<p> Adaptive radiations offer unique insight into how diversification is initiated in novel or changing environments but the value of such studies is often limited by incomplete or lacking information on the ancestral species. The threespine stickleback species complex is proving to be particularly valuable in enhancing our understanding of evolutionary processes because there is reason to believe a surrogate for the ancestral group is extant and representative of the oceanic form that gave rise to most post-glacial freshwater populations during the last ~12,000 years. If we are to maximize the value of this radiation a thorough understanding of the putative ancestor group is needed. This dissertation explores the degree of phenotypic variation in oceanic stickleback in Cook Inlet, AK as well as the relative contributions of genetic and plastic aspects shaping the phenotypic variation revealed.</p><p> Geometric morphometrics were used to describe shape differences in two oceanic forms of stickleback, anadromous and fully marine. These groups differ in shape along the same benthic-limnetic axis described within the freshwater derived populations in the same region. A common-garden rearing study revealed high levels of body shape plasticity in both groups as well as likely genetic influences maintaining important aspects of shape differences between their stocks of origin. Interestingly, plasticity related to the salinity of early rearing environment differed across types suggesting that there may be a flexible dual stem in the threespine stickleback radiation, a surprising result that has not been considered to date in any system to my knowledge.</p><p> Additionally, because life-history traits are intimately linked to reproductive success and thus fitness, differences in life-history strategies between these two oceanic types should reflect meaningful adaptive variation, whether plastic or strictly genetic based. Established methodologies in stickleback life-history studies were employed to assess phenotypic variation across populations, types, and years in many important traits (e.g., egg and clutch size, reproductive effort, allometric relationships between reproductive effort and female body size). Life-history strategies differed significantly across type and year. Generally, marine females exhibit greater reproductive investment and have larger and more numerous eggs per clutch. Anadromous populations experience an apparent reproductive cost to the migration to freshwater relative to their fully-marine counterpart. It&rsquo;s unclear from these studies then where the fitness advantage to anadromy lies in the primitively oceanic species complex. However, important differences in mortality on the breeding grounds for adults and young as well as a possibly faster clutch production frequency in the anadromous lifestyle explains the apparent paradox in these data.</p><p> The finding of differences in genetic and plastic contributions to oceanic stickleback phenotypes body shape and life histories across two types in close geographic proximity which correlates with salinity regime suggest a flexible dual stem in the oceanic group(s). This could then influence evolution within the freshwater radiation. Thus, depending upon the freshwater populations (or watersheds) studied, the choice of representative oceanic type would need to be carefully considered. These data suggest that any near shore or inland sea areas within the stickleback oceanic distribution which experience a wide range of salinities is likely to show associated clinal variation in stickleback population reaction norms for (at least) body shape, life history strategies, and likely many other traits which are sensitive to salinity, such as genes involved in osmoregulation. Recent studies of Baltic and Sea of Japan oceanic stickleback further support this conclusion.</p>

<p> Species interactions can regulate a population&rsquo;s density and therefore can act as a selective force on that population. Such evolutionary responses have the potential to feedback and change ecological interactions between species. For species that compete for resources, the interaction between ecological and evolutionary dynamics will regulate the stability of the species interactions, determining whether competing species can coexist. The outcome of competition between species is determined by two factors: (1) niche overlap, or the similarity in how species use resources and are affected by their environment, and (2) fitness differences, or differences in how efficiently each species uses resources in their environment. Decreasing niche overlap will decrease competitive interactions, thereby stabilizing coexistence. Decreasing fitness differences makes species more equal in their competitive abilities, facilitating coexistence. In the absence of evolutionary constraints, both niche overlap and fitness differences among species are subject to change as a consequence of evolution among competitors, and thus ecological dynamics between two species will also change. In this dissertation, I develop a broader understanding of (1) how niche overlap and fitness differences between species change after evolution in response to competition, (2) how changes in niche overlap and fitness differences are mediated through changes in resource use of protists, and (3) what role evolutionary history plays in shaping ecological and evolutionary dynamics. </p><p> I address these goals with a suite of approaches including theoretical models, an experimental lab system, and comparative methods. I constructed a quantitative genetic model of trait evolution, where the trait of a species determined its resource use, and found that species are prone to change in their niche overlap as well as their fitness differences as a result of trait evolution. However, the magnitude of changes in niche overlap and fitness differences were determined by the resource availability within the environments. When resources were broadly available, species changed more in their niche overlap, whereas when resources were narrowly available, species changed more in their fitness difference. To test these predictions, I developed a system in the laboratory where protists competed for a bacterial resource. Species were allowed to evolve in either monoculture or a two-species mixture; the effects of evolution on competition, niche overlap and fitness differences were quantified using parameterized models. In general I found that species tended to converge in their niche as a result of evolution, however, changes in fitness differences between species were larger and more influential on coexistence than changes in niche differences. Both increases in niche overlap, and increases in fitness differences decreased coexistence among species pairs. By describing the bacterial communities associated with these protists before and after selection I determined that protists tended to converge or not change in which bacteria they were consuming as a result of selection. Additionally, for eleven protist species, I determined whether traits or relatedness predicted competitive ability by placing species on a molecular phylogeny and conducting pairwise competition experiments for all pairs. I found no correlations, suggesting neither traits, nor evolutionary history was informative for explaining current ecological and evolutionary interactions in this deeply divergent clade. </p><p> There are two major conclusions from this dissertation: (1) when species evolve in response to competition, changes in fitness differences may often be more important than changes in niche overlap, (2) evolution can, and may be likely to, decrease the ability of species to coexist through increases in niche overlap and increases in fitness differences. This work suggests that one must simultaneously consider the role of evolutionary and ecological processes to understand community processes. Specifically, when researchers are attempting to explain mechanisms of coexistence between species, they must consider how evolutionary dynamics may change the ecological interactions within communities of competitors.</p><p>

<p> One of the consequences of the development of landscapes for human uses is the release and accumulation of chemicals in the environment. The long-term effects of multigenerational exposure to this chemical pollution in wild populations are poorly understood. Both ecological and rapid evolutionary responses are likely, as both species and populations are known to vary in sensitivity to toxicant exposure. While we have observed frequent rapid evolutionary changes in wild populations, particularly in response to human impacts, we are only beginning to understand how important rapid evolution might be in shaping long-term ecological and evolutionary responses to environmental stressors such as chemical pollution. My dissertation uses freshwater zooplankton as a model to contribute to this knowledge gap, examining both ecological and evolutionary consequences of exposure to pollution stress across a variety of spatial and temporal scales. In chapter one I surveyed 51 small lakes in Connecticut, US to evaluate the relative importance of the lake physicochemical environment, habitat connectivity and broader spatial properties in shaping pelagic crustacean zooplankton communities. I found that the chemical environment, particularly dissolved ions, was far more important than space and connectivity in predicting zooplankton species distributions. This evidence suggests that for the most part in this system zooplankton dispersal is not limited and environmental filtering is playing a key role in the distribution of zooplankton species across the landscape. Chapters 2 through 4 examined long-term ecological and evolutionary changes in daphniid zooplankton taxa in four Connecticut lakes that have experienced differing degrees of pollution over the past century. Using paleolimnological techniques I reconstructed changes in eutrophication and heavy metal contamination in these lakes over time. Examination of daphniid diapausing egg banks deposited in sediments of these lakes uncovered evidence of taxonomic homogenization of the daphniid species over time in the three eutrophied lakes. I also found that eutrophication may have been more influential than metals in shaping species compositional patterns (chapter 2). Chapters 3 and 4 investigated phenotypic responses of <i>Daphnia ambigua</i> populations to heavy metal contamination. I found that <i>Daphnia</i> diapausing eggs from time periods when metal contamination was elevated were less likely to hatch and that those animals that did hatch had a higher rate of juvenile mortality (chapter 3). <i>Daphnia</i> hatched and successfully cultured from high copper and high cadmium time periods were more sensitive to exposure of these metals (chapter 4), a pattern consistent with rapid maladaptation to metals over multi-decadal timescales. Overall, my dissertation research uncovers widespread long-term effects of changes in lake chemical environments on both ecological and evolutionary trajectories of lake zooplankton communities. Future research into the drivers and consequences of these trends, particularly those observed in chapters 3 and 4, is warranted. It is important to understand, both for basic scientific and conservation purposes, whether exposure to widely distributed toxicants such as heavy metals is disrupting the evolutionary capacity of lake zooplankton, an important component to lake communities worldwide. </p>

<p> The unique nature of island ecosystems have fascinated generations of naturalists, ecologists, and evolutionary biologists. Studying island systems led to the development of keystone biological theories including: Darwin and Wallace's theories of natural selection, Carlquist's insights into the biology of adaptive radiations, MacArthur and Wilson's theory of island biogeography, and many others. Utilizing islands as natural laboratories allows us to discover the underlying fabric of ecology and evolutionary biology. This dissertation represents my attempt to contribute to this long and storied scientific history by thoroughly investigating two aspects of island biology: 1. the role of island climate in shaping drought tolerance of woody plants, and 2. the absence of mammalian herbivores from insular environments and its effects on woody plant defenses. </p><p> These goals were accomplished by quantifying functional trait patterns, seasonal water relations, and plant defenses among closely-related species pairs of chaparral shrubs from matched field sites on Santa Catalina Island and the adjacent Santa Ana Mountains in southern California. This experimental design allowed me to test for &#65532;repeated evolutionary divergences across island and mainland environments and to examine the evolutionary trade-offs between traits. </p><p> Chapter 1 focuses on differences in dry season water availability and hydraulic safety between island and mainland chaparral shrubs by measuring seasonal water relations and cavitation resistance. My results suggest that island plants are more buffered than mainland relatives from the harsh summer drought conditions that characterize the Mediterranean type climate region of California. Furthermore, island plants exhibit increased hydraulic safety margins that suggest island plants may fare better than mainland relatives during episodes of increasing aridity. </p><p> Chapter 2 examines an exhaustive suite of 12 functional traits that characterize the drought-related functional strategies of island and mainland chaparral shrubs. Island plants have more mesomorphic leaf and canopy traits than mainland relatives. However, stem hydraulic traits are surprisingly similar between the island and mainland environments despite large differences in seasonal water relations. The differences between patterns at the leaf and stem levels may be related to the existence of evolutionary correlations for leaf traits but not for stem traits. Multivariate principal component analyses suggest that island plants are employing a very different suite of functional traits than their mainland relatives that allows them to take advantage of the more moderate conditions that characterize the island environment without sacrificing increased vulnerability to drought at the stem level. </p><p> Chapter 3 tests the hypothesis that the absence of mammalian herbivores throughout most of Santa Catalina Island's history has selected for plants that are less defended and more palatable than mainland relatives that have experienced more consistent browsing pressure. My results confirm that island plants have fewer morphological defenses and are more preferred by mammalian herbivores compared to close relatives from the mainland. These findings also suggest that island plants are more vulnerable to browsing by introduced mammalian herbivores. This vulnerability should be taken into account when making management decisions concerning introduced herbivores on islands. </p><p> In conclusion, chaparral shrubs on Santa Catalina Island have different levels of drought tolerance and herbivore defenses compared to mainland relatives that affect how they are likely to be impacted by climate change and other anthropogenic alterations of the insular environment. Furthermore, the pattern of evolutionary divergences between island and mainland plants reported in this dissertation offer new insights into how drought tolerance and herbivore defenses are shaped by environmental factors. </p>

<p> Since at least the time of Darwin biologists have searched for a simple set of universal governing mechanisms that dictate the dynamics of biodiversity. While much progress has been made in understanding system-specific processes and in documenting the context-dependent roles of such mechanisms as competition and facilitation, we still lack a universal governing rule set. The goal of understanding and predicting biodiversity dynamics comes at a critical moment when human systems are disrupting those very dynamics. In this thesis I approach this long-standing problem with the hypothesis that general patterns in biodiversity emerge from a combination of the statistical mechanics of large systems and the unique non-equilibrium dynamics imparted to biological systems by their evolutionary history. Statistical mechanics provides the key analytical approaches to abstracting the complex details of biodiversity into general macroscopic predictions that I show receive support from empirical data. However, key deviations from the simplest statistical mechanics of biodiversity reveal the key role of biological evolution in driving systems away from the idealized steady state predicted by statistical mechanics. </p><p> In Chapter 1 I expand a branch of non-equilibrial statistical mechanics, known as super statistics, to explain previously unaccounted for wild fluctuations in the richness of taxa through the Phanerozoic marine invertebrate fossil record and show how this non-equilibrium is driven by clades' punctuated exploration of their adaptive landscapes. This theory provides a novel explanation for deep time diversity dynamics invoking emergence of lineage-level traits as the drivers of complexity via the same mechanisms by which complexity emerges in large physical and social systems. In the context of fossil diversity I show how this complexity arises naturally from the uniquely biological mechanisms of punctuated adaptive radiation followed by long durations of niche conservatism, and thus identify these mechanisms as sufficient and necessary to produce observed patterns in the fossil record. I test this theory using two seminal fossil datasets. </p><p> In Chapter 2 I use the chronosequence afforded by the Hawaiian Islands to capture evolutionary snapshots of arthropod communities at different ages and stages of assembly to understand how the history underlying an assemblage determine its contemporary biodiversity patterns. I apply static ecological theory of trophic networks based on statistical mechanics to these rapidly evolving ecosystems to highlight what about the evolutionary process drives communities away from statistical idealizations. This study indicates that rapid assembly from immigration and speciation in young ecosystems and extinction in old ecosystems could drive observed patterns. </p><p> In Chapter 3 I highlight and explain the computational requirements to testing one statistical theory of biodiversity&mdash;the Maximum Entropy Theory of Ecology&mdash;with real data and make those test available in a stream-lined framework via the R package meteR that I authored.</p>

<p> The study of contemporary evolution and eco-evolutionary dynamics is classically defined in terms of genetic evolution, but the actual suite of processes driving contemporary trait change is likely much more complex than often credited. This dissertation considers additional mechanisms of trait change that might be important to an emerging model system for study of contemporary evolution and eco-evolutionary dynamics. Specifically, the research focuses on phenotypically plastic and demographic trait variation in Eastern and Western Mosquitofish (<i>Gambusia affinis</i> and <i>G. holbrooki</i>) facing the major ecological gradient of predation risk. Plasticity experiments employed a common-garden rearing design to manipulate fish predator cues experienced by individuals, their parents, or their grandparents and in turn quantify reaction norms in mosquitofish size, shape, and behavior. The two species of mosquitofish showed divergent plastic responses in behavior, with the relatively bolder <i>G. holbrooki</i> becoming even bolder in response to predator cues. In contrast, males and females within species showed parallel behavioral responses. Despite strong sexual dimorphism, both sexes and both species showed parallel patterns of plasticity toward streamlining of body shape when exposed to predators. Interestingly, mosquitofish also showed evidence of transmitting predator cues across generations, where female <i>G. affinis</i> become shyer and more streamlined when their parents or grandparents experienced predators. In contrast, male <i>G. affinis</i> showed little evidence of transgenerational plasticity and appear to rely more heavily on their own experience. Another set of field surveys and experiments with <i>G. hoibrooki </i> considered the potential role of sexual dimorphism and demographic variation in sex ratios as another form of trait variation with possible community and ecosystem consequences. Natural population surveys revealed female-biased sex ratios and higher primary production in the absence of predators. Mesocosm experiments suggested males and females differed in dietary preferences and that both sex ratio and density influence community responses. Although these findings support a need to expand the current eco-evolutionary synthesis to mechanisms beyond just genetic evolution, they also support some general patterns in these mechanisms and ways in which they might work with evolution to produce an even more dynamic interaction of ecology and trait change in nature.</p>

<p> Natural selection, the driving force behind evolution, acts on individual phenotypes. Phenotypes are the result of an individual&rsquo;s genotype, but the development from genotype to phenotype is not always accurate and precise. Developmental instability (DI: random perturbations in the microenvironment during development) can result in a phenotype that misses its genetic target. In the current study I assert that developmental instability may itself be an evolvable trait. Here I present evidence for DI&rsquo;s heritability, selectability, and phenotypic variation in the form of empirical data and evidence from the literature from the years 2006 through 2016. Phenotypic variation contributed by DI was estimated using fluctuating asymmetry and was found to contribute up to 60% of the phenotypic variation in certain trait types. I suggest that selection against developmental instability in some traits may result in higher evolvabilities (i.e., rates of evolution) for those traits or for entire taxonomic groups.</p><p>

<p> Nutrient cycling plays a critical role in maintaining biodiversity and ecosystem services in agricultural, urban, and natural lands. However, across landscapes there is substantial unexplained heterogeneity in nutrient cycling. Classic thinking holds that abiotic factors are the source of this spatial heterogeneity with a secondary role of plant biomass. However, recent work suggests that higher trophic levels or variation in traits at the level of plant genotype may also play an important role in structuring nutrient environments. For instance, herbivores may indirectly create heterogeneity in cycling through the induction of chemical and structural changes in plants traits. Phenotypic plasticity due to anti-herbivore defense may then alter nutrient cycling rates by changing the microbial breakdown of plant litter inputs. Alternatively, variation among plant genotypes in the expression of these same traits may overwhelm the influence of phenotypic plasticity on soil processes. Both genetic and environmentally based changes in plant traits have separately been demonstrated to alter soil processes, but their interaction and the relative importance of these sources of variation across local landscapes is unknown.</p><p> I address this question by developing a plant trait-mediated, conceptual framework of nutrient cycling. I then evaluate this framework within an old-field ecosystem by focusing on the dominant plant species, <i>Solidago altissima </i>, and its dominant grasshopper herbivore, <i>Melanoplus femurrubrum </i>, using a combination of lab assays, a greenhouse pot experiment, a field mesocosm experiment, and field surveys. First, I demonstrate that goldenrod individuals exhibit both genotypic variation and phenotypic plasticity in plant defensive trait responses across a nutrient and herbivory gradient in the greenhouse. At low nutrient supply, genotypes tolerate herbivory (inducing plant physiological changes that decrease the negative impact on fitness) while at high nutrient supply, the same genotypes induce a resistance response detectable through lower herbivore growth rates. These environmentally mediated changes in plant trait expression then altered the ability of a common microbial community to decompose senesced litter harvested from the same plants. Induced resistance in the population of genotypes grown at high nutrient levels led to decreased litter decomposition of herbivore legacy litter. In contrast, at low nutrient supply, herbivore legacy litter decomposed more efficiently compared to control litter. This suggests that the interaction between herbivory and nutrient supply could cause context-dependent acceleration or deceleration of nutrient cycling. As a result, trait plasticity may mediate effects of multiple environmental conditions on ecosystem processes in this system.</p><p> I tested this hypothesis using a three-year, raised bed, field experiment examining the effect of plasticity and locally relevant genetic variation on ecosystem processes in a naturalistic setting. Genotype clone clusters were planted in homogenized soil in enclosed cages with varying nutrient supply and grasshopper herbivory. Again, I documented strong genetically and environmentally-based trait variation in plant allocation, growth, and leaf traits. I next explicitly linked these genetic and plastic functional trait changes to concurrent changes in a variety of soil processes (microbially available carbon, plant available nitrogen, nitrogen mineralization potential, and microbial biomass) and litter decomposition rates. Importantly, partitioning functional trait variation into genetic and environmental components improved explanatory power. I also documented potential differences in herbivore effects on "slow" vs. "fast" cycling in soil microbially available C pools. Within both experiments the magnitude of trait variation measured was similar to the variation expressed by individuals across a focal field.</p><p> Taken together, this dissertation demonstrates that plant genotype, herbivores, and nutrients can all modify litter decomposition and other soil processes within ecosystems through differential expression of plant functional traits. Due to the spatially clumped, clonal, and dominant nature of goldenrod, the genetic and herbivory-driven changes documented here could lead to a predictable mosaic of soil process rates across a single old field landscape. This work also highlights the complex interplay between genetically and environmentally-based trait variation in determining population and ecosystem processes within landscapes and improves our understanding of the often-overlooked indirect effects of plant/herbivore interactions on nutrient cycling It suggests that herbivores may shape not only the evolution of plant populations, but also the soil nutrient environment and microbial community in which plants live. This sets up the potential for eco-evolutionary feedbacks between plant defense expression and soil nutrient availability. More broadly, it suggests that biotic factors, in addition to abiotic ones, play a key role in determining local-scale soil nutrient availability patterns and should potentially be accounted for within ecosystem models. These results are particularly salient in a world where anthropogenic nitrogen inputs continue to rise and climate change is predicted to increase herbivory and thus plant defensive trait induction on landscapes. </p>