Selection in spatially heterogeneous environments is a convenient explanation for the high levels of genetic variation observed in natural populations. Indeed, theoretical studies predict that spatial heterogeneity leads to higher levels of variation in a variety of selection models. These models, however, have assumed quite restrictive parameters (e.g., two alleles, fixed gene flow and specific selection schemes). Therefore, the effect on spatial heterogeneity is still poorly understood for a wider range of parameters (e.g., multiple alleles, different levels of gene flow and more general selection schemes). We have relaxed some of the assumptions that have limited the previous models and studied the effect of spatial heterogeneity using simple single-locus viability selection models. First, we investigate the rarity of the parts of fitness space maintaining variation for multiple alleles and different levels of gene flow by randomly sampling that space using a "fitness space" approach. The volume of fitness space maintaining variation is always larger in a spatial model compared to a single-population model regardless of gene flow. Moreover, this volume is relatively larger for higher numbers of alleles, indicating that spatial heterogeneity is more efficient maintaining higher levels of variation. Second, we investigate the ease with which a more natural process of recurrent mutation and selection evolves to the particular area of fitness space maintaining variation using a "construction" approach. Depending on the amount of gene flow, the construction approach leads to both higher and lower levels of variation compared to a single-population model. Thus, spatial heterogeneity can both constrain and promote the ease with which a natural process of mutation and selection evolves to maintain variation. Also, the construction approach results in variation being maintained in a more stable subset of the volume of fitness space than the volume that resulted from the fitness space approach. Third, we investigate the effect of higher and lower levels of spatial environmental heterogeneity using the construction approach. The different levels of heterogeneity and gene flow interact to influence the amount of variation that is eventually maintained and this interaction effect is especially strong for intermediate levels of gene flow. More heterogeneous environments can maintain higher levels of variation, but selection in these environments also results in a higher level of migration load, lowering the final amount of adaptation that is achieved by the simulated evolutionary process. Finally, we investigate effect of genetic drift and finite populations using the construction approach. Interestingly, two different effects emerge for smaller and larger populations; in smaller populations genetic drift lowers the amount of variation as expected, whereas, more surprisingly, genetic drift increases the amount of variation in larger populations. Overall, spatial heterogeneity has profound effects on the outcome of selection, resulting in elevated levels of genetic variation for a wide variety of parameters.

Improving our understanding of the forces driving population decline and the processes that affect the dynamics of threatened populations is central to the success of conservation management. The application of genetic tools, including our ability to examine ancient DNA, has now revolutionised our ability to investigate these processes. The recent human settlement of the Pacific, particularly in New Zealand, provides a unique, accessible system for revealing anthropogenic impacts on native biota. In this thesis I use genetic analyses from modern, historic and subfossil DNA to investigate temporal and spatial genetic structuring of the endangered yellow-eyed penguin (Megadyptes antipodes), and use these analyses to answer questions related to the conservation of this species. The yellow-eyed penguin is endemic to the New Zealand region and currently breeds on the subantarctic Auckland and Campbell Islands and the southeast coast of the South Island. The current total population size is estimated around 6000-7000 individuals, of which more than 60% inhabit the subantarctic. Despite intensive conservation measures by governmental and local community agencies, population sizes have remained highly unstable with strong fluctuations in numbers on the South Island. The species was believed to be more widespread and abundant before human colonisation of New Zealand, thus current management assumed the mainland population to be a declining remnant of a larger prehistoric population. Genetic and morphological analyses of subfossil, historic and modern penguin samples revealed an unexpected pattern of penguin extinction and expansion. Only in the last few hundred years did M. antipodes expand its range from the subantarctic to the New Zealand mainland. This range expansion was apparently facilitated by the extinction of M. antipodes' previously unrecognised sister species, M. waitaha, following Polynesian settlement in New Zealand. The demise of M. waitaha is the only known human-mediated extinction of a penguin species. Despite M. antipodes' recent range expansion, genetic analyses of microsatellite markers reveal two genetically and geographically distinct assemblages: South Island versus subantarctic populations. We detected only two first generation migrants that had dispersed from the subantarctic to the South Island, suggesting a migration rate of less than 2%. Moreover, the South Island population has low genetic variability compared to the subantarctic population. Temporal genetic analyses of historic and modern penguin specimens further revealed that the harmonic mean effective population size of the M. antipodes South Island population is low (<200). These findings suggest that the South Island population was founded by only a small number of individuals, and that subsequent levels of gene flow have remained low. Finally, we present a novel approach to detect errors in historic museum specimen data in cases where a priori suspicion is absent. Museum specimens provide an invaluable resource for biological research, but the scientific value of specimens is compromised by the presence of errors in collection data. Using individual-based genetic analysis of contemporary and historic microsatellite data we detected eight yellow-eyed penguin specimens with what appear to be fraudulently labelled collection locations. This finding suggests errors in locality data may be more common than previously suspected, and serves as a warning to all who use archive specimens to invest time in the verification of specimen data. Overall, yellow-eyed penguins have a remarkable dynamic history of recent expansion, which has resulted in two demographically independent populations. These results reveal that anthropogenic impacts may be far more complex than previously appreciated.

<p>Although evolution results from differential reproduction and survival at the level of the individual, most research in evolutionary genetics is concerned with comparisons made at the level of divergent populations or species. This is particularly true in work focused on the evolutionary genetics of natural populations. While this level of inquiry is extremely valuable, in order to develop a complete understanding of the evolutionary process we also need to understand how traits evolve within populations, on the level of differences between individuals, and in the context of natural ecological and environmental variation. A major difficulty confronting such work stems from the difficulty of assessing interindividual phenotypic variation and its sources within natural populations. This level of inquiry is, however, the main focus for many long-term field studies. Here, I take advantage of one such field study, centered on the wild baboon population of the Amboseli basin, Kenya, to investigate the possibilities for integrating functional, population, and evolutionary genetic approaches with behavioral, ecological, and environmental data. First, I describe patterns of hybridization and admixture in the Amboseli population, a potentially important component of population structure. Second, I combine field sampling, laboratory measurements of gene expression, and a computational approach to examine the possibility of using allele-specific gene expression as a tool to study functional regulatory variation in natural populations. Finally, I outline an example of how these and other methods can be used to understand the relationship between genetic variation and naturally occurring infection by a malaria-like parasite, Hepatocystis, also in the Amboseli baboons. The results of this work emphasize that developing genetic approaches for nonmodel genetic systems is becoming increasingly feasible, thus opening the door to pursuing such studies in behavioral and ecological model systems that provide a broader framework for genetic results. Integrating behavioral, ecological, and genetic perspectives will allow us to better appreciate the interplay between these different factors, and thus achieve a better understanding of the raw material upon which selection acts.</p> / Dissertation

<p>What evolutionary processes and ecological patterns underlie the maintenance of asexual reproduction in natural populations? Although a vast body of literature offers theory to explain the existence of sexual and asexual reproduction, there has been little study of these forms of reproduction in the natural environment. In this dissertation I use a combination of field experiments, greenhouse studies, and genetic techniques to answer this question in the model plant system Boechera. </p><p>In Chapter 1, I review the utility of this system for studying ecological and evolutionary questions in general. Boechera offers an array of genetic and genomic tools, facilitated in part by a close evolutionary relationship with the model plant Arabidopsis thaliana, as well as undisturbed ecology and habitat that extends across much of North America. Additionally, the presence of apomixis (asexual reproduction via parthenogenetic formation of seeds) at the diploid level makes Boechera an ideal system for studying sex without the often-confounding factor of polyploidy; Boechera is one of very few plant groups in which this is possible. </p><p>In Chapter 2, I use a combination of microsatellite markers, flow cytometry, chromosome squashes, and morphological work to characterize apomixis, polyploidy, and species diversity in over 100 natural populations collected from central Idaho and western Montana. As in many other apomictic systems, I find that apomixis in Boechera is strongly linked to hybridization between species or between genetically divergent intraspecific lineages. I then explore associations between apomixis and ecological and topographical variables, as well as variables underlying differentiation between apomictic and sexual lineages. I find that ecological variables associated with apomixis are largely in congruence with the hypothesis of geographic parthenogenesis, and that geographic parthenogenesis is likely driven by the consequences of interspecific hybridization. We also find that apomixis is linked with disturbance and slope, with apomicts occurring in flatter locations than sexuals. </p><p>In Chapter 3, I use a large-scale field experiment comprising three years of data from two cohorts of sexual and asexual lineages to compare fitness between these two groups. I find that, despite herbivory levels that are much higher in apomicts than sexuals, apomictic fitness is consistently higher than sexual. Viability selection strongly favors apomicts, which results in a total fitness advantage for apomicts, despite variable fecundity selection. Selection varies in intensity between cohorts and among gardens. The results of a complementary greenhouse experiment show that the effects of herbivory differ by reproductive mode. Together, these experiments suggest that Red Queen dynamics may contribute to the coexistence of sex and asex in this group.</p><p>In Chapter 4, I use inter- and intraspecific F2 crosses to conduct a greenhouse study and a field experiment to explore the effects of hybridization and heterozygosity on fitness. I find that heterozygosity is favored in the field, with viability selection strongly favoring outcrossed over inbred lineages. However, hybridization results in lower survival, reproduction, and total fitness of interspecific F2 crosses, although hybrids that do reproduce produce more fruits than selfed parental lineages of both species, resulting in fecundity selection for hybrids. It is clear that the benefits of apomixis are due to hybridization, as hybrids are less fit overall. Evidence for both heterosis and outbreeding depression, dependent on lineage and on trait, are found in the field; these phenomena are not clearly associated with geographic distance between parental populations. Ongoing SNP genotyping will facilitate assessment of heterozygosity-fitness correlations as well as correlation of fitness and heterozygosity.</p> / Dissertation

Androphilia refers to sexual attraction and arousal to adult males, whereas gynephilia refers to sexual attraction and arousal to adult females. Prehistoric artifacts such as art and pottery indicate that male-male same sex behaviour has existed for millennia. Bearing this in mind, and considering that male androphilia has a genetic component yet androphilic males reproduce at a fraction of the rate than do gynephilic males, how the genes for male androphilia have been maintained in the population presents an evolutionary puzzle. This thesis tests two hypotheses that attempt to address this Darwinian paradox. Chapter one reviews the current literature on the kin selection hypothesis and the sexually antagonistic gene hypothesis. In addition, rationales for testing these hypotheses in Canada are provided. Chapter two tests the kin selection hypothesis for male androphilia within a Canadian population. Results and implications are discussed. Chapter three tests the sexually antagonistic gene hypothesis within a Canadian population. Results and implications are discussed. Chapter four summarizes the results of the two studies and discusses how these findings may be interpreted from an evolutionary perspective. The impacts of gene-environment interaction on the functional behavioral expression of traits are emphasized. / viii, 113 leaves ; 29 cm

Thesis (Ph.D.)--McMaster University, 2006. / Supervisor: Jianping Xu). Includes bibliographical references.

Thesis (M.Sc.). / Written for the Dept. of Biology. Title from title page of PDF (viewed 2008/01/16). Includes bibliographical references.

Thesis (M. S.)--Chemistry and Biochemistry, Georgia Institute of Technology, 2008. / Committee Chair: Hud, Nicholas V.; Committee Member: Fox, Ronald F.; Committee Member: Lynn, David G.; Committee Member: Powers, James C.; Committee Member: Wartell, Roger M.; Committee Member: Williams, Loren D.

Thesis (Ph. D.)--University of Chicago, Committee on Genetics, March 2003. / Includes bibliographical references. Also available on the Internet.

Thesis (Ph. D.)--West Virginia University, 2006. / Title from document title page. Document formatted into pages; contains vi, 143 p. : ill. (some col.). Vita. Includes abstract. Includes bibliographical references.