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1
Steiger, Silke. "Evolution of avian olfaction." Diss., lmu, 2008. http://nbn-resolving.de/urn:nbn:de:bvb:19-91757.
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Steiger, Silke S. Fidler Andrew Eric Kempenaers B. Mueller Jakob C. "Evolution of avian olfaction." Connect to this title online (Universität München site) Connect to this title online (Deutsche Nationalbibliothek site), 2008. http://d-nb.info/991247264/34.
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Thesis (doctoral)--Ludwig-Maximilians-Universität München, 2008.<br>Title from PDF t.p. (viewed on Jan. 8, 2009). Some chapters co-authored with others. Includes bibliographical references (p. 117-127).
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Steiger, Silke S. "Evolution of avian olfaction." kostenfrei, 2008. http://edoc.ub.uni-muenchen.de/9175/.
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Maxwell, Erin. "Evolution of avian ossification sequences." Thesis, McGill University, 2008. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=21942.
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The relative timing and sequence of events during embryonic development plays an important role in adult shape and thus in evolution. The sequence in which bones form in the developing embryo should therefore contain a component capable of revealing evolutionary history, however processes relating to ossification sequence and the sequences themselves are poorly known and rarely discussed. In this thesis, I describe the embryonic skeletal development of Meleagris gallopavo, Sterna hirundo, Somateria mollissima, Anas platyrhynchos, Cairina moschata, Dromaius novaehollandiae, Rhea americana and Struthio camelus for the first time in the scientific literature, focusing on ossification. All species exhibited intraspecific variation in ossification sequence, but the level of polymorphism present was generally quite low. Specimens collected from the wild did not show more variability in ossification sequence than those incubated under constant conditions in the lab. Dermal bones did not always ossify before endochondral bones, nor did neural-crest derived elements always form before elements derived from the paraxial mesoderm. All of this suggests that the factors controlling ossification sequence are complex, and more than one variable may play a role. In order to examine sequences in a more explicit phylogenetic context, I converted them into a form that is easily analyzed (event-pairs) and used these as characters for phylogenetic reconstruction. While this technique is plagued with problems involving logical and biological non-independence, it is an efficient tool for surveying conservation and divergence in ossification sequences at different levels of phylogenetic relatedness. I also reconstructed shifts on an accepted topology. The analysis indicates that ossification sequences are influenced by relative evolutionary reduction or expansion in element size. Reduced elements ossify late in sequence, and also temporally later, as measured by stage. Enlarged elements<br>Le temps de formation et la séquence d'événements du développement embryonnaire jouent un rôle important dans la forme adulte et dans l'évolution. La séquence selon laquelle les os se forment dans l'embryon devrait donc contenir des informations capables de révéler l'histoire évolutionnaire. Cependant, les facteurs qui influencent la séquence d'ossification et les séquences elles-mêmes sont mal compris et rarement étudiés. Dans cette thèse, je décris le développement squelettique embryonnaire chez Meleagris gallopavo, Sterna hirundo, Somateria mollissima, Anas platyrhynchos, Cairina moschata, Dromaius novaehollandiae, Rhea americana et Struthio camelus pour la première fois dans la littérature scientifique, en me concentrant sur l'ossification. Une variabilité intraspécifique entre les séquences d'ossification a été observée chez toutes espèces, mais le niveau de polymorphisme était généralement bas. Les spécimens d'espèces sauvages n'ont pas montré plus de variabilité dans la séquence d'ossification que ceux incubés dans les conditions constantes du laboratoire. Les os membraneux n'ossifient pas toujours avant les os de cartilage, et les os dérivés de la crête neurale ne se forment pas toujours avant les éléments dérivés du mésoderme paraxial. Ceci suggère que les facteurs qui contrôlent la séquence d'ossification sont complexes et que plus qu'une facteur peuvent y jouer un rôle. Afin d'examiner les séquences dans un contexte phylogénetique, je les ai convertis en une forme facile à analyser (‘paires d'événements') et ai utilisé les caractères de séquence d'ossification pour la reconstruction phylogénetique. Bien que cette technique présente des problèmes liés à un manque d'indépendence logique et biologique, c'est un outil efficace pour examiner la conservation et la divergence des séquences d'ossification à différents niveaux de rélation phylogénetique. J'ai aussi reconstruit les changements$
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Wharton, Deborah Susan. "The evolution of the avian brain." Thesis, University of Bristol, 2002. http://hdl.handle.net/1983/04463ee9-0d16-4d96-a891-d09f0f3661c0.
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Uebbing, Severin. "On the Evolution of the Avian Transcriptome." Doctoral thesis, Uppsala universitet, Evolutionsbiologi, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-259487.
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Change in gene expression is a powerful tool for evolution, because seemingly small expression changes can contribute important steps towards adaptation without necessarily affecting the whole organism. There is still much to learn about how gene expression evolves on genome- and population-wide levels, especially in non-model organisms. This thesis addresses some important questions in gene expression evolution via the quantitative measurement of RNA and protein levels in birds. First, I confirmed the state of incomplete dosage compensation in birds by sequencing the transcriptome of collared flycatchers (Ficedula albicollis). I showed that pleiotropy governs the evolution of expression male-bias from the Z chromosome. Sex-linked genes in females were more highly expressed than half the male expression level, indicative of a partial up-regulation. A comparison with data from ostrich (Struthio camelus), a bird with non-degenerated sex chromosomes, showed that sex-linked expression male-bias evolved following sex chromosome degradation. Second, using a combination of RNA sequencing and proteome mass spectrometry in chicken (Gallus gallus), I asked whether complete dosage compensation was achieved through regulation at translation. I showed that this was not the case and that incomplete dosage compensation extends to the protein level in birds. In addition, sex-linked genes showed more often an increased amount of regulation at translational level than autosomal genes. Third, I investigated gene expression divergence between collared and pied flycatchers (Ficedula hypoleuca) using RNA sequencing in multiple tissues and individuals. Tissues differed in the degree of expression variance and in the number of divergent genes, which I identified using expression QST. Variance within species was negatively correlated with expression breadth and protein interactivity, indicating that evolutionary constraints act predominantly within interbreeding populations. Among genes unique to one of the species, I identified one gene, DPP7, falling into a large genomic deletion fixed in pied flycatchers. Fourth, I investigated allele-specific expression (ASE) in the two flycatcher populations. ASE was identified from genetic variants within transcripts using RNA sequencing reads. We developed a Bayesian negative binomial approach that gained statistical power by estimating expression variance from combined SNPs within a transcript and overdispersion from the whole dataset.
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Felice, Ryan N. "Evolution and Integration of Avian Caudal Skeletal Morphology." Ohio University / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1427117367.
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Vicario, Andrade Alba. "Development and evolution of the avian extended amygdala." Doctoral thesis, Universitat de Lleida, 2015. http://hdl.handle.net/10803/314572.
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En esta Tesis Doctoral hemos identificado los componentes de la amígdala extendida (EA) de aves, en base a su posición topológica, perfil genético y origen embrionario. En EA central de pollo y pinzón, identificamos las masas intercaladas y amígdala central, con células de origen estriatal dorsal y/o ventral, pero con subpoblaciones menores de otros orígenes. Además, el núcleo lateral de la estria terminal, de origen palidal, contiene subpoblaciones de células inmigrantes de origen estriatal, preóptico o eminencial. En EA medial del pinzón, hemos identificado distintas subpoblaciones celulares en la amígdala medial y el núcleo medial de la estria terminal con origen palidal, preóptico, hipotalámico o eminencial. Nuestros datos indican que EA está formada por múltiples corredores celulares con distinto origen y perfil genético, lo que supone un cambio de paradigma para entender la conectividad y función de cada tipo celular en el control de las emociones, motivación y comportamiento social.<br>In this Ph.D. Dissertation, we have identified the components of the avian extended amygdala (EA), based on their topological position, genetic profile and embryonic origin. In central EA of chicken and zebra finch, we identified the intercalated masses and the central amygdala, with cells derived from the dorsal and/or ventral striatal domains, but with minor subpopulations from other origins. Moreover, the lateral bed nucleus of the stria terminalis, with pallidal origin, contains subpopulations of immigrant cells with striatal, preoptic or eminential origins. In medial EA of zebra finch, we identified different cell subpopulations with pallidal, preoptic, hypothalamic or eminential origins. Our data indicate that EA is formed by multiple cell corridors with different origin and genetic profile, which opens new venues for investigating the connections and function of each neuron subtype in the control of emotions, motivation and social behavior.<br>En aquesta Tesi Doctoral hem identificat els components de l'amígdala estesa (EA) d'aus, en base a la seva posició topològica, perfil genètic i origen embrionari. En EA central de pollastre i pinsà, hem identificat les masses intercalades i l'amígdala central, amb cèl·lules estriatals dorsal i/o ventral, però amb subpoblacions menors d'altres orígens. A més, el nucli lateral de l’estria terminal, d'origen palidal, conté subpoblacions de cèl·lules immigrants d'origen estriatal, preòptic o eminèncial. En EA medial del pinsà, hem identificat diferents subpoblacions cel·lulars en l'amígdala medial i el nucli medial de l’estria terminal amb origen palidal, preòptic, hipotalàmic o eminèncial. Les nostres dades indiquen que EA està formada per múltiples corredors cel·lulars amb diferent origen i perfil genètic, la qual cosa suposa un canvi de paradigma per entendre la connectivitat i funció de cada tipus cel·lular en el control de les emocions, motivació i comportament social.
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Lindholm, Anna Kristina. "Evolution of host defences against avian brood parasitism." Thesis, University of Cambridge, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.627230.
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Middleton, Kevin Mallory. "Morphology, evolution, and function of the avian hallux /." View online version; access limited to Brown University users, 2003. http://wwwlib.umi.com/dissertations/fullcit/3087312.
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Thesis (Ph.D.)--Brown University, 2003.<br>Available in film copy from University Microfilms International. Vita. Thesis advisor: Stephen M. Gatesy. Includes bibliographical references (leaves 117-147). Also available online.
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Allen, Vivian Richard. "The evolution of avian hindlimb conformation and locomotor function." Thesis, Royal Veterinary College (University of London), 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.559019.
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Dalsätt, Johan. "Fossil birds: Contributions to the understanding of avian evolution." Doctoral thesis, Stockholms universitet, Institutionen för geologiska vetenskaper, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-75015.
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The study of the evolution of birds began about 150 years ago with the finding of Archaeopteryx. Yet, many unsolved questions about avian evolution remain to be answered. This thesis aims at addressing some of these questions. The Early Cretaceous Confusiusornis is the most well-represented Mesozoic bird in the fossil record. The abundance of fossils facilitates a study of the preservation of specimens in the two geological formations in which this taxon is found. It was demonstrated that specimens in the Yixiang Formation always are represented by complete, articulated skeletons, while those in the Jiofutang Formation often lack the pectoral girdle and the wings. Despite the many specimens available of Confusiusornis few clues to the diet of this taxon have been found. We describe a Confusiusornis specimen with a pellet of fish remains preserved in the throat region. The enantiornithid birds probably constituted the most species-rich and diverse bird group during the Cretaceous. Several well-preserved specimens have been found in China, e.g. Grabauornis lingyuanensis described herein. The mass extinction at the end of the Cretaceous probably gave the only surviving group of birds,Neornithes,chance to radiate and evolve into new niches. One such group is the Strigiformes (owls). We describe a new species from the Eocene Green River Formation in USAthat we suggest is closely related to the contemporary European Prosybris antique and P. medius. Although birds are known from several Miocene localities in Europe, the discovery of vertebrate fossils in the Hambach opencast lignite mine was thus unexpected and remarkable. The most significant bird found in Hambach is a specimen of darter, genus Anhinga. It agrees in size, proportions and morphology the fossil species Anhinga pannonica to which we refer the Hambach specimen. Fossils of ducks and galliforms have also been found in deposits at Hambach dated to the Pliocene.<br><p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 1: Submitted. Paper 4: Submitted.<strong></strong></p>
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Skelhorn, John. "Avian chemical perception and the evolution of insect defences." Thesis, University of Newcastle Upon Tyne, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.420011.
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Temperley, Nicholas David. "Evolution and Genetic Variation of Avian Toll-like Receptor Genes." Thesis, University of Kent, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.499778.
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Stoddard, Mary Caswell. "The evolution of colour, pattern and structure in avian eggs." Thesis, University of Cambridge, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.610588.
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Rands, Chris M. D. "Analyses of functional sequence in mammalian and avian genomes." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:27e0ac20-eb27-423c-9493-a8a1c6cc57b8.
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The first draft sequence of the human genome was published over a decade ago, yet interpreting the functional importance of nucleotides in genomes is still an ongoing challenge. I took a comparative genomic approach to identify functional sequence using signatures of natural selection in DNA sequences. Mutations that are purged or propagated by selection mark sequences of significance for biological fitness. I developed and refined methods for estimating the quantity of sequence constrained with respect to insertions and deletions (indels) between two genome sequences, a quantity I termed α<sub>selIndel</sub>. This sequence is evolving more slowly than surrounding neutral sequence due to the purging of deleterious indel variants, and thus this sequence is likely to be functional. I estimated α<sub>selIndel</sub> between diverse mammalian and avian species pairs, and found a strong negative correlation between α<sub>selIndel</sub> and the divergence between the species’ genome sequences. This implies that functional sequence turns over rapidly as it is lost and gained over time. I quantified the variable levels of sequence constraint, and rates of sequence turnover, for different types of human biochemically annotated element. Furthermore, I found that similar rates of functional turnover have occurred across mammalian and avian evolution. Finally, I identified positively selected amino acid residues that may be important for Darwin’s finch beak development, and found evidence of adaptively evolving reproductive proteins in the ancestral songbird lineage. Collectively these results demonstrate the wide-spread nature of lineage-specific functional sequence with implications for understanding species traits and the use of model organisms to inform human biology.
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Biskis, Veronika N. "Feathered dinosaurs and the origin of avian flight." Thesis, Boston University, 2013. https://hdl.handle.net/2144/21125.
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Thesis (M.A.) PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you.<br>It is now widely accepted that modern day birds originated from the clade Theropoda represented by bipedal carnivorous dinosaurs that thrived between the late Triassic and Cretaceous period. New research illustrates how the evolutionary assembly of the avian body plan began in these theropods with small fore limbs, large hind limbs and stiff tails, and progressed through a series of increasingly bird-like, transitional anatomical stages. There is also a great deal of homoplasy among dinosaurs however, or evolution of the same traits in distantly related groups, which makes it even more difficult to pinpoint the phylogenetic relationships among theropods. A limited fossil record and confusing temporal inconsistency has also led paleontologists and ornithologists alike to dismiss this crucial connection. They often attribute the origin of birds instead to a basal archosaur, ancestor to both dinosaurs and crocodilians.
However the recent discoveries of feathered non-avian theropods, especially from the Late Jurassic and Early Cretaceous of Liaoning, China may finally lay the argument to rest. The scientific community has remained especially divided over to what degree feathers and other flight characteristics are present amongst the advanced theropods, and Dinosauria in general. Understanding this distinction helps separate each species into separate clades along the cloudy phylogenetic timeline as a function of feather development, and therefore offers insight into where they initially became functional for flight. Because fossils depicting defined integumental structures have been recently uncovered by the hundreds over the last 20 years, there is more evidence of this transition than ever. Through studies of theropod and avian physiology, we can gain more insight into the macroevolutionary principles and selective pressures that led dinosaurs to take to the sky.<br>2031-01-01
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DuRant, Sarah Elizabeth. "The role of incubation temperature in determining avian phenotype: implications for avian ecology, life history evolution, and conservation." Diss., Virginia Tech, 2011. http://hdl.handle.net/10919/28494.
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The early developmental environment has a profound influence on an individualâ s life history trajectory and parents have tremendous influence over this environment. Despite the wealth of research demonstrating that incubation temperature affects a suite of traits important to fitness in reptiles, we are only now discovering that nest temperatures are a defining component of the avian developmental environment. Aspects of the nest environment may be an important and overlooked maternal effect in birds as nearly all birds physically incubate their eggs, thus providing a clear link between parental behavior and the developmental environment of the avian embryo. My research used an interdisciplinary approach, uniting concepts from life history theory, bioenergetics. immunology, and physiological ecology to investigate the importance of incubation temperature to avian phenotype. I found that incubation temperature affects a suite of traits important for future development, survival and reproduction in a species of birds. Using a population of wood ducks (Aix sponsa) that has been the subject of long term studies I investigated the effects of incubation temperature on embryonic developmental patterns and energy expenditure, and body size and condition, stress endocrinology, thermoregulatory performance, and immunocompetence in hatchling wood ducks. In all experiments freshly laid wood duck eggs were collected from nest boxes located in SC, transported to Virginia Tech and incubated at one of three temperatures (35.0, 35.9, 37.0Ë C) that fell within the range of naturally-incubated wood duck nest temperatures. I found that less than 1Ë C differences in incubation temperature affected duckling growth and body condition, stress endocrinology, immune responses, and energy expended to thermoregulate. Many of these effects persisted days to weeks after hatching. In most cases, ducklings that hatched from eggs incubated at lowest temperature performed poorer than ducklings that hatched from eggs incubated at the higher temperatures. Incubation temperature also affected wood duck embryonic developmental trajectories and energy expended during incubation with embryos from the low incubation temperature expended more energy and developing slower than ducklings incubated at the higher temperatures. Embryonic energy expenditure could contribute to effects observed on hatchling phenotype. Because I demonstrate that incubation temperature affects hatchling phenotypic quality, the variability upon which natural selection acts, my findings have implications for avian ecology, life history evolution and conservation.<br>Ph. D.
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Cooney, Christopher Richard. "Global patterns and processes in avian diversification." Thesis, University of Oxford, 2015. http://ora.ox.ac.uk/objects/uuid:cf2dcbf2-892f-48e3-97b2-70a25d2a20fd.
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The natural world consists of a vast array of forms, some more plentiful than others, yet our understanding of the processes responsible the production of biological diversity remains surprisingly limited. Here I combine novel datasets with powerful phylogenetic modeling techniques and computer simulations to test the effects of both biotic and abiotic factors on the dynamics of species radiations and the evolution of organism traits in birds. In the first part of this thesis, I develop our understanding of the importance of abiotic factors for diversification by showing that in the early stages of lineage diversification at least, rapid adaptation to novel climatic conditions is likely to represent a prominent driver of avian diversification. In the second part I concentrate on the role of biotic factors, in particular that of sexual selection. I show that not only is sexual selection associated with accelerated rates of speciation and secondary sympatry—as well as faster rates of net diversification across the entire avian tree of life—but also that across-species variation in rates of phenotypic evolution is best understood with reference to the focus and intensity of sexual selection. Finally, given that the relative importance of such processes appears to vary predictably across latitudes, in the final part of the thesis I argue that latitudinal differences in the speciation process offers a potentially powerful explanation for conflicting viewpoints regarding the contribution of speciation to high tropical diversity. Overall, this work provides fresh insight into the processes governing broad-scale patterns in biodiversity.
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Van, Doorslaer Koenraad, Valeria Ruoppolo, Annie Schmidt, et al. "Unique genome organization of non-mammalian papillomaviruses provides insights into the evolution of viral early proteins." OXFORD UNIV PRESS, 2017. http://hdl.handle.net/10150/627073.
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The family Papillomaviridae contains more than 320 papillomavirus types, with most having been identified as infecting skin and mucosal epithelium in mammalian hosts. To date, only nine non-mammalian papillomaviruses have been described from birds (n = 5), a fish (n = 1), a snake (n = 1), and turtles (n = 2). The identification of papillomaviruses in sauropsids and a sparid fish suggests that early ancestors of papillomaviruses were already infecting the earliest Euteleostomi. The Euteleostomi clade includes more than 90 per cent of the living vertebrate species, and progeny virus could have been passed on to all members of this clade, inhabiting virtually every habitat on the planet. As part of this study, we isolated a novel papillomavirus from a 16-year-old female Adelie penguin (Pygoscelis adeliae) from Cape Crozier, Ross Island (Antarctica). The new papillomavirus shares similar to 64 per cent genome-wide identity to a previously described Adelie penguin papillomavirus. Phylogenetic analyses show that the non-mammalian viruses (expect the python, Morelia spilota, associated papillomavirus) cluster near the base of the papillomavirus evolutionary tree. A papillomavirus isolated from an avian host (Northern fulmar; Fulmarus glacialis), like the two turtle papillomaviruses, lacks a putative E9 protein that is found in all other avian papillomaviruses. Furthermore, the Northern fulmar papillomavirus has an E7 more similar to the mammalian viruses than the other avian papillomaviruses. Typical E6 proteins of mammalian papillomaviruses have two Zinc finger motifs, whereas the sauropsid papillomaviruses only have one such motif. Furthermore, this motif is absent in the fish papillomavirus. Thus, it is highly likely that the most recent common ancestor of the mammalian and sauropsid papillomaviruses had a single motif E6. It appears that a motif duplication resulted in mammalian papillomaviruses having a double Zinc finger motif in E6. We estimated the divergence time between Northern fulmar-associated papillomavirus and the other Sauropsid papillomaviruses be to around 250 million years ago, during the Paleozoic-Mesozoic transition and our analysis dates the root of the papillomavirus tree between 400 and 600 million years ago. Our analysis shows evidence for niche adaptation and that these non-mammalian viruses have highly divergent E6 and E7 proteins, providing insights into the evolution of the early viral (onco-)proteins.
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Heath, Lesley Annette. "The molecular biology of avian visual pigments : evolution and spectral tuning." Thesis, University College London (University of London), 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.298706.
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Olson, Valérie Anne. "The evolution of avian carotenoid pigmentation : behavioural, biochemical and comparative approachers /." St. Lucia, Qld, 2002. http://www.library.uq.edu.au/pdfserve.php?image=thesisabs/absthe16733.pdf.
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Cheung, Chung-lam, and 張仲林. "Genesis and evolution of H6N1 virus in terrestrial poultry in southernChina." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2011. http://hub.hku.hk/bib/B47158311.
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During the 1997 Hong Kong ‘bird flu’ incident, three subtypes of influenza
viruses, including H5N1, H9N2 and H6N1, were co-circulated at the live-poultry markets. Genetic analyses revealed that all these viruses shared the same internal gene complex and might have been all involved in generation of the HK/97-like H5N1 virus. Subsequent epidemiological and genetic studies found that both H6N1 and H9N2 viruses became established and prevalent in minor poultry in the region. However, the genesis pathway for each of these viruses has not been defined. It is also unclear about these three subtypes further interact with each other and evolve in the field, along with the emerging reassortant variants.
To address these questions, H6 subtype of avian influenza viruses isolated
from terrestrial minor poultry from 2000 to 2005, and from 2006 to 2007 in our
influenza surveillance in southern china has been genetically and antigenically
analyzed in this study. Genetic and phylogenetic analyses of representative strains indicated that all H6N1 isolates from 2000 to 2007 had W312-like hemagglutinin and neuraminidase genes. These H6N1 viruses have become established in the minor poultry, mainly in quail and chukar, in this region. However, phylogenetic analyses revealed that the internal genes of the H6N1 virus lineage were derived from multiple origins with different evolutionary pathways. Evolution analyses of different gene segments of H6N1 viruses revealed imbalance dynamic evolutionary rates between surface genes and internal genes, which suggests that this virus lineage was more likely a descendant of the HK/97-like H5N1, rather than its precursor virus.
Similar to what have been observed in the H5N1 and H9N2 virus lineages, the
internal gene complex of the H6N1 viruses was found to undergo extensive
reassortment. Many novel internal gene segments of H6N1 viruses were first
recognized in the reassortant H9N2 virus particles, suggesting that the gene flow is likely from H9N2 to H6N1. The co-circulation of different virus lineages in southern China has greatly increased the genetic diversity of influenza viruses in this region. Analyses of the dynamics of different H6N1 reassortant variants also showed that some of them became persistent, but others were transient in the field. The increasingly diversified H6N1 and other subtypes of viruses will naturally increase the opportunity of interspecies transmission and dissemination, and may pose renewal threat for public health.<br>published_or_final_version<br>Microbiology<br>Doctoral<br>Doctor of Philosophy
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Chu, Ying-cheung, and 朱盈彰. "Continuing evolution of H9N2 avian influenza A viruses in poultry in southern China." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2011. http://hub.hku.hk/bib/B47326852.
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Our systematic influenza surveillance in southern China revealed that two lineages
of H9N2 influenza viruses, represented by Chicken/Beijing/1/94 and Quail/Hong
Kong/G1/97, became endemic in the poultry in southern China since 1990’s. These
established H9N2 lineages continually evolved to generate many different
reassortants (or genotypes) and caused sporadic human infection cases. As
co-circulating with H5N1 influenza viruses, the increasing genetic diversity and the
capability to cause sporadic human infection make the H9N2 viruses become one of
the major candidates with pandemic potential.
Even though highly pathogenic H5N1 influenza viruses were seldom detected at
the live-poultry markets of Hong Kong since 2002, H9N2 viruses were still
commonly isolated in our surveillance program. The accumulated H9N2 isolates
provided an opportunity to get insights into the continual evolution of this subtype
virus in the region. In present study, we have systematically analyzed the H9N2
influenza viruses isolated from 2005 to 2010. Antigenic and phylogenetic analyses of
60 representative H9N2 viruses showed that the Ck/Bei-like H9N2 virus lineage
continued endemic in the terrestrial poultry during the survey period in southern
China. Genotyping analyses revealed four prevalent genotypes or reassortant variants
in the field. Fifty-three of the viruses analyzed belonged to genotype B14 and B15,
which were also the major reassortant variants prevailing in southern China from
2000 to 2005. The remaining seven viruses belonged to novel genotypes that have not
been identified before. Our findings suggested that the Ck/Bei-like lineage continually
maintained high genetic diversity in this region.
The epidemiological findings showed that the isolation rate of H9N2 virus at the
marketing poultry in Hong Kong was dramatically dropped down since 2009, which
was different from what have observed in other provinces in southern China, but was
closely correlated with the hygiene measures implemented in live-poultry markets in
Hong Kong, e.g. not keeping live chicken overnight. These findings suggest the
proper market policy would directly impact the prevalence of influenza virus in the
field.<br>published_or_final_version<br>Microbiology<br>Master<br>Master of Philosophy
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Halpin, Christina. "Avian cognition and the evolution of defences and warning signals in insects." Thesis, University of Newcastle Upon Tyne, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.491835.
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Many insects are chemically defended and toxic to predators. Whilst some species avoid detection, so-called 'aposematic' insects use conspicuous colour pattems to advertise their toxins to potential predators. Although the initial evolution of aposematism is often considered a paradox due to the increased detection risk associated with conspicuousness, the role of learned avoidance and memory in naive predators is widely described as the major driving force. However, many insects have extemally detectable defences, and may be taste-rejected by predators. This role of taste-rejection has been largely overlooked, but could offer support for the theory of the evolution of aposematism by individual selection.
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Gutowska, Maria Weronika. "Comparative evolutionary and structural analysis of the avian and mammalian CSF1R systems." Thesis, University of Edinburgh, 2015. http://hdl.handle.net/1842/15852.
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Macrophages, phagocytic cells of the immune system involved in host defence, homeostasis and development, are controlled and influenced by a variety of growth factors. In mammals, the colony stimulating factor 1 (CSF1) is a secreted cytokine that controls macrophages survival, proliferation and differentiation. It acts through the CSF1 receptor (CSF1R), a transmembrane receptor tyrosine kinase, expressed mainly in mononuclear phagocytes. Mammalian CSF1R is found exclusively at the surface of the mononuclear phagocytes and their progenitors. CSF1R-/- knockout mice display more severe phenotypes than the CSF1-deficient mice, thus suggesting the existence of another CSF1R ligand. Indeed, recent studies have shown that interleukin 34 (IL34) also binds to and activates CSF1R and regulates monocyte viability in vitro. While the exact role of this protein is yet to be fully elucidated, studies in mammals thus far implied its involvement in embryogenesis and development. CSF1R system is highly conserved within vertebrates and has been identified in variety of mammals. Chicken has been used extensively as a model for vertebrate development and to identify fundamental biological processes. Previous studies by colleagues in the lab demonstrated that the CSF1R system is conserved in the chicken, where it controls the generation of monocytes and tissue macrophages. This thesis provides a thorough evolutionary and structural analysis to fully demonstrate the similarities and differences between avian and mammalian CSF1R systems. The primary objective of this thesis was the comparative functional and structural analyses of the three proteins in birds and mammals, using evolutionary and experimental approaches. Here the presence of CSF1, CSF1R and IL34 genes and protein products is identified in a number of evolutionary diverse birds, indicating that the system is well maintained within the group. Avian genes were cloned and sequenced or otherwise extracted from different databases, and the mammalian sequences were gathered from available online sources. Whilst the gene regulation and the differential expression of the mammalian CSF1R, CSF1 and IL34 are reasonably well understood, they have not been extensively studied in birds. Preliminary comparison between these two groups provided in this thesis suggests a number of similar patterns are involved in regulation of avian CSF1R system. The mammalian CSF1/CSF1R and IL34/CSF1R ligand:receptor peptide interface has been previously resolved and was used to model similar structures in the chicken. The models were then utilised to determine which amino acids are involved in receptor binding in birds. The apparent lack of cross-species reactivity between the chicken CSF1 and zebra finch CSF1R provided a basis for an experimental validation of the in silico binding site predictions. Altogether the structural modelling, evolutionary analysis and experimental confirmation provided sufficient proof for the location of avian CSF1/CSF1R interface. Finally, an extensive bioinformatics analysis has been performed on both the coding DNA and the protein structures of the CSF1R system. The results uniformly showed that IL34 remains under purifying selection in both groups. CSF1 is diverse amongst most mammalian species, while avian CSF1 is only positively selected along particular lineages. This implies the rapid evolution of mammalian CSF1, probably in response to the selection pressure from pathogens. Contrasting situation is found in the CSF1R. Whilst mammalian CSF1R remains positively selected only along particular branches, avian CSF1R presents a number of pervasively positively selected sites, found mostly in the extracellular domains of the receptor. That suggests that in birds it is the receptor, not CSF1, which remains under strong selective pressure. These indicates that birds employ a unique way of competing in the hostpathogen arms race, suggesting the existence of yet unknown pathogen-encoded protein interacting with the avian receptor.
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Daly, Benjamin. "Avian malaria in the montane tropics." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:70284964-36b6-4135-98d4-4ec8d22c8b45.
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Understanding the unequal distribution of life on earth is a fundamental goal of ecology and evolutionary biology. Past efforts to explain large-scale patterns in diversity have tended to focus on two broad classes of explanation, one invoking the importance of abiotic factors (i.e. climate and vegetation) and the other biotic (i.e. competition); but neither has proven entirely adequate. Parasites are a major but poorly understood component of life that may offer some answers. Yet despite widespread theoretical support and some empirical evidence, the role of parasites in explaining patterns in the diversity, distribution, and abundance of species remains largely untested in natural communities. In this thesis I use a mega-diverse elevation gradient of birds as a model system to study the role of avian malaria in explaining these macroecological patterns. In the first data chapter I tested the extent to which patterns of infection across species is predictable. I found that the effects of host ecology and environment were weakly related to infection prevalence and were not consistent across different malaria lineages. Instead, I show that hosts coexisting with many close phylogenetic relatives consistently experience higher infection than evolutionarily distinct host species. In the second chapter I tested if parasite sharing may help explain these observed relationships and show that parasite sharing among host pairs declines with the time since divergence. Spatial contiguity between host pairs was also positively associated with parasite sharing. In the third chapter I tested how infection prevalence varies across species ranges in accordance with expected variation in host abundance. I show that birds are more likely to be infected at the centre of their elevation range, where host abundance is expected to be highest. Intriguingly, I also found that the incidence of host infection is unrelated to the position within the geographic range of the parasite. In the fourth data chapter, I tested whether parasites may regulate diversity by limiting geographic ranges of their hosts through ‘apparent competition’ in which a non-lethal parasite in a primary host, may be lethal in a secondary host. In support of this, I found that more observed bird ranges end at parasite infection zones than would be expected by chance. Taken together, my results suggest that parasites may play a major role in shaping patterns in the distribution and diversity of species, over both ecological and evolutionary scales. This is likely to arise and be maintained by host parasite interactions in which distantly related hosts are less likely to be infected by local parasites than close relatives, thus promoting the build up of diversity locally. On the basis of my analyses, I conclude that across montane elevation gradients in birds, and across diversity gradients more generally, parasites are likely to play a crucial role in the origin and maintenance of high biological diversity.
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Watanabe, Junya. "Comparative ontogeny of avian limb skeleton: implications for ontogenetic ageing and evolutionary variability, with special emphasis on the evolution of avian flightlessness." Kyoto University, 2016. http://hdl.handle.net/2433/217730.
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Mooers, Arnie Øyvind. "Patterns of diversification revealed by phylogenies." Thesis, University of Oxford, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.386648.
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Wright, Alison Elizabeth. "Mating system, sex-specific selection and the evolution of the avian sex chromosomes." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:89079fac-7196-4c15-ac0e-ceae0c4b0264.
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Sex chromosomes experience distinct evolutionary environments, due to their unusual pattern of inheritance, and studies of sex chromosome evolution can shed light on the fundamental evolutionary forces acting across the genome as a whole. Here, I combine genomic and transcriptomic data across a wide range of avian species to explore the evolutionary processes governing sex chromosome evolution. Birds are female heterogametic and therefore it is possible, via comparisons with male heterogametic species, to identify the fundamental factors driving sex chromosome evolution, versus those associated with sex. In this thesis, I uncover a complex mosaic of recombination suppression between the Z and W chromosomes, characterized by repeated and independent divergence of gametologs, together with ongoing genetic exchange. Additionally, I highlight the role of mating system, and interplay between evolutionary forces, in driving coding and expression evolution on the Z and W chromosomes. My findings indicate that although the Z chromosome is masculinized for male-specific effects, the magnitude of genetic drift acting on Z-linked genes is elevated in promiscuous relative to monogamous mating systems. In contrast, evolution of the female-limited W chromosome is governed predominately by purifying selection. Together, my results suggest that the role of the Z chromosome in encoding sexual dimorphisms may be limited, but that W-linked genes play a significant role in female-specific fitness. In conclusion, my findings reveal the power of mating system in shaping broad patterns of genome evolution.
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McKeown, Jennifer J. "Modelling the evolution of sexual behaviour." Thesis, University of Stirling, 2014. http://hdl.handle.net/1893/21823.
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This thesis presents two studies where natural and sexual selection have interacted to evolve sexual behaviours. The thesis uses mathematical modelling to understand how these forces have caused each behaviour to evolve. This is useful because the results allow for reflection on the potential role of sexual selection in adaptation of these species to a changing environment. The first study is of early male arrival to spring breeding grounds in migratory avian species, this is termed protandry. The study explores the main hypotheses for avian protandry and then tests the susceptibility of each hypothesis to changing environment. The second study is of convenience polyandry in species where there is conflict over mating rate. Females have multiple strategies to avoid harassive males but strategies vary in cost and success rate; she must balance her strategy use to minimise her fitness depreciation. The study identifies the main factors that cause convenience polyandry to evolve and paves the way for future studies to investigate if sexual selection over resistance strategy provides these species a future advantage in adaptation to a changing environment.
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Leung, On-cheung. "Molecular characterization of H3N2 influenza viruses isolated from ducks at a single Hong Kong farm : their diversity and evolution in natural reservoirs /." Hong Kong : University of Hong Kong, 2002. http://sunzi.lib.hku.hk/hkuto/record.jsp?B25155118.
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Wang, Jia, and 王嘉. "Genesis, evolution and dissemination of highly pathogenic avian H5N1 influenza A virus in Southern China." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2010. http://hub.hku.hk/bib/B45816840.
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Cerio, Donald Greene. "The Visual Apparatus of Avian Dinosaurs and Other Diapsids: Anatomical Correlates of Behavior and Evolution." Ohio University / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1565617073174635.
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Bokma, F. (Folmer). "Why most birds are small – a macro-ecological approach to the evolution of avian body size." Doctoral thesis, University of Oulu, 2004. http://urn.fi/urn:isbn:9514273451.
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Abstract There are more small-bodied species of birds than those having large bodies. Generally, and relative to occurrance in any one place, small-bodied species also contain more individuals than large-bodied species. The same patterns have been documented for several groups of higher organisms for example, snakes, flowering plants and mammals, which suggests that there exists a general reason "why", which applies to other groups of species as well as to birds. This thesis attempts to identify this reason. In the first place, it is possible that most species happened to become small-bodied by chance. Simulations of neutral body-size evolution indicate however that the observed bias towards small size is stronger than that accounted for by neutral evolution. Then, the most plausible explanation for why most species are small is that small-bodied species speciate faster. However, statistical analyses accounting for historical relatedness of present-day species indicate no relation between body size and the rate of speciation. Finally, instead of little by little, the dominance of small species may have arisen suddenly, when approximately 65 million years ago (presumably) a large meteorite hit the earth, causing mass extinctions. However, analysis of body sizes and genetic differences of extant species reveals that while avian species numbers were approximately halved, the catastrophe affected small and large species equally. Thus, the reason why most species are small does not seem to be due to differential rates of speciation or extinction. Instead, the cause appears to be in the tempo and mode of evolution. It was found by analysis of extant species' body size that probably most differences in body size between species arise at the moment of speciation. Differences between small-bodied species are smaller than between large-bodied species and probably this difference also has its origin at the moment of speciation. Consequently, groups of small species stay small whereas groups of large species are more variable in body size, so that in the end most species are small<br>Tiivistelmä Maailman noin 10 000 lintulajin joukossa pienikokoisia lajeja on enemmän kuin suurikokoisia. Yleensä pienkokoiset lajit ovat myös yksilömääriltään suurempia kuin samalla paikalla esiintyvät suurikokoiset lajit. Koska sama ilmiö on havaittu monissa muissa suurissa eliöryhmissä (esim. nisäkkäät, käärmeet ja kukkakasvit), on ilmeistä, että on olemassa yhteinen syy, joka pätee niin linnuissa kuin muissakin eliöryhmissä. Tämän väitöskirjan tavoite on selvittää, mikä tämä yhteinen syy voisi olla. Ensinnäkin on mahdollista, että suurin osa lajeista on kehittynyt pienikokoisiksi aivan sattumalta. Ruumiin koon evoluution simulaatiot kuitenkin osoittavat, että on hyvin epätodennäköistä, että neutraali evoluutio olisi johtanut pienikokoisten lajien suuriin määrään havaitussa määrin. Toinen mahdollinen selitys ilmiölle on, että pienikokoiset lajit lajiutuvat nopeammin. Tilastolliset analyysit, jotka ottavat huomioon nykyisin elävien lajien sukulaisuussuhteet, osoittavat ettei ruumin koon ja lajiutumisen vauhdin välillä ole yhteyttä. Kolmas mahdollinen selitys pienikokoisten lajien suurelle määrällä on historiallinen. On mahdollista, että pienikokoisten lajien suhteellisen suuri määrä syntyi nopeasti noin 65 miljoonaa vuotta sitten tapahtuneen massasukupuuton seurauksena, joka fossiiliaineiston perusteella kohdistui erityisesti suurikokoisiin maaeläimiin (esimerkiksi dinosauruksiin). Vertaileva analyysi nykyään elävien lintulajien ruumiin koosta ja geneettisistä eroista osoittaa, että vaikka suuri osa lintulajeista hävisi massasukupuutossa, tämä katastrofi karsi lajeja riippumatta niiden ruumiin koosta. Näyttää siis siltä, etteivät erot lajiutumisen tai sukupuuttojen esiintymisessä selitä sitä, että suurin osa lajeista on pienikokoisia. Tämän tutkimuksen tulosten perusteella syy näyttäisi sen sijaan olevan ruumiin koon kehityksen vauhdissa ja siinä tavassa, jolla kehitys yleensä etenee. Analyysi nykyisten lajien ruumiin koosta paljasti, että suurin osa eroista lajien välillä syntyy (evolutiiviessa aikataulussa) suhteellisen nopeasti lajiutumistapahtuman yhteydessä (punktualismi) eikä vähitellen pitkien aikojen kuluessa (gradualismi), kuten yleensä oletetaan. Kehityslinjojen sisällä pienikokoisten lajien väliset erot ruumiin koossa olivat pienempiä kuin isokokoisten lajien väliset erot - ja todennäköisesti myöskin tämä ero syntyy lajiutumisen yhteydessä. Tämä johtaa evoluution kuluessa tilanteeseen, että alunperin pienikokoisista lajeista kehittyneet lajit ovat myös pienikokoisia, kun taas isokokoisten lajien kehityslinjoissa on nähtävissä huomattavasti paljon enemmän vaihtelua ruumiin koossa. Näiden seurauksena eliöstöissä suurin osa lajeista lopulta on pienikokoisia
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Heij, Maaike Elisabeth de. "Costs of avian incubation how fitness, energetics ans behaviour impinge on the evolution of clutch size /." [S.l. : [Groningen : s.n.] ; University Library Groningen] [Host], 2006. http://irs.ub.rug.nl/ppn/297673424.
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Damas, Joana Daniela Mendes. "Avian genomics : from improvement of sequenced genomes to ancestral karyotypes and novel patterns of chromosomal evolution." Thesis, Royal Veterinary College (University of London), 2017. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.766310.
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Yaklichkin, Sergey Yu, Diana Darnell, Maricela Pier, Parker Antin, and Sridhar Hannenhalli. "Accelerated evolution of 3'avian FOXE1 genes, and thyroid and feather specific expression of chicken FoxE1." BioMed Central, 2011. http://hdl.handle.net/10150/610379.
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BACKGROUND:The forkhead transcription factor gene E1 (FOXE1) plays an important role in regulation of thyroid development, palate formation and hair morphogenesis in mammals. However, avian FOXE1 genes have not been characterized and as such, codon evolution of FOXE1 orthologs in a broader evolutionary context of mammals and birds is not known.RESULTS:In this study we identified the avian FOXE1 gene in chicken, turkey and zebra finch, all of which consist of a single exon. Chicken and zebra finch FOXE1 are uniquely located on the sex-determining Z chromosome. In situ hybridization shows that chicken FOXE1 is specifically expressed in the developing thyroid. Its expression is initiated at the placode stage and is maintained during the stages of vesicle formation and follicle primordia. Based on this expression pattern, we propose that avian FOXE1 may be involved in regulating the evagination and morphogenesis of thyroid. Chicken FOXE1 is also expressed in growing feathers. Sequence analysis identified two microdeletions in the avian FOXE1 genes, corresponding to the loss of a transferable repression domain and an engrailed homology motif 1 (Eh1) C-terminal to the forkhead domain. The avian FOXE1 proteins exhibit a significant sequence divergence of the C-terminus compared to those of amphibian and mammalian FOXE1. The codon evolution analysis (dN/dS) of FOXE1 shows a significantly increased dN/dS ratio in the avian lineages, consistent with either a relaxed purifying selection or positive selection on a few residues in avian FOXE1 evolution. Further site specific analysis indicates that while relaxed purifying selection is likely to be a predominant cause of accelerated evolution at the 3'-region of avian FOXE1, a few residues might have evolved under positive selection.CONCLUSIONS:We have identified three avian FOXE1 genes based on synteny and sequence similarity as well as characterized the expression pattern of the chicken FOXE1 gene during development. Our evolutionary analyses suggest that while a relaxed purifying selection is likely to be the dominant force driving accelerated evolution of avian FOXE1 genes, a few residues may have evolved adaptively. This study provides a basis for future genetic and comparative biochemical studies of FOXE1.
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Ewart, Kyle Marc. "Phylogeography and population genetics of Australian threatened and invasive birds." Thesis, The University of Sydney, 2020. https://hdl.handle.net/2123/22592.
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Amidst the current extinction crisis avian biodiversity is decreasing dramatically, with declining populations in over 40% of bird species worldwide. The red-tailed black-cockatoo (Calyptorhynchus banksii) and the pink cockatoo (Lophochroa leadbeateri), iconic parrots endemic to Australia, are both variously listed under State and Federal conservation legislation. These species suffer from habitat degradation, particularly the destruction of old hollow-bearing trees, and are both poached for the illegal pet trade. Despite concerns related to their conservation, little population genetic or phylogeographic information is available to inform the management of either species. Some bird species, such as the common myna (Acridotheres tristis), are invasive in Australia and may present a major threat to endemic fauna. Various programs have been implemented to control this species, yet no genetic information is available to guide population management. Population genomic methods can be applied to inform conservation of threatened species, and can also be used to characterize invasive species populations. The aim of this thesis was to study the evolution and phylogeography of the two aforementioned native cockatoo species, and the introduced common myna using high throughput sequencing technologies. I generated genome-wide single nucleotide polymorphism (SNP) data from frozen tissues and aged museum specimens for these three species, and performed a range of population genomic and phylogenetic analyses. These results will inform conservation management and policy for the two cockatoo species, and facilitate the development of a wildlife forensic toolbox to monitor and prosecute the illegal trade. My results on the population genomics of the Australian common myna invasion will inform population management/eradication programs to help control their expansion. I generated genomic data from museum specimens not specifically collected for DNA analysis, and was able to systematically assess errors and biases associated with data from historical specimens and investigate how they affect biological inference. These results have important implications for future studies that incorporate museum samples.
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Early, Catherine Michele. "Quantitative Assessments of Avian Endocasts as Tools for Inferring Neuroanatomical Traits and Potential Functional Capabilities." Ohio University / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1554132803369615.
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Thi, Diep Nguyen. "Comparative molecular epidemiology and antigenic characterisation of highly pathogenic avian influenza A(H5) virus in Vietnam." Thesis, University of Oxford, 2017. https://ora.ox.ac.uk/objects/uuid:ed44c640-d83e-4766-85d7-ccf85e531b5e.
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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 ï¬ndings 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.
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Lyons, Amanda C. "Characterization of major histocompatibility complex class I loci of the lark sparrow (Chondestes grammacus) and insights into avian MHC evolution." Bowling Green State University / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1383578046.
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Dookie, Amanda. "Safe and Sound: Studies on the Function and Evolution of Defence Sounds in Bombycoidea Caterpillars." Thesis, Université d'Ottawa / University of Ottawa, 2017. http://hdl.handle.net/10393/35680.
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Defence sounds are widespread and diverse amongst insects. Despite their ubiquity and variability, hypotheses explaining their functions and evolutionary origins have been understudied. My thesis focused on these topics using silk and hawkmoth Bombycoidea caterpillars as a model system. In Chapter Two I investigated why defence sounds have evolved in some caterpillars but not others by testing the hypothesis that large body size is a factor in the evolution of defence sounds. To test this hypothesis, I followed the development of defence sounds in four Bombycoidea species from hatching to pupation. I predicted that early instars would not produce defence sounds, and that within sound producing instars defence sounds would be more likely to occur in larger caterpillars. Results showed that defence sounds were absent in the first and second instar, and that they developed in the third through to the fifth instar in all species. Moreover, the onset of sound production occurred when all species were the same relative size (~1.12 g, ~26.37 mm), despite the fact that the species differed in their final instar size. I concluded that early instar caterpillars do not make defence sounds, and that there is a critical size when defence sounds develop. I further tested the hypothesis that smaller caterpillars do not have enough energy to make defence sounds, by analyzing the relationship between size and several temporal characteristics of the sounds. I predicted that smaller caterpillars would signal less than larger caterpillars, and produce shorter signal units and trains, with lower duty cycles. Results partly supported the hypothesis, showing that in two species there was a positive relationship between size and the number of units produced within two seconds following an attack, the mean number of units per train, and the mean duration of the units in one species. I also tested the hypothesis that sounds of small caterpillars are not in the hearing range of predators. I predicted that there would be a relationship between caterpillar size, and the sound pressure levels and dominant frequencies of the sounds. Results showed no significant relationships with dominant frequencies or sound pressure levels and size. I concluded that the caterpillars made sounds that were within the hearing range of major predators from the onset of sound production. In Chapter Three I followed the other antipredator defences of the four species throughout development. I investigated whether the frequency of defences changed with instar. I found that the caterpillars employed up to seven different secondary defences throughout development. In one species the frequency of dropping and major thrashing increased in the late instars, and in a different species the frequency of regurgitation increased. I concluded that in some cases defence sound production accompanies other secondary defences that increase with the size of caterpillars during development. In Chapter Four I tested the hypothesis that the defensive whistle of the walnut sphinx caterpillar, Amorpha juglandis (Sphingidae: Sphinginae), functions to startle birds. I predicted that the birds would startle to the sounds, and habituate upon repeated exposure within a trial. Results showed that play-back recordings of the whistles elicited a startle response in captive red-winged blackbirds (Agelaius phoeniceus) and caused them to hesitate and/or flee from prey. I concluded that the whistles function as a startle display. Together, the experiments conducted within my thesis addressed important outstanding questions regarding the evolutionary origins of defence sounds in caterpillars, and their functions in predator-prey interactions.
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梁安祥 and On-cheung Leung. "Molecular characterization of H3N2 influenza viruses isolated from ducks at a single Hong Kong farm: theirdiversity and evolution in natural reservoirs." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2002. http://hub.hku.hk/bib/B31226310.
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Zhao, Ziming. "Exploiting phylogenetics to understand genome evolution in both modern and ancestral organisms." Diss., Georgia Institute of Technology, 2012. http://hdl.handle.net/1853/48988.
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Computational evolutionary analyses, particularly phylogenetics and ancestral reconstruction, have been extensively exploited under different algorithms and evolutionary models to better understand genome evolution from both small- and large-scale perspectives in order to assign genotypes based on assortment, resolve species relationships and gene annotation issues, further understand gene gain/loss within individual gene families, measure functional divergence among homologs, and infer ancestral character states. These evolutionary studies provide us with insights into biologically relevant issues including paleoenvironments inferred from resurrected proteins, developmental physiology associated with functional divergence of duplicated genes, viral epidemics and modes of transmission in attempt to better prepare, prevent and control diseases, evolution of lineage-specific pathogenicity, and attempts to create a synthetic ancient organism that would benefit the field of synthetic biology. Our work also provides us with greater insights into the accuracies and limitations of ancestral sequence reconstruction methods. In total, our work highlights the diverse questions that evolutionary studies attempt to address and the different biological levels that can be studied to answer these questions.
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Boyle, Alice. "Why do Birds Migrate? The Role of Food, Habitat, Predation, and Competition." Diss., The University of Arizona, 2006. http://hdl.handle.net/10150/195068.
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The ultimate causes of bird migration are largely unknown despite more than a century of research. By studying partially migratory short-distance tropical migrants and by employing comparative methods, some difficulties in testing hypotheses for evolution of migration can be overcome. Using comparative methods I tested the evolutionary precursor hypothesis, a major hypothesis for why migration evolved in some lineages and not in others. The results of this study conflicted with many assumptions and predictions of the evolutionary precursor hypothesis. Most importantly, migratory behavior was not related to diet and habitat in simple ways. The interaction between diet and habitat, as well as consistent associations between flocking behavior and migration suggested that food variability is poorly captured by the surrogates embodied in the evolutionary precursor hypothesis. I then employed comparative methods to studying tropical altitudinal migration. Comparisons of diets and fruit preferences between species pairs showed that migrants are more frugivorous, eat a broader diversity of fruits, and have diets that more strongly resemble their preferences than do residents. Although providing evidence that food limitation plays a role in altitudinal migration, these results do not support the hypothesis that interspecific competition explains variation in migratory behavior. Next, I provided the first test of a predation-based hypothesis to explain altitudinal migration. Migrants breed at higher elevations than where they spend their non-breeding season. Thus, birds may migrate uphill to escape high nest predation risk at lower elevations. Results from this experimental study are largely consistent with this hypothesis, but anomalies between predicted and observed patterns suggest that either migration of lowland birds occurs in response to other factors, or that anthropogenic change has altered the tradeoffs involved in migratory decisions. Finally, I focus on a single migrant species and evaluate (a) two food-based hypotheses to explain the destination of migration movements, and (b) mechanisms underlying intra-specific differences in migratory strategy. Food can explain why Corapipo altera migrate uphill, but not why they migrate downhill. My data on sex bias and body condition leads to a new hypothesis explaining the complete annual cycle of this tropical migrant bird.
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Shen, Peter S. "The Characterization of Avian Polyomavirus, Satellite Tobacco Mosaic Virus, and Bacteriophage CW02 by Means of Cryogenic Electron Microscopy." BYU ScholarsArchive, 2011. https://scholarsarchive.byu.edu/etd/3069.
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Viruses are the most abundant biological entity in the biosphere and are known to infect hosts from all domains of life. The aim of my work is to identify conserved and non-conserved features among the capsid structures of related and divergent icosahedral viruses via cryogenic electron microscopy, sequence analysis, molecular modeling, and other techniques. Bird polyomaviruses often cause severe disease in their hosts whereas mammalian polyomaviruses generally do not. Avian polyomavirus is a type of bird polyomavirus with an unusually broad host range compared to the restricted tropism of other polyomaviruses. Although most polyomaviruses have a conserved, rigid capsid protein structure, avian polyomavirus has a flexible capsid shell and a non-conserved C-terminus in its major capsid protein. A β-hairpin motif appears to stabilize other polyomaviruses but is missing in avian polyomavirus. The lack of this structure in avian polyomavirus may account for its capsid flexibility and broad host range. A minor capsid protein unique to bird polyomaviruses may be located on the inner capsid surface. This protein may have a role in the acute disease caused by bird polyomaviruses. The solution-state capsid structure of satellite tobacco mosaic virus was unexpectedly different than the previously solved crystalline structure. The conformational differences were accounted for by a shift of the capsid protein about the icosahedral fivefold axis. Conversely, the RNA core was consistent between solution and crystalline structures. The stable RNA core supports previous observations that the viral genome stabilizes the flexible capsid. Halophage CW02 infects Salinivibrio bacteria in the Great Salt Lake. The three-dimensional structure of CW02 revealed a conserved HK97-like fold that is found in all tailed, double-stranded DNA viruses. The capsid sequence of CW02 shares less than 20% identity with HK97-like viruses, demonstrating that structure is more conserved than sequence. A conserved module of genes places CW02 in the viral T7 supergroup, members of which are found in diverse aquatic environments. No tail structure was observed in reconstructions of CW02, but turret-like densities were found on each icosahedral vertex, which may represent unique adaptations similar to those seen in other extremophilic viruses.
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Holliday, Casey M. "Evolution and function of the jaw musculature and adductor chamber of archosaurs (crocodilians, dinosaurs, and birds)." Connect to this title online, 2006. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1147280827.
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Sepil, Irem. "The secret in their MHC : variation and selection in a free living population of great tits." Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:dd753cf0-9ec5-4d63-b318-57f037d73ee5.
Full textAbstract:
Understanding the genetic basis of fitness differences has been a major goal for evolutionary biologists over the last two decades. Although there are many studies investigating how natural selection can promote local adaptation, few have succeeded to find the link between genotype and fitness of the phenotype. Polymorphic genes of the major histocompatibility complex (Mhc) are excellent candidates for such associations as they are a central component of the vertebrate immune system, playing an important role in parasite resistance, and hence can have direct effects on survival of their bearers. Although associations between Mhc and disease resistance are frequently documented, the epidemiological basis of the host-parasite interaction is often lacking and few studies have investigated the role that Mhc genes play in individual variation in fitness; thus comparatively little is known about the fitness consequences of Mhc in wild populations. Furthermore, the majority of work to date has involved testing associations between Mhc genotypes and disease. However, the mechanism by which any direct selection on the Mhc acts, depends on how genotypes map to the functional properties of Mhc molecules. The aim of this thesis was to characterize Mhc alleles in terms of their predicted functional properties and to investigate whether and how selection operates on Mhc class I functional variation using the great tit (Parus major) population at Wytham Woods as a model host species. Through a comprehensive characterization effort and the use of 454 pyrosequencing platform, I performed a detailed analysis of genetic variation at Mhc class I exon 3 and grouped alleles with similar antigen-binding affinities into supertypes to classify functionally distinct Mhc types. There was extreme complexity at the Mhc class I of the great tit both in terms of allelic diversity and gene number. A total of 862 alleles were detected from 857 individuals; the highest number yet characterized in a wild bird species. The functional alleles were clustered into 17 supertypes; there was clear evidence that functional alleles were under strong balancing selection. To understand the role of Mhc in disease resistance, I examined the linkage between Mhc supertypes, Plasmodium infection and great tit survival, and showed that certain functional variants of Mhc confer resistance to two divergent Plasmodium parasite species that are common in the environment. I further investigated the fitness consequences of functional variation at Mhc, using mark-recapture methods and long-term breeding data; and tested the hypotheses that selection: (i) maximizes Mhc diversity; (ii) optimizes Mhc diversity, or (iii) favours specific functional variants. I found that the presence of three different supertypes was associated with three different components of individual fitness: adult survival, annual recruitment probabilities and lifetime reproductive success. In contrast, there was no evidence for a selective advantage of Mhc functional diversity, either in terms of maximal or optimal supertype diversity. Finally, I explored the role that Mhc plays in female mate choice decisions and examined the reproductive fitness consequences of Mhc-dependent mating patterns. There was little evidence to suggest that functional dissimilarity at Mhc has any influence on female mate choice decisions or that dissimilarity at Mhc affects the reproductive output of the social pair. Overall, this thesis provides strong support for the suggestion that selection favours specific functional variants of Mhc, possibly as a result of supertype-specific resistance or susceptibility to parasites that exert strong selective pressures on their hosts; whereas there is no support for selection favouring maximal or optimal Mhc diversity. More importantly it demonstrates that functional variants of Mhc class I loci are an important determinant of individual fitness in natural populations.
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Hill, Sarah. "Genomic approaches to virus discovery and molecular epidemiology." Thesis, University of Oxford, 2017. http://ora.ox.ac.uk/objects/uuid:5cef9f8e-d305-4207-8742-d8dde1683f50.
Full textAbstract:
Viral sequence data has great potential for answering questions about the epidemiological dynamics and evolution of viruses. Classical approaches have sought amino acid changes that alter pathogenesis or transmissibility by influencing a virus's ability to enter or replicate within cells. However, this approach rarely recognises the fundamental impact of heterogeneous host contact structures and existing immunological responses on viral transmission. This thesis draws heavily on ecological and immunological concepts to explore the epidemiological dynamics, diversity and evolution of viruses using molecular sequence data. A number of different research approaches and study systems are used in this thesis. I begin by describing a novel polyomavirus in a European badger, and apply phylogenetic techniques to analyze the evolutionary history of the Polyomaviridae. I subsequently describe a large metaviromic study in a population of wild mute swans, for which host demographic data are available. I describe nine new viral species and test whether age and season are associated with differences in abundance and prevalence of different viral taxonomic groups. The study highlights the potential of metaviromics for investigating viral epidemiological dynamics in natural populations. Influenza A viruses of avian origin (AIV) threaten human and animal health. Using phylogeographic methods, I reconstruct the spatial spread of an H5N8 virus at a regional scale, and investigate how bird density and migration shaped this dispersal. Despite the importance of acquisition of humoral immunity to different strains throughout the lifespan of wild birds for epidemiological dynamics, this topic is poorly understood. I assess the accumulation of immune responses to AIV with age in mute swans. I consider how ecological factors, including age-structured immunity, might have affected the epidemiology of an H5N8 outbreak in the population.