The analysis of the publicly available Hox gene sequences from the sea lamprey Petromyzon marinus provides evidence that the Hox clusters in lampreys and other vertebrate species arose from independent duplications. In particular, our analysis supports the hypothesis that the last common ancestor of agnathans and gnathostomes had only a single Hox cluster which was subsequently duplicated independently in the two lineages.

Thioredoxins (TRXs) and glutaredoxins (GRXs) are ubiquitous small redox proteins belonging to the thioredoxin (TRX) superfamily. They regulate several cellular functions via mediating a dithiol/disulphide exchange in target proteins. Thioredoxins have been classified into several subgroups based on their structural homologs. In an attempt to identify thioredoxin proteins which have not been characterized, an EST database survey of Lycopersicon esculentum, Glycine max, Helianthus annus, Secale cereale, Solanum tuberosum, Apis mellifera ligustica, Oncorhynchus mykiss, Salmo salar, and whole genome survey for Drosophila melanogaster, Rattus norvegicus and Caenorhabditis briggsae was performed. Several glutaredoxin and glutaredoxin-like proteins from Ricinus communis, Vercinia fordii, Lycopersicon esculentum, Tilia platyphyllos, Populus tremuloides, Triticum aestivum and Oryza sativa were also characterized. The deduced amino acid sequences were aligned and phylogenetic trees were constructed to determine the consensus sequences and for establishing interrelationships amongst the new and established thioredoxin and glutaredoxins. Based on the alignments, proteins were designated to their respective classes and subcellular localization predictions were used to predict their possible site of actions. In silico analysis has identified several new thioredoxins, glutaredoxins and related proteins and provided insight into their evolutionary relationships.

Central to the study of Life is knowledge both about the underlying relationships among living things and the processes that have molded them into their diverse forms. Phylogenetics provides a powerful toolkit for investigating both aspects. Bayesian phylogenetics has gained much popularity, due to its readily interpretable notion of probability. However, the posterior probability of a phylogeny, as well as any dependent biological inferences, is conditioned on the assumed model of evolution and its priors, necessitating care in model formulation. In Chapter 1, I outline the Bayesian perspective of phylogenetic inference and provide my view on its most outstanding questions. I then present results from three studies that aim to (i) improve the accuracy of Bayesian phylogenetic inference and (ii) assess when the model assumed in a Bayesian analysis is insufficient to produce an accurate phylogenetic estimate. As phylogenetic data sets increase in size, they must also accommodate a greater diversity of underlying evolutionary processes. Partitioned models represent one way of accounting for this heterogeneity. In Chapter 2, I describe a simulation study to investigate whether support for partitioning of empirical data sets represents a real signal of heterogeneity or whether it is merely a statistical artifact. The results suggest that empirical data are extremely heterogeneous. The incorporation of heterogeneity into inferential models is important for accurate phylogenetic inference. Bayesian phylogenetic estimates of branch lengths are often wildly unreasonable. However, branch lengths are important input for many other analyses. In Chapter 3, I study the occurrence of this phenomenon, identify the data sets most likely to be affected, demonstrate the causes of the bias, and suggest several solutions to avoid inaccurate inferences. Phylogeneticists rarely assess absolute fit between an assumed model of evolution and the data being analyzed. While an approach to assessing fit in a Bayesian framework has been proposed, it sometimes performs quite poorly in predicting a model’s phylogenetic utility. In Chapter 4, I propose and evaluate new test statistics for assessing phylogenetic model adequacy, which directly evaluate a model’s phylogenetic performance. / text

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An efficient purification procedure of Ascaris suum muscle utilizing ion exchange column chromatography has been developed.

Thesis advisor: Elizabeth A. Kensinger / Neural and behavioral responses to emotional stimuli often are discussed within an evolutionary framework. Although some of the information that elicits an emotional response is likely to have had evolutionary significance (e.g., snakes, spiders), many other stimuli would not have been evolutionarily relevant (e.g., guns, grenades). The present study re-analyzed data from two fMRI studies (Kensinger et al., 2007; Kensinger & Schacter, 2008) to examine whether the neural systems that respond to emotional stimuli differ depending upon whether those stimuli were of phylogenetic or ontogenetic significance. The results revealed that when stimuli were ontogenetic, activity was increased in regions of the anterior cingulate and orbitofrontal cortices. By contrast, when stimuli were phylogenetic, activity was increased in a region spanning the lingual and fusiform gyri. These results suggest that there can be differences in how emotional stimuli are processed, and those differences can depend upon the stimuli’s evolutionary significance. / Thesis (BA) — Boston College, 2009. / Submitted to: Boston College. College of Arts and Sciences. / Discipline: College Honors Program. / Discipline: Psychology Honors Program. / Discipline: Psychology.

Made available in DSpace on 2014-06-11T19:30:56Z (GMT). No. of bitstreams: 0 Previous issue date: 2009-02-06Bitstream added on 2014-06-13T20:21:24Z : No. of bitstreams: 1 arnoldi_fgc_dr_rcla.pdf: 2897071 bytes, checksum: fa1429945e5319eef834777ced11123a (MD5) / A partir dos coleópteros luminescentes, mais de 20 luciferases já foram clonadas e seqüenciadas. Dessas, a maioria é de lampirídeos das regiões Neártica e Paleártica, quatro de elaterídeos jamaicanos e uma de um fengodídeo asiático. Apenas outras cinco são oriundas da América do Sul, o continente mais rico em espécies de coleópteros luminescentes e o provável berço evolutivo de Lampyridae, a família com maior número de coleópteros luminescentes. Espécies desta região apresentam a maior variedade de cores de bioluminescência. No presente trabalho clonamos e seqüenciamos luciferases dos gêneros Brasilocerus sp., Phrixothrix sp. e Taximastinocerus sp., da família Phengodidae. Com base na análise filogenética dessas luciferases e outras já publicadas, concluímos que as luciferases das lanternas laterais e cefálicas são codificadas por genes parálogos, e propusemos um modelo para a evolução das cores da bioluminescência nessa família. Também determinamos o genoma mitocondrial de Pyrophorus divergens, membro da família Elateridae. A partir desse genoma e outros já publicados, analisamos a evolução da bioluminescência na superfamília Elateroidea sensu Lawrence e Newton (1995) e concluímos que essa pode ter surgido três vezes independentemente nesse grupo. / From luminescent Coleopteran's, more than 20 luciferases have already been cloned and sequenced. Among them, most part is from lampyrids of Neartic and Paleartic regions, four are from Jamaican elaterids and one is from Asiatic phengodids. Just five are from South American species, the richest continent in luminescent Coleopteran's and, probably, the evolutionary cradle of Lampyridae. Species from this region display the greatest range of bioluminescence colors. At the present work, we cloned and sequenced luciferases from the genera Brasilocerus sp., Phrixothrix sp. and Taximastinocerus sp., from Phengodidae family. Based on the phylogenetic analysis of these genes and other already published, we concluded that head and lateral lantern luciferases are coded by paralogous genes, and we also proposed a model for bioluminescence color evolution in this family. We also sequenced the mitochondrial genome of Pyrophorus divergens, an Elateridae member. Based on this genome and other already published, we analysed the evolutionary history of bioluminescence in Elateroidea superfamily sensu Lawrence e Newton (1995) and concluded that it could have appeared three times independently in this group.