The Trinidad Piping Guan, Pipile pipile synonym Aburria pipile (Jaquin, 1784) is the only endemic Cracid on the island of Trinidad. The species is currently listed as Critically Endangered and is considered to be in ‘on-going decline’ by the IUCN, BirdLife International and Cracid Specialist Group. This study aims to examine aspects of genetic variation and the evolution of the mitochondrial genome in the Trinidad Piping Guan utilising, for the first time, samples collected from individuals in the wild and reference specimens of the genus Pipile sourced from museum collections. In this study the complete mitochondrial genome of the Trinidad Piping Guan was sequenced for the first time. Analysis of intra-specific variation of wild Trinidad Piping Guan individuals using single nucleotide polymorphisms demonstrates extremely limited variation within the genes of the mitochondrial genome and nuclear gene intron sequences. Limited variation within this population is consistent with both historical and contemporary contractions of populations within a restricted island system, which may have serious implications for the future of this species in terms of both genetic diversity and conservation management. Phylogenetic analysis of the complete mitochondrial genome of the Trinidad Piping Guan enabled placement of the genus Pipile within the Galliforme evolutionary tree for the first time, and subsequently places the genus within the broader context of the Aves class. Mito-genomic analysis confirms that the Cracids are one of the basal Galliforme clades, and sister taxa to the Megapodidae. Phylogenetic placement of the Pipile genus is basal to that of the Crax species within the Cracidae family, indicative of an earlier evolutionary origin of the Piping Guans. The inclusion of the Trinidad Piping Guan, in the avian evolutionary tree using the whole mitochondrial genomes expands the current genetic phylogeny of the Cracid family, yielding a better understanding of evolutionary relationships among the Galliforme order and the diversification of modern avian lineages. This study has established novel molecular techniques for the analysis of mitochondrial DNA in historical specimens of the genus Pipile from museum reference collections. The analysis of inter-specific relationships within the genus Pipile has clarified the evolutionary and biogeographic relationships between the Piping Guan species. Additionally, the Trinidad Piping Guan is genetically defined for the first time as an evolutionarily significant unit, which represents a unique evolutionary pathway within this important genus in a closed island system on the island of Trinidad.

<p> Plants and the insects that feed on them dominate diversity in terrestrial ecosystems: half of all named species are contained within these two groups. Herbivorous insects (herbivores) are abundant and diverse, yet paradoxically, two thirds of insect orders contain no major lineages of herbivores, implying barriers to the evolution of this trophic interaction. How herbivory evolves and why herbivores are so diverse are questions that are key to understanding the processes that have shaped global biodiversity. Yet, most lineages of herbivores are ancient with sister groups either absent or too divergent for a comparative genomic analysis to yield a mechanistic understanding of both their origin and diversification. Many of the exceptions to this pattern are among the Diptera, where lineages such as the leaf-mining drosophilids in the genus <i>Scaptomyza</i> have emerged within the last 10 million years. <i>Scaptomyza</i> is particularly well-suited for identifying the adaptations associated with the evolution of herbivory because it is embedded within the paraphyletic genus <i>Drosophila</i>, which contains species with 25 sequenced genomes, and is closely related to <i>D. melanogaster </i>, the genetic model, and a taxon with one of the most well-studied nervous systems. </p><p> Behavior is thought to be one of the earliest adaptations during the evolution of herbivory and niche shifts in general. Insects undergoing a niche shift likely lose their preferences for their ancestral diet, and also evolve an attraction to novel cues indicative of their new oviposition substrate. Once females lay eggs in a new environment, herbivores must consume the new diet, despite the fact that it may contain aversive chemicals and a different balance of macronutrients compared to the ancestral diet. Using the herbivorous <i> Scaptomyza flava</i> as a model system, the primary aim of my dissertation was to use methods in comparative genomics, chemical ecology, ethology, and neural imaging to characterize the mechanistic basis of behavioral changes associated with the evolution of herbivory in insects. </p><p> Using a comparative genomics approach, I found that targeted gain- and loss-of-function mutations were associated with the evolution of herbivory in the genus <i>Scaptomyza</i>. First, four Odorant (Olfactory) Receptor (OR) genes were lost in herbivorous species of <i>Scaptomyza </i>, which are deeply conserved among microbe-feeding drosophilids. The OR genes lost code for receptors that detect yeast-volatiles and are known to stimulate oviposition, feeding and attraction behaviors in <i>Drosophila </i> species. Consistent with these losses was also a loss of detection sensitivity to ligands of these ORs, specifically short-chain aliphatic esters such as ethyl and propyl acetate, major yeast-produced odorants. <i> S. flava</i> female flies were also unresponsive to volatiles produced by active yeast cultures, in contrast to <i>D. melanogaster</i> flies. </p><p> In contrast to some other specialized lineages of <i>Drosophila </i>, I found no evidence of increased or mass chemosensory gene loss, with one interesting and novel exception. The majority of the genes encoding the Plus-C subfamily of Odorant Binding-like proteins (OBPs) are deleted or pseudogenized in <i>Scaptomyza</i>. Additional conserved cysteine residues that form disulfide bonds that stabilize the tertiary structure characterize this subfamily. Interestingly the extra disulfide bonds in Plus-C OBPs are known to be vulnerable to attack by toxic breakdown products of glucosinolates, isothiocyanates, chemicals that are characteristic of <i>S. flava</i>'s host plants in the mustard family. Other than the loss of OBPs, I found <i> S. flava</i> to have multiple duplications of genes encoding ORs, OBPs, gustatory receptors (GRs) and ionotropic receptors (IRs), some of which showed evidence for positive selection (<i>Or67b, Obp49a, Gr33a, Ir67a</i> and <i>Ir76a</i>). Among receptors expressed in the gustatory system, losses, duplications and genes with selection regime changes were more often orthologs of genes expressed in bitter gustatory neurons in <i>D. melanogaster </i>, especially gustatory sensory neurons with a broad expression of gustatory receptor genes. Changes, such as deletions, duplications and increased amino acid substitution rates, were also found among genes encoding receptors implicated in reproductive behavior including the loss of an anti-aphrodisiac receptor, <i>Gr68a</i>, which could be associated with a switch from males chemically guarding mated females with anti-aphrodisiacs to physical guarding behavior where males remain on the backs of females post-mating. (Abstract shortened by ProQuest.)</p><p>

The divergence of the two superfamilies belonging to the Infraorder Catarrhini – Cercopithecoidea (Old World monkeys) and Hominoidea (apes, including humans) – is generally assumed to have occurred during the Oligocene, between 38 and 20 million years ago. Genetic studies indicate that this time period was one of active genetic evolution under strong purifying selection for catarrhine primates. This includes selective pressures on the glycoprotein galactosyltransferase 1 (GGTA1) gene and subsequent inactivation "clocked" at approximately 28 ma, possibly prior to the Cercopithecoidea/Hominoidea split. The GGTA1 gene codes for an α1,3 galactosyltransferase (GT) enzyme that synthesizes a terminal disaccharide, αgalactosyl (αGal), found on glycoproteins and glycolipids on the surface of cells in the tissues of most mammals. Currently, catarrhines are the only mammals studied for the terminal αGal residue that do not express this sugar on their cell surfaces. The proposed selective advantage of this mutation for catarrhines is the ability to produce anti-Gal antibodies, which may be an effective immune component in neutralizing αGal-expressing pathogens, as certain helminthes, many bacteria, including those found in primate guts, and some viruses derived from GGTA1 positive species express αGal on their surfaces. However, many viruses are known to utilize host cell carbohydrates in various ways such as binding receptors or attachment proteins, making these moieties "hot spots" for selective evolution. Cell surface αGal may have predisposed ancestral catarrhines to pathogens and toxins that could utilize the terminal sugar moieties on host cells as binding sites or in other capacities during infection. I found that, in fact, the presence or absence of cell surface αGal affects the course of certain viral infections. Infections of paired cell lines with differential expression of GT showed that Sindbis viruses (SINV) preferentially replicate in αGal-positive cells, whereas herpes simplex viruses type 1 and type 2 (HSV-1 and HSV-2) preferentially grow in cells lacking αGal. In both cases, differences in infection levels resulted from the ability of the virus to successfully initiate infection. This points to a role for αGal in the early stages of viral infections. I also showed that GT knockout mice infected with HSV-2 had higher viral load and greater pathology compared to WT B6 mice that naturally express αGal. The increased susceptibility of KO mice to HSV-2 was not due to an immune component as differences in viral load and pathology were even more evident in immunocompromised mice. This clearly indicates that αGal expression in cells or animal hosts can affect the course of viral infections. I was not able to further confirm differences in susceptibility to HSV 1 and 2 using mouse backcrosses (KO x WT). Unknown genetic factors, that are independent of αGal expression, may be introduced during the crosses that need to be further investigated. Infections of KO and WT mice with other herpes viruses did not yield definitive data and require further studies with suitable reagents. The mechanism by which GT-dependent differential susceptibility to viruses operates still remains to be deciphered. However, it is clear that susceptibility to certain viral infections is tied to the presence or absence of αGal on the surface of host cells. Overall, these results have implications for the evolution of resistance to viral infections in catarrhines. Pathogens exert great selective pressure on their hosts, and it is possible that a pathogen, able to exploit αGal, could have helped shape primate lineage evolution during the Oligocene.

Oceanographic features such as currents, fronts and upwelling cells have been recognised as possible factors driving population differentiation within species. The Benguela Current is one of the oldest upwelling systems in the world, located off the west coast of Southern Africa, and represents a biogeographical boundary between the Atlantic and Indo-Pacific Oceans. Previous studies have reported the influence of this system in isolating several marine taxa between the two oceans. However, few have been conducted within the Benguela Current boundaries, in order to understand its role in shaping population genetic structure of fish species at a regional level. The present study documents the influence of the Benguela Current oceanographic features on the genetic differentiation, population connectivity and evolutionary history of five coastal fish species (Diplodus capensis, Argyrosomus inodorus, Argyrosomus coronus, Atractoscion aequidens and Lichia amia), and one oceanic pelagic fish species (Thunnus albacares). Results for both mitochondrial and nuclear marker variation in all coastal species revealed a similar geographical pattern of population genetic structuring despite distinct differences in life history features. The oceanic species exhibited shallow population differentiation between Atlantic and Indian Oceans. For coastal species, different depths of differentiation were observed, ranging from speciation events (A. aequidens, A. coronus and A. japonicus) to shallow structuring (A. inodorus and T. albacares). Furthermore, in these cases, population structures were coincident with the Benguela Current oceanographic features, suggesting that the system may represent a vicariant barrier to dispersal of coastal fish species. Congruence between mitochondrial and nuclear markers suggests that population isolation was not a single historical event, but has persisted over large timescales and is still active. The existence of cryptic speciation events, and the high levels of genetic diversity and differentiation documented make the Benguela Current a natural laboratory to study evolutionary mechanisms shaping biodiversity and genetic population structure of marine fish species.

W.D. Hamilton has been celebrated as the twentieth-century Darwin. His extension of evolutionary theory to explain social behaviours has been extensively documented. Current accounts, however, have often overlooked the extent to which his early research goals were tied to his desire to see that a better world was created through a scientific understanding of society. In fact, when his interests in humans, and especially his eugenic concerns, have been acknowledged, they have been distanced from his scientific achievements and treated separately. Using new sources to reexamine the development of Hamilton’s most famous idea, the theory of inclusive fitness, we may better understand how his perception of cultural upheaval shaped his reading of social behaviours as evolved characters following universal laws. Understanding this, we may see that however successful Hamilton was, he never realized his original dream, which was to devise a theory that would inform the human world, replacing religious and ideological beliefs. As he sought to solidify his career in the 1970s, he moved away from publicly disclosing his more controversial ideas. This meant that by the time the science of social behaviour inspired heated debates, he was almost always absolved from political critiques. Many assumed that his theory was derived from observations of insects, and his eugenic ideas were forgotten, ignored, or not understood. He was therefore well positioned to become the objective figurehead of a new discipline, sociobiology. This does not mean that his desire to understand society as the result of genetic laws subsided, and by placing inclusive fitness against its social and political background, we might reimagine its trajectory and its impact in new ways. We might also begin to see Hamilton not as an isolated scholar unengaged with society but as an individualist whose extra-scientific beliefs paralleled his scientific theories in meaningful ways.

As an outcome of very active arbovirus monitoring programs that began in Australia in the 1950s, some of the most diverse and unusual rhabdoviruses in the world have been isolated from this continent. These novel rhabdoviruses represent an important and valuable pool of highly diverse viruses; however, most of them have remained poorly characterised. In light of the significant disease potential of numerous rhabdoviruses, the characterisation of novel rhabdoviruses is indispensable for threat assessment to livestock, wildlife and humans and preparedness for outbreaks. The genetic characterisation of novel viruses is also an essential step for the development of molecular detection assays for improved monitoring and investigations into unidentified disease cases. In this study, the complete genomes of four novel rhabdoviruses have been sequenced and a fifth is close to completion. The substantial new data generated has significantly extended the understanding of the biology and evolution of the Rhabdoviridae. Wongabel virus (WONV), isolated from the biting midge Culicoides austropalpalis, was found to contain a unique genome structure encoding ten genes, including five novel genes (Chapter 2). Analysis by western blotting suggested that four out of the five novel genes were expressed in infected cell cultures. Ngaingan virus (NGAV), isolated from Culicoides brevitarsis, was found to have the largest genome of any rhabdovirus sequenced to date, and with thirteen genes has the largest number of genes of any (-) ssRNA virus sequenced to date (Chapter 3). Seven of the thirteen genes are novel. Similar to viruses in the genus Ephemerovirus (bovine ephemeral fever virus and Adelaide River virus), NGAV contains a second glycoprotein with an unknown function. Phylogenetic analysis places this virus alongside WONV and the north-American bird and mosquito-associated Flanders virus within the Hart Park group that remains to be classified by the ICTV. Screening of various wildlife and livestock sera collected in northern Australia indicated a strong association of NGAV with macropods. Tibrogargan virus (TIBV) and Coastal Plains virus (CPV) were isolated from cattle and Culicoides brevitarsis (TIBV). Past serological surveys reported both viruses to be highly prevalent in cattle in northern Australia and demonstrated that the two viruses share a relatively close relationship at the antigenic level. The genomic analyses revealed that these two viruses have a unique genome organization, with three additional genes (Chapter 4). These additional genes are highly diverged at the sequence level but the encoded putative proteins share a significant conservation of secondary structure elements. The sequencing of these two related viruses has provided a unique opportunity to gain insights into the characteristics and evolution of novel proteins in two different rhabdoviruses. Phylogenetic analyses showed that TIBV and CPV form an independent cluster which does not appear to belong to any of the current genera, but which is most closely related to the genus Ephemerovirus based on N protein analysis. Although neither virus has been associated with disease, a serological survey of various animal sera collected in northern Australia showed that these viruses are currently highly prevalent in sentinel cattle and buffalo. Oak Vale virus (OVRV) was isolated from mosquitoes, Culex edwardsi and Ochlerotatus vigilax, from two geographically diverse regions of Australia located approximately 3000 km apart. The genome of OVRV was found to contain only one novel gene (Chapter 5). Comparatively, the genome of this virus is much less complex than the others in this study, but this virus displays considerable divergence from all other rhabdoviruses. A high seroprevalence for this virus was found in the feral pig population in northern Australia. The data generated from this study represents a considerable increase in the quantity of genetic data available for this viral family, and has revealed the existence of a large number of previously unidentified genes, highlighting that that the potential for complexity within the prototype genomic model of a rhabdovirus is much greater than previously thought. The novel nature of the additional genes provides grounds for further research into rhabdovirus evolution. Analysis of this new data suggests that these viruses cannot be classified into existing genera under the current criteria and it is clear that the taxonomy of the Rhabdoviridae requires revision. The observation that these viruses are currently circulating in livestock and wildlife in northern Australia accentuates the need for closer monitoring of animals and the need for further study of this diverse and fascinating group of viruses.

Thesis (Master)--İzmir Institute of Technology, İzmir, 2005. / Includes bibliographical references (leaves. 111-115).

Meningococcal disease, caused by the bacterium Neisseria meningitidis, is an important cause of morbidity and mortality in young children and adolescents worldwide. There are 12 serogroups with most disease due to meningococci expressing one of five capsular polysaccharide antigens corresponding to serogroups A, B, C, Y and W135. In Europe, the majority of disease-causing strains are of serogroups B and C. No comprehensive vaccine is available against the bacterium due to the difficulty in producing serogroup B vaccines. A number of countries, e.g. UK and the Republic of Ireland have implemented routine meningococcal conjugate C (MCC) vaccine strategies. Due to the high proportion of disease accounted for by serogroup B in Europe and other developed countries, much research is currently being carried out to unearth vaccine candidates that would be protective and give as wide coverage as possible. Such candidates include the antigens PorA, FetA and factor H-binding protein. Potential drawbacks with antigens such as these which are under immune selection are high degrees of variability and lack of cross-immunity. Determination of the distribution, both geographically and temporally, of antigens and their association with clonal complex can aid in the formulation of novel vaccines and assess their potential coverage across Europe. Serological typing schemes involving characterisation of the polysaccharide capsule (serogroup) and outer membrane proteins such as PorA (serosubtype) and PorB (serotype) have been used for a number of years with some success. However, drawbacks associated with these methods include insufficient discrimination, limitations in panels of monoclonal antibodies used in the typing procedures and difficulty in comparison of results among labs. Consequently, in recent years genotypic methods such as multi-locus enzyme electrophoresis (MLEE) and subsequently multi-locus sequence typing (MLST) have been developed. These methods measure the variation in slowly evolving housekeeping genes whereas serological methods measure variation in antigens which are under immune pressure and are therefore more diverse. Combination of phenotypic and genotypic typing methods can offer high levels of discrimination. Molecular studies into meningococcal diversity have offered many important insights into its population biology, which have implications for prevention and control of meningococcal disease. These have included the identification of hyperinvasive lineages and the correlation of genetic type with antigenic type and disease epidemiology. The EU-MenNet programme was established as a pan-European infrastructure for the research and surveillance of European meningococcal disease. Its aim was to coordinate and disseminate the latest molecular isolate characterisation techniques (MLST) and electronic data transfer via the Internet to exploit epidemiological and population genetic studies. Within the EU-MenNet, the European Meningococcal MLST Centre (EMMC) was set up to carry out molecular typing — MLST, PorA and FetA — of European disease isolates from 18 countries over three years 2000, 2001 and 2002. The output of this project will be the largest representative molecular epidemiological study of meningococcal disease in Europe. Assessment of the data produced will give insights into the geographic and temporal distribution and structuring of disease-associated clonal complexes and antigens and their associations. This will give an indication of the meningococcal disease population in Europe and will be invaluable for the current, and ongoing, development and introduction of new meningococcal vaccines.

How long has the extant flora been present in the Antarctic? Glaciological reconstructions propose that most areas in Antarctica were covered by thick ice sheets throughout the Last Glacial Maximum (LGM; ~22-18 kya) as well as previous glaciations, suggesting terrestrial life must have been extremely limited during these periods. In contrast, recent biogeographic and genetic studies support most extant groups of Antarctic terrestrial fauna having survived past glaciations in situ. However, studies on the origin and age of the Antarctic flora remain sparse. Applying population genetic, phylogeographic and divergence time analyses I assessed the global biogeography, origin and age of several abundant Antarctic moss species, including: four Polytrichaceae mosses, characterised by having bipolar distributions, the most common (~45% of species) distribution pattern amongst Antarctic mosses; the globally widespread moss Ceratodon purpureus; the bank-forming moss Chorisodontium aciphyllum, also known for its old sub-fossils in Antarctica and long-term viability from revival experiments; and, lastly, the genus Schistidium, the most species-rich moss genus in Antarctica, including many endemic species. Genetic analyses revealed evidence of long-term (multi-million year) survival of plants in Antarctica (several species of Schistidium, Ceratodon purpureus, and possibly Polytrichum juniperinum). However, evidence for a likely more recent (< 100 ky) arrival of Chorisodontium aciphyllum was also found. Some species revealed multiple separate dispersal events to the Antarctic, suggesting the region may be less isolated for spore-dispersed organisms than previously thought. Evidence for increased genetic diversity in the northern maritime Antarctic compared to other regions point at it including potential refugial areas. Furthermore, genetic patterns revealed geographic features that enable and limit the connectivity of bryophytes globally as well as in Antarctica. This study suggests that, despite the harsh polar climate during glaciation periods, many bryophytes have had a much longer presence in Antarctica than previously thought.

Orientador: Gonçalo A. Guimarães Pereira / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-15T02:44:59Z (GMT). No. of bitstreams: 1 Tiburcio_RicardoAugusto_D.pdf: 13957444 bytes, checksum: 5d1ae127f2574323a433b1478aeb3efe (MD5) Previous issue date: 2010 / Resumo: Moniliophthora perniciosa (Stahel) Aime & Phillips-Mora é um fungo basidiomiceto hemibiotrófico causador da vassoura de bruxa no cacau (Theobroma cacao L.). Esta doença é caracterizada pela produção de ramos hiperplásicos e hipertróficos e frutas partenogênicos durante a fase biotrófica, seguido por necrose dos tecidos infectados durante a fase necrotrófica. Esta é a principal doença da produção de cacau na América do Sul e no Caribe, tendo causado uma diminuição de mais de 65% na produção no sul da Bahia, a principal região produtora do país. Vários genes relacionados à patogenicidade foram encontrados em M. perniciosa como parte do Projeto Genoma da Vassoura de Bruxa. No entanto, os padrões de evolução destes genes, que poderiam ajudar a compreender a evolução da fitopatogenicidade dessa espécie, ainda não foram estudados. Também não foram estudados as mudanças ocorridas no genoma desta espécie durante a sua evolução. Estas mudanças são particularmente relevantes uma vez que a maioria das espécies estreitamente relacionadas com M. perniciosa não é fitopatogênica. Desta forma a compreensão da evolução deste modo de vida na espécie poderia ajudar a entender a evolução de fungos fitopatógenos em geral. Este trabalho tem como objetivo ampliar o conhecimento sobre o surgimento da patogenicidade em M. perniciosa analisando a evolução dos genes potencialmente relacionados a ela, aumentando assim o conhecimento sobre a vassoura de bruxa e ajudando na busca por uma maneira de controlar a doença. Para isso, foram estudados os padrões de evolução de diversos genes ligados ao processo de necrose característica da vassoura de bruxa e genes candidatos a terem sido obtidas por transferência horizontal de genes (HGT). Os resultados indicam que a evolução da patogenicidade em M. perniciosa envolveu tanto à aquisição de novos genes quanto a utilização para novas funções de outros já presentes nos ancestrais saprotróficos. Em particular, a busca de genes horizontalmente transferidos encontrou dois genes potencialmente envolvidos na doença que ainda não tinham sido estudados, sugerindo que a análise evolutiva a nível genômico é um instrumento relevante para a escolha de genes candidatos para análises em bancada. / Abstract: Moniliophthora perniciosa (Stahel) Aime & Phillips-Mora is a hemibiotrophic basidiomycete fungus that causes witches' broom disease in cocoa (Theobroma cacao L.). This disease is characterized by the production of hyperplasic and hypertrophic stems and parthenogenetic fruits during biotrophic life-phasee, followed by necrosis of infected tissues during necrotrophic life-phase. This is the main disease affecting the cocoa production in South America and the Caribbean, causing a decrease of more than 65% in the production in southern Bahia, the main producing region. Several genes related to pathogenicity were found in M. perniciosa as part of the Witches' Broom Genome Project. However the patterns of evolution of these genes, that could help to understand the evolution of plant pathogenicity in this species, were not yet studied. Also the changes occurred in this species at a genomic level during its evolution were not studied. These changes are particularly relevant since the majority of species closely related to M. perniciosa is not phytopathogenic and so the understanding of this evolution would help to understand the evolution of plant pathogens in general. This work attempts to increase the knowledge about the emergence of pathogenicity in M. perniciosa studding the evolution of genes potentially related to it, therefore increasing the knowledge about the witches' broom and helping in the search for a way to control the disease. To do that, it were studied the evolutionary patterns of several genes related with the necrosis process characteristic of witches' broom and genes candidate to have been obtained by horizontal gene transfer (HGT). These later were detected by a genome level screening. The results indicate that the evolution of plant pathogenicity in M. perniciosa involved both the acquisition of new genes and the use of genes already present in the saprotrophic ancestral in new functions. In particular, the search for horizontally transferred genes found two genes potentially involved in the disease which were not yet studied, suggesting that the evolutionary analysis at the genomic level is a relevant tool to the choice of genes candidate to laboratory analysis. / Doutorado / Genetica de Microorganismos / Doutor em Genetica e Biologia Molecular