Thesis (Ph. D.)--University of Wisconsin--Madison, 1981. / Typescript. Vita. Includes bibliographical references (leaves 155-158).

O elemento transponível hobo pode estar presente sob três formas no genoma de Drosophila simulans: como cópias autônomas completas (ou canônicas), como cópias defectivas internamente deletadas e como seqüências relacionadas a hobo (ou “relics”). Algumas evidências indicam que cópias completas e internamente deletadas são aquisições recentes desse genoma, enquanto os “relics” são componentes antigos, normalmente degenerados, defectivos e até recentemente considerados imóveis. O estudo desse tipo de seqüências pode ajudar a desvendar algumas questões sobre sua origem, dinâmica e seu papel na história evolutiva da família hobo. No presente trabalho, buscamos contribuir ao entendimento de algumas dessas questões estudando a dinâmica de uma família particular de seqüências relacionadas a hobo de D. simulans. Primeiramente, isolamos uma seqüência “relic” hobo envolvida no surgimento de uma mutação white de novo em uma linhagem hipermutável de D. simulans. Esta seqüência, denominada hobov-a, apresenta divergência típica de elemento “relic” em relação ao elemento canônico, é defectiva como outras já descritas, porém, mobilizável, pois apresentando estruturas essenciais para mobilização bem conservadas. Além disso, apresenta alta similaridade estrutural e de seqüência com um elemento “relic” de Drosophila sechellia, mas parece estar ausente do genoma de Drosophila melanogaster. A análise populacional de hobov-a revela que estes elementos são bem conservados entre diferentes populações de D. simulans. Apresentam, ainda, polimorfismo de sítios de inserção e variabilidade no número de cópias, o que nos dá fortes indícios de atividade atual ou recente desses elementos no genoma dessas populações. Pela similaridade compartilhada com elementos MITEs em muitas de suas características estruturais e funcionais, sugerimos, apontando algumas evidências, que elementos hobov-a podem ser ou uma nova família de MITEs de Drosophila ou, mais provavelmente, estariam se encaminhando para esse destino, utilizando o elemento canônico como fonte para sua mobilização.

O elemento transponível hobo pode estar presente sob três formas no genoma de Drosophila simulans: como cópias autônomas completas (ou canônicas), como cópias defectivas internamente deletadas e como seqüências relacionadas a hobo (ou “relics”). Algumas evidências indicam que cópias completas e internamente deletadas são aquisições recentes desse genoma, enquanto os “relics” são componentes antigos, normalmente degenerados, defectivos e até recentemente considerados imóveis. O estudo desse tipo de seqüências pode ajudar a desvendar algumas questões sobre sua origem, dinâmica e seu papel na história evolutiva da família hobo. No presente trabalho, buscamos contribuir ao entendimento de algumas dessas questões estudando a dinâmica de uma família particular de seqüências relacionadas a hobo de D. simulans. Primeiramente, isolamos uma seqüência “relic” hobo envolvida no surgimento de uma mutação white de novo em uma linhagem hipermutável de D. simulans. Esta seqüência, denominada hobov-a, apresenta divergência típica de elemento “relic” em relação ao elemento canônico, é defectiva como outras já descritas, porém, mobilizável, pois apresentando estruturas essenciais para mobilização bem conservadas. Além disso, apresenta alta similaridade estrutural e de seqüência com um elemento “relic” de Drosophila sechellia, mas parece estar ausente do genoma de Drosophila melanogaster. A análise populacional de hobov-a revela que estes elementos são bem conservados entre diferentes populações de D. simulans. Apresentam, ainda, polimorfismo de sítios de inserção e variabilidade no número de cópias, o que nos dá fortes indícios de atividade atual ou recente desses elementos no genoma dessas populações. Pela similaridade compartilhada com elementos MITEs em muitas de suas características estruturais e funcionais, sugerimos, apontando algumas evidências, que elementos hobov-a podem ser ou uma nova família de MITEs de Drosophila ou, mais provavelmente, estariam se encaminhando para esse destino, utilizando o elemento canônico como fonte para sua mobilização.

O elemento transponível hobo pode estar presente sob três formas no genoma de Drosophila simulans: como cópias autônomas completas (ou canônicas), como cópias defectivas internamente deletadas e como seqüências relacionadas a hobo (ou “relics”). Algumas evidências indicam que cópias completas e internamente deletadas são aquisições recentes desse genoma, enquanto os “relics” são componentes antigos, normalmente degenerados, defectivos e até recentemente considerados imóveis. O estudo desse tipo de seqüências pode ajudar a desvendar algumas questões sobre sua origem, dinâmica e seu papel na história evolutiva da família hobo. No presente trabalho, buscamos contribuir ao entendimento de algumas dessas questões estudando a dinâmica de uma família particular de seqüências relacionadas a hobo de D. simulans. Primeiramente, isolamos uma seqüência “relic” hobo envolvida no surgimento de uma mutação white de novo em uma linhagem hipermutável de D. simulans. Esta seqüência, denominada hobov-a, apresenta divergência típica de elemento “relic” em relação ao elemento canônico, é defectiva como outras já descritas, porém, mobilizável, pois apresentando estruturas essenciais para mobilização bem conservadas. Além disso, apresenta alta similaridade estrutural e de seqüência com um elemento “relic” de Drosophila sechellia, mas parece estar ausente do genoma de Drosophila melanogaster. A análise populacional de hobov-a revela que estes elementos são bem conservados entre diferentes populações de D. simulans. Apresentam, ainda, polimorfismo de sítios de inserção e variabilidade no número de cópias, o que nos dá fortes indícios de atividade atual ou recente desses elementos no genoma dessas populações. Pela similaridade compartilhada com elementos MITEs em muitas de suas características estruturais e funcionais, sugerimos, apontando algumas evidências, que elementos hobov-a podem ser ou uma nova família de MITEs de Drosophila ou, mais provavelmente, estariam se encaminhando para esse destino, utilizando o elemento canônico como fonte para sua mobilização.

Field-based mesocosm studies may be used as conceptual experiments to examine theoretical questions using the generated empirical data. A field-based Drosophilidae-nectarine mesocosm, comprising sun and shaded microclimate treatments arranged in a checkerboard design, was used in this thesis to examine four theoretical objectives. First, the efficacy of spatial analysis for detecting empirical pattern was examined. Natural variation weakened spatial structuring. However, hypothesis generation was shown not to be affected by this inclusion. Second, enhancing the hypothesis generating capacity of spatial methods was assessed, and confirmed to be possible, through the use of a sensitivity analysis method developed here. The method ( distinguished between mechanism categories (intrinsic, extrinsic and natural variation) and assessed the relative strength of each category. Next, an empirical test of the He and Gaston (2000a) parameterisation method and model to predict abundance from occupancy was conducted. Abundance estimates derived using the parameterisation method were underestimated because individuals were highly aggregated within fruit. This model and method require further exploration at fine scales for highly aggregated species. The incorporation of spatially explicit information may improve abundance predictions. Finally, the influence of spatial variation in temperature on adult body size in Drosophila simulans Sturtevant was investigated. The simple developmental effects of temperature differences, or the simple effects of stressful temperatures on thorax length, were overridden by interactive effects between temperature and larval density. As a result, flies attained the same final sizes in the shade and sun. Under natural conditions both mortality and non-lethal effects of temperature and/or crowding are likely to playa role in the evolution of body size. The results of this thesis provide i) an improved understanding of the influence of natural variation on spatial pattern, ii) an additional tool for spatial hypothesis generation, iii) an empirical test of an abundance-prediction model and iv) an understanding of interactive and non-lethal effects on body size under field conditions. The thesis therefore provides empirical support for the usefulness of field-based mesocosms to examine theoretical objectives. / Thesis (PhD (Entomology))--University of Pretoria, 2007. / Zoology and Entomology / unrestricted

Over the last century, sexual selection has grown from a controversial theory into a vast field of theoretical and empirical research. Although Darwin outlined two major mechanisms within his theory, male-male competition and female mate choice, the latter has promoted a wealth of research by virtue of its complexity. Despite decades of research into how female preferences and sexually selected traits have evolved, there is still little consensus as to why females prefer the males they do. Preferences are thought to evolve from either direct selection on the preference, as females themselves benefit directly from mating with a preferred male, or through indirect selection on the preference via offspring fitness. In all cases however, female preferences should compensate for the costs of discriminating between potential mates, if they are to remain overall beneficial. The fitness benefits of mating with preferred males were investigated here using the fruitfly Drosophila simulans, employing a range of behavioural, phenotypic and quantitative genetic approaches. The findings presented here indicate that female Drosophila simulans do not gain directly from mating with a preferred male. Multiple mating can increase fecundity, although costs from male harassment can reduce the net benefit. They also indicate that females may benefit indirectly from mating with attractive males as attractiveness is heritable and sons of preferred males are themselves preferred. There is also evidence that attractive males are successful in both the pre- and post-copulatory sense, as preferred males are better sperm competitors than less-preferred males. However, although there appear to be benefits from preferred males via their sons, there appear to be no benefits from males via their daughters’ fitness. These findings collectively indicate that female preferences in Drosophila simulans are driven by indirectly selected benefits (via Fisherian sons), and that females benefit directly from mating multiply.

Drosophila is involved in a wide range of interactions with parasites and pathogens (parasitoid wasps, bacteria, fungi, viruses). Drosophila hosts vary greatly at the species, population and individual level, in their response against such organisms, and much of this variation has a genetic basis. In this thesis I explored three aspects of this variation. First, using recombination mapping based on SNPs and a variation of bulk segregant analysis, I identified a QTL region on the right arm of the third chromosome of D. melanogaster associated with resistance to at least some of the parasitoid species / strains used in the experiments. The location of the QTL was further explored with deficiency complementation mapping and was narrowed down to the 96D1-97B1 region. The success of the deficiency mapping suggests that the resistant allele is not completely dominant. Second, I investigated patterns of molecular evolution in a set of immunity-related genes, using sequences from a D. melanogaster and a D. simulans population and a set of genes without known involvement in immunity for comparison. I found evidence that several of these genes have evolved under different selection pressure in each species, possibly indicating interactions with different parasites. The immunity genes tested appear to be evolving faster compared to non-immunity genes, supporting the idea that the immune system is evolving under strong selective pressure from parasites. Finally, in a D. melanogaster – sigma virus system, I measured genetic variation in the transmission of different virus genotypes, in different environments. There was poor correlation between temperatures, suggesting that environmental heterogeneity could constraint evolution of resistance (to virus transmission). The correlation between viral genotypes was also low, although relatively stronger for more closely phylogenetically related viral strains. Such interactions between host genotypes, virus genotypes and environmental conditions can maintain genetic variation in virus transmission.

Cette thèse a été consacrée à l'évolution du transcriptome de Drosophila simulans, et à son rôledans l'adaptation et la spéciation. L'étude a comporté deux parties. La première utilisant des pucesà ADN pour comparer les transcriptomes de populations de D. simulans, de son espèce jumelleD. sechellia, et de leurs hybrides. La seconde basée sur la quantification des transcrits par séquen-çage haut débit pour comparer une population de la zone d'origine (Afrique), et une populationd'une zone récemment envahie (France métropolitaine). Ces analyses ont mis en évidence plusieursgroupes ou familles de gènes montrant des variations d'expression.Un résultat majeur est l'implication prépondérante de la famille des cytochromes P450 dansl'adaptation. Cette superfamille composée de 85 gènes chez D. simulans est notamment importantepour la détoxi_cation des xénobiotiques. L'expression de plusieurs gènes de cette famille estfortement réduite chez D. sechellia, probablement à cause de la spécialisation de cette espèce surla plante Morinda citrifolia (plante toxique pour les autres drosophiles). On peut s'attendre alorsà un relâchement des contraintes de sélection sur cette famille de gènes, dû à une forte réductionde la diversité des toxines auxquelles cette espèce est exposée.Ces gènes sont également impliqués dans la différenciation entre les populations de la zoneancestrale de D. simulans et les populations dérivées. La zone ancestrale, en Afrique de l'est etdans les îles de l'Océan Indien occidental, est encore peu anthropisée. A contrario, la plupartdes populations dérivées, comme ici notre population de la vallée du Rhône, sont exposées à descontraintes chimiques sous la forme de pesticides utilisés massivement sur les grandes cultures.Ces pesticides contraignent les populations dérivées à s'adapter, ce qui peut se réaliser par uneaugmentation de l'expression. Nous avons détecter une augmentation de l'expression de treizeP450, dont un gène très bien connu pour ses fonctions de détoxifcation : Cyp6g1. Ce gène montreune augmentation d'expression corrélée à une résistance aux pesticides et à l'insertion d'élémentstransposables en 5' ; ceci a été montré en détail chez D. melanogaster, et dans une moindre mesurechez D. simulans. Nous avons mis en évidence chez cette dernière espèce un nouvel évènementd'insertion.Nos résultats montrent également que d'autres familles de gènes impliqués dans les détoxi_-cations sont concernées par ces augmentations d'expression liées à l'anthropisation des milieux,notamment les Glutathion transfèrases (GST).Nous avons également examiné la plasticité d'expression liée au changement de ressource, enélevant une partie de nos populations sur la ressource d'origine (fruits), et une autre partie sur lemilieu axénique, milieu d'élevage standard de laboratoire (stérile). Les drosophiles élevées sur unmilieu "naturel" montrent une forte activation du système immunitaire, et notamment une forteinduction des gènes effecteurs de l'immunité innée, codant les peptides anti-microbiens. Cela estprobablement dû à la présence de microorganismes sur ce milieu (ici, la banane). En conclusion,cette thèse a révélé des familles de gènes fortement impliquées dans les différenciations d'expressionentre populations, espèces, et ressources, posant les jalons d'une meilleure compréhension desmécanismes d'adaptation du transcriptome. / The topic of this thesis was the evolution of the transcriptome of Drosophila simulans, andits role in adaptation and speciation. First, we used microarrays to compare transcriptomes ofpopulations of D. simulans, its sister species D. sechellia and their hybrids. Second, we useda RNA-seq like approach to quantify gene expression of a population from the ancestral range(Africa) on the one side, and a population from a recently invaded zone (France) on the other side.These analyses revealed several gene groups or families showing gene expression variations.One main result is the major involvement of the cytochrome P450 gene family in adaptation.This superfamily is composed of 85 genes in D. simulans, and is notably important in detoxificationof xenobiotics. The expression of several genes of this family is strongly reduced in D. sechellia,likely due to the specialization of this species on Morinda citrifolia (a plant toxic for any otherdrosophila). This specialization may strongly reduce the diversity of toxines this species is exposedto, thus relaxing selective constraints on this gene family.These genes are also involved in the differentiation between populations of the ancestral range ofD. simulans and derived populations. The ancestral range, in eastern Africa and in the occidentalislands of the Indian Ocean, is not highly anthropized yet. Contrasting with this pattern, manyderived populations (here our population from the Rhône valley) are exposed to chemical pressuresdue to the massive use of pesticides on agricultural zones. These pesticides force derived populationsto adapt, which can happen via increased expression in genes such as the very famous exampleof Cyp6g1. This gene shows a strong increase in expression correlated with pesticide resistance aswell as the insertion of transposable elements upstream of the gene ; this was described in detailsin D. melanogaster, and to some extent in D. simulans. We have shown a novel insertion event inthe latter species.Our results also reveal the involvement of other gene families in detoxification linked withanthropized environment via increase of gene expression, notably the Glutathione transferases(GST).We also examined expression plasticity linked with resource change, raising half our _ies ontheir natural food resource (fruits), and the other half on axenic medium (standard sterile laboratorymedium). Drosophila raised on their natural medium show a strong activation of their immunesystem, and notably an induction of the effectors of teir innate immunity, the anti-microbial peptides.This observation can be explained by the presence of microorganisms on this medium (here,banana). To conclude, this thesis revealed gene families strongly involved in expression differentiationamong populations, species and food resources, paving the way of a better understanding ofmechanisms of adaptation of the transcriptome.

Une grande partie du génome des eucaryotes est constituée d’éléments transposables(ET). Ces séquences d’ADN répétées ont la capacité de se déplacer d’un site chromosomiqueà un autre et de multiplier le nombre de leurs copies, pouvant ainsi être la cause d’uneinstabilité génétique. Face à ce potentiel de mutagénèse, un certain nombre de systèmes ontété sélectionnés dans les génomes eucaryotes qui conduisent à une réduction de l’activité desET. Notamment, chez la drosophile, on a récemment mis en évidence des mécanismes derégulation impliquant les modifications d’histones, et une nouvelle classe de petits ARN,appelés piARN, qui contrôlent spécifiquement les éléments transposables dans les tissusreproducteurs.tirant est un rétrotransposon à LTR de la drosophile, de type Gypsy, isolé au sein dulaboratoire dans les populations naturelles de D. simulans, où le nombre de ses copies estvariable entre populations. Cet ET possède la même structure génomique que les rétrovirus.Dans la première partie de cette thèse, j’ai caractérisé un élément tirant actif dans lespopulations naturelles de D. simulans. Je me suis intéressé en particulier au gène de laprotéine d’enveloppe (env), qui confère le caractère infectieux du rétrovirus. La comparaisondes transcrits et de la protéine du gène env entre populations de D. simulans a montré quetirant est actif dans une population, et cette activation est associée à sa mobilisation, alors quedans les autres populations tirant est présent, mais régulé.Dans la deuxième partie de mon travail, je me suis intéressé à l’étude de l’influence detirant sur la structure de la chromatine au niveau de son site d’insertion et à son influence surl’expression des gènes voisins. J’ai étudié trois modifications d’histones dans troispopulations naturelles, dont une où tirant est inséré dans un intron du gène tkv. Les résultatsobtenus montrent que tirant est capable de modifier la structure de la chromatine au niveau deson site d’insertion, mais aussi en amont, par l’hétérochromatinisation d'un promoteur du gènetkv, en affectant ainsi son taux de transcription.Enfin, je me suis intéressé à la régulation post-transcriptionnelle de tirant par lespiARN. Par l’analyse de croisements intraspécifiques entre des souches contenant ou non descopies de tirant dans l’euchromatine, j’ai montré qu’une régulation post-transcriptionnelle parles piARN germinaux qui contrôle tirant dans les cellules folliculaires de l’ovaire. J’ai aussipu montrer une expression variable entre populations des gènes de la voie piARN. / Eukaryotic genomes harbor a wide variety of repeated sequences, such as transposableelements (TE). These sequences are able to move from one chromosomal site to another, tomultiply their number of copies, and can be the cause of a genetic instability. Sophisticatedgenomic defenses have evolved to restrict their activity. In Drosophila, epigeneticmodification such as post-translational histone modifications and RNAi interference areinvolved in TE silencing in reproductive tissues. The silencing of an LTR like element, tirant,has been deeply analyzed in this work. Tirant is a Gypsy like element, isolated in ourlaboratory in natural populations of D. simulans, in which a high level of copy numbervariability is observed between strains.Here, I first describe an active tirant element in natural populations of D. simulans. Ihave focused on the envelope protein gene (env), which confers the infectious behavior to theretrovirus. By comparison of tirant transcripts level and protein localization between naturalpopulations of D.simulans, I showed that tirant is active in one population, and this activationis correlated with its mobilization.I then focused on the effects of TE insertions on chromatin structure and in its influenceon the expression of the nearby genes. I studied three histone modification marks in threenatural populations, in the locus in which tirant was inserted. I show that tirant is associatedwith repressive marks and active marks, which explains the activity of the element. We alsoshowed that tirant modifies the structure of the chromatin at the level of its site of insertion,but also upstream, by the heterochromatinization of the promoter of tkv gene, interfering withthe level of transcription of the gene.Finally, I was interested in the post-transcriptional regulation of tirant involving thepiRNA pathway. By crossing D.simulans strains which contains different copy numbers ofthe tirant element, I showed that tirant is regulated in the follicular cells by the germ linepiRNA pathway. I was also able to show a variable expression between populations of theproteins of the piRNA pathway.

Transposable elements are DNA sequences that can change their location within the genome and can be found in almost all organisms. The mariner transposable element belongs to Class II, Tc1-mariner superfamily. An inactive insertion of this element in the gene white (w+) located on the X chromosome, causes a phenotypic change in color's eyes becoming them a peach color in the place of the wild coloration, being for this reason called whitepeach (wpch). Crossing of mutant females with males obtained from nature, an offspring with eyes the color of peach or variegated with spots of wild color is formed enabling estimate transposicional activity in natural populations. From the use of this system, several studies have been performed to understand if the number of copies and the activity of the mariner element are involved with environmental factors, historical and/or populational. In this study, the existence of intrapopulation variability of D. simulans collected in two places at Santa Maria (RS) city was investigated by crossing with a line of D. simulans wpch. Moreover, data on another species, D. melanogaster, were also obtained and analyzed: interspecific crosses generated progeny with variegation. The isolines that showed these properties were studied using of molecular research tools, such as PCR, cloning and sequencing, it was also necessary. The results suggest the existence of intrapopulation variability in D. simulans and indicate the discovery of sequences very similar to the element mariner in the genome of natural populations of D. melanogaster. / Os elementos transponíveis são seqüências de DNA capazes de alterar sua localização dentro do genoma e podem ser encontrados em praticamente todos os organismos. O elemento transponível mariner pertence à classe II, superfamília Tc1-mariner. Uma inserção inativa deste elemento no gene white (w+) localizado no cromossomo X de Drosophila simulans, causa uma alteração fenotípica na cor dos olhos tornando-os cor de pêssego no lugar da coloração selvagem, sendo por este motivo denominada white-peach (wpch). Do cruzamento de fêmeas mutantes com machos coletados na natureza, uma prole com olhos cor de pêssego ou variegados com pontos de coloração selvagem é formada, possibilitando estimar a atividade transposicional em populações naturais. A partir do uso deste sistema, diversos estudos têm sido realizados para compreender se o número de cópias e a atividade do elemento mariner estão envolvidos com fatores ambientais, históricos e/ou populacionais. Neste trabalho, a existência de variabilidade intrapopulacional de D. simulans coletadas em dois pontos da cidade de Santa Maria RS foi investigada através de cruzamentos com uma linhagem de D. simulans wpch. Além disso, dados sobre uma outra espécie, D. melanogaster, também foram obtidos e analisados: cruzamentos interespecíficos que geraram descendência com variegação fez com que o uso de ferramentas de pesquisa molecular, como PCR, clonagem e seqüenciamento, também fossem necessárias. Os resultados obtidos sugerem a existência de variabilidade intrapopulacional em D. simulans e indicam a descoberta de seqüências semelhantes ao elemento mariner no genoma de populações naturais de D. melanogaster.