O presente estudo objetivou estimar parâmetros genéticos visando quantificar a variabilidade genética de uma população de café robusta (Coffea canephora Pierre ex A. Froehner) introduzida da Costa Rica e analisar o seu potencial genético para o desenvolvimento de futuras cultivares clonais para o estado de São Paulo. Outro intuito foi verificar a possibilidade de submeter essa população à seleção recorrente, tornando-a, assim, fonte de alimentação e sustentação de programas de melhoramento genético do café robusta. O experimento foi composto por 25 tratamentos, sendo 21 progênies de C. canephora e quatro cultivares de C. arabica, plantados em Mococa (SP). O delineamento experimental utilizado foi em látice balanceado 5x5 quadruplicado, com seis repetições e uma planta por parcela. Foram realizadas doze colheitas e após a sexta colheita as plantas foram podadas. Em 2004, foi realizada uma seleção fenotípica dessa população a fim de clonar os melhores indivíduos. Essa seleção resultou em novo experimento, instalado em Campinas, seguindo o delineamento de blocos ao acaso, com três repetições, 28 clones e quatro plantas por parcela, sendo realizadas cinco colheitas consecutivas. As análises estatísticas e biométricas foram realizadas considerando os modelos lineares mistos (procedimento REML/BLUP), por meio do software Selegen, cujos componentes de variância são estimados pelo método da máxima verossimilhança restrita (REML) e os valores genotípicos preditos pela melhor predição linear não viesado (BLUP). As análises mostraram que, na população em estudo, observou-se elevada variabilidade genética, passível de ser explorada tanto para a extração de clones quanto para a seleção recorrente. As adversidades climáticas severas fizeram com que a seleção fosse prejudicada. Nessa situação é preferível não considerar o período afetado e analisar os dados após a recuperação das plantas. A seleção baseada em seis colheitas forneceu estimativas de parâmetros e ganhos genéticos similares aos obtidos na seleção baseada em duas colheitas de alta produção. Os ganhos genéticos esperados nas duas formas de propagações foram elevados e a seleção clonal proporcionou maiores ganhos do que a sexual. No experimento clonal foi possível identificar materiais com potencial produtivo e que poderão vir a ser recomendados para o cultivo no estado de São Paulo. Apesar de a interação genótipos x colheitas ter sido do tipo complexa, devido ao veranico ocorrido, esta não afetou significativamente o ordenamento dos melhores clones e nem comprometeu as estimativas dos parâmetros genéticos. Os coeficientes de variação experimental e genético bem como seu valor relativo deverão ser analisados conjuntamente com o número de repetições e a acurácia seletiva. A seleção recorrente deverá ser conduzida concomitantemente com o programa de seleção clonal, a fim de evitar o esgotamento da variabilidade genética e o comprometimento do programa de melhoramento genético visando o desenvolvimento de cultivares clonais. Tendo em vista que a população inicial foi constituída por um pequeno número de progênies, é aconselhável o monitoramento do tamanho efetivo populacional e do grau de endogamia ao longo dos ciclos de seleção recorrente. / The objective of this research was to estimate genetic parameters to quantify the variability of a population of robusta coffee (Coffea canephora Pierre ex A. Froehner) introduced into Brazil from Costa Rica in 1974 aiming at determining its genetic potential for the development of clonal or seedling cultivars for the state of São Paulo, Brazil. The feasibility has also been studied to submit this population to recurrent selection, making it a continuous source of improved base material in support of varietal improvement of robusta. An experiment consisting of 21 open pollinated seedling progenies of robusta and four cultivars of arabica was established in Mococa (SP) in 1975. Yield was observed for twelve harvests and after the sixth harvest the plants were pruned. The experimental lay out was a balanced 5x5 quadruple lattice design, with six replicates and one plant per plot. In 2004 a phenotypic selection of this population for yield was carried out aiming at cloning the best individuals. These 28 clones were planted in an experiment in Campinas in 2005, following a completely randomized block design, with 28 treatments (clones), three replications and four plants per plot. In total, yields were collected over five harvests. Statistical and biometrical analyzes were performed considering the linear mixed models (REML/BLUP), through software Selegen, where the variance components are estimated by restricted maximum likelihood (REML) and genotypic values predicted by best linear unbiased prediction (BLUP). The analyzes showed that the population had high genetic variability, which can be exploited for the extraction of both clones and seedling progenies, used for recurrent selection. Selection was impaired by severe adverse weather conditions. In such situations it is preferable not to consider the affected period and analyze the data after recovery of the plants. Due to the moisture stress that occurred in the clonal trial, genotype x environment interaction was complex. However this did not affect the ranking of superior clones nor compromised the genetic parameter estimates. Selection for yield based on six yield resulted in genetic parameters and genetic gains similar to those obtained by selection based on two high yielding harvesting periods. The expected genetic gains both for clones as for open pollinated progenies were high. However, clonal selection resulted in higher genetic gains for yield than the seedling selection. In the clonal experiment it was possible to identify materials with high yield potential that may become to be recommended for cultivation in São Paulo State. The experimental, genetics and relative coefficients of variation, should be analyzed together with the number of replications and selective accuracy. Recurrent selection should be conducted concurrently with the clonal selection program in order to avoid depletion of genetic variability and to impairthe breeding program aiming at the development of clonal cultivars. Considering that the initial population was composed of a small number of progeny, it will be important monitoring adequately the effective size and the inbreeding coefficient during recurrent selection cycles.

Caracteres importantes em espécies vegetais estão, em sua maior parte, sob o controle de vários locos gênicos, denominados locos de caracteres quantitativos (QTLs). A expressão fenotípica desses caracteres produz uma distribuição contínua de valores devido à segregação genotípica, aos efeitos ambientais e à interação genótipos por ambientes. Com o advento dos marcadores moleculares e de modelos estatístico-genéticos adequados tornou-se possível a detecção e o mapeamento de regiões cromossômicas que controlam estes caracteres. Este trabalho foi realizado para analisar caracteres quantitativos em uma população de milho tropical com os objetivos: (1) obter estimativas das variâncias genéticas aditiva e de dominância, e do grau médio de dominância; (2) construção de um mapa genético utilizando marcador molecular do tipo microssatélite; (3) detecção de QTLs e estimação de seus efeitos genéticos, e de suas interações com ambientes, utilizando o delineamento III. Neste trabalho foram utilizadas 250 progênies F2:3 retrocruzadas para ambos os genitores, totalizando 500 progênies, que foram avaliadas em seis ambientes para a obtenção de dados fenotípicos. Foi realizada a genotipagem com 140 marcadores moleculares para as 250 plantas F2 genitoras. O mapa genético foi construído utilizando o programa MAPMAKER/EXP V.3.0. Os componentes das variâncias genéticas e o grau de dominância dos caracteres foram estimados utilizando-se o delineamento III. A detecção de QTLs e as estimativas de seus efeitos genéticos foram efetuados utilizando a metodologia de Cockerham & Zeng (1996). Os resultados das análises de variâncias evidenciaram sobredominância para produção de grãos e dominância parcial para os outros nove caracteres. Por causa do desequilíbrio de ligação nesta população, estas estimativas estão, provavelmente, superestimadas. O mapa genético com 140 marcadores tem 1.730,1 centiMorgans (cM) de extensão e intervalo médio de 12,4 cM entre marcadores adjacentes. Foram detectados QTLs em todos os cromossomos para todos os caracteres, indicando que os locos que controlam estes caracteres estão distribuídos pelo genoma. A análise genética utilizada permitiu a estimação dos efeitos aditivos, dominantes e epistáticos dos QTLs. Efeitos aditivos, dominantes e epistáticos foram detectados para todos os caracteres. As magnitudes, em módulo, dos efeitos aditivos e dominantes foram maiores do que os efeitos epistáticos para todos os caracteres, exceto para posição relativa da espiga onde os efeitos epistáticos foram um pouco maiores do que os efeitos dominantes. A porcentagem de marcadores que detectaram efeitos epistáticos variou de 10,71% para teor de umidade nos grãos a 50,71% para número de folhas. Para produção de grãos, os efeitos epistáticos foram detectados em 32,14% dos marcadores, sendo encontrados valores altos para alguns marcadores. Os efeitos dos QTLs detectados variaram muito em magnitude e sinal entre marcadores adjacentes, demonstrando que os QTLs contribuem de forma diferenciada para as expressões dos caracteres. Os efeitos dos QTLs tiveram pequena ou nenhuma interação genótipos por ambientes para os caracteres avaliados, exceto para teor de umidade nos grãos. / Most of the agronomic traits in crop species are under the control of unknown number of loci, which have been termed quantitative trait loci (QTL). Because of genotypic segregation, environmental effects, and of genotype by environment interaction, the phenotypic values of these traits present continuous variation. The advent of molecular markers, and of sophisticated statistical-genetic models allowed the analysis of quantitative traits at the DNA level, by detecting and mapping chromosomal regions with loci affecting those traits. This research was carried out to analyze quantitative traits in a tropical maize population by (1) estimating genetic parameters as additive and dominance genetic variance, and the level of dominance; (2) developing a genetic map with microsatellites as molecular markers; (3) detecting and estimating genetic effects of QTLs as well as QTLs by environment interaction by using the Design III methodology. The genetic material was a set of 250 F2:3 progenies developed from a cross of two inbred lines. The F2 plants, parents of the F2:3 progenies, were genotyped with microsatellites and a genetic map was developed by using MAPMAKER/EXP V.3.0 software. The F2: 3 progenies were backcrossed to both parental inbred lines giving rise to 500 backcrossed progenies, which were evaluated in six environments. The components of genetic variances and the level of dominance of the traits were estimated by using the Design III approach. The detection of QTLs and estimates of their genetic effects were computed by using Cockerham & Zeng (1996) methodology. Average level of dominance was overdominance for grain yield (GY), and partial dominance for the other nine traits. Because of the linkage disequilibrium in this population, probably these estimates are overestimated. The genetic map with 140 markers spanned 1,730.1 centimorgans (cM) in length with an average interval of 12.4 cM between adjacent markers. QTLs were detected at all chromosomes for all traits, indicating that the genes controlling the quantitative traits assessed are spread in the genome. The genetic analysis used allowed the estimation of additive, dominance and epistatic effects of the QTLs. Additive, dominance and epistatic effects were detected for all traits, although the magnitudes, in module, of additive and dominance effects were larger than epistatic effects for all traits, except for ear placement where epistatic effects were slightly larger than dominance effects. The percentage of markers that detected significant epistatic effects ranged from 10.71% for grain moisture to 50.71% for number of leaves. For GY, the dominance effects were more important than additive effects; epistatic effects were detected in 32.14% of the markers, whereas in some markers high values were found. The magnitudes and signs of the QTLs effects were highly variable among the markers, showing that the contribution of the QTLs for the expression of the traits was very different, and that epistatic effects are important for the expression of all traits. Also, fewer QTL effects by environment interactions were detected for all traits, except for grain moisture.

Dans le contexte des changements climatiques prévisibles et d'une demande évaporative accrue vis à vis des cultures, ce travail de thèse vise à évaluer la variabilité génétique du pommier pour sa réponse à la contrainte hydrique. Cette évaluation est d'un intérêt certain pour l'amélioration future de l'espèce, qu'il s'agisse de mieux tolérer le stress pouvant résulter d'une sécheresse temporaire du sol, ou d'une efficience accrue d'utilisation de l'eau. Les méthodes de phénotypage actuellement disponibles pour l'étude de la réponse à la contrainte hydrique ne permettent pas un haut débit de mesure compatible avec les comparaisons simultanées entre de nombreux individus. En conséquence, ce travail de thèse s'est focalisé sur l'application de l'imagerie multi-spectrale aéroportée comme outil de phénotypage à haut débit en condition de plein champ et sur l'évaluation de sa pertinence pour l'analyse quantitative des réponses à la contrainte hydrique et la recherche des déterminismes génétiques associés. Les essais ont été réalisés sur une population hybride de pommiers (croisement Starkrimson x Granny Smith) âgée de 4 ans au début de l'étude, implantée dans le sud de la France. A partir d'images acquises dans les longueurs d'onde du visible, du proche infrarouge et de l'infrarouge thermique, à une résolution spatiale proche de 30cm, différents indices de végétation et de stress ont été calculés permettant d'apprécier la vigueur des arbres et leur transpiration. La prise en compte, dans des modèles linéaires mixtes, de six dates d'expérimentation, couvrant deux campagnes d'acquisitions, et de régimes d'irrigation différenciés sur la population a permis de mettre en évidence l'héritabilité des indices phénotypiques et conduit à la détection de nombreux QTLs. 18 QTLs se sont révélés indépendants de la date d'acquisition. Pour quatre de ces QTLs, dits adaptatifs, c'est-à-dire exprimés en conditions de stress, un certain nombre de gènes candidats potentiellement impliqués dans les réponses précoces responsables de la régulation stomatique ont été identifiés. / In the context of foreseen climate changes and higher evaporative demand in crops, this PhD work is aiming at assessing the apple tree variability in response to hydric constraints. This could be of great interest for future breeding programs in this species, either in respect to temporary abiotic stress tolerance, or looking at a better water use efficiency. Phenotyping methods presently available for evaluating the plant response to hydric constraints do not allow the high-throughput that could be compatible with simultaneous comparison of a high number of individuals. As a consequence, this thesis focused on the application of airborne multispectral imagery as a tool for high-throughput field phenotyping, and it assessed the relevancy of this method for quantitative analysis of response to drought and further dissection of associated genetic determinisms. Trials were realized on a segregating hybrid apple population (Starkrimson x Granny Smith cross), 4-year old at the beginning of study, installed in the South of France. Images acquired in visible, near infrared and thermal infrared, with a spatial resolution close to 30cm, were the calculation basis of various vegetation and stress indices, allowing estimation of individual tree vigor and transpiration. Linear mixed models taking account of six flight dates, covering two acquisition campaigns and including two contrasted irrigation regimes over the apple population, made it possible to highlight the heritability of phenotypic indices and to perform numerous QTLs mapping. Eighteen QTLs were revealed independently from the acquisition date. Out of this QTLs set, a further analysis on 4 of them, which were adaptative i.e. expressed in stress conditions, allowed first identification of putative candidate genes potentially involved in the early stomatal closure.

Sistemas morfológicos quantitativos são descritos por medidas contínuas. A relação genética entre essas características dos indivíduos é representada pela matriz de covariância genética aditiva, a matriz G. Entender a evolução da matriz G, portanto, é de suma importância para compreender os padrões de diversificação encontrados na natureza. Neste trabalho estudamos modelos computacionais para a evolução de traços contínuos em populações naturais, sujeitas a variados tipos de seleção e condições internas, focando no problema da evolução dos padrões de integração e modularidade nessas populações. Testamos dois modelos com diferentes combinações de parâmetros em sua capacidade de reproduzir e elucidar padrões naturais. Seleção direcional correlacionada se mostrou uma força importante na criação desses padrões de covariação e a seleção estabilizadora correlacionada se mostrou fundamental para a manutenção desses padrões / Quantitative morphological systems are described by continuous measurements. The genetic relation between these characteristics of the individuals is represented by the genetic additive co-variance matrix, the G matrix. Understanding the evolution of the G matrix is, therefore, of paramount importance for proper interpretation of the patterns of diversification we observe in nature. In this work we study computational models for the evolution of quantitative traits in natural populations, subject to different natural selection and internal conditions, focusing on the problem of the evolution of the pattern of morphological integration and modularity. We test two models with different sets of parameters in their ability to reproduce and elucidate natural patterns. Directional correlated selection was necessary for the shaping of the patterns of morphological integration, and correlated stabilizing selection was fundamental to the maintenance of these patterns

Recent empirical studies have demonstrated inter-generational morphological and life-history changes in fish stocks that have been impacted by size-selective harvest. Evolutionary processes in biological populations occur through differential survival and reproductive success based, in part, upon individual phenotypic variability. Fishing is a source of directional selection resulting in the directed removal of some phenotypes; however, many aspects of the evolutionary effects of fishing remain have yet to be described. In order to better understand the life-history and morphological changes that occur as a result of size-selective fishing, and their effect on fishery dynamics, I first determined the suitability of Japanese medaka (Oryzias latipes) for selection experiments. I performed selection experiments using Japanese medaka and report how morphology and life-history characteristics changed over multiple generations of selection. I then used these patterns of change in life-history and morphology to validate individual-based simulation candidate models to test general mechanisms of life-history relationships. Finally, I applied the individual-based simulation modeling approach in order to describe how biological and fishery characteristics change in a large, age-structured population exposed to size-selective fishing over multiple generations. I found that the Japanese medaka has attractive characteristics for biological investigation. The selection experiments indicated large changes in the age-atmaturity, including a nearly 50% decrease over four generations in the most intense sizeselective removal regimes. However, I did not observe significant changes in length-at-age or weight-at-age over the course of the experiment. Candidate simulation models were poor at predicting some aspects of the life-history characteristics of Japanese medaka. The simulation model to determine fishery characteristics predicted large decreases in yield and egg production as a result of decreases in length-at-age. Understanding the relationships of life-history characteristics and their role in determining population resilience is a step toward understanding the importance of evolutionary processes in fishery management. / Ph. D.

Genotypes adapted to contrasting environments are expected to behave differently when placed in common controlled conditions, if their sensitivity to environmental cues or intrinsic growth behaviour are set to different thresholds, or are limited at distinct levels. This allows natural variation to be exploited as an unlimited source of new alleles or genes for the study of the genetic basis of quantitative trait variation. My doctoral work focuses on analysing natural variation for shoot growth and response to the environment in A. thaliana. Natural variation analyses aim at understanding how molecular genetic or epigenetic diversity controls phenotypic variation at different scales and times of plant development and under different environmental conditions, and how selection or demographic processes influence the frequency of those molecular variants in populations for them to get adapted to their local environment. As such, the analysis of A. thaliana natural variation can be addressed using a variety of approaches, from genetics and molecular methods to ecology and evolutionary questions. During my PhD, I got the chance to tackle several of those aspects through my contributions to three independent projects which have in common to exploit A. thaliana natural variation. The first one is the analysis of the pattern of polymorphism from a set of 102 A. thaliana accessions at the MOT1 gene coding for a molybdate transporter (an essential micronutrient) and responsible for contrasted growth and fitness among accessions in response to Mo availability in the soil. I showed at different geographical scales that MOT1 pattern of polymorphisms is not consistent with neutral evolution and shows signs of diversifying selection. This work helped reinforce the hypothesis that in some populations, mutations in MOT1 have been selected to face soils rich in Mo and potentially deleterious despite their negative effect on Mo-limiting soils. The second project consists in the characterisation and functional analysis of two putative receptor-like kinases (RLKs) identified from their effect on shoot growth specifically under mannitol-supplemented media and not in response to other osmotic constraints. The function of such RLKs in A. thaliana, which is not known to synthesize mannitol was intriguing at first but, through different experiments, we built the hypothesis that those RLKs could be activated by the mannitol produced by some pathogens such as fungi and participate to plant defensive response. The third project, in collaboration with Michel Vincentz's team from CBMEG (Brasil) and Vincent Colot (IBENS, Paris), consists in the analysis of the occurrence of natural epigenetic variants of the QQS gene in different populations from Central Asia and their possible phenotypic and adaptive consequences. Overall, these analyses of the genetic and epigenetic molecular variation leading to the biomass phenotype(s) in interaction with the environment provide clues as to how and where in the pathways adaptation is shaping natural variation.

L'évolution contemporaine des organismes vivants est de plus en plus dépendante des perturbations d'origine anthropique. En particulier, la pollution amplifie l'intensité des pressions de sélection auxquelles sont soumises les populations. Or ces changements peuvent avoir des effets négatifs sur la vie des individus, la démographie des populations, mais aussi, au cours des générations, sur leurs caractéristiques phénotypiques et génétiques. Ainsi en réponse aux pressions de sélection, des changements microévolutifs sont susceptibles de se manifester. Mais ces phénomènes entraînent en parallèle la mise en place de coûts adaptatifs qui fragilise le maintien des populations. Il est donc indispensable de développer nos connaissances sur l'évolution des populations en milieu pollué. Dans ce contexte, cette étude vise à déterminer les réponses microévolutives de populations de C. elegans, exposées à diverses pollutions et à mesurer les coûts adaptatifs de ces microévolutions. Ces populations ont été exposées expérimentalement, durant 22 générations, à une forte concentration en uranium et/ou en chlorure de sodium. Nous avons mis en évidence une différentiation génétique des populations exposées, associée à augmentation de la résistance, au cours du temps. La vitesse des réponses évolutives était dépendante des conditions d'exposition et de leurs effets sur l'expression de la structure génétique des traits d'histoire de vie. Ces phénomènes ont pu être reliés à des coûts adaptatifs, comme une réduction de la fertilité, dans de nouveaux environnements stressants (ex : augmentation de la température) ou en l'absence de stress. Ce projet nous a permis de mieux identifier comment une exposition à un ou deux polluants peut affecter la réponse évolutive de populations de C. elegans et d'évaluer les conséquences sur leur sensibilité. / The contemporary evolution of organisms is largely dependent on anthropogenic disturbances. In particular, the pollution amplifies the intensity of selection pressures suffered by populations. However, these changes may have negative effects on the life of individuals, the demographics of the populations, and its phenotypic and genetic characteristics over generations. Thus, microevolutionary changes are likely to occur in response to selection pressures. These phenomenon lead to collateral damages: adaptive costs. Populations can be more susceptible to many environmental changes. Hence, it is essential to expand our knowledge on the evolution of populations in polluted environment. In this context, our study aims to determine the microevolutionary response of C. elegans populations exposed to different pollutions, and to measure their costs of adaptation. Populations were experimentally exposed for 22 generations to a high concentration of uranium and/or sodium chloride. We confirmed the genetic differentiation between populations with an increase of resistance in populations exposed to different pollutions. The speed of evolutionary responses depended on exposure conditions and their effects on the expression of the genetic structure of life history traits. Microevolutionary changes were linked to costs of adaptation, such as reduced fertility, in stressful novel environments (e.g. fast temperature raise) or in the absence of stress. This project allowed us to better identify how exposure to one or two pollutants affects the evolutionary response of C. elegans populations and evaluate the impact on their sensitivity to environmental conditions.

Die vorliegende Dissertation verbindet Ergebnisse aus neuroethologischen, verhaltensbiologischen, quantitativ genetischen und genomischen Ansätzen bei Feldgrillen (Gryllus), um neue Erkenntnisse über die Rolle von sexueller Selektion bei Artbildung zu erlangen. Es wird gezeigt dass multivariate Gesangspräferenzen von Grillenweibchen von wenigen Merkmalen abhängen und zwischen Arten ähnlich sind, während sich Männchengesänge in allen Merkmalen unterschieden. Verschiedene Ebenen der Gesangserkennung sind durch unterschiedliche Präferenzfunktionen charakterisiert. Multivariate Präferenzen können also gleichzeitig verschiedene Indikatoren für Paarungspartnerqualität aus den Gesangsmerkmalen erkennen. Eine polygene genetische Architektur der Gesangsmerkmale und der Präferenz wurde beobachtet und weist auf eine eher langsamere Divergenz hin, obwohl gonosomale Vererbung mehrerer Gesangsmerkmale höhere Evolutionsraten zulässt. Starke Kovarianz zwischen den Merkmalen die direkt sexueller Selektion unterliegen und Merkmale, die nicht direkt von Weibchen gewählt werden, zeigen, dass indirekte Selektion teilweise für die markante Divergenz der Gesänge verantwortlich sein könnte, trotz begrenzter Divergenz der Präferenzen. Ferner zeigte ein Artvergleich der multivariaten Gesangsmerkmale, dass die Form der Präferenzfunktion die Ausrichtung der Kovarianzen und damit die erwartete Selektionsantwort der männlichen Gesänge beeinflussen kann. Simulationen ergaben starke Hinweise auf Genfluss zwischen zwei nahverwandten Arten über einen langen Zeitraum . Nur wenige Contigs zeigten hohe genetische Divergenz und hohe Raten nicht-synonymer Polymorphismen. Diese stimmten aber mit Genen überein, die experimentell nachgewiesene Funktionen in neuromuskulärer Entwicklung und im Paarungsverhalten haben. Zusammen zeigen die Ergebnisse das Potential von sexueller Selektion bei der Entstehung und Aufrechterhaltung von reproduktiver Isolation zwischen Arten. / This thesis integrates insights from neuro-ethological, behavioural, quantitative genetics, and genomic approaches in field crickets to provide novel insights in the role of sexual selection in speciation, in particular focusing on speciation with gene flow. It was shown that song preferences depend on few traits and are similar across species while the male song has diverged strongly in all traits. Because the different levels of song recognition are characterized by different types of preference functions, it is conceivable that multivariate preferences can extract various cues for mate quality from different traits simultaneously. A polygenic genetic architecture was found for song traits and preferences, probably limiting divergence rates. However, sex-chromosomal inheritance of some song traits may have allowed for somewhat higher rates. Strong covariance was found between traits that are under sexual selection and traits that are not directly selected by females. This indicates that indirect selection may be responsible in part for striking multivariate divergence in the male calling song despite limited divergence in female preferences. Furthermore, comparing multivariate song traits among species showed that the shape of the preference function can affect the orientation of trait covariance and thereby the selection responses of the male song. Coalescent simulations revealed evidence for a long history of gene flow between two closely related cricket species. Only few contigs with high genetic divergence and high rates of non-synonymous SNPs were found, but many of those that were highly diverged matched genes with experimentally proven functions in neuromuscular development and courtship behavior. Together, these findings underline the potential for sexual selection to drive reproductive isolation.

Pour lutter contre les agents phytopathogènes, la sélection de plantes résistantes est la stratégie la plus rentable et la plus écologique. Les résistances quantitatives, basées sur des mécanismes de résistances complexes, sont connues pour être sujettes à l’érosion, en cas d’évolution de l’agressivité des agents pathogènes. L’objectif de ce travail basé sur le pathosystème peuplier – rouille du peuplier (Melampsora larici-populina) est d’évaluer le potentiel évolutif des caractères d’agressivité et morphologiques du parasite par des approches de génétique quantitative et d'identifier les bases génétiques par génétique d'association. Pour estimer la plasticité, l’héritabilité et les compromis évolutifs d’un ensemble de caractères quantitatifs, nous avons précisément mesuré leurs variations dans quatre populations contrastées du champignon. Nous avons montré que le volume des spores est un caractère héritable qui évolue rapidement. La quantité de mycélium in planta est aussi héritable mais très conservée car sous sélection stabilisante dans les populations étudiées. Le temps de latence, la taille des lésions et le taux de sporulation présentent une héritabilité faible, ce qui explique l’absence d’évolution observées au cours du temps pour ces trois caractères. Les caractères liés à la fonction de sporulation semblent être les plus plastiques le long d’un gradient de maturité foliaire. Cependant, l’absence de mise en évidence de compromis évolutifs ne nous a pas permis d’identifier des caractères d’agressivité qui seraient les meilleures cibles pour les résistances quantitatives chez le peuplier. Si aucune base génétique de ces caractères quantitatifs n’a été mise en évidence, nous avons localisé un locus d’avirulence potentiel (Avr7) sur lequel une caractérisation fonctionnelle est envisagée / To control plant pathogens, breeding resistant plants is the most cost-effective and ecological strategy. Quantitative resistances, which are based on complex plant mechanisms, are known to be exposed to erosion through an increase of pathogens aggressiveness. Through the study the poplar – poplar rust (Melampsora larici-populina) pathosystem, this work aims to estimate the evolutionary potential of aggressiveness and morphological traits using quantitative genetic approaches and to identify molecular bases through genome-wide association study. To estimate plasticity, heritability, and trade-offs for a set of quantitative traits, we precisely measured their variation in four contrasted pathogen populations. It appeared that spore volume is highly heritable and evolved rapidly. In planta mycelium quantity is also heritable but constant because of stabilizing selection occurring in the studied populations. Latent period, lesion size and sporulation rate exhibit low heritability, which explains the absence of evolution during the studied time period. Traits involved in the sporulating function seem to be the most plastic ones along a leaf maturity gradient. However, the lack of evidence of trade-offs did not allow us to identify aggressiveness traits that would be the best targets for the construction of durable resistance in poplar. No genetic underpinning has been found for quantitative traits, but we have identified a potential avirulence locus (Avr7), opening the way for its functional characterization

O fenótipo de caracteres complexos é o produto final da inter-relação entre genes, vias ontogenéticas e efeitos ambientais. A variação desses fatores não apenas influencia o fenótipo final, mas também como caracteres covariam e evoluem de forma integrada. A seleção natural pode influenciar a integração entre caracteres, levando a mudança de padrões de correlação ao longo do tempo. Assim, uma visão integrativa e dinâmica de fenótipos complexos é essencial para a compreensão da história evolutiva destas estruturas. Na tese atual investiguei a integração morfológica de caracteres cranianos em Caniformes sob duas perspectivas. Em uma primeira abordagem investiguei o padrão de integração morfológica das espécies a partir da comparação das variâncias e covariâncias dos caracteres. Os resultados evidenciam dois principais pontos. O primeiro é que houve uma considerável estabilidade na covariância entre caracteres ao longo de toda a história evolutiva de Carnivora, sugerindo a manutenção dos padrões de desenvolvimento no grupo como um todo. O segundo ponto é que, apesar desta estabilidade, espécies da família Canidae apresentam modificações em sua integração morfológica que os tornam mais similares entre si e mais dissimilares com os demais Carnivora. Essas diferenças estão relacionadas principalmente com caracteres da região facial, que apresentaram maior flexibilidade evolutiva, maiores correlações entre caracteres, e contêm uma maior proporção da variância em Canidae que nos demais Carnivora. Em uma segunda abordagem investiguei as propriedades estatísticas de dois testes baseados na teoria de genética quantitativa: o teste de regressão de autovalores e o teste de correlação de componentes principais (PCs). Estes testes avaliam a proporcionalidade entre padrões de covariância genética e entre-espécies como forma de testar a hipótese nula de deriva genética. Os resultados mostram que o uso de contrastes filogenéticos independentes (PIC) reduz erros do tipo I inflados, principalmente no caso do teste de correlação. Quando PIC são utilizados, o teste de correlação apresenta taxas de erro tipo I nominais para todos os números de espécies. Entretanto, a flutuação do número efetivo populacional (Ne) infla o erro tipo I deste testes. O teste de regressão, apesar de apresentar erro do tipo I inadequado para número de espécies baixo, é robusto a flutuações de Ne. A redução do número de PCs reduz o erro do tipo I a valores nominais à custa de uma redução no poder do teste. O poder de ambos os testes é similar nos diversos cenários avaliados, com uma leve tendência de maior poder para o teste de correlação em números amostrais mais baixos. Adicionalmente, as famílias de Caniformes foram utilizadas como estudo de caso para ambos testes. Os testes foram realizados com métodos paramétricos e não-paramétricos (simulações) e com e sem PIC. Houve rejeição de deriva para quase todas as famílias, com exceção de Mephitidae e Ursidae. Os testes de regressão baseados em simulações se mostraram consistentes com e sem o uso de PIC, apresentando intervalos de confiança menores que os testes paramétricos. Os resultados da presente tese abrem diversas possibilidades de investigação futura, tanto do ponto de vista empírico (em relação a modificações de Canidae e dos processos evolutivos deste grupo e de Ursidae e Mephitidae), assim como metodológicos (aprofundamento das investigações sobre as propriedades dos métodos para investigações macroevolutivas baseados em genética quantitativa) / The phenotype of complex characters is the end-product of the interrelations between genes, ontogenetic pathways and environmental effects. The variation in these factors influences not only the final phenotype, but also how characters covary and evolve in an integrated way. Natural selection can influence the interaction among characters, leading to changes in the patterns of integration. Therefore, a integrative and dynamic view of complex phenotypes is essential to the understanding of the evolutionary history of such structures. In the present thesis I investigated the morphological integration of cranial characters in Caniform species in two perspectives. In the first approach I investigated the pattern of morphological integration of the species through the comparison of character variances and covariances. The results of this investigation highlighted two points. The first is that there is considerable stability in the covariance among characters along the evolutionary history of Carnivora, suggesting the maintenance of ontogenetic pathways in the group. The second is that, despite this stability, Canidae species show changes in their morphological integration that make them more similar among each other and more different from the rest of Carnivora. These changes are related mainly to characters from the facial region, which showed a greater evolutionary flexibility, greater correlation among characters, and concentrate a greater proportion of the variance in Canidae than in the rest of Carnivora. In a second approach I evaluated the statistical properties of tests based on quantitative genetics theory: the test of regression of eigenvalues and the test of correlation of principal components (PCs). These tests investigate the proportionality between patterns of genetic and between-species covariance as a way to test the null hypothesis of genetic drift. The results show that the use of phylogenetic independent contrasts (PIC) reduces the inflated type I error, especially in the case of the correlation test. When PIC are employed, the correlation test shows nominal type I error rates for all species sample sizes. However, the oscillation of the effective population size (Ne) inflates type I error rates of these tests. The regression test, despite showing inadequate type I error rates at small species sample sizes, is robust to the oscillation of Ne. The reduction of the number of PCs reduces type I error rates to nominal values at the expense of statistical power. The power of both tests is similar under different scenarios evaluated, with a slight tendency of the correlation test to perform better at small number of species. Additionally, the Caniform families were used as case studies for both tests. Tests were performed using parametric and non-parametric (simulations) techniques, with and without PIC. The drift hypothesis was rejected for almost all families, with the exception of Mephitidae and Ursidae. The regression tests based on simulations were consistent with and without the use of PIC, showing narrower confidence intervals than the ones for parametric tests. The results of the present thesis open a wide range of future investigation opportunities, both from the empirical (relative to the differences in Canidae patterns of morphological integration or the evolutionary processes underlying Ursidae and Mephitidae diversification) and methodological (further investigations of the properties of the quantitative genetics-based tests for macroevolution) points of view