Foxtail pine (Pinus balfouriana) is a subalpine conifer endemic to California, notably separated into two disjunct subspecies. Previous studies have described the northern subspecies,Pinus balfouriana subsp. balfouriana,as having an uncommonly high level of genetic differentiation and no discernible spatial patterns in phenotypic variation. This study seeks to characterize the spatial genetic structure and patterns of selection of the northern subspecies (Pinus balfouriana subsp. balfouriana) using genome-wide data and to identify the influence of ecology and environment on the unique genetic patterns. I show that genetic differentiation among populations is much less than previously estimated (FST= 0.000644) and there is weak isolation-by-distance structure, but ongoing gene flow is unlikely. Within populations, stand density and competitor effects contribute to inbreeding. I also show that previously measured traits are predominantly determined by genetics. Analyzing by sliding window in the genome, I show that connectivity patterns vary widely throughout the genome and identify several areas that are important to the genetic architecture of the phenotypic traits and plasticity (GxE). Overall, there is high connectivity, genetic similarity, and genetically based trait variation among and within populations of the northern subspecies of foxtail pine due to historical processes, despite biotic interactions driving inbreeding. Persistent genetic isolation, however, may make adaptation to future climate a challenge for the subspecies.

L’anthropométrie est le domaine scientifique qui étudie les dimensions du corps humain. La complexité de la morphologie du corps nécessite une analyse 3D, aujourd’hui permise par les progrès des scanners 3D. L’objectif de cette étude est de comparer les populations et utiliser les résultats pour mieux adapter les produits sportifs à la morphologie des utilisateurs. Des campagnes de mensuration 3D ont été réalisées et des algorithmes de traitement automatique ont été créés pour analyser les nuages de points des sujets scannés. Basés sur les méthodes d’images et de géométrie, ces algorithmes repèrent des points anatomiques, calculent des mesures 1D, alignent les sujets scannés et créent des modèles anthropométriques 3D représentatifs des populations. Pour analyser les caractéristiques anthropométriques, des statistiques de premier ordre et factorielles ont été adaptées pour être utilisées dans l’espace 3D. Les méthodes ont été appliquées à trois parties : le pied, la tête et la poitrine. Les différences morphologiques entre les populations, mais également au sein d’une population donnée, ont été révélées. Par exemple, la différence à chaque point de la tête entre des têtes a été calculée. Les statistiques en trois dimensions ont aussi permis de mettre en évidence l’asymétrie de la tête. La méthode de création de modèles anthropométriques est plus adaptée à nos applications que les méthodes dans la littérature. L’analyse en trois dimensions permet d’obtenir des résultats qui ne sont pas visibles par les analyses 1D. Les connaissances acquises par cette étude sont utilisées pour la conception de différents produits vendus dans les magasins DECATHLON à travers le monde. / Anthropometry is the scientific field that studies human body dimensions (from the greek άνθρωπος (human) + μέτρον (measure)). Anthropometrical analysis is based actually on 1D measurements (head circumference, length, etc). However, the body’s morphological complexity requires 3D analysis. This is possible due to recent progress of 3D scanners. The objective of this study is to compare population’s anthropometry and use results to adapt sporting goods to user’s morphology. For this purpose, 3D worldwide measurement campaigns were realized and automated treatment algorithms were created in order to analyze the subjects’ point cloud. Based on image processing methods and on shape geometry, these algorithms detect anatomical landmarks, calculate 1D measurements, align subjects and create representative anthropometrical 3D models. In order to analyze morphological characteristics, different statistical methods including components’ analysis, were adapted for use in 3D space. The methods were applied in three body parts: the foot, the head and the bust. The morphological differences between and inside the populations were studied. For example, the difference in each point of the head, between Chinese and European head, was calculated. The statistics in three dimensions, permitted also to show the asymmetry of the head. The method to create anthropometrical models is more adapted to our applications than the methods used in the literature. The analysis in three dimensions, can give results that they are not visible from 1D analyses. The knowledge of this thesis is used for the conception of different products that they are sold in DECATHLON stores around the world.

Despite long-term study, the mechanism explaining the parapatric distribution of two Australian reptile ticks species, Bothriocroton hydrosauri and Amblyomma limbatum, is not understood. This project aimed to use molecular genetic data to investigate aspects of the population biology of these two tick species, such as population structure and dispersal, to gain further insights into the cause and maintenance of this parapatric boundary. I developed and subsequently tested for Mendelian inheritance a suite of B. hydrosauri and A. limbatum species-specific microsatellites markers. Pedigree analysis showed one B. hydrosauri locus and all of the A. limbatum loci to be inherited in a non-Mendelian manner. Thus I could not investigate A. limbatum population structure and focused solely on B. hydrosauri. The first part of this study tested predictions of a model formulated to explain B. hydrosauri transmission dynamics. The “ripple” model, based on detailed ecological and behavioural data on B. hydrosauri and Tiliqua rugosa, B. hydrosauri’s most common host, predicts higher relatedness among larvae than among nymphs or adults on a host, and significant spatial autocorrelation in larvae extending further than for the later life stages. The model also predicts that adult ticks are likely to encounter related partners and that this will generate inbreeding within the population. I tested those predictions using nine microsatellite loci on a sample of 848 ticks (464 larvae, 140 nymphs and 244 adults) collected from 98 T. rugosa hosts at the northern edge of B. hydrosauri’s distribution range. My data did support all of the predictions of the “ripple” model and indicated that the dynamics of transmission among hosts play an important role in parasite population structure. The second part of this project focused on investigating the population genetic structure of B. hydrosauri at the edge of its geographic range and testing the predictions of a population model derived to explain B. hydrosauri’s parapatric boundary with A. limbatum. The “ridge and trough” model suggested the tick population was organised spatially into a series of “ridges” where tick density was high and “troughs” where it was low. Genetically, the expectation was to find clusters of more closely related individuals associated with the ridges. Cluster analysis of microsatellite allele frequencies and analysis of molecular variance of mitochondrial haplotype frequencies revealed the presence of four genetic clusters within a sample of 244 B. hydrosauri adults. As the highly genetically divergent clusters had overlapping distributions, and in some cases were syntopic, the genetic population structure predicted for these ticks by the “ridge and trough” model was not observed. Several explanations were considered for the observed B. hydrosauri genetic population structure, but syntopy of the clusters suggested that assortative mating is the most likely. I speculated that the clusters have formed in allopatry, when the environment was extremely heterogeneous, such that the ticks (and their hosts) were confined to isolated patches of high-quality habitat. Given sufficient time, this could have resulted in reproductive incompatibility between ticks occupying different patches. The population structure I uncovered indicates subsequent secondary recontact of divergent groups. Although my study allowed for a better understanding of B. hydrosauri biology and population structure, the reasons for the parapatric distributions of B. hydrosauri and A. limbatum are still unclear. Further research should focus on investigating the population genetic structure of A. limbatum at the edge of its range, as well as on performing a larger-scale study of B. hydrosauri population genetic structure and a more detailed investigation of the applicability of the “ridge and trough” model to this tick species. Moreover, it will be useful to inspect the population structure of both these species within the centers of their ranges and compare these findings with population structure found at the edge of the range.

Population structure, gene flow and dispersal are some of the most commonly estimated population parameters in population genetics, evolutionary biology and conservation genetics. The primary aim of thesis is to test the precision and accuracy of genetic estimates of population structure, gene flow and dispersal. The controlled replicated Drosophila melanogaster experiments of known effective population size (Ne = 14.3) and dispersal rate (m = 0.0025 - 0.04) all adhered to Wright??s demographic island model. Three statistical approaches were empirically tested: 1) the conversion of population structure to gene flow using FST, RST, SHUA and PhiST ; 2) the private alleles method to estimate gene flow; 3) a Bayesian assignment method to estimate dispersal (BAYESASS 1.2). Even in the best-case scenario, almost all current methods except SHUA significantly underestimate population structure, and consequently overestimate gene flow and dispersal when applied to real populations. It was crucial to ensure that the manipulated rate of gene flow was correctly defined. This led to three supporting investigations of hybrid performance, inversion polymorphisms and effective population size. The hybrid performance investigation demonstrated that the manipulated rate of gene flow had not been unexpectedly inflated by hybrid vigour or reduced by breakdown. These experiments also demonstrated that close inbreeding is not a necessary precondition for hybrid vigour or breakdown, which is important for conservation strategies involving induced dispersal. The investigation of inversion polymorphisms ensured that the manipulated rate of gene flow was not affected by selection on inverted regions. The effective population size investigation used a temporal estimation method to confirm that the Ne was accurately predicted by an N:Ne ratio of 0.286. Additionally this experiment showed that the single-sample estimation methods implemented by ONeSAMP or LDNE resulted in downwardly biased estimates of Ne in structured populations. In conclusion these results call into question the confidence that biologists may have in some of the most widely used molecular tools in conservation biology.

Processes that influence the early life stages of fishes can significantly impact population dynamics, yet they continue to be poorly understood. This dissertation examined relationships between the environment, early life history traits (ELHTs), behavior, and post-settlement survival for a coral reef fish, Stegastes partitus, in the upper Florida Keys, to elucidate how they influence juvenile demography. Otolith analysis of settlers and recruits coupled with environmental data revealed that S. partitus surviving the early juvenile period settled at larger sizes and grew slower post-settlement. Water temperature also influenced the ranges of these and other ELHTs as well as the intensity and direction of selective mortality processes acting on some of these traits (i.e., pelagic larval duration, mean larval growth). Otolith analysis was paired with behavioral observations of newly settled juvenile S. partitus in the field to reveal that the relationship between size-at-settlement, early juvenile growth and survival is behaviorally-mediated. Individuals that were larger at settlement were more active (i.e., spent less time sheltered, swam farther from shelters) and grew more slowly post-settlement. Likewise, slower juvenile growth was associated with greater activity, more conspecific aggression, and faster escape swimming speeds. A six-year time series of recruitment densities revealed substantial temporal (interannual, seasonal, lunar) and spatial (by microhabitat, conspecific density) variability in recruitment which influenced the composition of recruits. For instance, larvae settling during the darkest phases of the moon were larger at settlement, but selective mortality processes during brighter periods removed more of the smallest settlers, resulting in juveniles with similar sizes-at-settlement regardless of when they arrived to the reef. Because recruitment strength and composition varied temporally, genetic markers (6 microsatellite and 1 mitochondrial loci) were used to determine if the genetic composition of monthly cohorts of settling larvae and juveniles also varies interannually, monthly, or across life stages. A lack of genetic structure suggested that S. partitus has a large effective population size and variation in ELHTs is not likely the result of successful spawning of a disproportionately small group of adults. As a whole, these results reveal processes associated with larval supply and post-settlement life that collectively shape juvenile demography.

Near the beginning of the last century, R. A. Fisher and Sewall Wright devised an elegant, mathematically tractable model of gene reproduction and replacement that laid the foundation for contemporary population genetics. The Wright-Fisher model and its extensions have given biologists powerful tools of statistical inference that enabled the quantification of genetic drift and selection. Given the utility of these tools, we often forget that their model - for reasons of mathematical tractability - makes assumptions that are violated in many real-world populations. In particular, the classical models assume fixed population sizes, held constant by (unspecified) sampling mechanisms. Here, we consider an alternative framework that merges Moran’s continuous time Markov chain model of allele frequencies in haploid populations of fixed size with the density dependent models of ecological competition of Lotka, Volterra, Gause, and Kolmogorov. This allows for haploid populations of stochastically varying – but bounded – size. Populations are kept finite by resource limitation. We show the existence of limits that naturally generalize the weak and strong selection regimes of classical population genetics, which allow the calculation of fixation times and probabilities, as well as the long-term stationary allele frequency distribution.

University of Macau / Faculty of Social Sciences and Humanities / Department of Government and Public Administration

Texte remanié de: Thèse de doctorat--Histoire contemporaine--Paris 4, 2002. Titre de soutenance : Société et démographie dans le sud de l'Allier au XIXe siècle : Bellenaves et Ébreuil, deux bourgs en Médioromanie bourbonnaise. / Bibliogr. p. 463-472. Notes bibliogr.

Texte constitué d'une partie de: Tesis--Universidad de Cádiz. / Bibliogr. p. 169-190.

Thèse d'État--Lettres--Clermont-Ferrand, 1946. / Bibliogr. p. 507-519. CRÉER = Centre de réalisations, d'études et d'éditions régionales.