No / Numerous landscape genomic studies have identified single-nucleotide polymorphisms (SNPs) and genes potentially involved in local adaptation. Rarely, it has been explicitly evaluated whether these environmental associations also hold true beyond the populations studied. We tested whether putatively adaptive SNPs in Arabidopsis halleri (Brassicaceae), characterized in a previous study investigating local adaptation to a highly heterogeneous environment, show the same environmental associations in an independent, geographically enlarged set of 18 populations. We analysed new SNP data of 444 plants with the same methodology (partial Mantel tests, PMTs) as in the original study and additionally with a latent factor mixed model (LFMM) approach. Of the 74 candidate SNPs, 41% (PMTs) and 51% (LFMM) were associated with environmental factors in the independent data set. However, only 5% (PMTs) and 15% (LFMM) of the associations showed the same environment-allele relationships as in the original study. In total, we found 11 genes (31%) containing the same association in the original and independent data set. These can be considered prime candidate genes for environmental adaptation at a broader geographical scale. Our results suggest that selection pressures in highly heterogeneous alpine environments vary locally and signatures of selection are likely to be population-specific. Thus, genotype-by-environment interactions underlying adaptation are more heterogeneous and complex than is often assumed, which might represent a problem when testing for adaptation at specific loci.

No description available.

The spatial spread of populations is one of the most visible and fundamental processes in population and community ecology. Due to the potential negative impacts of spatial spread of invasive populations, there has been intensive research into understanding the drivers of ecological spread, predicting spatial dynamics, and finding management strategies that best constrain or control population expansion. However, understanding the spread of populations has proved to be a formidable task and our ability to accurately predict the spread of these populations has to date been limited. Microbial populations, during their spread across agar plate environments, can exhibit a wide array of spatial patterns, ranging from relatively circular patterns to highly irregular, fractal-like patterns. Work analysing these patterns of spread has mainly focused on the underlying mechanistic processes responsible for these patterns, with relatively little investigation into the ecological and evolutionary drivers of these patterns. With the increased recognition of the links between microbial and macrobial species, it is possible that many of the ecological/evolutionary mechanisms responsible for these patterns of spread at a microbial level extrapolate to the spatial spread of populations in general. Through an interdisciplinary approach, combining empirical, computational and analytical methods, the principal aim of this thesis was to investigate the ecological and evolutionary basis of microbial spatial dynamics. The first section of this thesis utilises the Pseudomonas microbial model system to show that the rate of microbial spatial spread across agar plate surfaces is affected by both intrinsic and extrinsic factors, thereby causing the exhibited rates of spread to deviate from the predictions made by the classical models in spatial ecology. We then show the spatial dynamics of microbial spread depends on important environmental factors, specifically environmental viscosity and food availability and that these spatial dynamics (particularly the shape of spread) has conflicting impacts on individual- and group-level fitness. From this, we used a geometric framework representing the frontier of a population, combined with an individual based model, to illustrate how individual-level competition along the leading edge of the population, driven by geometric factors and combined with simple life-history rules, can lead to patterns of population spread reminiscent of those produced by natural biofilms. The thesis finishes by establishing that the spatial pattern of spread is not seemingly amenable to artificial selection, although based on other results in this thesis, we believe it remains likely that the patterns of spatial spread and the strategies responsible for them have evolved over time and will continue to evolve. Combined, the results of this thesis show that the array of evolutionary factors not accounted for by the simple ecological models used to help manage invasive species will often cause these models to fail when attempting to accurately predict spatial spread.

Competition plays a fundamental role in structuring ecological communities, and is a particularly important interaction for sessile organisms such as plants (Goldberg & Fleetwood 1987; Tilman 1994). To mitigate the negative effects of competition on fitness, plants can alter their phenotypes and reproductive traits through plastic responses. For example, decreases in the red to far-red ratio of light signal the presence of competitors, inducing a suite of responses known as shade avoidance syndrome (Franklin 2008). My thesis examines the impact of the competitive environment on reproductive output, the phenotypes Impatiens capensis produce and natural selection acting on shade avoidance responses. I found that heterospecific competitors affect both the phenotypes of I. capensis, and selection on shade avoidance traits. I also found evidence of population differentiation in hypocotyl lengths and flowering time. My thesis elucidates the influence of competition on the evolution of phenotypic plasticity in Impatiens capensis.

Competition plays a fundamental role in structuring ecological communities, and is a particularly important interaction for sessile organisms such as plants (Goldberg & Fleetwood 1987; Tilman 1994). To mitigate the negative effects of competition on fitness, plants can alter their phenotypes and reproductive traits through plastic responses. For example, decreases in the red to far-red ratio of light signal the presence of competitors, inducing a suite of responses known as shade avoidance syndrome (Franklin 2008). My thesis examines the impact of the competitive environment on reproductive output, the phenotypes Impatiens capensis produce and natural selection acting on shade avoidance responses. I found that heterospecific competitors affect both the phenotypes of I. capensis, and selection on shade avoidance traits. I also found evidence of population differentiation in hypocotyl lengths and flowering time. My thesis elucidates the influence of competition on the evolution of phenotypic plasticity in Impatiens capensis.

As animals age, they are expected to invest successively more energy in reproduction as they have fewer subsequent chances to reproduce (the “restraint” hypothesis). Conversely, the oldest animals may show restraint in reproduction because even a small increase in energy expended during reproduction may lead to death. Alternatively, both young and very old animals may lack the ability to maintain high levels of energy expenditure (the “constraint” hypothesis), leading to reduced reproductive success. Many studies have observed an increase in reproductive success with age followed by a reduction at the end of life, but fewer studies have examined the proximate mechanisms, which provide a context for understanding ultimate causes. I examined over 30 behavioural and physiological metrics of aging in two species of free-living long-lived seabirds (thick-billed murres Uria lomvia and black-legged kittiwakes Rissa tridactyla) and a short-lived passerine (tree swallows Tachycineta bicolor). For all species, reproductive success was high at intermediate ages. In support of the “restraint” hypothesis, when birds were stressed glucocorticoid hormones, which direct energy away from reproduction and towards survival, were higher in young birds (swallows) and both young and very old birds (kittiwakes and murres). When birds were handicapped older birds expended more energy. When challenged exogenously, there was no change in hormone levels with age, implying that they were “choosing” to be restrained. Resting metabolic rate (RMR) declined linearly with age in both seabird species. T3, which I show is indicative of RMR in birds, also declined with age, demonstrating that the reduction in metabolism was strategic and not due to changing body composition. In contrast, daily energy expenditure in both seabird species during breeding was constant with age while antioxidant capacity became elevated during middle age, and further increased with age. Several measures of behavioural performance did not vary with age. I conclude that hormonal cues lead to greater investment in adult’s energy stores over its offspring’s energy reserves (restraint hypothesis) at the start of life. At the end of life, both hypotheses were supported; energy expenditure was constrained by senescence, leading to increased restraint in investing additionally in offspring.

With global climates changing rapidly, animals must adapt to new environmental conditions with altered weather and phenology. Key to adapting to these new conditions is adjusting the timing of reproduction to have offspring when the conditions are best to maximize growth and survival. Using a long-term dataset on a wild population of yellow-bellied marmots (Marmota flaviventer) at the Rocky Mountain Biological Laboratory (RMBL), we investigated how the timing of reproduction changed with changing spring conditions over the past 50 years. Marmots are hibernators with a four-month active season. It is thus crucial to reproduce early enough in the season to have time to prepare for hibernation, but not too early so as snow cover prevents access to food. Importantly, climate change in this area has increased spring temperatures by 5 °C and decreased spring snowpack by 50 cm over the past 50 years. This directional change in climate may have caused adaptation. Given that adaptation to environmental conditions could arise from either microevolution or phenotypic plasticity, we evaluated how female marmots adjust the timing of their reproduction and estimated the importance of both genetic variance and plasticity in the variation in this timing. We show that, within a year, the timing of reproduction is not as tightly linked to the date a female emerges from hibernation as previously thought. We report a positive effect of spring snowpack but not of spring temperature on the timing of reproduction. There is inter-individual variation in the timing of reproduction but not in its response to changing spring conditions. Genetic variance in the timing of reproduction is low, and heritability was 8%. Earlier pup emergence date increases the number and weighted proportion of pups surviving their first winter, indicative of directional selection on this trait. The same pattern is not found for litter size with no effect of pup emergence date on the number of pups born. Further, all three of these traits are not under stabilizing selection. Taken together, it seems that we should expect some changes in this population with changing climatic conditions, but because of plasticity and not due to natural selection. Further, future studies on the marmots should not operate under the assumption that females reproduce immediately following their emergence.

The study of archaeology within an ecological and evolutionary framework began with the study of changes in human subsistence through time. Within the last few decades archaeologists have expanded applications of evolutionary ecology (EE) beyond the dietary emphasis of the prey choice model toward increasingly complex and novel applications. The chapters in this dissertation provide several examples of this expansion, through novel examinations of the complex relationships between humans and their environment, as well as thoughtful examinations of social systems and non-subsistence related behavior through the prism of EE. Appendix A asks at what transport distance from a central place does big game become costly to procure relative to smaller local game? Results from this study show that big game is an economical choice at a one-way transport distance of over 100 km. These results are then used in Appendix B where isotope geochemistry is used to show both large and small game from Pueblo Bonito, Chaco Canyon were transported over 70 km to the Canyon. Without the results from Appendix A, one would be inclined to describe the long-distance transport of large game as a costly signal, when in fact it is an economical choice, particularly in a depressed or low productivity habitat. Appendix C, demonstrates the applicability of costly signaling theory to non-dietary artifacts, by showing how geochemically sourced non-local goods contain a variety of social meaning.

This study presents an analysis of the zooarchaeological remains from Klissoura Cave 1, a Middle Paleolithic through Mesolithic site in Peloponnese, Greece. Changes in subsistence patterns are evaluated across a long sequence (ca. 80,000-10,000 BP) against a backdrop of environmental change. Results are interpreted using models from evolutionary ecology, specifically prey choice, central place foraging, and patch choice models. Two major trends are apparent in the series. One is a decline in the exploitation of high-ranked ungulate species with an overall increase in lower-ranked small game animals. The second is an increase in low-ranked small, fast-fast moving animals (e.g., hares and partridges) at the expense of higher-ranked small, slow-moving animals (e.g., tortoises). These changes cannot be accounted for by environmental shifts alone, though shifts in ungulate diversity likely track the expansion and contraction of plant communities. The increase in use of low-ranked prey indicates human population growth and demographic pressure in southern Greece during the late Pleistocene and early Holocene. In addition to these overarching trends, there are changes in site use during the sequence. In the Middle Paleolithic, foragers used Klissoura Cave 1 more during the winter and overwhelmingly hunted prime-aged adult animals, maternal herds of fallow deer in particular. In the Upper Paleolithic and later periods, the site continued to be used during the winter, in addition to other times of year, but the mortality profiles reflect a natural fallow deer herd structure. There was an intense period of occupation during the Aurignacian period. This is evidenced by numerous clay-lined hearth features, a possible rock-lined structure, and increases in ornaments, as well as abundant lithic and faunal materials. The ungulate faunas are particularly rich during this period, but there is evidence of resource intensification based on increased bone marrow processing and the transport of marrow-rich elements to the site. After this period there was a gradual decline in site use through the end of the Upper Paleolithic and into the Mesolithic, though the exploitation of low-ranked resources (e.g., small, fast-moving game) indicates that populations were on the rise in there region as a whole.

Experiments with microbes are a powerful tool for addressing general questions in evolutionary ecology. Microbial evolution is also interesting in its own right, and often clinically relevant. I have used experimental evolution of bacteria (Pseudomonas spp.) in controlled laboratory environments to investigate the role of environmental heterogeneity in the evolution of phenotypic diversity. Some of my results provide insight on general processes, while others are specific to bacteria. (1) I have shown that variation in resource supply affects the evolution of niche breadth in complex environments containing a range of available resources, leading to a peak in phenotypic diversity at intermediate levels. (2) I have found that resource availability also affects selection against redundant phenotypic characters, which is strongest when resources are scarce. (3) Using experiments with bacteria and their protozoan predators, I have found that selection for predator resistance varies with resource supply during a model adaptive radiation. (4) I have looked at the role of periodic bottlenecks in population size in the evolution of antibiotic-resistant bacteria. My results highlight the importance of biochemical constraints specific to different resistance mutations. (5) Finally, I have shown that bacterial adaptation to novel carbon substrates affects different growth parameters simultaneously, and that the same response is seen in environments that maintain different levels of phenotypic diversity. These findings emphasize the role of environmental heterogeneity in the evolution of phenotypic diversity, but also show how ecological and genetic factors can constrain adaptation to a given niche within a heterogeneous environment.