The past fifteen years have seen a revolution in human population genetics. We have gone from anecdotal genetic data from a few individuals at a few genetic loci to an avalanche of genome-wide sequencing data, from many individuals in many different human populations. These new data have opened up many new directions of research in human population genetics. In this work, I explore two such directions. Genomic data have uncovered that recent changes in human population size have had dramatic effects of on the genomes of different human populations. These effects have raised the question of whether historic changes in population size have led to differences in the burden of deleterious mutations, or mutation load, between different human populations. In Chapter 1 of this thesis, I show that despite earlier arguments to the contrary only minor differences in load are expected and indeed observed between Africans and Europeans. Over the past decade, genome-wide association studies (GWAS) have begun to systematically identify the genetic variants underlying heritable variation in quantitative traits. The number, frequencies and effect sizes of these variants reflect the selection, and other evolutionary processes, acting on traits. In Chapter 2, I develop a model for traits under pleiotropic, stabilizing selection, relate the model’s predictions to GWAS findings, and show that GWAS findings for height and BMI indeed follow model predictions. In Chapter 3, I develop a method to infer the distribution of selection coefficients acting on genome-wide significant associations made by GWAS.

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Southwest Louisiana Creoles underwent great change between World Wars I and II as they confronted American culture, people, and norms. This work examines that cultural transformation, paying particular attention to the processes of cultural assimilation and resistance to the introduction and imposition of American social values and its southern racial corollary: Jim Crow. As this work makes clear, the transition to American identity transmuted the cultural foundations of French- and Creole-speaking Creole communities. World War I signalled early transformative changes and over the next three decades, the region saw the introduction of English language, new industries, an increasing number of Protestant denominations, and the forceful imposition of racialized identities and racial segregation. Assimilation and cultural resistance characterized the Creole response, but by 1945, southwest Louisiana more closely resembled much of the American South. Creole leaders in churches, schools, and the tourism industry offered divergent reactions; some elite Creoles began looking to Francophone Canada for whitened ethnic identity support while others turned toward the Catholic establishment in Baltimore, Maryland to bolster their faith. Creoles were not the only distinct community to undergo Americanization, but Louisiana Creoles were singular in their response. As this study makes clear – in ways no historian has previously documented – Louisiana Creoles bifurcated as a result of Americanization. This study also contributes to, and broadens, the literature on Acadian identity. Previously, scholars simply assumed that whitened Latins in Louisiana had always identified with Acadia and their black-racialized brethren with Haiti. This thesis, however, suggests that Cajun and Creole are not opposites. Rather, they derive from the same people and culture, and their perceived and articulated difference emerged in response to Americanization. Through a critical analysis of that bifurcation process, this thesis demonstrates how Acadianized identity and culture emerged in the first half of the 20th century.

This thesis explores the stochastic features of models of ecological systems in discrete and in continuous time. Our interest lies in models formulated at the microscale, from which a mesoscopic description can be derived. The stochasticity present in the models, constructed in this way, is intrinsic to the systems under consideration and stems from their finite size. We start by exploring a susceptible-infectious-recovered model for epidemic spread on a network. We are interested in the case where the connectivity, or degree, of the individuals is characterised by a very broad, or heterogeneous, distribution, and in the effects of stochasticity on the dynamics, which may depart wildly from that of a homogeneous population. The model at the mesoscale corresponds to a system of stochastic differential equations with a very large number of degrees of freedom which can be reduced to a two-dimensional model in its deterministic limit. We show how this reduction can be carried over to the stochastic case by exploiting a time-scale separation in the deterministic system and carrying out a fast-variable elimination. We use simulations to show that the temporal behaviour of the epidemic obtained from the reduced stochastic model yields reasonably good agreement with the microscopic model under the condition that the maximum allowed degree that individuals can have is not too close to the population size. This is illustrated using time series, phase diagrams and the distribution of epidemic sizes. The general mesoscopic theory used in continuous-time models has only very recently been developed for discrete-time systems in one variable. Here, we explore this one-dimensional theory and find that, in contrast to the continuous-time case, large jumps can occur between successive iterates of the process, and this translates at the mesoscale into the need for specifying `boundary' conditions everywhere outside of the system. We discuss these and how to implement them in the stochastic difference equation in order to obtain results which are consistent with the microscopic model. We then extend the theoretical framework to make it applicable to systems containing an arbitrary number of degrees of freedom. In addition, we extend a number of analytical results from the one-dimensional stochastic difference equation to arbitrary dimension, for the distribution of fluctuations around fixed points, cycles and quasi-periodic attractors of the corresponding deterministic map. We also derive new expressions, describing the autocorrelation functions of the fluctuations, as well as their power spectrum. From the latter, we characterise the appearance of noise-induced oscillations in systems of dimension greater than one, which have been previously observed in continuous-time systems and are known as quasi-cycles. Finally, we explore the ability of intrinsic noise to induce chaotic behaviour in the system for parameter values for which the deterministic map presents a non-chaotic attractor; we find that this is possible for periodic, but not for quasi-periodic, states.

The systematic relationship of two species of the Peromyscus truei group (P. truei and P. difficilis) was analysed through the application of starch gel electrophoresis, numerical taxonomy, and chromosomal techiques. Of 20 loci examined, 11 were monomorphic in all populations, two exhibited variation in only two populations, and seven loci were polymorphic in two or more populations. The mean number of polymorphic loci per population was 0.186, the mean number of polymorphic loci per individual was 0.024, and the proportion of loci heterozygous per individual was 2.4%. Chromosomal forms of P. truei, P. t. gentilis (FN 54) and P. t. truei (FN 62), and P. difficilis, P. d. petricola (FN 56) and P. d. nasutus (FN 58), were consistent for their karyotypes throughout their geographic ranges. No chromosomal hybrids were detected. Numerical analysis of morphological characters and similarity values based on allelic frequencies utilizing Roger's coefficient (S) demonstrated a distinct seperation of karyotypic forms of P. truei (S = 0.902) and P. difficilis (S = 0.924) and were below the mean value of S for conspecifics (S = 0.950). All data indicates that each chromosomal form of the P. truei group examined represents four distinct species. The oldest available name for chromosomal forms of P. true with a fundamental number of 62 is Peromyscus truei Shufeldt (1885) and the oldest available name for chromosomal forms with a fundamental number of 54 is Peromyscus gratus Merriam (1898). The oldest available name for chromosomal forms of P. difficils with a fundamental number of 58 is PeromYSCus nasutus Allen (1891) and the oldest available name for chromosomal forms with a fundamental number of 56 is Peromyscus difficilis Allen (1891).

Xu Jiawu. / "March 2005." / Thesis (Ph.D.)--Chinese University of Hong Kong, 2005. / Includes bibliographical references (p. 103-120) / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Mode of access: World Wide Web. / Abstracts in English and Chinese.

Horizontal gene transfer (HGT) and gene loss are important processes in the evolution of prokaryotic lineages. HGT involves the movement of genetic material between distantly related species, and can facilitate adaptation when gained genes confer advantageous phenotypes to recipient lineages. However, high levels of gene gain and loss are predicted to obfuscate patterns of vertical descent and homogenise nucleotide diversity across ecological and phylogenetic boundaries. Thus, a holistic understanding of the role of genome fluctuation in the emergence and maintenance of genetically and ecologically cohesive bacterial groups remains to be fully elucidated. In this thesis, I use the plant-associated bacterium Pseudomonas syringae as a model system to investigate the impact of HGT and gene loss on evolutionary processes such as adaptation, diversification and speciation. The Gram-negative Gammaproteobacterium P. syringae is an opportunistic plant pathogen, and has been used for decades as a model system with which to study the interaction between plants and their microbial pathogens. Recently, the diversification of lineages within this species has involved a number of host jumps onto a range of woody host plant species, resulting in the emergence of diseases such as bacterial canker of kiwi and bleeding canker of the European horse chestnut. Using whole-genome sequence data and a range of comparative genomics and phylogenetics methods, I quantitatively reconstruct the history of gene gain and loss in P. syringae and show HGT to be the predominant evolutionary force in this species. Genomes of this species are under constant permutation, are subject to a highly diverse HGT genepool and show marked differences in patterns of codon usage between imported and core genes. I then generate additional genome data for 26 strains of P. syringae that are pathogenic on a range of different woody plants, and investigate the contribution from HGT to the adaptation of these strains into the woody niche. Using a method that accounts for the underlying phylogenetic relationships among P. syringae strains, I look for the correlated evolution between gained genes and the woody niche, and find that a substantial proportion of the genome is associated with this ecological niche. I then investigate the recent adapitation of P. syringae pv. aesculi onto the European horse chestnut, and show that a number of genomic events that include both homologous and non-homologous recombination are likely to have led to the evolution of this bacterium onto its host, where it has become the causal agent of the bleeding canker disease that is currently epidemic across much of northern and central Europe. Overall, this thesis is an investigation into how HGT contributes to niche adaptation in P. syringae, and aims to further our understanding of the mechanisms that underlie bacterial evolution.

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The thesis examines the migration decision-making and everyday experiences of young highly skilled professional migrants through the case study of German migration to the UK. It develops a framework combining the twin notions of transnational urbanism and translocal subjectivities, allowing a strong focus on migrants' subjective experiences, perceptions and emotionalities of mobility, while acknowledging the centrality of spaces and places for them. The geographical setting of the case study further serves to accentuate the relatively small-scale disruption occurring during the migration process, and the subjectivities connected to this. Data was collected in the UK (mainly London) during thirteen months of fieldwork, using participant observation, in-depth interviews and expert interviews. The research reveals a previously unacknowledged high ambivalence and diversity of this migrant group. Young German highly skilled migrants display various mobility and migration patterns with regard to the translocal connections they maintain, the emotional importance they attach to these connections, and their previous internal and international migration history. Three mobility types emerge from this: 'bi-local', 'multi-local' and 'settled' migrants. The close translocal connections practiced by migrants can lead to conflict, particularly for bi-local migrants, as judging of the migration project can occur by friends and families; meaning the spatial and emotional proximity between the migrants and their social network can be both positive and negative. The expectations towards the UK are also highly complex, and strongly influence micro-scale personal geographies. Lastly, the diversity of migration projects leads to widely varying attitudes towards fellow German migrants, as well as tensions and potentially conflicts within German social spaces. Overall, a strong and pervasive ambivalence about the migration experience emerges, which is experienced differently by the three migrant groups and the geographical proximity between Germany and the UK plays a large role in this. This thesis adds empirical and analytical insight to the academic debate regarding young professional migrants within the EU, and German contemporary migration in particular. Theoretically, it contributes to the discussion around lifestyle migration and middling transnationalism, and it enhances the practical use of the concept 'emotional geographies' for migration studies.