Abstract In social insects a major cost of social life is the high number of pathogens found in large societies and the greater likelihood of transmission of pathogens among closely related individuals. The aim of this thesis was to investigate the effect of high pathogen pressure on the molecular evolution of genes involved in the innate immune system in social insects. In addition, the transmission dynamics of the intracellular bacteria Wolbachia in wood ants was examined. By comparing DNA sequences from diverse species of ants and honeybees it was shown that the immune genes in hymenopteran social insects have evolved rapidly. However, by using codon-based likelihood models of evolution positive selection was detected in only two ant genes. This may reflect behaviourally based colony-level defences that can reduce selective pressure on the immune genes. The transmission modes of Wolbachia were studied by comparing DNA sequence variation of the bacteria with that of the host ants. First, it was found that all the studied ants carry Wolbachia. Second, Wolbachia have been transmitted both vertically from mother to offspring and horizontally between individuals of the same as well as of different species. / Tiivistelmä Yhteiskuntahyönteisten (muurahaiset, ampiaiset, mehiläiset ja termiitit) ekologisen menestyksen kääntöpuolena on ollut jatkuva riesa taudinaiheuttajista, joita suurissa yhteisöissä tavataan runsaammin kuin yksittäin elävissä eliöissä. Taudinaiheuttajien tuoman paineen myötä yhteiskuntahyönteisille on kehittynyt käyttäytymiseen perustuvia puolustusmekanismeja täydentämään kaikille monisoluisille eliöille yhteistä synnynnäistä, fysiologista immuniteettia. Nämä puolustusmekanismit ovat todiste siitä, että taudeilla on ollut suuri merkitys yhteiskuntahyönteisten käyttäytymisen evoluutiossa. Toisaalta taudinaiheuttajien vaikutuksista synnynnäiseen immuunipuolustukseen tiedetään hyvin vähän. Väitöstutkimuksen ensisijainen kohde oli taudinaiheuttajien merkitys yhteiskuntahyönteisten synnynnäisen immuunipuolustuksen evoluutiossa. Tutkimuksessa tarkasteltiin, miten immuunijärjestelmän geenit ovat ajan mittaan muuttuneet. Tulokset osoittivat että muutoksia, jotka johtavat proteiinien aminohappojen vaihtumiseen on tapahtunut tiuhempaan tahtiin muurahaisilla ja mehiläisillä kuin yksittäin elävällä banaanikärpäsellä. Merkkejä erityisen voimakkaasta luonnonvalinnasta löydettiin kuitenkin yllättävän pienestä määrästä geenejä. Tämä voi johtua siitä, että käyttäytymiseen perustuvat puolustusmekanismit lieventävät taudinaiheuttajien vaikutusta synnynnäiseen immuunipuolustukseen. Väitöstutkimukseen sisältyi myös hyönteisten solunsisäisen bakteerin, Wolbachian, siirtymismekanismien kartoitus kekomuurahaisilla. Wolbachia on loinen, joka siirtyy yleensä äidiltä jälkeläisille munasolussa. Leviäminen voi tapahtua myös horisontaalisesti lajitoverien ja jopa eri lajien edustajien kesken. Geenisekvensseihin perustuvassa tutkimuksessa kaikista muurahaisista löytyi Wolbachia-bakteereja, ja samasta yksilöstä saattoi löytyä useaa eri bakteerikantaa. Koska muurahaislajien väliset geneettiset erot olivat paljon suurempia kuin erot niissä elävien bakteerien välillä, voitiin päätellä että bakteerien pääasiallinen leviämistapa tutkituilla muurahaisilla on ollut horisontaalinen.

As taxas de resposta viral ao tratamento com Interferon- associado com Ribavirina ainda não estão bem definidas. Muitos estudos associam vários fatores virais e do hospedeiro, tais como a idade, sexo, peso, etnia, nível de enzimas hepáticas, estágio de fibrose, genótipo do HCV com os níveis de RNA viral. Outros estudos associam as células CD8+ específicas para epítopos do HCV com o controle da viremia. O objetivo desse trabalho foi verificar se há aumento na pressão seletiva contra o vírus nos pacientes em tratamento com Interferon- associado à Ribavirina respondedores em comparação com os pacientes não respondedores e associar esse aumento com a ação antiviral do tratamento e/ou com o aumento da resposta imune devido à ação imunomoduladora do Interferon-, utilizando-se modelos de máxima verossimilhança, de cálculo da razão dN/dS e realizando o mapeamento dos epítopos das proteínas NS5A. Nossos resultados demonstram que usando modelos par a par não foi detectado evidência de seleção positiva, entretanto utilizando modelos de máxima verossimilhança nós observamos evidência no grupo que não responde a terapia. O mapeamento dos epítopos revelou que o epítopo VLSDFKTWL estava associado com a resposta efetiva do tratamento com suporte estatístico. Estes resultados indicam que a resposta imunológica aumenta durante o período de tratamento, auxiliando na eliminação do vírus. Além das análises, foi desenvolvida uma ferramenta de mapeamento automático dos epítopos do HCV e análise de seleção natural aplicando modelos de máxima verossimilhança / The reason for low rates of sustained viral response (SVR) in HCV patients remains unknown. Several studies suggest that viral load is closely associated to viral and host factors, such age, sex, body weight, transaminase levels and HCV genotype. Moreover, an strong CD8+ T-cell immunity in acute resolving hepatitis C is matched by strong and sustained CD4+ T-cell proliferation to multiple recombinant structural and non-structural viral proteins is responsible for the control of viraemia in HCV infection. Here, we investigate the differences in CD8 epitopes frequencies from Los Alamos database between groups of patients that showed distinct response to pegylated alpha interpheron with ribavirin therapy, and test for evidence of natural selection on virus in treatment failure group, using five maximum likelihood evolutionary models. Our results indicated no evidence of positive selection by using pairwise models, however we identify evidence of positive selection in non responder group by applying maximum likelihood models. The epitope mapping showed that the epitope VLSDFKTWL was associated with efective therapy outcome, with statistical support. Those results suggest that the immune response increase during the treatment period, allowing the virus clearance. We also developed a tool for automatic mapping of epitopes of HCV that tests for evidence of natural selection by applying maximum likelihood models

The Selection during Niche AdaPtation (SNAP) hypothesis aims to explain how the gene order in bacterial chromosomes can change as the result of bacteria adapting to a new environment. It starts with a duplication of a chromosomal segment that includes some genes providing a fitness advantage. The duplication of these genes is preserved by positive selection. However, the rest of the duplicated segment accumulates mutations, including deletions. This results in a rearranged gene order. In this work, we develop a method to identify SNAP in bacterial chromosomes. The method was tested in Salmonella and Bartonella genomes. First, each gene was assigned an orthologous group (OG). For each genus, single-copy panorthologs (SCPos), the OGs that were present in most of the genomes as one copy, were targeted. If these SCPos were present twice or more in a genome, they were used to build duplicated regions within said genome. The resulting regions were visualized and their possible compatibility with the SNAP hypothesis was discussed. Even though the method proved to be effective on Bartonella genomes, it was less efficient on Salmonella. In addition, no strong evidence of SNAP was detected in Salmonella genomes.

Islands have been considered natural laboratories to study evolutionary processes. Ibiza is a  small island in Spain whose population stands out from other Spanish populations due to its  particular demographic and historical processes. War, famine, and several epidemics have af fected Ibizans, and these phenomena could have left signatures of positive selection in their  genomes. Here, we used three different methodologies to detect positive selection: The Popu lation Branch Statistic (PBS), the Integrated Haplotype Score (iHS), and the Cross-Population  Extended Haplotype Homozygosity (XP-EHH). We used a sliding windows approach to control  for spurious results. The candidate windows for selection were chosen using three different  criteria for each test: maximum and mean score within each window, and proportion of high  scores in each window. Only the windows being simultaneously on the top of each of the three  criteria were selected for annotation and enrichment analyses. The most common traits asso ciated with the SNPs present in the candidate windows were blood function, cardiovascular  diseases, body mass measures, lipid metabolism, renal function, and skin diseases. We sug gest some hypotheses to explain the selection signatures related to some of these traits and  some recommendations for further studies to overcome the present research's limitations.

No description available.

No description available.

Ancestral Sequence Reconstruction is a technique used to statistically infer the most likely ancestor of a set of evolutionarily related sequences, but research which relies solely on protein data has the disadvantage of sequence information being lost upon translation of a protein from its gene transcript, due to the redundancy inherent in the genetic code. In this project, the amino acid sequences, and separately the corresponding codon sequences, of 184 homologous Acetylcholine receptor protein sequences were aligned, and phylogenetic analysis and ancestral sequence reconstruction was performed based on both alignments to infer several ancestral sequences representing important milestones in the evolutionary history of the homologous protein family. To further extract meaningful information from the nucleotide sequences, positive selection analysis was performed on the codon alignment using the Mixed Effects Model of Evolution method, which estimates and compares between the rates of synonymous and non- synonymous mutations across the alignment to detect the occurrence of positive selection events throughout their evolution. The Mixed Effects Model of Evolution can infer positive selection across both sites and evolutionary branches in a sequence alignment, thus highlighting residues along the evolutionary trajectory of the proteins which may have been functionally important in their evolution. Positive selection analysis detected positive selection at a multitude of sites and branches, and by mapping signatures at which selection is strongest with changes in the trajectory of ancestral states, several important sites were chosen as likely to be most valuable for future experimental testing. The implications of this study on the benefits of conducting ancestral sequence reconstruction with protein and codon sequences are discussed.

This study is primarily concerned with assessing the influence of the sex determination genes, transformer (tra), doublesex (dsx) and fruitless (fru) on three sexually dimorphic traits within Drosophila; pheromone blend, courtship song and sex comb tooth number. The sex determination loci have all been implicated as possible candidate genes affecting these important traits that contribute to sexual isolation, which is a major cause of speciation. Quantitative Trait Loci (QTL) analysis is used to assess the effects of these known candidate genes on the naturally occurring variation of mean interpulse interval (IPI) of courtship song and the differing pheromone blend profiles between Drosophila simulans and D. sechellia. The QTL analysis for both song and pheromone blend variation incorporated Multiple Interval Mapping (MIM), which enables the detection for epistasis. The desaturase loci desat1, desat2 and desatF were also included in the assessment on pheromone blends (cuticular hydrocarbon compounds), since they facilitate ecological adaptation and are also candidate genes, which are likely to exert a large affect on this particular trait. The sex determination genes were not significantly influential on the interspecific variation of the cuticular hydrocarbon compounds between these two sibling species. However significant effects were detected from two of the desaturase loci. desat1 was associated with a strong effect on the interspecific variation of a saturated hydrocarbon chain compound (unbranched-23). Additionally the candidate gene desatF potentially exerts an influence on the variation of 7,11-heptacosadiene, through a large epistatic effect with unidentified loci, situated between the markers pros and Mtn. The candidate gene eloF is situated in this region, and is known to affect the elongation of unsaturated hydrocarbon chains. The QTL associated with the marker desatF influenced the variation of both diene compounds (7,11-heptacosadiene and 7,11-pentacosadiene). Intriguingly epistasis was only detected for the variation of these two diene compounds. The MIM analysis assessing the affects of the sex determination genes on interspecific variation of mean IPI detected the candidate gene fru as the closest marker associated with a significant QTL on the third chromosome. The MIM also found a significant QTL associated with the marker Dgα situated on the second chromosome. Moreover significant epistatic interactions were detected between a further QTL situated nearest the marker forked on the X-chromosome with both of the other significant QTL situated on the third and second chromosomes. The analysis of a number of Recombinant Inbred (RI) lines was also carried out to test for the affects of the sex determination genes on both mean IPI and sex comb tooth number. The fru locus was associated with a significant increase in mean IPI, whereas the opposite was true for the dsx locus. In the analysis of sex comb tooth variation, it appears that all RI lines homozygous for D. sechellia alleles at the sex determination loci had significantly higher numbers of sex comb teeth. The final data chapter involves the sequence analysis of the fruitless locus, including all 13 fru proteins between ten recently sequenced Drosophilid genomes. The PAML program was used to detect the possible influence of natural selection on sequence divergence. There was no significant positive selection detected at the BTB functional domain and the sequences encoding for this domain were extremely conserved. Positive selection was found to be acting on the exon encoding for the Zinc-finger C domain. This domain is present in two protein isoforms including the male sex-specific isoform FRUMC, and the common non-sex-specific isoform FRUComC. Interestingly positive selection was also found at the non sex-specific Zinc-finger D domain.

In mammals, before fertilisation can occur, sperm have to bind to, and penetrate, the extracellular coat of the oocyte, the zona pellucida (ZP). In the laboratory mouse, which has been used as a model system for fertilization studies, sperm-ZP binding has been found to be mediated by a region near the carboxy terminal, encoded by exon 7 of the Zp3 gene. This region shows considerable interspecific sequence diversity in North American cricetid rodents, with some evidence of adaptive evolution, suggesting that this may contribute to species specific sperm-ZP binding. However, by contrast, in a preliminary study of three species of Australian murine rodents an identical protein sequence of the region encoded by exon 7 of Zp3 was found to be present. The aim of this present study was to determine the pattern of sequence diversity of this region in the most speciose subfamily of mammals, the murine rodents, and to obtain insight into the selective pressures involved in its evolution. For this, DNA was extracted from murine rodents of Africa, Eurasia, South-east Asia, New Guinea and Australia. The nucleotide and predicted amino acid sequence of exons 6 and 7 of Zp3 in 96 murine species from 14 divisions, as recently defined by Musser and Carleton (2005), was determined and compared. Generally, it was found that closely related species shared a highly similar ZP3 sequence. Maximum likelihood analyses of codon substitution models using representatives from 14 murine divisions, suggested that positive selection had occurred within only a few lineages at several different codon sites adjacent to, or within, the putative combining-site for sperm of ZP3. Positive selection was not evident when the analysis was restricted to the Australian taxa which showed low levels of both intra- and inter-generic sequence divergence. There was no good evidence that this region contributes to species specificity of sperm-ZP binding in these species. These findings thus suggest that the selective forces acting on the Zp3 exon 7 region during the evolution of the murine rodents have varied possibly due to a range of selective pressures not necessarily restricted to the prevention of hybridization. It seems unlikely, therefore, that the amino acid sequence of the exon 7 coding region contributes to species specificity of sperm-ZP binding within most of the lineages from this most speciose subfamily of eutherian mammals. / http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1294654 / Thesis(Ph.D.)-- School of Medical Sciences, 2007

<p>To shed light on forces that shape the molecular evolution of bird genomes, and in turn avian adaptations, comparative analyses of avian DNA sequences are important. Moreover, contrasting findings in birds to those of other organisms will lend a clearer view on general aspects of molecular evolution. However, few such analyses have been conducted in birds. Progress is presented in this thesis.</p><p>Theories predict a reduction in the mutation rate of the Z chromosome as the harmful effects of recessive mutations are exposed in female birds. We find no evidence for this. Instead, the substitution rates of sex chromosomes and autosomes are largely compatible with expectations from male-biased mutation. This suggests that a majority of mutations arise during DNA replication.</p><p>Substitution rates also vary across chicken autosomes. For instance, microchromosomes accumulate ~20% more substitutions than macrochromosomes. We show that a majority of the autosomal variation in substitution rate can be accounted for by GC content, mainly due to the incidence of mutable CpG-dinucleotides.</p><p>Sequence comparisons also show that the pattern of nucleotide substitution varies in the chicken genome and this reinforces regional differences in base composition. </p><p>The level of selective constraint in at least some avian lineages is higher than in mammalian lineages as indicated by low<i> d</i><i>N</i><i>/d</i><i>S</i><i> </i>– ratios. Larger historical population sizes of birds relative to mammals could explain this observation. Within the avian genome, the<i> d</i><i>N</i><i>/d</i><i>S</i> is lower for genes on micro- than macrochromosomes, potentially owing to a higher incidence of house-keeping genes in the former category.</p><p>Contrasting data on non-synonymous and synonymous substitution for divergence and polymorphism shows that positive selection has contributed more to the evolution of Z-linked than autosomal genes. This is likely explained by the full exposure of beneficial recessive mutations on Z when in female birds.</p>