With rapid advances in sequencing technologies and precipitous decreases in cost, public sequence databases have increased in size apace. However, experimental characterization of novel genes and their products remains prohibitively expensive and time consuming. For these reasons, bioinformatics approaches have become increasingly necessary to generate hypotheses of biological function. Phylogenomic approaches use phylogenetic methods to place genes, chromosomes, or whole genomes within the context of their evolutionary history and can be used to predict the function of encoded proteins. In this thesis, two new phylogenomic methods and software implementations are presented that address the problems of subcellular localization prediction and functional divergence prediction within protein families respectively. Most of the widely used programs for subcellular localization prediction have been trained on model organisms and ignore phylogenetic information. As a result, their predictions are not always reliable when applied to phylogenetically divergent eukaryotes, such as unicellular protists. To address this problem, PhyloPred-HMM, a novel phylogenomic method was developed to predict sequences that are targeted to mitochondria or mitochondrion-related organelles (hydrogenosomes and mitosomes). This method was compared to existing prediction methods using an existing test dataset of mitochondrion-targeted sequences from well-studied groups, sequences from a variety of protists, and the whole proteomes of two protists: Tetrahymena thermophila and Trichomonas vaginalis. PhyloPred-HMM performed comparably to existing classifiers on mitochondrial sequences from well-studied groups such as animals, plants, and Fungi and better than existing classifiers on diverse protistan lineages. FunDi, a novel approach to the prediction of functional divergence was developed and tested on 11 biological datasets and two large simulated datasets. On the 11 biological datasets, FunDi appeared to perform comparably to existing programs, although performance measures were compromised by a lack of experimental information. On the simulated datasets, FunDi was clearly superior to existing methods. FunDi, and two other prediction programs, was then used to characterize the functional divergence in two groups of plastid-targeted glyceraldehyde-3-phosphate dehydrogenases (GAPDH) adapted to roles in the Calvin cycle. FunDi successfully identified functionally divergent residues supported by experimental data, and identified cases of potential convergent evolution between the two groups of GAPDH sequences.

A estruturação em comunidades biológicas sugere que há fatores que determinam quais espécies poderão ocorrer juntas. Os pequenos mamíferos sul-americanos (marsupiais e roedores cricetídeos) apresentam um padrão de dispersão no continente sul-americano bastante distinto. Os marsupiais chegaram ao continente há cerca de 100 milhões de anos e os roedores cricetídeos o colonizaram apenas na formação do Istmo do Panamá em aproximadamente 2,5 milhões de anos. Atualmente esses dois grupos ocupam nichos bastante diversos e também específicos. O objetivo geral desta dissertação é explorar padrões funcionais entre pequenos mamíferos sul-americanos, apresentando uma nova métrica de análise e discriminando os principais mecanismos que estruturam esses padrões. Assim, ela está dividida em dois capítulos: o primeiro apresenta uma nova abordagem analítica para o cálculo de divergência funcional entre clados coocorrentes na mesma comunidade; o segundo trata de avaliar os principais determinantes da divergência funcional entre marsupiais e roedores cricetídeos sul-americanos. A métrica desenvolvida no primeiro capítulo foi adaptada da abordagem de diversidade beta funcional, entretanto, ao invés de compararmos pares de comunidades, comparamos pares de clados que coocorrem na mesma comunidade, distinguindo o quanto similiar ou diferente funcionalmente esses clados são. No segundo capítulo, verificamos que fatores ambientais, funcionais, históricos e evolutivos influenciam a divergência funcional entre os dois clados aqui estudados. Além disso, nós encontramos uma tendência de aumento da diferenciação de nicho entre marsupiais e roedores cricetídeos em direção ao norte do continente sul-americano. Nós podemos inferir que a porta de entrada da colonização dos roedores cricetídeos no continente determina, ainda hoje, padrões de funcionalidade dos ambientes, além de outros fatores importantes como o clima. / The existence of structure in biological communities suggests that there are factors that determine which species may occur together. Small mammals of South America (marsupials and cricetid rodents) show a pattern of dispersal in this continent quite different and interesting. Marsupials arrived on South American continent about 100 million years and cricetid rodents only colonized it in the formation of the Isthmus of Panama, approximately 2.5 million years. Currently, these two groups occupy several and specific niches. The major goal of this thesis is to explore functional patterns among small mammals in South America, presenting an analytical novelty and discriminating mechanisms that driving these patterns. Thus it is divided into two chapters: the first presents a new functional approach for the calculation of functional divergence among clades co-occurring in the same community; the second evaluates the main drivers of functional divergence between marsupials and cricetid rodents in South America. The metric developed in the first chapter was adapted from the approach of functional beta diversity, however, instead of comparing pairs of communities, we compared pairs of clades co-occurring in the same community, discriminating how functionally similar or different these clades are. In the second chapter, we found that environmental, functional, evolutionary and historical factors determine the functional divergence among two clades studied here. Furthermore, we found a trend of increased niche differentiation between marsupials and cricetid rodents northward South American continent. We may infer that the gateway of cricetid rodents already determines patterns of functionality in environments nowadays, beyond other important factors, like climate.

A estruturação em comunidades biológicas sugere que há fatores que determinam quais espécies poderão ocorrer juntas. Os pequenos mamíferos sul-americanos (marsupiais e roedores cricetídeos) apresentam um padrão de dispersão no continente sul-americano bastante distinto. Os marsupiais chegaram ao continente há cerca de 100 milhões de anos e os roedores cricetídeos o colonizaram apenas na formação do Istmo do Panamá em aproximadamente 2,5 milhões de anos. Atualmente esses dois grupos ocupam nichos bastante diversos e também específicos. O objetivo geral desta dissertação é explorar padrões funcionais entre pequenos mamíferos sul-americanos, apresentando uma nova métrica de análise e discriminando os principais mecanismos que estruturam esses padrões. Assim, ela está dividida em dois capítulos: o primeiro apresenta uma nova abordagem analítica para o cálculo de divergência funcional entre clados coocorrentes na mesma comunidade; o segundo trata de avaliar os principais determinantes da divergência funcional entre marsupiais e roedores cricetídeos sul-americanos. A métrica desenvolvida no primeiro capítulo foi adaptada da abordagem de diversidade beta funcional, entretanto, ao invés de compararmos pares de comunidades, comparamos pares de clados que coocorrem na mesma comunidade, distinguindo o quanto similiar ou diferente funcionalmente esses clados são. No segundo capítulo, verificamos que fatores ambientais, funcionais, históricos e evolutivos influenciam a divergência funcional entre os dois clados aqui estudados. Além disso, nós encontramos uma tendência de aumento da diferenciação de nicho entre marsupiais e roedores cricetídeos em direção ao norte do continente sul-americano. Nós podemos inferir que a porta de entrada da colonização dos roedores cricetídeos no continente determina, ainda hoje, padrões de funcionalidade dos ambientes, além de outros fatores importantes como o clima. / The existence of structure in biological communities suggests that there are factors that determine which species may occur together. Small mammals of South America (marsupials and cricetid rodents) show a pattern of dispersal in this continent quite different and interesting. Marsupials arrived on South American continent about 100 million years and cricetid rodents only colonized it in the formation of the Isthmus of Panama, approximately 2.5 million years. Currently, these two groups occupy several and specific niches. The major goal of this thesis is to explore functional patterns among small mammals in South America, presenting an analytical novelty and discriminating mechanisms that driving these patterns. Thus it is divided into two chapters: the first presents a new functional approach for the calculation of functional divergence among clades co-occurring in the same community; the second evaluates the main drivers of functional divergence between marsupials and cricetid rodents in South America. The metric developed in the first chapter was adapted from the approach of functional beta diversity, however, instead of comparing pairs of communities, we compared pairs of clades co-occurring in the same community, discriminating how functionally similar or different these clades are. In the second chapter, we found that environmental, functional, evolutionary and historical factors determine the functional divergence among two clades studied here. Furthermore, we found a trend of increased niche differentiation between marsupials and cricetid rodents northward South American continent. We may infer that the gateway of cricetid rodents already determines patterns of functionality in environments nowadays, beyond other important factors, like climate.

A estruturação em comunidades biológicas sugere que há fatores que determinam quais espécies poderão ocorrer juntas. Os pequenos mamíferos sul-americanos (marsupiais e roedores cricetídeos) apresentam um padrão de dispersão no continente sul-americano bastante distinto. Os marsupiais chegaram ao continente há cerca de 100 milhões de anos e os roedores cricetídeos o colonizaram apenas na formação do Istmo do Panamá em aproximadamente 2,5 milhões de anos. Atualmente esses dois grupos ocupam nichos bastante diversos e também específicos. O objetivo geral desta dissertação é explorar padrões funcionais entre pequenos mamíferos sul-americanos, apresentando uma nova métrica de análise e discriminando os principais mecanismos que estruturam esses padrões. Assim, ela está dividida em dois capítulos: o primeiro apresenta uma nova abordagem analítica para o cálculo de divergência funcional entre clados coocorrentes na mesma comunidade; o segundo trata de avaliar os principais determinantes da divergência funcional entre marsupiais e roedores cricetídeos sul-americanos. A métrica desenvolvida no primeiro capítulo foi adaptada da abordagem de diversidade beta funcional, entretanto, ao invés de compararmos pares de comunidades, comparamos pares de clados que coocorrem na mesma comunidade, distinguindo o quanto similiar ou diferente funcionalmente esses clados são. No segundo capítulo, verificamos que fatores ambientais, funcionais, históricos e evolutivos influenciam a divergência funcional entre os dois clados aqui estudados. Além disso, nós encontramos uma tendência de aumento da diferenciação de nicho entre marsupiais e roedores cricetídeos em direção ao norte do continente sul-americano. Nós podemos inferir que a porta de entrada da colonização dos roedores cricetídeos no continente determina, ainda hoje, padrões de funcionalidade dos ambientes, além de outros fatores importantes como o clima. / The existence of structure in biological communities suggests that there are factors that determine which species may occur together. Small mammals of South America (marsupials and cricetid rodents) show a pattern of dispersal in this continent quite different and interesting. Marsupials arrived on South American continent about 100 million years and cricetid rodents only colonized it in the formation of the Isthmus of Panama, approximately 2.5 million years. Currently, these two groups occupy several and specific niches. The major goal of this thesis is to explore functional patterns among small mammals in South America, presenting an analytical novelty and discriminating mechanisms that driving these patterns. Thus it is divided into two chapters: the first presents a new functional approach for the calculation of functional divergence among clades co-occurring in the same community; the second evaluates the main drivers of functional divergence between marsupials and cricetid rodents in South America. The metric developed in the first chapter was adapted from the approach of functional beta diversity, however, instead of comparing pairs of communities, we compared pairs of clades co-occurring in the same community, discriminating how functionally similar or different these clades are. In the second chapter, we found that environmental, functional, evolutionary and historical factors determine the functional divergence among two clades studied here. Furthermore, we found a trend of increased niche differentiation between marsupials and cricetid rodents northward South American continent. We may infer that the gateway of cricetid rodents already determines patterns of functionality in environments nowadays, beyond other important factors, like climate.

Production of mutant biological molecules for understanding biological principles or as therapeutic agents has gained considerable interest recently. Synthetic genes are today being widely used for production of such molecules due to the substantial decrease in the costs associated with gene synthesis technology. Along one such line, we have engineered tRNA genes in order to dissect the effects of G:U base-pairs on the accuracy of the protein translation machinery. Our results provide greater detail into the thermodynamic interactions between tRNA molecules and an Elongation Factor protein (termed EF-Tu in bacteria and eEF1A in eukaryotes) and how these interactions influence the delivery of aminoacylated tRNAs to the ribosome. We anticipate that our studies not only shed light on the basic mechanisms of molecular machines but may also help us to develop therapeutic or novel proteins that contain unnatural amino acids. Further, the manipulation of the translation machinery holds promise for the development of new methods to understand the origins of life. Along another line, we have used the power of synthetic biology to experimentally validate an evolutionary model. We exploited the functional diversity contained within the EF-Tu/eEF1A gene family to experimentally validate the model of evolution termed ‘heterotachy’. Heterotachy refers to a switch in a site’s mutational rate class. For instance, a site in a protein sequence may be invariant across all bacterial homologs while that same site may be highly variable across eukaryotic homologs. Such patterns imply that the selective constraints acting on this site differs between bacteria and eukaryotes. Despite intense efforts and large interest in understanding these patterns, no studies have experimentally validated these concepts until now. In the present study, we analyzed EF-Tu/eEF1A gene family members between bacteria and eukaryotes to identify heterotachous patterns (also called Type-I functional divergence). We applied statistical tests to identify sites possibly responsible for biomolecular functional divergence between EF-Tu and eEF1A. We then synthesized protein variants in the laboratory to validate our computational predictions. The results demonstrate for the first time that the identification of heterotachous sites can be specifically implicated in functional divergence among homologous proteins. In total, this work supports an evolutionary synthetic biology paradigm that in one direction uses synthetic molecules to better understand the mechanisms and constraints governing biomolecular behavior while in another direction uses principles of molecular sequence evolution to generate novel biomolecules that have utility for industry and/or biomedicine.