Herbivory by ungulates is a known agent of disturbance in many ecological systems around the globe. At high abundances and through a selective foraging behaviour herbivory may inflict significant direct and indirect effects on local plant and animal communities. Direct effects referto ungulates directly interacting with another species by foraging on plants and incidentally on insect eggs, larvae and/or adults. Indirect effects in this context describes ungulate feeding on plants which indirectly alters the availability and quality of food resources utilized by local insect fauna. Ungulates have even been considered as a potential conservation threat topersistence of some insect species. This aim of this thesis was to study the interaction between a common ungulate, the roe deer (Capreolus capreolus), and the rare butterfly Scolitantides orion by sharing the same plant resource, orpine (Hylotelephium telephium).  S. orion is a butterfly species of high conservation concern in Sweden. It is classified as endangered (EN) and has over the last decades experienced significant decrease in population size, mainly as a result of habitat loss and fragmentation. Roe deer has been considered as a potential threat to the population, but the magnitude of the threat has not been studied in detail. The objective of this thesis was to analyse the direct and indirect consequences of roe deer herbivory on S. orion population in the island of Mörtö, Stockholm archipelago. I predicted that roe deer alters the abundance of suitable host plants for oviposition and consumes egg and/or larvae, producing significant differences between protected and unprotected plants. The study was conducted in May-June 2020 in seven selected sites in Mörtö. At the onset of the butterfly season, 47 mesh cages were established sheltering 10.4% of the 1310 plants included in the study. Five inventories were conducted over a five-week time period, where each plant was examined by measuring the height, number of leaves, plant damage and the number of eggs and larvae. These data were used to examine the direct and indirect effect of roe deer foraging.  The results of this study could not confirm that roe deer has a significant direct or indirect effect on S. orion population in Mörtö. Hence, roe deer may not pose as large of a threat as initially expected, at least in this island at this time period. However, this was not the only result from this study. Plant properties such as leaf number and plant height (although not significant) as well as plant quality influenced the host choice for oviposition, with significantly more eggsbeing found on plants with more leaves and less plant damage. Hence, it seems that roe deer and other herbivores indirectly affects the host choice of S. orion by altering plant attractiveness. The reason for this behaviour needs to be studied in detail, but a proposed reason was that females choose plants with less damage to avoid competition and/or predation. Another finding was that a substantial number of eggs were lost over the season, some of which due to incidental feeding by roe deer and other herbivores. However, many eggs were lost without an identified reason, which likely is a result of disease or predators, but this needs to be studiedfurther. Finally, the cage experiment was successful in keeping the roe deer out but not able to cause a difference in egg survival between protected and unprotected plants. This was likely due to low roe deer herbivory in general.  Even though the effect of roe deer on S. orion population was not as significant as expected, it is still important to consider roe deer as a potential threat to the species at its most vulnerable stages as the species is dependent on the host plant for its survival. Hence, it would be interesting to do a similar experiment in a locality with higher deer density to further investigate the effect of roe deer on S. orion populations.

The cause and effect paradigm underlying medical research has led to an enhanced etiological understanding of many diseases and the development of many lifesaving drugs, but the paradigm does not always include an understanding of the pathways involved. Causal mediation analysis extends the cause and effect relationship to the cause and effect through a mediator, an intermediate variable on the causal pathway. The total effect of an exposure on an outcome is decomposed into two parts: 1) the indirect effect of the exposure on the outcome through the mediator and 2) the direct effect of the exposure on the outcome through all other pathways. In this dissertation, I describe various counterfactual causal mediation frameworks with identifiability assumptions that all lead to the Mediation Formula. The indirect and direct effects can be estimated from observable data using a semi-parametric algorithm derived from the Mediation Formula that I generalize to different types of mediators and outcomes. With an increased interest in causal mediation analysis, thoughtful consideration is necessary in the application of the Mediation Formula to real-world data challenges. Here, I consider three motivating causal mediation questions in the areas of HIV curative research and cardio-respiratory fitness. HIV curative treatments typically target the viral reservoir, cells infected with latent HIV. Quantifying the effect of an HIV curative treatment on viral rebound over a set time horizon mediated by reductions in the viral reservoir can inform future directions for improving curative treatments. In cardiorespiratory fitness research, metabolites, molecules involved with cellular respiration, are believed to mediate the effect of physical activity on cardiorespiratory fitness. I propose three novel adaptations to the semi-parametric estimation algorithm to address three data challenges: 1) Numerical integration and optimization of the observed data likelihood for mediators with an assay lower limit (left-censored mediators); 2) Pseudo-value approach for time-to-event outcomes on a restricted mean survival time scale; 3) Elastic net regression for high-dimensional mediators. My novel approaches provide estimation frameworks that can be applied to a broad spectrum of research questions. I provide simulation studies to assess the properties of the estimators and applications of the methodologies to the motivating data. / 2025-06-16T00:00:00Z

Frugivorous insects, specialised herbivores that consume fruit and seeds, are considered detrimental to host plant fitness. Their direct link to genetic fitness via consumption of plant reproductive tissue, and their negative socioeconomic association with agriculture exacerbates their harmful status. However, empirical testing of insect frugivore effects on host plants, and ecological research on the contribution of insect frugivores to multitrophic frugivory systems, is lacking. In the current study, direct effects of a non-mutualistic, insect frugivore/host plant system were tested and results showed variable effects. Beneficial, detrimental, but predominantly neutral effects on germination and seed production were observed between the Queensland fruit fly (Bactrocera tryoni) and tomato and capsicum plants. Significant effects on seed production were unexpected because infestation occurs after seed set. It was also found that eggplant, although a recorded host of B. tryoni, is inconsistent in its ability to sustain B. tryoni larvae through to its final instar. These results confirmed a simplification and presumption associated with insect frugivore (specifically fruit fly)/host plant interactions. Larval movement, infestation-induced fruit decay, pulp removal and germination were then investigated. For all hosts (tomato, apple and paw paw), treatments infested by B. tryoni decayed significantly quicker and to a greater extent than uninfested treatments, with obvious but variable changes to the texture and appearance. The movement of B. tryoni larvae, pattern of infestation-induced decay and pulp removal was unique and host dependent for all hosts. Only seeds from infested tomato were shown to germinate during the experiment. This indicated that host fruit characteristics are responsible, in part, for variable direct effects on host plant fitness by insect frugivores. Variable direct effects between insect frugivores and host plants, combined with the more rapid decay of infested fruits is likely to have implications for seed dispersal and seed predation by a third trophic level. The characteristics of fruit that are changed by infestation by an insect frugivore were then tested for their effect on a vertebrate frugivore, to illustrate the importance of recognising multitrophic interactions and indirect effects in frugivory. Specifically, seed predating rodents were incorporated into the study and their response to infested and uninfested fruits were recorded, as well as their reaction to the changes in fruit caused by insect frugivores (i.e. texture, smell, larvae presence and sound). Apple and pear infested with B. tryoni larvae were found to attract rodents, while infested tomato and paw paw had a neutral effect on the native rats. This differed from the predominant finding in the literature, which was a deterrent effect on avian seed dispersers. Vertebrate response to fruit infested with insect frugivores therefore, is variable. Assessing the indirect effect of insect frugivores on host plant fitness by attracting or deterring another trophic level requires knowledge of the direct effect between the introduced trophic level and the host plant. For example, the attraction of a seed predator may be as detrimental to host plant fitness as the deterrence of a seed disperser. This illustrates the complexity associated with assessing insect frugivore effects on host plant fitness. Results also indicated that differences in pulp texture, caused by infestation, have a significant effect on rodent preference for infested or uninfested treatments. Pulp texture is likely to effect rodent foraging efficiency, whereas the presence of B. tryoni larvae was observed to be inconsequential to rodent response to fruits. For rodents, and indeed any trophic level motivated by foraging efficiency, this finding raises the issue that for long lived fruiting plants, outside factors such as food abundance and competition for food, may cause a variable response to fruits infested by insect frugivores. From these investigations it has become apparent that insect frugivores are not consistently harmful to host plant fitness, as suggested by their negative stigma, but are likely to contribute variable effects, directly and indirectly, on multiple components of plant fitness and multitrophic frugivory systems.