Uma hipótese de relacionamento e proposta para o gênero Rhopalurus Thorell, 1876 (Scorpiones: Buthidae). O gênero possui 19 espécies e duas subespécies validas, e e diagnosticado principalmente pela presença de aparelho estridulatorio e dilatação dos segmentos do metassoma. O monofiletismo de Rhopalurus nunca foi testado com uma analise filogenetica, e nem a validade desses caracteres para suportar o gênero. A análise foi feita com 14 spp de Rhopalurus e 17 spp de outros seis gêneros de Buthidae. Utilizamos cinco regiões gênicas (18S, 28S, 12S, 16S e COI) e 86 caracteres morfológicos em uma analise de evidencia total, através de parcimônia com otimização direta. O gênero Rhopalurus e parafiletico e dividido em quatro gêneros aqui descritos: Rhopalurus, Heteroctenus (revalidado), gên. nov. A e gên, nov. B. Sinonimias: R. amazonicus e R. crassicauda paruensis com R. crassicauda, R. virkkii com H. abudi, R. acromelas com gên. nov. B agamemnon, R. pintoi kourouensis com gên. nov. B pintoi. Alguns dos gêneros sul-americanos (Rhopalurus, Physoctonus e gên. nov. B) relacionam o nordeste brasileiro com o norte da America do Sul, e os padrões encontrados sugerem um cenário de especiações alopatricas nesses gêneros. Os padrões de Heteroctenus sugerem dispersão da America do Norte para as Grandes Antilhas, com eventos de especiação posteriores em cada ilha. Também discutimos uma possível estruturação populacional de gên. nov. B rochae. A presença do aparelho estridulatorio não agrupa as antigas espécies do gênero. Alem disso, um estudo detalhado mostra que existem três tipos morfológicos distintos. Com base na filogenia obtida, relacionamos cada um desses tipos com os gêneros onde eles ocorrem (Rhopalurus, Heteroctenus e gên. nov. B). / A relationship hypothesis is proposed for the genus Rhopalurus Thorell, 1876 (Scorpiones: Buthidae). The genus has 19 valid species and two valid subspecies, and is diagnosed mainly by the presence of an stridulatory apparatus and by the expansion of the metassomal segments. The monophyly of Rhopalurus was never tested within a phylogenetic analysis, neither was the useness of those characters to support the genus. The analysis was made with 14 spp of Rhopalurus and 17 spp from other six Buthidae genera. We have used five genes (18S, 28S, 12S, 16S, and COI) and 86 morphological characters in a total evidence analysis, through parsimony and direct optimization. The genus Rhopalurus is paraphyletic and divided in four genera, here described: Rhopalurus, Heteroctenus (revalidation), gên. nov. A, and gên, nov. B. Synonymies: R. amazonicus and R. crassicauda paruensis with R. crassicauda, R. virkkii with H. abudi, R. acromelas with gên. nov. B agamemnon, R. pintoi kourouensis with gên. nov. B pintoi. Some of the South American genera (Rhopalurus, Physoctonus, and gên. nov. B) relate the Brazilian northeast with the north of South America, and the found patterns suggest allopatric speciation within these genera. The Heteroctenus patterns suggest dispersion from North America to the Greater Antilles, with later speciation events in each island. We also discuss a putative populational structure of gên. nov. B rochae. The presence of the stridulatory apparatus doesn\'t gather the former species of the genus. Furthermore, a detailed study reveals the existence of three different morphological types. Based on the obtained phylogeny, we related each one of these types with the genera where they occur (Rhopalurus, Heteroctenus, and gên. nov. B).

A subtribo Pericopina (Lepidoptera: Erebidae: Arctiinae: Arctiini) compreende 37 gêneros com distribuição exclusivamente Neotropical. Estudos acerca da taxonomia e relações filogenéticas para esse grupo são escassos. Entre os gêneros arrolados em Pericopina, Dysschema Hübner, 1818 é o mais especioso. O gênero é representado por 146 nomes válidos e 88 espécies, conta com 12 sinonímias genéricas e não há um consenso sobre o número de espécies que o compõem, uma vez que há suspeita por parte de alguns autores (WATSON & GOODGER 1986; LAMAS & GRADOS 1996) de que alguns nomes atualmente válidos para algumas espécies sejam, de fato, sinonímias. Recentemente Becker (2013) estabeleceu uma série de sinônimos, e o gênero passou a somar 59 espécies. O presente trabalho propõe, através do levantamento de caracteres morfológicos de adultos, analisar as relações filogenéticas de Pericopina e das espécies arroladas em Dysschema, atualizar a distribuição das espécies atualmente arroladas no gênero, além de uma melhor delimitação taxonômica. A análise cladística baseada em 156 caracteres morfológicos não corroborou a monofilia da subtribo Pericopina; o gênero Scearctia Hering se mostrou morfologicamente associado à Lithosiini e o gênero Pteroodes Butler se mostrou morfologicamente associado à Phaegopterina. Esses gêneros são realocados nos grupos supragenéricos anteriormente citados, com os quais mostraram maior afinidade filogenética, como taxonomicamente incertae sedis. Adicionalmente o gênero Seileria Dognin é aqui considerado sinônimo junior subjetivo de Thyrgis Walker A monofilia de Dysschema é corroborada apenas com a inclusão dos gêneros monotípicos Sermyla Walker e Are Walker. São descritas quatro novas espécies em Dysschema, 14 novos sinônimos estabelecidos, nove espécies revalidadas, oito sinônimos revalidados e duas combinações novas. Pericopis thyridia é um nome novo proposto em substituição a Pericopis fenestrata Butler, 1872, homônimo júnior de Coborisa fenestrata Walker, 1855. Para garantir a estabilidade taxonômica dos nomes arrolados em Dysschema foram designados 67 lectótipos e fixados 19 holótipos por evidência de monotipia / Pericopina (Lepidoptera: Erebidae: Arctiinae: Arctiini) comprises 37 genera distributed exclusively in the Neotropical region. Studies on the taxonomy and phylogenetic relationships for the species included in this group are scarce. Among the genera enrolled in Pericopina, Dysschema Hübner, 1818 is the most specious genus. The genus is represented by 146 valid names and 88 species, Dysschema has 12 generic synonyms and there is no consensus on the number of species that compose it, as it is suspected by some authors (Watson & Goodger 1986; Lamas & Grados1996) based on that currently valid names for some species are, in fact, synonyms. Recently Becker (2013) introduced several synonyms and the genus currently has 59 species . The present study proposes, through a survey of morphological characters of adults, to analyze the phylogenetic relationships of Pericopina and of the species enrolled in Dysschema, to update the distribution of the species currently enrolled in this genus, and a better taxonomic delimitation. A cladistic analysis based on 156 morphological characters did not corroborate the monophyly of Pericopina. Scearctia Hering is morphologicaly associated to the Lithosiini and Pteroodes Butler is morphologicaly associated to the Phaegopterina. These genera are enrroled in the supra-generic groups which their share phylogenetics afinities as taxonomically incertae sedis. Aditionally, Seileria Dognin is a junior subjective synonym of Thyrgis Walker. The monophyly of Dysschema was supported only with the inclusion of the monotypic genera Sermyla Walker and Are Walker. Four new species are described in Dysschema, 14 new synonyms are established, nine species are revalidated, eight synonyms are revalidated and two new combinations are established. Additionally, Pericopis thyridia is a new name proposed to replace the Pericopis fenestrata Butler, 1872, a junior homonym of Coborisa fenestrata Walker, 1855. In order to assure the estability of the names enrroled in Dysschema 67 lectotypes were designated and 19 holotypes were fixed by evidence of monotypy

Chloroplasts are organelles that convert light energy to chemical energy through photosynthesis. The movement of chloroplasts within the cell for the optimization of light absorption is crucial for plant survival. Cellular motor proteins and cytoskeletal tracks can facilitate transport of organelles. As an ancient superfamily of microtubule-dependent motors, kinesins participate in various cellular activities including cytokinesis, vesicle and organelle movements. Based on phylogenetic relationships and functional analysis, the kinesin superfamily has been subdivided into more than 14 families, most of which can be found in plants. With the ever increasing amount of genomic information, it is important and beneficial to systematically characterize and document kinesins within an organism. As a result of my collaborative work with other members of the Vidali lab, a detailed phylogenetic characterization of the 76 kinesins of the kinesin superfamily in the moss Physcomitrella patens is reported here. We found a remarkable conservation of families and subfamily classes with Arabidopsis, which is important for future comparative analyses of functions. Some of the families are composed of fewer members, while other families are greatly expanded in moss. To improve the comparison between species, and to simplify communication between research groups, we proposed a classification of subfamilies based on our phylogenetic analysis. As part of my efforts in studying chloroplasts motility, I investigated the function of two members of Physcomitrella kinesin family 14 class V proteins, Ppkin14-Va and -Vb. These two proteins are orthologs of the Arabidopsis KAC proteins which mediate actin-based chloroplast movement in Arabidopsis thaliana. In contrast, in the Physcomitrella both actin filaments (AFs) and microtubules (MTs) participate in chloroplast movement. Our results show that Ppkin14-Vs are important for maintaining chloroplast dispersion. They also function during chloroplast light avoidance responses via an AF-dependent, rather than MT-dependent mechanism. Although two Ppkin14- Vs do not act as MT-based motors, our phylogenetic study on moss kinesins provides an important source of information to track other potential kinesins that are predicted to move chloroplasts on MTs.

Camarea St.-Hil. (Malpighiaceae) é um gênero endêmico da América do Sul, constituído por nove espécies. O objetivo do trabalho foi a reconstrução da filogenia do gênero, por meio de evidências químicas e moleculares. Foram avaliados nove terminais, sete dos quais são espécies correntemente reconhecidas, um é uma espécie que entrou em sinonímia (C. triphylla = C. axillaris) e outro é um suposto híbrido. Como grupos externos, foram utilizadas as espécies Peixotoa reticulata e Janusia guaranitica. Foram analisados os n-alcanos das ceras epicuticulares e os flavonóides de todas as espécies. Os n-alcanos principais foram C29, C31 e C33, todos da série normal. Como flavonóides característicos de Camarea, foram identificados glicosídeos de apigenina, luteolina, crisoeriol, campferol e quercetina. A análise de agrupamentos baseada na distribuição de alcanos, usando UPGMA e distâncias euclideanas, resultou em dois grupos principais, um com C29 como homólogo principal, constituído por C. hirsuta, C. affinis x C. hirsuta, C. affinis e C. ericoides. O outro grupo caracteriza-se por homólogos principais C31 ou C33, e é formado por C. elongata, C. humifusa, C. sericea, C. axillaris e C. triphylla (= C. axillaris). Esses dois principais agrupamentos contêm grupos internos menores. Uma análise de UPGMA usando coeficiente de DICE e baseada na distribuição de agliconas de flavonóides forneceu um dendrograma com alguns agrupamentos coerentes com as afinidades reveladas pela distribuição de alcanos, como as associações: 1) C. hirsuta, C. affinis e C. affinis x hirsuta; 2) C. elongata e C. axillaris; 3) C. sericea e C. humifusa. Uma inferência filogenética molecular foi obtida com seqüências de duas regiões do cloroplasto (trnL-F e rps16) e uma nuclear (ITS). Dentre as análises com um só marcador, resultados mais consistentes foram conseguidos com ITS, que forneceu 49 caracteres filogeneticamente informativos, enquanto trnL-F e rps16 forneceram 10 e 18 caracteres informativos, respectivamente. A análise de consenso estrito de quatro árvores mais parcimoniosas de uma análise combinando-se as três seqüências resultou em um cladograma em que Camarea é um grupo monofilético, com \"bootstrap\" (BS) 100, várias politomias e clados com baixa consistência. Foi realizada análise por AFLP utilizando quatro combinações de iniciadores seletivos, obtendo-se 217 fragmentos polimórficos. Uma análise combinando as evidências moleculares resultantes de seqüências de DNA e marcadores AFLP forneceu uma única árvore mais parcimoniosa com uma politomia agrupando C. affinis, C. ericoides, C. hirsuta e C. affinis x C. hirsuta, mas boa resolução e elevada sustentação em outros clados. A combinação de todas as evidências moleculares e químicas (estas compreendendo três caracteres derivados da análise de alcanos e cinco de flavonóides) resultou numa única árvore mais parcimoniosa completamente resolvida. Os resultados apóiam a fusão de C. triphylla em sinonímia com C. axillaris e indicam forte associação entre: 1) C. humifusa e C. sericea (BS 94); 2) C. affinis, C. affinis x hirsuta, C. hirsuta e C. ericoides (BS 83); 3) C. axillaris e C. elongata (BS 100). C. affinis, C. hirsuta e C. affinis x C. hirsuta compartilham a presença crisoeriol. C. affinis e C. affinis x C. hirsuta, compartilham também luteolina e formam um clado com BS 70. O presente trabalho demonstra a utilidade de caracteres químicos para melhorar a resolução de filogenias e elevar a sustentação de clados. / Camarea St.-Hil. (Malpighiaceae) is a genus with eight species endemic in South America. The purpose of the present work was the attainment of a phylogenetic inference of the genus by means of chemical and molecular evidences. Nine accessions were analyzed: seven correspond to currently recognized species; one is a species sunk into synonymy (C. triphylla = C. axillaris); and a last one is a hypothesized hybrid. Peixotoa reticulata and Janusia guaranitica were used as out-groups. n-Alkanes from epicuticular waxes and flavonoids were analyzed from all species. The main alkanes of all distributions were either C29 or C31 or C33, all from the normal series. The characteristic flavonoids of Camarea were shown to be apigenin, luteolin, chrysoeriol, kaempferol and quercetin. A cluster analysis based on the alkane distribution using UPGMA and Euclidean distances provided two main clusters. One cluster is characterized by C29 as main homologue and is formed by C. hirsuta, C. affinis, C. affinis x hirsuta and C. ericoides. The other cluster has species with either C31 or C33 as main homologue and is formed by C. elongata, C. humifusa, C. sericea, C. axillaris and C. triphylla (= C. axillaris). These two main clusters contain smaller inner clusters. An analysis using UPGMA and DICE coefficients and based on the distribution of flavonoid aglycones provided a dendrogram with clusters congruent with affinities revealed by the alkane evidence, such as the groupings: 1) C. hirsuta, C. affinis and C. affinis x hirsuta; 2) C. elongata and C. axillaris; 3) C. sericea and C. humifusa. A phylogenetic molecular inference was obtained with sequences from two chloroplast (trnL-F and rps16) and one nuclear (ITS) DNA regions. Among the analyses based on a single marker, more consistent results were obtained with ITS, which provided 49 informative phylogenetic characters, while trnL-F and rps16 provided 10 and 18 informative characters, respectively. A strict consensus analysis based on four more parsimonious trees from an analysis combining sequences of the three DNA regions gave a cladogram showing Camarea as a monophyletic group with bootstrap support (BS) 100. The cladogram contains several polytomies and clades with low support. An AFLP analysis, using four combinations of selective primers, provided 217 polymorphic fragments. Data from sequencing and AFLP were combined in a phylogenetic analysis. A sole more parsimonious tree was obtained, with most clades completely resolved with and high support. A polytomy remained, grouping C. affinis, C. ericoides, C. hirsuta and C. affinis x hirsuta. The combination of all molecular and chemical evidences (the latter comprising three alkane and five flavonoid characters) was used for a phylogenetic analysis. A sole more parsimonious tree was obtained, completely resolved and with clades highly supported. The results support sinking C. triphylla into synonymy of C. axillaris and indicate strong kinship: 1) between C. humifusa and C. sericea (BS 94); 2) among C. affinis, C. affinis x C. hirsuta, C. hirsuta and C. ericoides (BS 83); 3) between C. axillaris and C. elongata (BS 100). C. affinis, C. hirsuta and C. affinis x C. hirsuta share the possession of chrysoeriol. C. affinis and C. affinis x C. hirsuta share the possession also of luteolin and form a clade with BS 70. The present work reveals the utility of chemical characters to improve resolution of phylogenies and increment clade support.

Dengue é uma doença infecciosa não contagiosa causada pelo vírus da dengue (gênero Flavivirus, família Flaviviridae), transmitida pela picada de artrópodes do gênero Aedes, principalmente Aedes aegypti, e sendo atualmente um importante problema de saúde pública em todo o mundo. Segundo a Organização Mundial de Saúde, cerca de 50 a 100 milhões de pessoas se infectam anualmente em mais de 100 países de todos os continentes. A dengue apresenta-se em três formas clínicas principais; doença febril indiferenciada, febre clássica do dengue (DF) e dengue hemorrágico com ou sem choque (DHF/DSS). Recentemente, viu-se um dramático aumento do número de casos de DHF/DSS nas Américas, e este aumento coincidiu com a introdução do dengue tipo 3, genótipo III. Neste trabalho, caracterizamos completamente o genoma de um vírus brasileiro de dengue tipo 3 (D3BR/RP1/2003) isolado de um paciente com dengue clássica. O genoma viral possui um tamanho de 10707 nucleotídeos e contém uma única região codificadora (posição 95 a 10264) flanqueada por duas regiões não codificadoras (RNC5, 1 a 94; RNC3, 10268 a 10707). A comparação do genoma viral com outros vírus isolados de pacientes com DF e DHF não mostrou diferenças significativas que sugerissem a presença de um fator genético associado à virulência. A analise filogenética baseada no genoma completo, mostra que a cepa D3BR/RP1/2003 pertence ao genótipo III e encontra-se proximamente relacionada a outro vírus isolado no Rio de Janeiro em 2002. Entretanto, quando essa análise filogenética é realizada com as regiões codificadoras das proteínas E e NS5 individualmente, a cepa D3BR/RP1/2003 encontra-se mais proximamente relacionada a um vírus isolado na Ilha de Martinica no Caribe. Este achado sugere que o isolado D3BR/RP1/2003 pode ter sido originado através de um evento de recombinação entre duas cepas virais distintas antes ou após sua introdução no Brasil. Dados sugestivos de recombinação foram observados também quando analisada a relação filogenética entre vírus isolados na Ásia. / Dengue is an infectious disease caused by dengue virus (genus Flavivirus, family Flaviviridae), transmitted by the bite of arthropods of the Aedes genus, mainly Aedes aegypti, and being currently an important problem of public health worldwide. According to the World Health Organization, about 50 the 100 million people are infected annually in more than 100 countries of all continents. Dengue can be presented in three main clinical forms; undifferentiated febrile illness, classic dengue fever (DF) and hemorrhagic dengue fever with or without shock (DHF/DSS). Recently, a dramatically increase of DHF/DSS cases in the Americas have been seen, and this increase coincided with the introduction of the dengue type 3, genotype III. In this work, we have completely characterized the genome of a Brazilian dengue type 3 (D3BR/RP1/2003 strain) isolated from a DF patient. The viral genome possesses a size of 10707 nucleotides and has a unique open reading frame (position 95 to 10264), flanked by two untranslated regions (UTR5\', 1 to 94; UTR3\', 10268 to 10707). The comparison of the viral genome with other viruses isolated from patients with DF and DHF did not show significant differences to suggest the presence of a genetic factor associate with virulence. Phylogenetic analysis based on the complete genome showed that D3BR/RP1/2003 strain belongs to genotype III and is close related to another virus isolated in Rio de Janeiro in 2002. However, when the phylogenetic analysis was based on the individual coding regions of E and NS5 proteins, D3BR/RP1/2003 strain was closely related to a virus isolated in the Island of Martinique in the Caribbean. This finding suggests that D3BR/RP1/2003 strain could have been originated through an event of recombination between different virus strains before or after its introduction to Brazil. Data supporting recombination events between viruses isolated in Asia have also been observed.

<p>This dissertation is primarily focused on the <i>Buellia</i> species with pluriseptate spores, often referred to the section or genus <i>Diplotomma</i>, and secondarily on the Physciaceae. An ultrastructural study at family level gives new information on spore characters. Variations in the composition and structure of the spore wall layers and septa are described.</p><p>A phylogenetic analysis of the Physciaceae, based on morphological and chemical characters, is presented. In the resulting trees the species with pluriseptate spores appear in a poorly resolved clade together with other crustose species with 1-septate spores. A subsequent analysis, excluding foliose and fruticose species, shows that the species with pluriseptate spores do not form a monophyletic group, and that only a few are grouped together with the type species of <i>Diplotomma</i>. Due to low resolution, poor branch support, and uncertainty concerning the typification of <i>Buellia</i> all species treated are retained in <i>Buellia</i>.</p><p>Altogether 35 species with pluriseptate spores are treated, including ten new to science, viz. <i>B. aeruginosa</i>, <i>B. morsina</i>, <i>B. muriformis</i>, <i>B. oidaliella</i>, <i>B. pallido-marginata</i>, <i>B. romoletia</i>, <i>B. rubroreagens</i>, <i>B. terricola</i>, <i>B. tombadorensis</i>, and <i>B. tri-septata</i>. Historical outlines are presented, and information on life strategy, morphology, chemistry, ecology, and distribution is given. All species are similar and macroscopically not easily distinguished, having crustose thalli and blackish apothecia, but there is a great variation in microscopic characters, secondary chemistry, substrate preferences, habitat ecology, and distribution range. Several names are typified and many synonyms are listed. References are given to all species referred to <i>Diplotomma</i> in literature.</p>

Background: Mitochondrial genomes are a valuable source of data for analysing phylogenetic relationships. Besides sequence information, mitochondrial gene order may add phylogenetically useful information, too. Sipuncula are unsegmented marine worms, traditionally placed in their own phylum. Recent molecular and morphological findings suggest a close affinity to the segmented Annelida. Results: The first complete mitochondrial genome of a member of Sipuncula, Sipunculus nudus, is presented. All 37 genes characteristic for metazoan mtDNA were detected and are encoded on the same strand. The mitochondrial gene order (protein-coding and ribosomal RNA genes) resembles that of annelids, but shows several derivations so far found only in Sipuncula. Sequence based phylogenetic analysis of mitochondrial protein-coding genes results in significant bootstrap support for Annelida sensu lato, combining Annelida together with Sipuncula, Echiura, Pogonophora and Myzostomida. Conclusion: The mitochondrial sequence data support a close relationship of Annelida and Sipuncula. Also the most parsimonious explanation of changes in gene order favours a derivation from the annelid gene order. These results complement findings from recent phylogenetic analyses of nuclear encoded genes as well as a report of a segmental neural patterning in Sipuncula.

This dissertation is primarily focused on the Buellia species with pluriseptate spores, often referred to the section or genus Diplotomma, and secondarily on the Physciaceae. An ultrastructural study at family level gives new information on spore characters. Variations in the composition and structure of the spore wall layers and septa are described. A phylogenetic analysis of the Physciaceae, based on morphological and chemical characters, is presented. In the resulting trees the species with pluriseptate spores appear in a poorly resolved clade together with other crustose species with 1-septate spores. A subsequent analysis, excluding foliose and fruticose species, shows that the species with pluriseptate spores do not form a monophyletic group, and that only a few are grouped together with the type species of Diplotomma. Due to low resolution, poor branch support, and uncertainty concerning the typification of Buellia all species treated are retained in Buellia. Altogether 35 species with pluriseptate spores are treated, including ten new to science, viz. B. aeruginosa, B. morsina, B. muriformis, B. oidaliella, B. pallido-marginata, B. romoletia, B. rubroreagens, B. terricola, B. tombadorensis, and B. tri-septata. Historical outlines are presented, and information on life strategy, morphology, chemistry, ecology, and distribution is given. All species are similar and macroscopically not easily distinguished, having crustose thalli and blackish apothecia, but there is a great variation in microscopic characters, secondary chemistry, substrate preferences, habitat ecology, and distribution range. Several names are typified and many synonyms are listed. References are given to all species referred to Diplotomma in literature.

Understanding how protein sequence, structure and function coevolve is at the core of functional genome annotation and protein engineering. The fundamental problem is to determine whether sequence variation contributes to functional differences or if it is a consequence of evolutionary divergence that is unrelated to functional specificity. To address this problem, we cannot merely analyze sequence variation between homologous proteins that have different functions. For comparison, we need to understand the factors that determine sequence variation in proteins that have the same function, such as a set of orthologous enzymes. Here, we address this problem by analyzing the evolution of functionally important residues in the o-succinylbenzoate synthase (OSBS) family. The OSBS family consists of several hundred enzymes that catalyze a step in menaquinone (Vit. K2) synthesis. Based on phylogeny, the OSBS family can be divided into eight major subfamilies. We assayed wild-type OSBS enzyme activities. The results show that the enzymes from γ-Proteobacteria subfamily 1 and Bacteroidetes have relatively low values, the enzyme from Cyanobacteria subfamily 1 is intermediate, and the values for the proteins from the Actinobacteria and Firmicutes subfamilies are relatively high. We are using computational and experimental methods to identify functionally important amino acids in each subfamily. Our data suggest that each subfamily has a different set of functionally important residues, even though the enzymes catalyze the same reaction. These differences may have accumulated because different mutations were required in each subfamily to compensate for deleterious mutations or to adapt to changing environments. We assessed the roles of these amino acids in enzyme structure and function. Our method achieved 70% successful rate to identify positions that play important roles in one family but not another. The residues P119 and A329 play important role in D. psychrophila but not in T.fusca OSBS. We also observed two class switch mutations in T.fusca, P11 and P22. The mutations at these two position have a similar kinetic parameters as wild-type D. psychrophila OSBS.

Phylogenetic analysis, or the inference of evolutionary history is done routinely by biologists and is one of the most important problems in systematic biology. In this thesis, we study two computational problems in the area. First, we study the evolutionary tree reconstruction problem under the character compatibility (CC) paradigm and give a polynomial time approximation scheme (PTAS) for a variation of the formulation called fractional character compatibility (FCC), which has been proven to be NP-hard. We also present a very simple algorithm called the Ordinal Split Method (OSM) to generate bipartitions given sequence data, which can be served as a front-end to the PTAS. The performance of the OSM and the validity of the FCC formulation are studied through simulation experiments. The second part of this thesis presents an efficient algorithm to compare evolutionary trees using the quartet metric. Different evolutionary hypothesis arises when different data sets are used or when different tree inference methods are applied to the same data set. Tree comparisons are routinely done by biologists to evaluate the quality of their tree inference experiments. The quartet metric has many desirable properties but its use has been hindered by its relatively heavy computational requirements. We address this problem by giving the first O(n^2) time algorithm to compute the quartet distance between two evolutionary trees.