abstract: Megafauna species worldwide have undergone dramatic declines since the end of the Pleistocene, twelve thousand years ago. In response, there have been numerous calls to increase conservation attention to these ecologically important species. However, introduced megafauna continue to be treated as pests. This thesis evaluates the extent of this conservation paradox in relation to changing megafauna diversity from the Pleistocene to the Anthropocene and finds that introductions have provided refuge for a substantial number threatened and endangered megafaunal species and has restored generic diversity levels per continent to levels closer to the Pleistocene than the Holocene. Furthermore, this thesis describes a previously unstudied behavior of wild burros (Equus asinus), an introduced megafauna whose pre-domestic ancestors are Critically Endangered. Wild burros dig wells to access groundwater and in doing so substantially increase water availability on several scales, create sites that are visited by numerous species and are comparable to natural water sources in terms of species richness, and provide germination nurseries for important riparian pioneer plant species. My results suggest that relaxing concepts of nativity in an age of extinction will provide new understandings of ecological function and can help focus attention on broader conservation goals. / Dissertation/Thesis / Appendix C / Appendix F / Masters Thesis Biology 2017

abstract: Quagga mussels are an aquatic invasive species capable of causing economic and ecological damage. Despite the quagga mussels’ ability to rapidly spread, two watersheds, the Salt River system and the Verde River system of Arizona, both had no quagga mussel detections for 8 years. The main factor thought to deter quagga mussels was the stratification of the two watersheds during the summer, resulting in high temperatures in the epilimnion and low dissolved oxygen in the hypolimnion. In 2015, Canyon Lake, a reservoir of the Salt River watershed, tested positive for quagga mussel veligers. In this study, I used Landsat 7 and Landsat 8 satellite data to determine if changes in the surface temperature have caused a change to the reservoir allowing quagga mussel contamination. I used a location in the center of the lake with a root mean squared error (RMSE) of 0.80 and a correlation coefficient (R^2) of 0.82, but I did not detect any significant variations in surface temperatures from recent years. I also measured 21 locations on Canyon Lake to determine if the locations in Canyon Lake were able to harbor quagga mussels. I found that summer stratification caused hypolimnion dissolved oxygen levels to drop well below the quagga mussel threshold of 2mg/L. Surface temperatures, however were not high enough throughout the lake to prevent quagga mussels from inhabiting the epilimnion. It is likely that a lack of substrate in the epilimnion have forced any quagga mussel inhabitants in Canyon Lake to specific locations that were not necessarily near the point of quagga veliger detection sampling. The research suggests that while Canyon Lake may have been difficult for quagga mussels to infest, once they become established in the proper locations, where they can survive through the summer, quagga mussels are likely to become more prevalent. / Dissertation/Thesis / Masters Thesis Civil, Environmental and Sustainable Engineering 2018

Master of Science / Department of Animal Sciences and Industry / K C Olson / We evaluated effects of annual, prescribed burning on vigor of the noxious weed, sericea lespedeza (Lespedeza cuneata; SL) in native tallgrass prairie over a 4-yr period. We hypothesized that annual prescribed burning conducted during the growing season would selectively pressure SL, whereas locally-conventional, dormant-season prescribed burning would have no effect on SL. A 50-ha native tallgrass pasture infested with SL (initial basal frequency = 2 ± 1.3%, initial aerial frequency = 36 ± 3.4%) was used for our study. It was divided along watershed boundaries into 9 fire-management units (5 ± 2.6 ha) for this experiment. Burn units were assigned randomly to 1 of 3 prescribed-burning times (n = 3 / treatment): early spring (1 April; EARLY), mid-summer (1 August; MID), or late summer (1 September; LATE). Forage biomass, SL aerial frequency, SL stem length, SL seed production, soil cover, and plant species composition were measured along single, permanent 100-m transects in each burn unit. Treatment and measurement date influenced forage biomass and SL stem length (treatment × time). Forage biomass was not different (P ≥ 0.43) between treatments on 17 July; however, forage biomass was greater (P < 0.01) in EARLY than MID and greater in MID than LATE on 10 October. Maximum stem length of SL was less (P ≤ 0.02) in MID and LATE than in EARLY on 17 July and on 10 October. Aerial frequency of SL was least (main effect – P < 0.01) in LATE, intermediate in MID, and greatest in EARLY, whereas basal frequency of SL was less (P < 0.01) in MID and LATE compared with EARLY. Whole-plant dry weight and seed production of SL at dormancy were greatly diminished (P ≤ 0.02) in MID and LATE compared with EARLY. Occurrence of bare soil, litter cover, and total basal plant cover were not different (P ≥ 0.21) between treatments. Similarly, basal cover of grasses, forbs, and shrubs were not different (P ≥ 0.24) between treatments. We interpreted these data to indicate that annual prescribed burning during the growing season had strong suppressive effects on SL compared to locally-conventional, early-season prescribed burning and produced no apparent detrimental effects on soil cover or non-target plant species. Post-fire regrowth was sufficient to prevent erosion and soil-moisture loss during the subsequent dormant season and would have allowed light to moderate grazing during the ensuing winter. Key words: Lespedeza cuneata, prescribed fire, range improvement

Precise descriptions and comprehensive taxonomies of species and their ecology are essential in monitoring changes in marine biodiversity at multiple spatial scales. A currently undescribed species of commensal amphipod in the genus Leucothoe is reported from New Zealand, collected from the endemic tunicate Cnemidocarpa bicornuta. This species differs from others in the genus in having a one-articulate first maxilla palp and an apically produced tuberculate lobe on the inner margin of the outer plate of the maxilliped. Previous taxonomic surveys in New Zealand waters did not document this species, indicating that it may be a recent arrival. This research highlights the importance of biodiversity monitoring and taxonomic surveys to record occurrences of undescribed or recently-arrived taxa.

Fire is a natural component of, and serves as a tool for, the restoration of forested ecosystems worldwide; however, disturbance due to fire also has been implicated in the proliferation of invasive species. How these fires affect occupancy and use of the forest by wildlife is of great concern, in particular, the differential response of non-native and native species. In the North American Southwest, prior to European settlement, frequent wildfires helped to maintain forest structure. We examined the effect of a large wildfire on an introduced population of the Abert's squirrel (Sciurus aberti) that has invaded the high elevation forests inhabited by the critically endangered Mt. Graham red squirrel (Tamiasciurus fremonti grahamensis). We found that introduced Abert's squirrels were more common than native red squirrels in burned areas. Abert's squirrels did not abandon burned areas but nested, foraged, and did not adjust their home range size in burned areas. This suggests that invasive Abert's squirrels are better able to exploit burned areas than native red squirrels and that fire can favor non-native species. This interaction between non-native species, native species, and fire adds new insight into the complexities of conservation and restoration of ecosystems and helps to inform conservation activities worldwide.

The emerald ash borer (EAB, Agrilus planipennis Fairmaire) (Coleoptera: Buprestidae) is a non-native wood boring beetle that is causing extensive ash (Fraxinus spp.) mortality in eastern North America, affecting both urban and wildland forests and drastically altering forest structure and composition. As EAB-induced ash mortality progresses, native arthropod associates of ash forests are impacted by the effects of rapid and broad scale tree mortality. These include loss of food source, increased canopy gap formation, alterations in litter inputs causing shifting temperature and moisture regimes on the forest floor, and significant accumulation of coarse woody debris. I assessed the sub-canopy arthropod community in five forests, all in different stages of the invasion process, from introduction through impact. Additionally, I assessed the ground level arthropod community in a post EAB-invaded forest with 100% mature ash mortality. Arthropod communities were assessed at the ordinal level, and with a focus on coleopterans, they were further classified to families and trophic guilds to analyze abundance, richness, and diversity. Due to their overwhelming abundance, I identified scolytines collected in the post EAB-invaded forest to species to see if the EAB-invasion was part of a greater invasional meltdown. My results indicate that the EAB-invasion in North America is affecting the native coleopteran communities associated with these forests.

Doctor of Philosophy / Department of Biology / Theodore J. Morgan / Natural populations are highly complex and consist of genetically variable individuals that belong to continuously varying age classes. Genotype and age interact to determine how individuals respond to environmental stress, which ultimately determines the evolutionary trajectories and persistence of populations in variable environments. For small ectothermic species, seasonal and diurnal variation in temperature is an important source of environmental stress that impacts activity patterns and suites of phenotypes directly related to whole organism fitness. I used the genetic and ecological model Drosophila melanogaster to investigate the influence of seasonal and diurnal thermal variability on survival and reproduction in genetically diverse populations. First, I characterized changes in cold tolerance and phenotypic plasticity within a natural population as it responded to seasonal shifts in developmental and short-term acclimation and thermal selection. I found that seasonal variation in cold tolerance was significantly influenced by developmental acclimation that occurred in the field as well as in the lab, where flies that developed under warmer conditions had reduced cold tolerance relative to flies that developed under cooler conditions. Second, I characterized the effect of variation in age on stress response phenotypes in a genetically variable population. I measured genotype- and age-specific responses to multiple environmental stressors, and identified regions of the genome that were associated with age-specific stress tolerance. Genome-wide association mapping revealed that age-specific phenotypes were influenced by distinct sets of polymorphisms and genes, suggesting that the evolution of age-related decline in phenotypes is driven by mutation accumulation within phenotypes, but both mutation accumulation and antagonistic pleiotropy between phenotypes. Next, I characterized the costs and benefits of acclimation for survival and reproduction to understand how physiological and behavioral plasticity interact to determine fitness. I found that phenotypic plasticity and the capacity for acclimation significantly influenced behavioral reproductive success, but the thermal cues that led to adaptive acclimation response in survival also led to decreased reproductive success. However, genotypes with the capacity to acclimate were more likely to survive thermal variation and more likely to reproduce, suggesting that genetic capacity for phenotypic plasticity has important implications for whole organism fitness. Finally, I measured the effect of acclimation on the induction of diapause and ability to survive cold stress in the recently introduced invasive species Drosophila suzukii. D. suzukii is endemic to Asia and was first detected in California in 2008 and in Topeka, KS in 2013. Its recent invasion history thus provides an interesting model to understand the role of plasiticy in the response to a novel and variable environment. I found that diapause was induced through a plastic response to acclimation and short photoperiod, though diapause was more drastically induced by acclimation. Overall, my research provides critical insights into how organisms respond to thermal variation by intergrating quantitative genetics, ecology, evolution, and life history tradeoffs. Collectively, my research demonstrates that the ability of organisms to survive thermal stress is a function of genetic capacity to tolerate stress, genetic capacity for phenotypic plasticity, prior exposure to thermal variation, and the age of the individual.

La diversité biologique constitue l’un des piliers du fonctionnement des écosystèmes, etun potentiel pour l’adaptation et l’évolution de la vie dans le contexte du changement climatique. Les espèces constituant cette biodiversité sont étroitement connectées de différentes façons. Une diminution de cette biodiversité peut déclencher des effets de cascade et des conséquences largement imprévisibles, bien au delà de la seule réduction apparente du nombre ou de la distribution des espèces. La grande complexité de l’organisation écologique est très souvent un cauchemar pour la prise de décision. Les difficultés commencent avec le choix d’une mesure adéquate de la biodiversité. Une telle mesure est cependant une étape nécessaire si nous voulons prioriser nos actions de gestion de la biodiversité, afin de préserver le plus de diversité possible avec des ressources limitées. Bien que cette thèse ne prétende pas produire des réponses complètes à ces problèmes complexes, elle offre quelques points de réflexion pour la gestion de la biodiversité.Elle se compose de quatre chapitres. Le premier chapitre soulève la question de la gestion d’une biodiversité mélangée, au sein de laquelle des espèces invasives peuvent également s’inviter. Ce chapitre souligne les interconnections entre la sévérité des impacts des invasions biologiques et le contexte dans lequel cette invasion intervient. Considérant les impacts des invasions comme “ambivalents” — i.e. pouvant être positifs, négatifs, ou neutres pour le système dans lequel l’invasion s’installe — nous proposons une typologie afin d’évaluer l’ambivalence des impacts, sur la base de l’identification des sources potentielles de variabilité des impacts. Pour le second chapitre, nous nous concentrons sur la mesure de la biodiversité lorsque l’on tient compte des interactions entre espèces, de façon à produire une version de la métaphore de l’Arche de Noé (Weitzman, 1998) mieux adaptée aux problèmes de conservation in situ. Nous montrons tout d’abord que, lorsque l’on tient compte d’interactions écologiques, le problème défini par Weitzman demeure une solution extrême ; et deuxièmement, qu’un renversement de la hiérarchie des espèces préservées est possible et entièrement déterminée par la catégorie des interactions. Dans le troisième chapitre, nous utilisons le cadre de coût-bénéfice in-situ développé dans le chapitre 2 afin de comparer les résultats de priorisation de deux indices de biodiversité, Weitzman et Rao. Ces deux indices combinent différemment l’information sur les probabilités autonomes de survie des espèces, les interactions écologiques et la dissimilitude entre espèces afin de mesurer la biodiversité. Nous analysons des plans simples de protection de la biodiversité pour chaque indice, et démêlons le rôle joué par les différents éléments d’information nécessaires au calcul du ranking par l’indicateur,dans un écosystème à trois espèces. Nous montrons que chaque indice réalise un compromis qui lui est propre entre ces éléments d’information, et que l’introduction d’interactions écologiques entre plus de deux espèces mène à des conclusions plus complexes. Les interactions écologiques donnent ainsi une information additionnelle importante afin de déterminer les objectifs de conservation. Notre dernier chapitre est une adaptation du cadre d’optimisation défini précédemment. Il élabore une règle de décision myope afin de déterminer quelles invasions doivent être contrôlées en priorité, en tenant compte des coûts de gestion relatifs et les impacts trophiques en cascade. Nous discutons le gradient de la fonction d’objectif composé d’une fonction de diversité W et d’une fonction d’utilité U, afin de déterminer si nous devrions conserver plusieurs ou seulement quelques espèces sous une contrainte de budget. / Biological diversity constitutes one of the major pattern of ecosystem functioning, and a potential for adaptation and evolution of life in the context of climate change. As species are in many ways tightly interconnected, biodiversity loss can trigger large cascade effects and might lead to largely unpredictable consequences, reaching far beyond the visible reduction in the number or distribution of species. The high complexity of ecological organization is often a nightmare for decision-making, starting from accurately measuring biodiversity. This is however a necessary step to take if we want to prioritize action in biodiversity management, in order to preserve as much diversity as possible under limited resources. Though this thesis does not pretend to provide complete answers to those quite complex issues, it provides some reflection points for biodiversity management. It is composed of four chapters. The first chapter raises the issue of dealing with a mixed biodiversity, in which invasive species can be guests. It highlights the interconnections between the severity of the impacts of biological invasions and the contexts in which this invasion occurs. Considering invasion impacts as inherently ''ambivalent'' - i.e. good, bad or neutral for the system in which it arrives - we propose a typology to assess ambivalence in impact, based on the identification of potential sources of impact variability. For the second chapter, we focus on the measurement of biodiversity when accounting for species interactions, which we incorporates into the Noah's Arch problem developed by Weitzman (1998). We then derive a general model for ranking in situ conservation projects. We show firstly that, when accounting for ecological interactions, the problem defined by Weitzman is still an extreme solution, and secondly, that a ranking reversal is possible and completely defined by the interaction categories. In the third chapter, we use the in situ cost-benefit framework developed in Chapter 2 to compare the outcomes of two biodiversity indices, Weitzman's and Rao's. Those two indexes combine information about species survival probability, ecological interaction and distinctiveness in a different way to measure biodiversity; We analyze simple biodiversity protection plans for each index, and disentangle the role played by the different data requirement in the rankings, in a three species ecosystem. We show that such pieces of information will come as a trade-off when considered simultaneously in the measure, and that the introduction of ecological interactions among more than two species lead to more complex conclusions. Ecological interactions thus give important additional information to determine conservation objectives. Our last chapter is an adaptation of the previously defined optimization framework for the prioritization of invasive species management. It elaborates a myopic rule to determine which invasions must be controlled in priority, taking into account relative management costs and trophic cascades impacts. We discuss the gradient of the objective function composed of a diversity function W and a utility function U, to see whether we should retain several or only a few species for management under a budget constraint.

Herbivory can have many effects on plant fitness, including altering plant-pollinator interactions and sexual reproduction in angiosperms. Pollinator-mediated interactions may be impacted when herbivores alter plant traits, such as floral display size, that can influence pollinator visitation rates, and, ultimately, the reproductive component of plant fitness. Here I describe an investigation into the indirect effects of feeding by beetles released as a biological control agent, Galerucella calmariensis and G. pusilla, on plant-pollinator interactions and reproductive output in the invasive plant Lythrum salicaria L. (purple loosestrife). During the summer of 2011, three treatments (low, ambient and mechanical herbivory) were applied to 105 plants during the pre-flowering period of growth. At the onset of flowering, a series of pollinator observations were conducted over the course of approximately 1.5 weeks. Several aspects of floral display were affected by the herbivory treatments, including increased inflorescence and flower production in the ambient and mechanical herbivory treatments, relative to the low herbivory treatment. Treatment type did not have a significant effect on the number of pollinator foraging bouts, but had marginally significant effects on the number of flowers probed per pollinator foraging bout and per 30-minutes. Moreover, treatment had a significant effect on the number of switches among the inflorescences on a single plant. I discuss the possibility that the differences in pollinator visitation were mediated by differences in the architecture and the size of floral display. There were no detectable differences in fruit or seed production (i.e., female fitness) among treatments. However, as I discuss, differences in pollinator visitation may affect other unmeasured aspects of fitness, such as the level of inbreeding or the number of seeds sired through male function.

The release of biological control agents into the environment is inherently risky: assessment of those risks through on-going, post-release monitoring is very important. Herbivores have the potential to inflict multiple impacts on a host plant’s performance and reproduction. Previous research demonstrates that the effects of herbivory on plants include changes to plant architecture, biomass allocation, flowering time and reproductive success, to list a few. Moreover, when herbivory significantly impacts the population ecology of a dominant community member, other species can be indirectly affected, ultimately influencing plant community ecology. Here I describe an investigation into the impacts of two introduced herbivorous biological control agents: the leaf beetle Galerucella calmariensis (Coleoptera: Chrysomelidae), and the flower-feeding weevil, Nanophyes marmoratus (Coleoptera: Brentidae) on several characteristics of the host plant species, invasive purple loosestrife (Lythrum salicaria), and its surrounding community. I collected data on 18 invaded communities from around eastern Ontario, including information on feeding damage and the density of each species of biological control, along with data on purple loosestrife’s height and biomass, inflorescence length, inflorescence number and fruit production. The history of each site’s colonization by Galerucella was also considered. I discovered that the density of both Galerucella and Nanophyes at a site was negatively associated with Lythrum fruit production. However, herbivore density was not significantly associated with Lythrum biomass, height or the species richness of the surrounding plant community. This study, conducted 20 years after the initial Ontario release of Galerucella, demonstrates that although vegetative traits of Lythrum do not appear to be significantly impacted by the presence of Galerucella or Nanophyes, reproductive traits are. Twenty years is likely too short a time period to adequately assess the impacts of the release on community species richness, although my data indicate that communities with smaller Lythrum plants tend to have higher species richness. This study covered a small geographical area and data collection was conducted for a single season only; adding additional years and/ or sites is recommended.