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.

In this thesis, I combined observational studies with field and greenhouse experiments to examine selection on life history traits and variation in tolerance and resistance against herbivores in natural populations of the annual herb Arabidopsis thaliana in its native range. I investigated (1) phenotypic selection on flowering time and plant size, (2) the effects of timing of germination on plant fitness, (3) the effect of leaf damage on seed production, and (4) correlations between resistance against a specialist and a generalist insect herbivore. In all three study populations, flowering time was negatively related to plant fitness, but in only one of the populations, significant selection on flowering time was detected when controlling for size prior to the flowering season. The results show that correlations between flowering time and plant fecundity may be confounded by variation in plant size prior to the reproductive season. A field experiment detected conflicting selection on germination time: Early germination was associated with low seedling survival, but also with large leaf rosette before winter and high survival and fecundity among established plants. The results suggest that low survival among early germinating seeds is the main force opposing the evolution of earlier germination, and that the optimal timing of germination should vary in space and time as a function of the relative strength of selection acting during different life-history stages. Experimental leaf damage demonstrated that tolerance to damage was lowest among vegetative plants early in the season, and highest among flowering plants later in the season. Given similar damage levels, leaf herbivores feeding on plants before flowering should thus exert stronger selection on defence traits than those feeding on plants during flowering. Resistance against larval feeding by the specialist Plutella xylostella was negatively correlated with resistance against larval feeding by the generalist Mamestra brassicae and with resistance against oviposition by P. xylostella when variation in resistance was examined within and among two Swedish and two Italian A. thaliana populations. The results suggest that negative correlations between resistance against different herbivores and different life-history stages of herbivores may contribute to the maintenance of genetic variation in resistance.

Population projection matrix (PPM) models are a central tool in ecology and evolution. They are widely used for devising population management practises for conservation, pest control, and harvesting. They are frequently employed in comparative analyses that seek to explain demographic patterns in natural populations. They are also a key tool in calculating measures of fitness for evolutionary studies. Yet, demographic analyses using projection matrices have, in some ways, failed to keep up with prevailing ecological paradigms. A common focus on long-term and equilibrium dynamics when analysing projection matrix models fits better with the outmoded view of ecosystems as stable and immutable. The more current view of ecosystems as dynamic and subject to constant extrinsic disturbances has bred new theoretical advances in the study of short-term "transient" dynamics. Transient dynamics can be very different to long-term trends, and given that ecological studies are often conducted over short timescales, they may be more relevant to research. This thesis focuses on the study of transient dynamics using population projection matrix models. The first section presents theoretical, methodological and computational advances in the study of transient dynamics. These are designed to enhance the predictive power of models, whilst keeping data requirements to a minimum, and borrow from the fields of engineering and systems control. Case studies in this section provide support for consideration of transient dynamics in population management. The second section applies some of these new methods to answer pertinent questions surrounding the ecology and evolution of transient dynamics in plants. Results show that transient dynamics exhibit patterns according to life form and phylogenetic history. Evidence suggests that this can be linked to the stage-structuring of life cycles, which opens up the possibility for new avenues of research considering the evolution of transient dynamics in nature.

Abstract A central goal in evolutionary biology is to identify the ecological and genetic mechanisms that give rise to adaptation and speciation. Importantly, a large body of theoretical work has modelled the adaptive evolution under selection, migration and drift. Yet to test these predictions on an empirical level has proven a challenging task. The aim of my thesis is to explore outstanding questions in local adaptation and reproductive isolation using natural populations of Arabidopsis lyrata: How does differential selection lead to adaptive divergence in the face of gene flow and drift? What traits underlie both short- and large-scale adaptive differentiation? And what reproductive barriers are involved in incipient speciation? By combining whole-genome based demography simulations with a multi-year reciprocal transplant experiment, I confirmed that alpine and lowland populations of A. lyrata are adapted to their local environments despite high gene flow and strong drift. Patterns of trait differentiation, supported by analysis of phenotypic selection, further suggested that flowering traits have contributed to the adaptive divergence. Selection patterns at the sequence level confirmed that the genetic architecture underlying the local adaptation conforms to theory: populations under higher levels of gene flow had fewer adaptive loci that were also found in areas of reduced recombination. Although most selection outliers were population specific, indicating conditional neutrality, a small proportion showed potential for genetic trade-offs (antagonistic pleiotropy). The analysis also revealed important traits and biological processes linked to alpine and lowland adaptation. The role of seed germination in large-scale adaptation and reproductive isolation was also studied. Populations representing the European and North American subspecies exhibited germination patterns consistent with adaptive differentiation. Comparisons against first- and second-generation hybrids then indicated that genetic incompatibilities impede germination of the hybrid seeds. Furthermore, genetic mapping helped to clarify the genetic basis of these phenotypic traits. Taken together, the three studies in this thesis highlight the value of combining traditional organismal methods with next-generation genomics, by providing novel insights into processes underlying adaptation and speciation. / Tiivistelmä Evoluutiobiologian keskeinen tehtävä on sopeutumiseen ja lajiutumiseen johtavien prosessien selvittäminen. Vaikka evoluutiovoimien – luonnonvalinnan, geenivirran ja geneettisen satunnaisajautumisen – vaikutusta adaptiivisen muuntelun määrään on mallinnettu laajalti, teoreettisten ennusteiden tarkastelu empiirisellä tasolla on usein osoittautunut haastavaksi. Tässä väitöskirjatyössä pyrin vastaamaan eräisiin paikallissopeutumisen ja lajiutumisen kannalta tärkeisiin kysymyksiin, hyödyntäen kasvilaji idänpitkäpalkoa (Arabidopsis lyrata) malliorganismina: Kuinka luonnonvalinta johtaa paikallissopeutumiseen tilanteessa, jossa geenivirta samankaltaistaa eriytyvien populaatioiden perimää? Mitkä ominaisuudet vaikuttavat adaptiiviseen erilaistumiseen eri etäisyyksillä olevien populaatioiden välillä? Sekä millaiset lisääntymisesteet johtavat alkavaan lajiutumiseen? Yhdistämällä genomisekvensointiin perustuvan demografia-analyysin ja monivuotisen siirtoistutuskokeen, selvitin kuinka idänpitkäpalkopopulaatiot ovat sopeutuneet elinympäristöihinsä runsaasta geenivirrasta ja voimakkaasta satunnaisajautumisesta huolimatta. Fenotyyppisen muuntelun ja kelpoisuuden yhteys vahvisti myös, että kukkimisominaisuudet ovat vaikuttaneet populaatioidenväliseen adaptiiviseen erilaistumiseen. Valinnan merkkien etsiminen sekvenssitasolla osoitti, että havaintoni paikallissopeutumisen geneettisestä arkkitehtuurista tukevat teoreettisia ennusteita: populaatioista, joihin kohdistuu voimakasta geenivirtaa, löytyi vähemmän adaptiivisia lokuksia ja ne olivat keskittyneet matalamman rekombinaation alueille. Suurin osa adaptiivisista lokuksista löytyi ainoastaan yhdestä populaatiosta, ollen näin todennäköisesti valinnan alla ainoastaan tietyssä elinympäristössä. Pieni osuus lokuksista vastasi kuitenkin harvoin havaittua tilannetta, jossa hajottava valinta on johtanut eri alleelien runsastumiseen populaatioissa, joita yhdistää geenivirta. Tutkin myös, miten itämisajan muuntelu vaikuttaa sopeutumiseen pitkällä aikavälillä. Eurooppalaista ja pohjoisamerikkalaista alalajia edustavat populaatiot itivät tavalla, joka viittaa adaptiiviseen erilaistumiseen. Ensimmäisen ja toisen hybridisukupolven siementen vertailu paljasti lisäksi, että geneettiset yhteensopimattomuudet haittaavat hybridien itämistä, toimien näin lisääntymisesteenä. Geenikartoitus auttoi myös selventämään näiden itämisominaisuuksien geneettistä taustaa. Tämän väitöskirjan kolme osatyötä korostavat miten perinteisten yhteiskenttäkokeiden ja uuden sukupolven genomimenetelmien yhdistelmä voi tuottaa arvokasta lisätietoa sopeutumisen ja lajiutumisen mekanismeista.

Cette thèse est divisée en deux parties reliées par un même fil conducteur. Elle porte sur l'étude théorique et l'application de modèles mathématiques décrivant des dynamiques de population où les individus se reproduisent et meurent à des taux dépendant de leur âge et d'un trait phénotypique. Le trait est fixé durant la vie de l'individu. Il est modifié au fil des générations par des mutations apparaissant lors de la reproduction. On modélise la sélection naturelle en introduisant un taux de mortalité densité-dépendant décrivant la compétition pour les ressources.Dans une première partie, nous nous intéressons au comportement en temps long d'une équation aux dérivées partielles de sélection-mutation structurée en âge décrivant une grande population d'individus. En étudiant les propriétés spectrales d'une famille d'opérateurs positifs sur un espace de mesures, nous montrons l'existence de mesures stationnaires pouvant admettre des masses de Dirac en les traits maximisant la fitness. Lorsque ces mesures admettent une densité continue, nous montrons la convergence des solutions vers cet (unique) état stationnaire.La seconde partie de cette thèse est motivée par un problème issu de la biologie du vieillissement. Nous voulons comprendre l'apparition et le maintien au cours de l'évolution d'un marqueur de sénescence observé chez l'espèce Drosophila melanogaster. Pour cela, nous introduisons un modèle individu-centré décrivant la dynamique d'une population structurée par l'âge et par le trait d'histoire de vie suivant : l'âge de fin de reproduction et celui où la mortalité devient non-nulle. Nous modélisons également l'effet Lansing, qui est l’effet suivant lequel « la descendance de parent jeune vit plus longtemps que celle de parents vieux » . Nous montrons, sous des hypothèses de grande population et de mutations rares, que l'évolution amène ces deux traits à coïncider. Pour cela, nous sommes amenés à étendre l'équation canonique de la dynamique adaptative à une situation où le gradient de fitness n'admet pas des propriétés de régularité suffisantes. L'évolution du trait n'est plus décrite par la trajectoire (unique) d'une équation différentielle ordinaire mais par un ensemble de trajectoires solutions d'une inclusion différentielle. / This thesis is divided into two parts connected by the same thread. It concerns the theoretical study and the application of mathematical models describing population dynamics. The individuals reproduce and die at rates which depend on age a and phenotypic trait. The trait is fixed duringthe life of the individual. It is modified over generations by mutations appearing during reproduction. Natural selection is modeled by introducing a density-dependent mortality rate describing competition for resources.In the first part, we study the long-term behavior of a selection-mutation partial differential equation with age structure describing such a large population. By studying the spectral properties of a family of positive operators on a measures space, we show the existence of stationary measures that can admit Dirac masses in traits maximizing fitness. When these measures admit a continuous density, we show the convergence of the solutions towards this (unique) stationary state.The second part of this thesis is motivated by a problem from the biology of aging. We want to understand the appearance and maintenance during evolution of a senescence marker observed in the species Drosophila melanogaster. For this, we introduce an individual-based model describing the dynamics of a population structured by age and by the following life history trait: the age of reproduction ending and the one where the mortality becomes non-zero. We also model the Lansing effect, which is the effect through which the “progeny of old parents do not live as long as those of young parents”. We show, under large population and rare mutation assumptions, that the evolution brings these two traits to coincide. For this, we are led to extend the canonical equation of adaptive dynamics to a situation where the fitness gradient does not admit sufficient regularity properties. The evolution of the trait is no longer described by the (unique) trajectory of an ordinary differential equation but by a set of trajectories solutions of a differential inclusion.