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Conselho Nacional de Desenvolvimento Científico e Tecnológico / Transposable elements (TEs) are DNA fragments that can move within and between genomes causing great impact on the evolution of organisms. The hAT superfamily belongs to class II, subclass I of TEs and despite having originally been described in insects and plants, it is now known that these elements have a wide distribution and are diverse in many groups of higher organisms. Phylogenetic studies show that this superfamily is very ancient and its occurrence in these groups may be related to events of horizontal transfer (HT). This work was performed in order to estimate possible cases of hATs elements' HT. The elements homo1 and howilli2 described by Ortiz and Loreto in 2009 in D. willistoni and D. mojavensis species were searched in Neotropical Drosophila genomes using PCR with degenerate primers and because they are very similar elements and described in distantly related species, it was suggested that these elements might be being transmitted horizontally. Amplification was detected in 18 of the 34 species analyzed and these elements showed a patch distribution and incongruities with the TEs and host species' phylogeny, suggesting possible cases of HT. In addition, the estimated divergence of sequences found showed that these elements are or recently were active in the genomes that were investigated. Thus, our results demonstrate that these elements could be in an expansion process in Neotropical drosophilid genomes due to the large amount of HT events observed. / Elementos transponíveis (TEs) são fragmentos de DNA que podem se mover dentro e entre genomas, causando grande impacto na evolução dos organismos. A superfamília hAT pertence a classe II, subclasse I dos TEs e apesar de originalmente terem sido descritos em insetos e plantas, hoje se sabe que esses elementos possuem uma ampla distribuição e são diversos em muitos grupos de organismos superiores. Estudos filogenéticos demonstram que esta superfamília é muito antiga e que sua ocorrência nesses grupos pode estar relacionada a eventos de transferência horizontal (TH). Este trabalho foi realizado com a finalidade de estimar possíveis casos de TH entre elementos hATs. Os elementos homo1 e howilli2, descritos por Ortiz e Loreto em 2009, nas espécies D. willistoni e D. mojavensis, foram buscados nos genomas de Drosophila Neotropicais por meio de PCR com primers degenerados, e por se tratarem de elementos muito similares e descritos em espécies distantemente relacionadas, foi sugerido que esses elementos poderiam estar sendo transmitidos horizontalmente. Das 34 espécies analisadas, houve amplificação em 18, e esses elementos apresentaram uma distribuição descontínua e incongruências com a filogenia das espécies hospedeiras, o que sugere eventos de TH. Além disso, a estimativa de divergência das sequências encontradas revelou que esses elementos são ou foram ativos muito recentemente nos genomas em que foram investigados. Sendo assim, nossos resultados demonstram que esses elementos podem estar em processo de expansão nos genomas de drosofilídeos Neotropicais devido a grande quantidade de eventos de TH que foram observados.

Genome evolution is not always shaped by a Darwinian-fashion of vertical inheritance from ancestral lineages. The historical gene content of a species contains many atypical gene sequences showing high similarity to those of distantly related taxa. This evolutionary phenomenon is referred to as lateral gene transfer (LGT). Lateral gene transfer permits the exchange of genetic material across lineages, completely ignoring any concept of taxonomic boundary. The rapid acquisition of foreign genes into bacterial genomes has greatly obscured the historical phylogeny of prokaryotes. In this thesis we calculate the rate of LGT on a Bacillaceae phylogeny, to determine the extent to which it controls species evolution. First, we examined the evolution of the phylogeny according to a simple model of maximum likelihood. We assume equal rates of gene insertion and deletion on the phylogeny and show high rates of evolution in the genomes of B. anthracis, B. cereus, and B. thuringiensis (Bc group), representative of adaptive evolution. We then improved the model to account for differential rates of gene insertion and deletion, thus offering a more realistic model of gene evolution. Again, we demonstrate that members of the Bc group are rapidly evolving, with the rate of gene insertion being significantly higher than the rated of gene deletion. Finally, we evaluate the sole effect of LGT on the phylogeny in a simple birth-death analysis with immigration. We show that LGT is the main vehicle of gene acquisition when the number of gene families substantially increases from external taxa to members of the Bc group. Collectively, our findings suggest that the Bacillaceae genome is rapidly expanding, and that laterally transferred genes may facilitate adaptive evolution and subsistence in a new niche. / Thesis / Master of Science (MSc)

The “risk allocation hypothesis” can predict how prey species will respond to predation risk, balancing vigilance with potentially risky behaviours. In order to maximize fitness, an optimal behavioural repertoire can evolve to respond to predation threat to allow for both survival and future fitness gains. High locomotor activity and time spent engaging in mating behaviours are expected to put Drosophila melanogaster at a greater risk to predation. With direct predator exposure, Drosophila are predicted to reduce activity and mating, which over years of exposure, will be reflected in evolved behavioural traits and evolved changes in the genome. Predation as a selective force shows alterations in flies genomes of experimentally evolved populations. Locomotor activity was found to be reduced in the presence of zebra jumping spiders (Salticus scenicus), presumably due to these spiders as visual hunters, using movement to detect prey. This behaviour is reflected in populations of Drosophila that have been constantly under selection by predators. Flies evolved with spider predators or mantid predators (Tenodera aridifolia sinensis) showed reduced locomotor activity when no predators are present. Interestingly, while alterations are seen for locomotory activity, the presumed risky behaviours of courtship and mating did not show an evolved response. Wild caught populations under threat from spiders, as well as the evolved populations when no predators were present showed no alterations in courtship or copulation behaviour. It appears that although there may be potential risks associated with mating behaviours, the benefits to future fitness when mating outweigh the potential costs from predation risks in Drosophila. / Thesis / Master of Science (MSc) / Predation is a profound selective force, with many anti-predator adaptations seen throughout the diversity of life. Antipredatory behavioural adaptations must balance immediate and future fitness effects, to maximize overall fitness. In Drosophila melanogaster, research into natural ecology and role of predation is generally lacking for behavioural & evolutionary studies. I will discuss research on the influence of predator exposure on Drosophila behaviours, as well as the evolution of Drosophila behaviours and genomes through experimentally evolved populations of Drosophila. While predation risk has resulted in changes in Drosophila locomotory activity, predation has not altered mating behaviours.

Hamiltonella defensa est un endosymbiote secondaire ayant établi deux associations très distinctes chez les insectes phloémophages. Chez les pucerons, la bactérie protège l'hôte contre les parasitoïdes. Elle infecte de nombreux tissus dans l'hôte, et notamment l'hémolymphe, ce qui favoriserait le contact avec les oeufs de parasitoïdes. Malgré ce phénotype protecteur, les coûts importants que sa présence inflige à son hôte empêchent sa fixation dans les populations. Chez l'aleurode Bemisia tabaci, on ne retrouve la bactérie que dans des cellules spécialisées dans l'hébergement des endosymbiotes, les bactériocytes. Elle s'y trouve entre autres en présence du symbiote primaire, Portiera aleyrodidarum, des conditions de vie propices aux échanges entre les deux symbiotes. Elle est fixée dans les populations d'insectes, ce qui suggère un rôle important pour le consortium, qui serait nutritif. Dans le cadre de cette thèse, nous nous sommes intéressés aux spécificités de chacun de ces systèmes. Nous nous sommes également attardés sur l'évolution génomique du genre Hamiltonella, en comparant des souches infectant B. tabaci à une souche de puceron. Pour finir, nous nous sommes intéressés aux phénomènes d'accélération des taux de mutations chez H. defensa, comparativement à son espèce-soeur Regiella insecticola, également endosymbiotique et protectrice du puceron. Après avoir éliminé l'hypothèse selon laquelle la transition vers la vie intracellulaire aurait eu lieu indépendamment dans les deux lignées, nous avons tenté d'établir un lien entre ces différentiels d'évolvabilité chez les endosymbiotes et leur contenu en gènes, notamment ceux impliqués dans l'écologie et la réparation de l'ADN. L'ensemble des résultats obtenus au cours de ce Doctorat ont permis de mieux comprendre l'évolution de l'espèce H. defensa, depuis le dernier ancêtre jusqu'aux espèces actuelles, en tâchant de faire le lien entre phénotype de la bactérie et évolution génomique / Hamiltonella defensa is a secondary endosymbiont that established two distinct associations with phloemophagous insects. In aphids, it protects the host against parasitoid attacks. Its ability to infect many host tissues, notably the hemolymph, could promote its contact with parasitoid eggs. Despite this protective phenotype, the high costs associated with its presence within the host prevent its fixation in the population. In the whitefly Bemisia tabaci however, this symbiont is found only in cells specialized in hosting endosymbionts, the bacteriocytes. In these cells, it cohabits with other symbiotic species, such as the primary symbiont Portiera aleyrodidarum, a proximity that favors potential exchanges between the two symbionts. It is fixed in populations of B. tabaci, which suggests an important role for the consortium, probably nutritious. As part of this PhD thesis, we studied the specificities of each of these systems. We also focused on the genomic evolution of the genus Hamiltonella, by comparing the strains infecting B. tabaci with a strain infecting the aphids. Finally, we studied the phenomenon of ‘accelerated mutation rate’ in H. defensa, compared to its sister species Regiella insecticola, which is also a clade of protective endosymbionts of aphids. After excluding the assumption that the transition to the intracellular life occurred independently in the two lineages, we tried to establish a link between these differences in terms of evolvability in the endosymbionts and of their gene contents, particularly for genes involved in ecology and DNA repair. All the results obtained during this PhD have provided insight into the evolution of the species H. defensa, since the last ancestor to the present species, by establishing a link between bacterial phenotype and genomic evolution

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