Vertebrate brain size is remarkably variable at all taxonomic levels. Brains of mammals forexample, range from 0.1 gram in small bats (Chiroptera) to about 8-9 kilos in Sperm whales(Physeter macrocephalus). But what does this variation in size really mean? The link between brainsize and cognition is debated due to, for instance the difficulties of comparing cognitive ability indifferent species. A large number of comparative studies continue to provide information aboutcorrelations found both within and between species. The relative size of the brain is an example of apopular measurement that correlates with cognitive ability. But to date, no experimental studieshave yielded any proof causality between relative brain size and cognitive ability. Here I usedguppies selected for either large or small relative brain size to investigate differences in cognitiveperformance of a quantity discrimination task. The results from this experiment provideexperimental evidence that relative brain size is important for cognitive ability, and that a differencein cognitive ability could be obtained already after two generations of selection experiments onrelative brain size in a vertebrate. / Artificial Selection on Relative Brain Size in the Guppy Reveals Costs and benefits of Evolving a Larger Brain

Variations in skeletal morphology have often been used to interpret an organism’s overall activity level when direct observation is not possible. Although skeletal change in response to exercise is well documented, the skeleton’s response to mechanical loading is modulated by several factors (e.g. age, hormones, sex). Additionally, variation in skeletal morphology is partially a result of genetic variation, which is rarely accounted for in inferences of locomotor activity from skeletal remains. However, blood flow to long bones serves as a proxy for bone metabolic activity, which can be used to infer locomotor activity. Long bones receive blood from three sources, with the nutrient artery supplying the bulk of total blood volume in mammals (50-70%). The size of the nutrient artery can be estimated from the dimensions of the nutrient canal, which is present long after the vascular tissue has degenerated. The literature on nutrient canals is sparse, with most studies consisting of anatomical descriptions from surgical proceedings, and only a few studies investigating the links between nutrient canals and physiology or behavior. Moreover, no study to date has accurately modelled the size and shape of the nutrient canal. For this study, mice from an artificial selection experiment for high voluntary wheel-running behavior were used. High Runner mice from the experiment are known to differ in both metabolic and locomotor activity, with mice from HR lines having increased VO2max and increased voluntary wheel-running behavior when compared to controls. 137 femora from mice of the 11th generation of this selection experiment were µCT scanned. Three-dimensional reconstructions of nutrient canals were measured for minimum cross-sectional area (an index of blood flow). Nutrient canals varied far more in number and shape than prior descriptions would indicate. Canals adopted non-linear shape and pathing as they traversed from the periosteum to the medullary cavity, occasionally even branching within the cortical bone. Additionally, mice from both HR and control lines had more than four nutrient canals per femur. Mice from HR lines had significantly larger nutrient canal area than controls, which was not the result of an increase in the number of nutrient canals, but rather an increase in their average size. This study demonstrates that mice with an evolutionary history of increased locomotor activity and metabolic rate have a concomitant increase in the size of their nutrient canals.

The multivariate distribution of genetic variance is key to understanding two fundamental and interrelated processes in evolution; the ability of populations to respond to selection, and the balance of forces that maintain the genetic variance that such a response is based upon. In this thesis, I develop an analytical framework for characterizing the multivariate distribution of genetic variance and how it evolves. I then apply this framework to explore the evolution of genetic variance in multiple sexually-selected traits under artificial selection using the Drosophila serrata experimental system. An analytical framework for characterizing the multivariate distribution of genetic variance and how it evolves: First, I present a method from the statistical literature to establish the statistical dimensionality of genetic variance in a suite of traits. I evaluate the ability of this and two other methods to predict the correct number and orientation of dimensions of genetic variance by conducting a simulation study for a suite of eight traits. Second, I present a method from the materials science literature that uses multi-linear algebra to characterize the variation among matrices. I show how variation in the multivariate distribution of genetic variance among populations can be analyzed by constructing a fourth-order genetic variance-covariance tensor, and how the spectral decomposition of this tensor reveals independent aspects of change in genetic variance. I use the tensor to explore the variation in the genetic variance of eight traits among nine populations of D. serrata, and show how this variation can be associated with variation in selection pressures to determine whether selection may have affected genetic variance within populations. The evolution of genetic variance in sexually-selected traits under artificial selection: Female D. serrata display a strong preference for a particular combination of male cuticular hydrocarbons (CHCs). Individually, these pheromones display substantial genetic variance, but the genetic variance is not distributed equally among all phenotypic dimensions. In the specific CHC combination preferred by females, genetic variance is low. This is compatible with the expectation that selection will deplete genetic variance, but is contrary to the typical observation of high levels of genetic variance in individual sexually-selected traits. By artificially selecting on the trait combination preferred by females, I show that male mating success can successfully respond to selection, but the evolution of the combination of CHCs preferred by females is constrained. I then show that a key prediction of mutation-selection balance (MSB) models that has rarely been observed holds for these traits. Under MSB, genetic variance is expected to be maintained by rare alleles with large effects. Therefore, when a trait that is usually under stabilizing selection is subjected to directional artificial selection, the genetic variance is predicted to increase. I show that genetic variance increases in the CHC combination preferred by females under artificial selection, but not when another combination of the same traits with greater genetic variance is artificially selected. Complex segregation analysis indicated that the observed increase in genetic variance was a consequence of at least one allele of major effect increasing in frequency. This experiment demonstrates the importance of the past history of selection on the nature of genetic variance. General conclusion: Mutation-selection balance (MSB) is appealing as an explanation for the maintenance of genetic variance because it is simple and intuitive: the total mutation rate must be sufficiently high to replenish the variation eliminated by selection. However, MSB models seem unable to adequately explain the coexistence of the observed levels of genetic variance and strength of selection on individual traits. I contend that the failure of MSB models to explain these data is not a failure of MSB theory itself; rather it is the data that has been used to evaluate MSB models that may not be appropriate. It is now clear that there are fewer genetically independent traits than measured phenotypes, and that selection gradients measured for individual traits do not adequately reflect the nature of selection on combinations of traits. In other words, it is not possible to understand the relationship between genetic variance and selection by simply associating median levels of genetic variance and selection collated across studies as levels of genetic variance are likely to be much lower in trait combinations associated with stronger selection. Together, these observations suggest that we should be looking at the distribution of genetic variance in suites of traits and pattern of correlated selection on those same traits if we are to understand MSB.

Alimentos produzidos de forma mais sustentável têm ganhado espaço e o controle biológico vem assumindo importância cada vez maior em programas de manejo integrado de pragas. Dentre os principais agentes de controle biológico estão os ácaros predadores pertencentes a família Phytoseiidae. Amblyseius tamatavensis Blommers é um ácaro predador pertencente a esta família, amplamente distribuído no Brasil e no mundo. Este predador apresentou resultados promissores em relação ao possível uso para o controle de Bemisia tabaci (Gennadius). Alguns estudos mostraram diferenças biológicas marcantes entre as populações de fitoseídeos. Portanto, espera-se que tais diferenças também possam ocorrer entre as populações brasileiras de A. tamatavensis. Por isso, 14 populações de diferentes regiões do Brasil (dos estados de Alagoas, Goiás, Minas Gerais e São Paulo) foram comparadas em relação ao potencial de predação e oviposição quando alimentadas com ovos de B. tabaci biótipo B. A população coletada em Olhos d\'Água das Flores (Alagoas) apresentou as maiores taxas de predação diária (7,9 ovos / fêmea) e oviposição (1,2 ovo / fêmea) e uma variabilidade entre os indivíduos da população que possibilitou um processo de seleção. O objetivo deste trabalho foi selecionar em laboratório uma linhagem de A. tamatavensis com maior potencial de predação e oviposição, sendo assim mais favorável para uso prático no controle de B. tabaci. Na seleção para predação, após seis gerações, foi observado um ganho genético de 1,1 ovo/fêmea/dia (aproximadamente 15% de aumento em relação à população) na taxa de predação, demonstrando resultado promissor para o melhoramento. Entretanto, o ganho genético foi praticamente nulo quando a população selecionada para predação foi submetida ao processo de seleção para oviposição, e também foi observado um baixo diferencial de seleção, mostrando um baixo potencial para a seleção das melhores fêmeas em relação a este parâmetro. Em função dos resultados promissores em relação ao aumento da eficiência da população de A. tamatavensis no controle de B. tabaci e das tabelas de vida de fertilidade não mostrarem custos adaptativos importantes, testes em plantas de pimentão mantidas em um telado foram realizados para avaliar a real eficiência desta linhagem. Foram comparadas diferentes populações, selecionadas e não selecionadas em laboratório. Os melhores resultados foram observados com a população que passou pelo processo de seleção, que teve uma eficiência maior quando comparada com as outras populações. Essa população apresentou uma redução nos imaturos de B. tabaci que variou de 82% a 90% após 14 dias da liberação dos predadores. Os resultados obtidos nas plantas de pimentão sugerem que, assim como observado nas tabelas de vida realizadas no capítulo anterior, não houve um custo adaptativo significativo na população que passou pelo processo de seleção. Estudos complementares devem ser realizados, para avaliar se essas populações estudadas mantém o mesmo comportamento em cultivos no campo. / More attention has been given recently to sustainable food production, and biological control has become increasingly important in integrated pest management programs. Predatory mites of the family Phytoseiidae are among the main biological control agents. Amblyseius tamatavensis Blommers is a predatory mite belonging to this family, widely distributed in Brazil and worldwide. This predator presented promising results regarding the possible use for the control of Bemisia tabaci (Gennadius). Some studies have shown marked biological differences among phytoseiid populations. It is expected that such differences may also occur among Brazilian populations of A. tamatavensis. Therefore, 14 populations of different regions of Brazil (from the states of Alagoas, Goiás, Minas Gerais and São Paulo) were compared in relation to predation and oviposition potential when fed with B. tabaci biotype B. The population collected in Olhos d\'Água das Flores (Alagoas) presented the highest rates of daily predation (7.9 eggs / female) and oviposition (1.2 egg / female) and sufficient variability among individuals of the population to enable a selection process. The objective of this work was to select in the laboratory a strain of A. tamatavensis with higher predation and oviposition potential, being thus more favorable for practical use in the control of B. tabaci. In the selection for predation, after six generations, a genetic gain of 1.1 eggs / female / day (approximately 15% increase in relation to the population) in predation rate was observed, showing promising result for breeding. However, the genetic gain was practically null when the population selected for predation was submitted to the selection process for oviposition, and a low selection differential was also observed, showing a low potential for the selection of the best females in relation to this parameter. As a result of the promising results in increasing the efficiency of the A. tamatavensis population in the control of B. tabaci and because the fertility life tables did not show important adaptive costs, tests on pepper plants were carried in a screen-house to evaluate the real efficiency of this strain. Different populations were compared, selected and not selected in the laboratory. The best results were observed with the population that passed by the selection process, which had a greater efficiency when compared with the other populations. This population showed a reduction in the immatures of B. tabaci that ranged from 82% to 90% after 14 days of predator release. The results obtained on the pepper plants suggest that, as observed in the life tables performed previously, there was no significant adaptive cost in the population that passed by selection process. Complementary studies should be carried out to evaluate whether these studied populations maintain the same behavior in field crops.

Natural and artificial selection cause changes in certain regions of the genome resulting in selection signatures. Thus, is expected to identify genes associated with the traits under selection in such regions. Selection signatures may be identified using different methodologies, and some are based on detecting of contiguous sequences of homozygous identical-by-descent haplotypes, called runs of homozygosity (ROH), or estimating fixation index (FST) of genomic windows that indicates genetic differentiation. In our study, we aimed to identify selection signatures in a paternal broiler line and to investigate the genes annotated in these regions as well as the biological phenomena involved. For such purpose, ROH and FST-based analysis were performed using whole genome sequence of twenty eight chickens from two different generations. ROH analysis identified homozygous regions of short and moderate length. Analyzing ROH patterns it was observed regions commonly shared among some animals and changes in ROH abundance and length between the two generations. The results also suggests that WGS outperforms SNPchip data, however the number of individuals analyzed must be properly chosen. FST-based analysis revealed genetic differentiation in some genomic windows. Annotation of the consensus regions of ROH and FST windows counted for many genes of which some were previously associated with traits of economic interest, such as APOB, IGF1, IGFBP2, POMC, PPARG, and ZNF423. Overrepresentation analysis of the genes resulted in biological terms of skeletal muscle, matrilin proteins, adipose tissue, hyperglycemia and diabetes, Salmonella infections and tyrosine. Therefore, suggested that ancient and recent selection in TT line acted over regions affecting performance traits. / Identificação de assinaturas de seleção envolvidas com características de desempenho em uma linhagem paterna de frangos de corte Seleção natural e artificial causam mudanças em determinadas regiões do genoma, resultando em assinaturas de seleção. Assim, espera-se identificar genes associados às características sob seleção nessas regiões. Assinaturas de seleção podem ser identificadas usando diferentes metodologias, e algumas delas são baseadas na detecção de sequências contíguas de haplótipos homozigotos idênticos por descendência, chamados segmentos de homozigose (ROH), ou na estimativa do índice de fixação (FST) de janelas genômicas que indicam diferenciação genética. Em nosso estudo, objetivamos identificar assinaturas de seleção em uma linha paterna de frangos de corte e investigar os genes anotados nessas regiões, bem como os fenômenos biológicos envolvidos. Para tal propósito, as análises de ROH e FST foram realizadas usando dados de sequenciamento completo do genoma (WGS) de vinte e oito aves de duas gerações diferentes. A análise de ROH identificou regiões em homozigose de comprimentos curto e moderado. Analisando os padrões de ROH, foram observadas regiões comumente compartilhadas entre alguns animais e mudanças na abundância e no comprimento da ROH entre as duas gerações. Os resultados também sugerem que dados de WGS apresentam vantagens sobre os dados de SNPchip, porém o número de indivíduos analisados deve ser levado em consideração. A análise baseada em FST revelou diferenciação genética em algumas janelas genômicas. Anotação das regiões consenso de ROH e das janelas FST identificaram diversos genes, alguns dos quais já foram associados a características de interesse econômico, como APOB, IGF1, IGFBP2, POMC, PPARG e ZNF423. Análises de enriquecimento dos genes resultaram em termos biológicos de músculo esquelético, proteínas matrilinas, tecido adiposo, hiperglicemia e diabetes, infecções por Salmonella e tirosina. Portanto, sugerimos que a seleção ocorrida durante várias gerações na linha TT atuou sobre as regiões que afetam as características de desempenho destes animais.

Le rôle des communautés de bactéries est essentiel dans les écosystèmes, mais aussi dans l’industrie, l’agriculture ou le secteur de la santé. La structure de ces communautés accroit leurs applications potentielles par rapport aux bactéries isolées. Si manipuler et faire évoluer une souche bactérienne est devenu courant, il n’existe pourtant pas de technologie permettant de cultiver, manipuler, sélectionner et en faire évoluer des communautés. Ce travail de thèse concerne la conception, le développement et la caractérisation d’un outil pouvant y aboutir en millifluidique digitale. Avec cet outil nous manipulons un millier de cultures de bactéries sous la forme de gouttes incubées et analysées en continu, et dont nous souhaiterions diriger l’évolution. La dérive génétique, les flux géniques, la diversification et la sélection sont les quatre agents de l’Évolution qui fixèrent les quatre axes de ce travail. La conservation des diversités spécifiques à une culture et entre elles conditionne la conception de notre outil. Son utilisation implique des échanges entre cultures que nous avons caractérisés. Nous avons créé un protocole permettant d’évaluer la diversité de ces cultures, et donc de les discriminer pour mieux les sélectionner. Nous avons finalement conçu un système permettant d’automatiser leur sélection artificielle : leur évolution dirigée est à portée de main. / The role of bacterial communities is essential in ecosystems, but also in the industry, agriculture and human health. Communities’ structure increases their potential applications unlike isolated bacteria. While the culture and engineering of a bacterial strain has become common, currently no technology exists to allow cultivation, handling, selection and evolution of bacterial communities. This work focuses on the design, development and characterization of a tool which can perform evolution of communities using digital millifluidics. With this tool, we handle one thousand cultures of bacteria in drops incubated and analyzed continuously, and the evolution of which we would like to manage. The genetic drift, the genic flows, the diversification and the selection are the four agents of the Evolution which fixes the four axes of this work. The preservation of the diversities, specific to a culture and between them, affect the design of our tool. Its use involves exchanges between cultures which we characterized. We created a protocol allowing to estimate the diversity of these cultures, and thus to discriminate them for robust selection. We finally conceived a system automating their artificial selection: their directed evolution is within easy reach.

The study of genetic variation in populations is of great interest for the study of the evolutionary history of humans and other species. Improvement in sequencing technology has resulted in the availability of many large datasets of genetic data. Computational methods have therefore become quite important in analyzing these data. Two important problems that have been studied using genetic data are population stratification (modeling individual ancestry with respect to ancestral populations) and genetic association (finding genetic polymorphisms that affect a trait). In this thesis, we develop methods to improve our understanding of these two problems. For the population stratification problem, we develop hierarchical Bayesian models that incorporate the evolutionary processes that are known to affect genetic variation. By developing mStruct, we show that modeling more evolutionary processes improves the accuracy of the recovered population structure. We demonstrate how nonparametric Bayesian processes can be used to address the question of choosing the optimal number of ancestral populations that describe the genetic diversity of a given sample of individuals. We also examine how sampling bias in genotyping study design can affect results of population structure analysis and propose a probabilistic framework for modeling and correcting sample selection bias. Genome-wide association studies (GWAS) have vastly improved our understanding of many diseases. However, such studies have failed to uncover much of the variation responsible for a number of common multi-factorial diseases and complex traits. We show how artificial selection experiments on model organisms can be used to better understand the nature of genetic associations. We demonstrate using simulations that using data from artificial selection experiments improves the performance of conventional methods of performing association. We also validate our approach using semi-simulated data from an artificial selection experiment on Drosophila Melanogaster.

If sexual selection acts in a sex-limited way on a trait that has a shared genetic basis between males and females, the resulting intralocus sexual conflict can have a considerable impact on the opposite sex. A prime example of sexual conflict affecting a shared characteristic would be the reproductive organs in males and females. This study investigates how artificial selection on the female-specific trait egg size influences male reproductive success, particularly male testes morphology, by analysing the density and number of seminiferous tubules within the testes. It was found that selection on female reproductive investment has a concordant effect on male reproductive success, by demonstrating increased density of seminiferous tissue in the testes of males originating from high investment selection lines. Interestingly, a non-significant trend suggested that the density of seminiferous tissue influences testes size in a negative way. This study therefore provides evidence that female-specific selection on reproductive investment influences testes morphology in males, and that testes size depends on more than sperm-producing tissue.

Fragmentation of rivers due to the rapid expansion of hydropower plants is one of the major factors responsible for the decline in the Atlantic salmon (Salmo salar L.) in the Baltic Sea. Current methods to aid downstream migrating salmon smolt still struggle with effectively stopping the smolt from going through the hydropower turbines, by guiding them towards the available salmon ladders. A promising guiding method is using a barrier of bubbles which may serve as a non-intrusive alternative to conventional guiding structures. This study evaluated the risk of artificial selection caused using bubble barriers and compared the results with an earlier study.  The three hypotheses tested were: i) the salmon display a scototaxis behaviour related to their boldness, ii) temperature, and size of arena affect the scototaxis of the salmon, and iii) the salmons reaction to a bubble barrier is correlated to their boldness. The hypotheses were tested in a controlled laboratory setting by conducting three scototaxis tests and an experiment with several bubble barriers, where the reaction of salmon to bubbles could be assessed. There was significant positive correlation (r = 0,62 & p = 0,012) between the boldness of an individual and the time it took to swim through the bubbles. Even though a significant difference in scototaxis as a result of lowered temperature were discovered, the difference was too small to have a noticeable effect on the overall results. A bubble barrier may therefore put artificial selection pressure on the salmon population.

Here we present the genome-wide association study of body weight at 8 weeks of age based onthe advanced intercross pedigree of two chicken lines gone through bi-directional selection.With improved marker density (~3M SNPs) and larger sample size (2667 individuals from F2-F15), 34 loci with suggestive significance are detected, of which 18 loci are novel, and the rest17 loci are consistent with the results of previous quantitative trait locus mapping studies onthis trait with smaller number of genetic markers and fewer individuals. The component traits,referring to traits related to body weight and possibly contributing to the body weight as well,are also measured and analysed. The combined result showed that one locus with significantmarginal effect on BW8 is associated with early growth, breast muscle development and shankdevelopment, while another locus with late development and bursa development.