Thesis (M.S.)--Brigham Young University. Dept. of Plant and Wildlife Sciences, 2008. / Includes bibliographical references (p.62-71).

Highly pathogenic avian influenza (HPAI) virus poses a significant economic disease burden to the poultry sector of Vietnam, and is a credible threat for emergence of novel zoonotic viruses. This thesis examines the molecular evolution and epidemiology of HPAI A(H5) viruses in Vietnam identified through the national poultry surveillance system. The investigations comprised analysis of detection rates and geographic distribution of A(H5) clade variants from samples collected in live bird markets (LBMs); comprehensive analysis of whole genome sequences of viruses collected from 2012 to 2015; development of laboratory protocols for production of reference chicken antisera; and in-depth antigenic characterisations of contemporary A(H5N1) isolates. The findings underscored the high prevalence and widespread distribution of HPAI A(H5) virus within apparently healthy poultry sampled in LBMs and the difficulties in designing appropriate and effective disease management strategies. Whole genome analysis revealed significant diversification and reassortment of A(H5) viruses, with substantial in-situ evolution of clade 1 and 2.3.4 viruses between 2010 and 2012 and lineage replacements involving clade 2.3.2.1 and 2.3.4.4 viruses during 2014-2015. Antigenic analysis of contemporary A(H5N1) clade variants using chicken antisera produced at the National Center for Veterinary Diagnostics (NCVD) proved to be feasible and reproducible, and recapitulated similar patterns of clade clustering as ferret antisera. Antigenic relationships between existing poultry vaccines and circulating field viruses also appeared aligned with in-vivo vaccine challenge studies, in terms of protection profiles. Given the co-circulation of multiple, antigenically distinct clade variants, there is a great need for vaccine strategies capable of inducing broadly cross-reactive immunity. If traditional inactivated vaccines are used, bivalent or trivalent formulations may be required. The results strongly suggest that antigenic data could ultimately be used as a surrogate (or as a precursor) to challenge studies that take time and resources to conduct, thus potentially enabling more rapid assessments and decisions about poultry vaccine selection by Vietnamese animal health authorities.

Genetic variation is the raw material of evolution. The sources of this variation within a population, and its maintenance within a species, have been mysterious since the birth of the field of evolutionary genetics. In this work, I study divergently adapted freshwater and marine populations of the threespine stickleback (Gasterosteus aculeatus) as an evolutionary model to track the origin of adaptive genetic variation and to describe the evolutionary processes maintaining variation across the genome. The stickleback is a small fish with a large geographic range encompassing the northern half of the Northern Hemisphere and composed of coastal marine habitats, freshwater lakes, and river systems. Populations of stickleback adapt rapidly to changes in habitat, and fossil evidence suggests that similar adaptive transitions have been ongoing in this lineage for at least ten million years. In this work, I develop a significant extension of restriction site-associated DNA sequencing (RAD-seq) to generate phased haplotype information to estimate gene tree topologies and divergence times at thousands of loci simultaneously. I find anciently derived clades of variation associated with marine and freshwater habitats in genomic regions involved in recent adaptive divergence; some divergence times extend to over ten million years ago. This history of adaptive divergence has had profound effects on genetic variation elsewhere in the genome: chromosomes harboring freshwater-adaptive variants retain anciently derived variation in linked genomic regions, while marine chromosomes have much more recent ancestry. I present a conceptual model of asymmetric selective and demographic processes to explain this result, which will form a nucleus for future research in this species. Lastly, by incorporating genome-wide recombination rates estimated from multiple genetic maps, I describe a recombination landscape that is favorable to the maintenance of marine-freshwater genomic divergence. Low recombination rates in key chromosomal regions condense widespread divergence of the physical genome, encompassing many megabases, into a small number of Mendelian loci. Combined, my results demonstrate the interconnectedness of evolutionary processes taking place on ecological and geological timescales. The genetic variation available for adaptive evolution today is a product of the long-term evolutionary history of a species.

Esta tese de doutorado versa sobre relações filogenéticas, evolução e biogeografia das espécies do gênero Ramphastos, representado pelos tucanos. / This PhD thesis is about phylogenetics, evolution and biogeography of the species of the genus Ramphastos (toucans).

Orientador: João Meidanis / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Computação / Made available in DSpace on 2018-08-08T13:34:53Z (GMT). No. of bitstreams: 1 Almeida_AndreAtanasioMaranhao_M.pdf: 3188069 bytes, checksum: b0743bc208c47e2d263f7d5503c22c07 (MD5) Previous issue date: 2007 / Resumo: Nas últimas décadas presenciamos grandes avanços na biologia molecular que levaram ao acúmulo de um grande volume de dados acerca de moléculas, tais como DNAs e proteínas, essenciais para a vida e para seu entendimento.O estágio atual é de busca por ferramentas que permitam extrair informações com relevância biológica destes dados. Neste contexto, a comparação de genomas surge como uma das ferramentas e nesta categoria incluímos rearranjo de genomas. Em rearranjo, o genoma é representado por uma seqüência de blocos conservados e, dados dois genomas e um conjunto de operações, busca-se pela que transformem um genoma no outro. Em 1995, Hannenhallie Pevzner apresentaram o primeiro algoritmo polinomial para o problema da ordenação por reversões orientadas. Tal algoritmo executa em tempo O(n4) e foi o primeiro algoritmo polinomial para um modelo realístico de rearranjo de genomas. Desde então, surgiram algoritmos que apresentam desempenho assintoticamente melhor. O melhor deles, apresentado por Tannier e Sagot em 2004, é capaz de executar em tempo O (n(n log n)1/2). Há um algoritmo linear, desenvolvido por Bader e colegas[2], mas este capaz de determinar a seqüência de reversões, apenas calcula a distância. Motivado pela carência de uma derivação algébrica mais formal da teoria desenvolvida em rearranjo de genomas, desenvolvemos uma solução formal para o problema da distância de reversão com sinal. Utilizamos, em tal solução, um formalismo algébrico para rearranjo de genomas que relaciona a recente teoria de rearranjo de genomas ?basicamente fundamentada no trabalho de Hannenhalli e Pevzner ? e a teoria de grupos de permutação de uma nova forma. Pretendemos criar a base para grandes avanços na área através de um formalismo algébrico forte / Abstract: In the last decades we have seen a great progress in molecular biology. That lead to a large volume of data on molecules, DNA and proteins, essential for life.The current stage of research lies in the pursuit of tools to extract information with biological relevance from this data. In this context, comparison of genomes is an important tool and genome rearrangements is a way of doing that comparison. In rearrangement analysis the genome is represented by a sequence of conserved blocks. The aim is to ?nd a minimum sequence of operations that transform a genome into another given as input two genomes and a set of allowed operations. In 1995, Hannenhalli and Pevzner presented the ?rst polinomial algorithm for sorting signed permutations by reversals. This algorithm has complexity O(n4) in time and was the ?rst polinomial algorithm for a realistic model of genome rearrangement. Since then, new algorithms with better asintotic performance had appeared. The fastest algorithm, with complexity O(n?n logn), was developed byTannier and Sagot in 2004. Motivated by a lack of a more formal derivation in the genome rearrangement developed theory, we developed a formal solution for the signed reversal distance problem. We use an algebraic formalism that relates the recent genome rearrangement theory ? basically based on a work of Hannenhalli and Pevzner ? to permutation group theory in a new form. We intend to build a solid theoretical base for further advances in the area through strong algebraic formalism / Mestrado / Teoria da Computação / Mestre em Ciência da Computação

Orientador: Michel Georges Albert Vincentz / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-11T18:45:34Z (GMT). No. of bitstreams: 1 DelBem_LuizEduardoVieira_M.pdf: 9371325 bytes, checksum: 4720605c3fed6784b51b26b99feff19c (MD5) Previous issue date: 2008 / Resumo: Introdução: Os xiloglucanos são os polímeros de açúcar mais abundantes na hemicelulose da maioria das espécies de plantas terrestres, em especial nas eudicotiledôneas. Possuem papel estrutural na parede celular vegetal, interagindo com os filamentos de celulose, e podem ser utilizados como reserva em sementes de várias espécies de eudicotiledôneas, como o Jatobá (Hymenaea courbaril), onde correspondem a quase 50% do peso seco da semente. Este polímero é formado por uma cadeia central de ß-glucano com ramificações que contêm xilose, galactose e fucose. O mecanismo de degradação deste polímero é realizado por cinco hidrolases: XTH, ß-Galactosidase, ß-Glucosidase,? a-Xilosidase e? a-Fucosidase. Estas enzimas são codificadas por genes que constituem famílias multigênicas nos genomas de plantas, e sua atividade na degradação seletiva de xiloglucano têm papel central na regulação do crescimento e morfogênese da célula vegetal. O Jatobá (Leguminosae) é uma árvore tropical, nativa do Brasil, que vem sendo utilizada como modelo vegetal para estudos de impacto ambiental por efeito estufa e estresses abióticos oriundos do aquecimento global. Foi observado que mudas de Jatobá, crescidas numa atmosfera com 720 PPM de CO2 (dobro da concentração atual), apresentam até 50% de aumento de biomassa aos 100 dias. O entendimento das respostas transcripcionais desta planta, em resposta a estes estresses, pode levar a conclusões à cerca de como as florestas tropicais responderão ao aumento inexorável na concentração de CO2, num quadro de aquecimento global. Resultados: Construímos bibliotecas de cDNA de folhas, caule, cotilédones e raízes de plântulas de 45 dias de Jatobá. Um seqüenciamento amostral dos ESTs levou à obtenção de 103 seqüências, parciais ou completas, de proteínas de Jatobá. São os primeiros dados de ESTs numa árvore tropical brasileira. Análises filogenéticas das enzimas que constituem o mecanismo de degradação de xiloglucano foram conduzidas ao longo de 13 genomas completos e 27 bancos de ESTs de espécies dos mais diversos grupos no reino Viridiplantae. Isso nos permitiu organizar a diversidade destas cinco famílias multigênicas em possíveis grupos de ortólogos (PoGOs). As XTHs foram divididas em seis grupos de genes homólogos e 19 PoGOs. As ß-Galactosidases foram divididas em dois grupos de genes homólogos e 10 PoGOs. As ß-Glucosidases foram divididas em dois grupos de genes homólogos e dois PoGOs. As? a-Xilosidase foram divididas em três PoGOs e as a-Fucosidase em dois PoGOs não relacionados evolutivamente. Conclusões e Perspectivas: As 103 seqüências peptídicas obtidas de Jatobá foram anotadas por comparação e serão disponibilizadas nos bancos de dados internacionais. A perspectiva de seqüenciar mais clones poderá levar à montagem do transcriptoma do Jatobá, algo inédito para uma árvore tropical. Concluímos, com as análises filogenéticas, que as XTHs, que formam um grupo monofilético de genes em Streptophyta, surgiram antes da conquista do ambiente terrestre. Estes genes foram progressivamente amplificados ao longo da evolução das plantas terrestres, o que sugere um ganho progressivo de complexidade, que teve seu auge nas Angiospermas. Apresentamos evidências que podem unir evolutivamente as XTHs exclusivas de plantas a enzimas transglicosiladoras de cadeias de ß -glucano em fungos, o que sugere uma origem comum do processo de transglicosilação de cadeias de ß-glucano como mecanismo de controle do crescimento e formato celular em eucariotos com parede celular. As ß-Galactosidases formam um grupo monofilético em Embryophytas com nove PoGOs, no entanto sua grande diversificação (seis PoGOs) ocorreu apenas em Angiospermas. As ß -Glucosidases formam um grupo monofilético em Embryophytas, seqüências similares em bactérias fotossintetizantes podem sugerir uma origem no ancestral dos cloroplastos. As a -Xilosidase, que são monofiléticas nas Spermatophytas, derivaram das ?a-Glucosidases que se encontram dispersas entre todos os eucariotos, é um caso de neofuncionalização. Duas linhagens distintas evolutivamente de a-Fucosidases foram encontradas, uma delas é monofilética em Embryophytas e a outra pertence a uma grande família multigênica (GDSL-motif) da qual pouco se sabe. Mostramos que o mecanismo completo (cinco hidrolases) de degradação de xiloglucano existia no ancestral comum das Spermatophytas (plantas com semente). Como perspectivas este trabalho permite a racionalização de estudos funcionais destas hidrolases o que, em longo prazo, pode contribuir com processos biotecnológicos que passem pela modificação seletiva da parede celular vegetal. / Abstract: Introduction: Xyloglucans are the main hemicelulose in most of land plants, especially in eudicots. It is a structural compound of plant cell-wall that interacts with cellulose and can be used as seed's energy storage of many species, like Jatoba (Hymenaea courbaril). Xyloglucan structure is composed of a ß-glucan backbone that it branched with xylose, galactose and fucose. Its degradation machinery is composed by five glycosil hydrolases: XTH, ß-Galactosidase, ß-Glucosidase,?a-Xylosidase and? a- Fucosidase. These enzymes are codified by multigenic families in plant's genomes and it plays a central role in key processes like growth and morphogenesis of plant cells. Jatoba (Leguminosae) is a tropical tree, native of Brazil. It's been used as a model tree in researches of plant's responses to stresses caused by global warming and high atmospheric CO2 concentration. It was observed a 50% increase in biomass of a 100 days Jatoba seedling when grown in a 720 PPM of CO2 atmosphere (two times bigger than today's atmospheric concentration). Understand the transcriptional responses to these stresses can lead to conclusions about how tropical forests will respond to high concentrations of CO2 and global warming. Results: We made cDNA libraries of leaves, stem, cotyledons and roots of 45 days seedlings of Jatoba. A preliminary sequencing of these libraries reveled 103 predict protein sequences (most partial sequences). Phylogenetic analyses of xyloglucan hydrolytic enzymes were conducted using 13 completed genomes and 27 ESTs assemblies, from a wild range of taxonomic groups in the Viridiplantae kingdom. It allowed us to divide XTH's diversity of genes into six homology groups and 19 possible groups of orthologues (PoGOs). ß-Galactosidases were divided into two groups of homologues and 10 PoGOs. ß -Glucosidases were divided into two groups of homologues and two PoGOs. a-Xylosidase were divided into three PoGOs and a-Fucosidase into two PoGOs evolutionarily unrelated. Conclusions and Perspectives: The 103 protein sequences of Jatoba were annotated by comparison to known proteins and will be deposited in international sequences assemblies. As a perspective, the sequencing of Jatoba ESTs will lead to the assembly of its transcriptome, something never done before in a tropical tree. We concluded that XTHs are monophyletic group o genes in Streptophyta, what means they emerged before lands conquest by plants. These genes were progressively amplified in land plants evolution, especially in Angiosperms, what suggests a progressive gain in complexity. We showed evidences of a possible evolutionary relation between plant's XTHs and fungus hydrolases/transglycosylases enzymes. It suggests a eukaryotic ancestral mechanism to control cell expansion and shape based in ß -glucan transglycosylation and its interaction to cellulose (in plants) or chitin (in fungus). The ß -Galactosidases are a monophyletic group in Embryophytas that were divided into nine PoGOs, six PoGOs only appeared in Angiosperms. The ß -Glucosidases belongs to a monophyletic group in Embryophytas that has sequence similarity to bacterial proteins, especially ones from photosynthetic bacteria species. The a-Xylosidases are a PoGO in Spermatophyta that probably emerged from a-Glucosidases presents in all eukaryotes. It's probably a neofunctionalization process. Two evolutionary distinct lineages of a-Fucosidases where found, one monophyletic in Embryophytas and another that belongs to the poorly understood multigenic family "GDSL-motif proteins". We showed that the complete machinery (all the five hydrolases) of Xyloglucan degradation already exists in Spermatophytas common ancestor. As a perspective, we expect to rationalize the functional characterization works among these multigenic families and to contribute in biotechnology processes that pass through cell-wall modification and selective control. / Mestrado / Genetica Vegetal e Melhoramento / Mestre em Genética e Biologia Molecular

A comparação de taxas de substituição não-sinônimas (dN) e sinônimas (dS) permite inferir quais regimes de seleção operaram sobre regiões codificadoras. Genes com d>N/dS > 1 são candidatos a estarem sob seleção positiva, e scans genômicos em busca dessa assinatura se revelaram uma ferramenta poderosa. Trata-se de um método robusto, uma vez que assume-se que tais sítios estão intercalados nas regiões do genoma sob estudo (e portanto partilham a mesma história demográfica), e que têm como foco a variação em genes específicos, eliminando ambiguidades acerca do alvo da seleção. Por outro lado, o critério de ω > 1 para que genes estejam sob seleção positiva é muito conservador. Isso ocorre porque geralmente apenas alguns códons estão sob seleção positiva, enquanto a maior parte das mutações não-sinônimas são deletérias e, portanto, estão sob seleção purificadora. Por isso, convencionou-se analisar subconjuntos de códons em busca de seleção, seja através de uma base de dados mais restrita ou através de modelos que estimam diferentes valores de ω para subconjuntos de códons, tornando possível inferir quais deles estão sob seleção positiva. Os genes das moléculas MHC têm vários padrões de variação que indicam que algum tipo de seleção balanceadora atuou sobre eles (alta diversidade, grande diferenciação entre alelos e a existência de polimorfismos trans-específicos). Os genes HLA constituem um subconjunto de genes do MHC humano e estão localizados no braço curto do cromossomo 6. Os genes clássicos de classe I (HLA-A, HLA-B e HLA-C) são expressos na maior parte das células somáticas e desempenham papel central no processo de resposta imune adaptativa, capturando e apresentando peptídeos na superfície celular. A região da molécula de MHC à qual antígenos são ligados para serem apresentados a linfócitos T, dessa forma iniciando a resposta imune adaptativa, é conhecida como sítio de reconhecimento do antígeno (ARS). É bem estabelecido que os códons ARS apresentam taxas de substituição não-sinônimas maiores que as taxas sinônimas para esses três locos, consistente com um efeito de seleção balanceadora levando a maior variabilidade funcional na região da molécula que interage com o peptídeo. Os genes HLA clássicos apresentam centenas de alelos, e esses constituem clados que reúnem alelos filogeneticamente relacionados e com similaridades funcionais. Apesar de não haver controvérsia sobre a existência de seleção sobre genes HLA, não existe consenso acerca da importância relativa da seleção sobre linhagens alélicas e sobre alelos individuais na diversificação dos alelos de HLA, e essa foi a questão que decidimos investigar. Nossa hipótese nula foi a de que as linhagens foram os alvos da seleção e a hipótese alternativa foi a de que os alelos individuais foram alvos da seleção ao longo da história evolutiva dos genes HLA. Buscamos, primeiramente, fazer uma validação do método de inferência de dN/dS usando como estudo de caso os códons ARS e sua relação com a capacidade de inferência. Constatamos que, dos códons que encontramos sob seleção positiva, todos (exceto um) estão também na classificação clássica dos códons ARS ou a ±1 códon de distância destes, mostrando que existem evidências de seleção em sítios vizinhos aos ARS. Portanto, uma classificação expandida, que inclua os códons sob seleção que não estão nas classificações ARS comumente utilizadas, deveria aumentar o poder estatístico de testes de modelos de seleção nos genes HLA. Ao comparar os resultados obtidos em análises filogenéticas com bases de dados com e sem recombinantes, verificamos que a remoção de alelos recombinantes altera as estimativas de parâmetros, a identificação de códons com evidência de seleção e a significância dos testes de comparação de modelos. Nossas análises mostraram que ω é significativamente maior para pares de alelos de linhagens diferentes do que para pares de alelos de uma mesma linhagem e que existe uma correlação positiva significativa entre o tempo de divergência dos alelos e as estimativas de ω. Verificamos, ainda, que é possível rejeitar um modelo nulo de uma razão ω estimada para todos os ramos da árvore filogenética e favorecer um modelo em que ω é estimado separadamente para ramos entre e intra-linhagens em HLA-C. Em HLA-A e HLA-C, ω é significativamente > 1 entre linhagens. Mostramos também, para os mesmos locos, ω é significativamente > 1 nos ramos internos. Em HLA-C, o modelo que estima ω separadamente para ramos internos e terminais foi favorecido. Nossos resultados mostram que a intensidade de seleção atuando entre linhagens é maior do que aquela dentro de linhagens. Entretanto, mesmo dentro de linhagens, há fortes evidências de desvios de neutralidade, sugerindo a ação da seleção natural. / The comparison of non-synonymous (dN) and synonymous (dS) substitution rates allows us to infer selection schemes which operated in coding regions. Genes with dN/dS > 1 are candidates to be under positive selection, and genome scans in search for this signature have proved to be a powerful tool. It is a robust method, since it is assumed that such sites are interspersed in regions of the genome under study (and therefore share the same demographic history), and which focuses on the variation in specific genes, eliminating ambiguities about the target of selection. On the other hand, the criterion of ω > 1 for genes to be considered under positive selection is very conservative. This is because usually only a few codons are under positive selection, while most non-synonymous mutations are deleterious and are thus under purifying selection. Therefore, it has been conventioned to analyze subsets of codons in search of selection, either through a narrower data set or through models that calculate different ω values for subsets of codons, making it possible to infer which of them are under positive selection. The MHC molecules genes have different variation patterns that indicate some sort of balancing selection acted upon them (high diversity, large differentiation between alleles and the existence of trans-specific polymorphisms). HLA genes are a subset of human MHC genes and are located on the short arm of chromosome 6. The classical class I genes (HLA-A, HLA-B and HLA-C) are expressed in most somatic cells and play a central role in the process of adaptive immune response, capturing and presenting peptides on the cell surface. The region of the MHC molecule to which antigens are bound to be presented to T lymphocytes, thereby initiating the adaptive immune response, is known as the antigen recognition site (ARS). It is well established that ARS codons have higher non-synonymous than synonymous substitution rates on these three loci, consistent with an effect of balancing selection leading to greater variability in the functional region of the molecule that interacts with the peptide. The classical HLA genes have hundreds of alleles, and these constitute clades which group phylogenetically related and functionally similar alleles. Although there is no controversy about the existence of selection acting on HLA genes, there is no consensus on the relative importance of selection on allelic lineages and on individual alleles on the diversification of HLA alleles, and that was the question we decided to investigate. Our null hypothesis was that lineages were targets of selection and the alternative hypothesis was that the individual alleles were targets of selection during the evolutionary history of HLA genes. We sought, first, to make a validation of the method of inference dN/d>S using as a case study the ARS codons and their relation to the ability of inference. Of all the codons under selection we found, all (except one) are also in the classification of classical ARS codons or ±1 codon away from these, showing that there is evidence of selection at nearby sites to the ARS. Therefore, an expanded classification, which includes the codons under selection that are not commonly used in the ARS classifications, should increase the statistical power of selecion model tests on the HLA genes. By comparing the results obtained in phylogenetic analysis using data sets with or without recombinants, we found that the removal of recombinant alleles alters the parameter estimates, the identification of codons with evidence of selection and the significance of model comparison tests. Our analysis showed that ω is significantly higher for pairs of alleles from different lineages than for pairs of alleles from the same lineage and that there is a significant positive correlation between time of divergence of alleles and estimates of ω. We also verified that it is possible to reject a null model of one ω estimated for all branches of the phylogenetic tree and favor a model where ω is estimated separately for branches within and between lineages of HLA-C. In HLA-A and HLA-C, ω is significantly > 1 between lineages. We also show that, for these same loci, ω fis significantly greater than one or internal branches. In HLA-C, the model that estimates ω separately for terminal and internal branches was favored. Our results show that the intensity of selection between lineages is greater then within them. However, even within lineages, there is a strong evidence of deviation from neutrality, suggesting the action of natural selection.

Retrovírus endógenos (ERVs) são vírus que infectaram células germinativas e proliferaram no genoma do hospedeiro. A família K está integrada apenas no genoma de primatas do Velho Mundo. Os ERVs promovem alterações estruturais nos genomas hospedeiros, sendo fundamentais para a sua evolução. Esse trabalho teve como objetivo realizar uma investigação da distribuição e dinâmica evolutiva de ERV-K nos diferentes hospedeiros. Foram identificados 58 ERV-K em humanos, 38 em chimpanzés, 35 em orangotangos e 19 em macaco rhesus. Análises filogenéticas evidenciaram dois grupos principais, Grupo O/N, que compreende os provirus mais antigos e os mais recentes, e Grupo I, com provirus com tempo de integração intermediário. A dinâmica de espalhamento de ERV-K diferiu entre os hospedeiros. A fixação e eliminação dos ERV-K é resultado de fatores demográficos e populacionais, como gargalos de garrafa e expansões sofridas ao longo da evolução. Análises de quais provírus são ativos em pacientes com HIV e com cancer demonstrou que distintos ERVs são transativados, sugerindo alguma consequencia biológica para o hospedeiro. Além disso, a atividade dos ERVs não depende exclusivamente do tempo de integração, mas sim da integridade de regiões específicas contidas na LTR. / Endogenous retroviruses (ERVs) are remains of ancient viral infection in the germ line cells and subsequent vertical transmission. The K family are integrated only in humans and the Old World monkeys. ERVs play a fundamental role on genome evolution and foster variability. The aim of this work was to investigate their distribution and evolutionary dynamics in primate hosts. We found 55 ERV-K genomes in the human genome, 38 in chimpanzee, 35 in orangutan and 19 in Rhesus monkey. Two main groups were recovered by phylogenetic inference, Group O/N, comprising the newest and the oldest proviruses and, Group I, enclosing those with intermediate integration time. Although the primary integration took place in the ancestral lineage of all primates investigated, their evolutionary dynamic was different among them. I propose that ERV-K dynamics depends on the host demography experienced throughout their evolution. This work also investigated the putative source of proviral transcripts detected in HIV carries and cancer patients. The differential expression found under these conditions suggested a biological role of the ERV-K overexpression. Finally, the results showed that the ERV-K overexpression depends on the integrity of specific promoters in their LTR.

The greater kudu (Tragelaphus strepsiceros) is a large spiral-horned antelope that occurs in sub-Saharan Africa. The species is predominantly a browser and inhabits a diverse range of habitats including savanna woodland, scrub and open forests. The geographical distribution extends from south-eastern Chad, northern Central African Republic (CAR), through eastern Africa, to southern Africa. Throughout its range the species is threatened by habitat loss, fragmentation, diseases and hunting for trophy. Consequently, many populations have reduced numbers and are at great risk of local extinction. In the absence of evidence from comprehensive studies, strategies for conservation and management of many species are often based on subspecies designations despite the fact that the original descriptions were based on few samples and morphological characters that vary extensively. To develop appropriate conservation and management measures, it is imperative to obtain information on population structure, historical demography and evolutionary history of the species. The information generated is used to define units for conservation of the species. In this study, the objective was to investigate population structure and evolutionary history of the greater kudu by analysing mitochondrial DNA (mtDNA) control region sequences and examining size variation in eight microsatellite loci. The mtDNA control region sequences were examined using a combined approach that included phylogeographic, nested clade and mismatch frequency distribution analyses. It was anticipated that use of the two types of genetic markers with contrasting patterns of inheritance and mutation would enhance the understanding and interpretation of the evolutionary history of the species throughout its range. The results were used to evaluate subspecies taxonomy, draw inferences on historical demography and provide information relevant for conservation and management of T. strepsiceros. Intraspecific variation in the mtDNA was examined in 94 samples from 12 locations and revealed low to medium levels of nucleotide diversity. The average nucleotide diversity was 2.7% (0.3% to 2.9%). The average sequence divergence between populations was 2.3% (0.0% to 5.7%). Eight microsatellite loci were analysed in 203 samples representing 13 locations. The number of alleles scored from these loci was 7-12 while the mean heterozygosity was 70.4% (66% to 76%). Microsatellite data showed shallow phylogeographic structure and the average measure of genetic differentiation <1>ST was 0.046. Comparisons of allelic variation across all populations revealed that the Eastern Cape had lower allelic diversity and showed significant differences in allele frequency distribution suggesting a genetic bottleneck in the population's evolutionary past. The combined analyses suggest that the greater kudu originated from Namibia and spread southwards before colonising other parts of its modern range. The results revealed weak geographic partitioning at the regional level, but showed two genetically distinct groups at the continental level. The first group comprised of populations from Namibia, Kimberley and the Eastern Cape from South Africa, while the second comprised of the remaining populations. The results suggest a single evolutionary significant unit (ESU) with two management units (MUs). In the long term, conservation efforts should focus on maintaining demographic connectivity over broad geographical areas within each MU in order to approximate the natural dispersal patterns of the species. / Thesis (PhD (Zoology))--University of Pretoria, 2005. / Zoology and Entomology / unrestricted

Motivated by the desire to investigate two of the largest outstanding problems in galactic evolution -- stellar feedback and galactic chemical evolution -- we develop the first set of galaxy-scale simulations that simultaneously follow star formation with individual stars and their associated multi-channel stellar feedback and multi-element metal yields. We developed these simulations to probe the way in which stellar feedback, including stellar winds, stellar radiation, and supernovae, couples to the interstellar medium (ISM), regulates star formation, and drives outflows in dwarf galaxies. We follow the evolution of the individual metal yields associated with these stars in order to trace how metals mix within the ISM and are ejected into the circumgalactic and intergalactic media (CGM, IGM) through outflows. This study is directed with the ultimate goal of leveraging the ever increasing quality of stellar abundance measurements within our own Milky Way galaxy and in nearby dwarf galaxies to understand galactic evolution. Our simulations follow the evolution of an idealized, isolated, low mass dwarf galaxy (Mvir ∼ 10^9 M ) for ∼ 500 Myr using the adaptive mesh refinement hydrodynamics code Enzo. We implemented a new star formation routine which deposits stars individually from 1 M to 100 M . Using tabulated stellar properties, we follow the stellar feedback from each star. For massive stars (M∗ > 8 M ) we follow their stellar winds, ionizing radiation (using an adaptive ray-tracing radiative transfer method), the FUV radiation which leads to photoelectric heating of dust grains, Lyman-Werner radiation, which leads to H2 dissociation, and core collapse supernovae. In addition, we follow the asymptotic giant branch (AGB) winds of low-mass stars (M∗ < 8 M ) and Type Ia supernovae. We investigate how this detailed model for stellar feedback drives the evolution of low mass galaxies. We find agreement with previous studies that these low mass dwarf galaxies exhibit bursty, irregular star formation histories with significant feedback-driven winds. Using these simulations, we investigate the role that stellar radiation feedback plays in the evolution of low mass dwarf galaxies. In this regime, we find that the local effects of stellar radiation (within ~ 10 pc of the massive, ionizing source star) act to regulate star formation by rapidly destroying cold, dense gas around newly formed stars. For the first time, we find that the long-range radiation effects far from the birth sites are vital for carving channels of diffuse gas in the ISM which dramatically increase the effect of supernovae. We find this effect is necessary to drive strong winds with significant mass loading factors and has a significant impact on the metal content of the ISM. Focusing on the evolution of individual metals within this galaxy, it remains an outstanding question as to what degree (if any) metal mixing processes in a multi-phase ISM influence observed stellar abundance patterns. To address this issue, we characterize the time evolution of the metal mass fraction distributions of each of the tracked elements in our simulation in each phase of the ISM. For the first time, we demonstrate that there are significant differences in how individual metals are sequestered in each gas phase (from cold, neutral gas up to hot, ionized gas) that depend upon the energetics of the enrichment sources that dominate the production of a given metal species. We find that AGB wind elements have much broader distributions (i.e. are poorly mixed) as compared to elements released in supernovae. In addition, we demonstrate that elements dominated by AGB wind production are retained at a much higher fraction than elements released in core collapse supernovae (by a factor of ~ 5). We expand upon these findings with a more careful study of how varying the energy and spatial location of a given enrichment event changes how its metal yields mix within the ISM. We play particular attention to events that could be associated with different channels of r-process enrichment (for example, neutron star - neutron star mergers vs. hypernovae) as a way to characterize how mixing / ejection differences may manifest themselves in observed abundance patterns in low mass dwarf galaxies. We find that -- on average -- the injection energy of a given enrichment source and the galaxy's global SFR at the time of injection play the strongest roles in regulating the mixing and ejection behavior of metals. Lower energy events are retained at a greater fraction and are more inhomogeneously distributed than metals from more energetic sources. However, the behavior of any single source varies dramatically, particularly for the low energy enrichment events. We further characterize the effect of radial position and local ISM density on the evolution of metals from single enrichment events. Finally, we summarize how this improved physical model of galactic chemical evolution that demonstrates that metal mixing and ejection from galaxies is not uniform across metal species can be used to improve significantly upon current state of the art galactic chemical evolution models. These improvements stand to help improve our understanding of galactic chemical evolution and reconcile outstanding disagreements between current models and observations.