given the topology of a model tree, how to infer the gene orders of the ancestor species. To assemble a MP phylogenetic tree constructor, there are multiple NP hard problems involved, unfortunately, they organized as one problem on top of other problems. Which means, to solve a NP hard problem, we need to solve multiple NP hard sub-problems. For phylogenetic tree construction with the input of unequal content genomes, there are three layers of NP hard problems. In this thesis, we will mainly discuss about our contributions to the design and implementation of the software package DCJUC (Phylogeny Inference using DCJ model to cope with Unequal Content Genomes), that can help to achieve both of these two goals. Aside from the biological problems, another issue we need to concern is about the use of the power of parallel computing to assist accelerating algorithms to handle huge data sets, such as the high resolution gene order data. For one thing, all of the method to tackle with phylogenetic problems are based on branch and bound algorithms, which are quite irregular and unfriendly to parallel computing. To parallelize these algorithms, we need to properly enhance the efficiency for localized memory access and load balance methods to make sure that each thread can put their potentials into full play. For the other, there is a revolution taking place in computing with the availability of commodity graphical processors such as Nvidia GPU and with many-core CPUs such as Cray-XMT, or Intel Xeon Phi Coprocessor with 60 cores. These architectures provide a new way for us to achieve high performance at much lower cost. However, code running on these machines are not so easily programmed, and scientific computing is hard to tune well on them. We try to explore the potentials of these architectures to help us accelerate branch and bound based phylogenetic algorithms.