Appendix A. Sensitivity analysis for fixed strategy management programs.

Sensitivity analysis for fixed strategy management programs

Proportions of unhealthy and hydroid-colonized branches

Proportions of unhealthy and hydroid-colonized branches for every coral colony at MC 294, MC 297 and MC 344

Post-overwintering response to microsite characteristics.

*<p>indicates significance of p≤0.05.</p>**<p>indicates significance of p≤0.01.</p>***<p>indicates significance of p≤0.001.</p><p>Generalized linear mixed-effects models were fit, using likelihood ratio tests to determine whether model fit was improved by including interactions. Where higher order interactions were present (such as analyses of germination for <i>C. nutans),</i> separate models were fit on clipped and fully disturbed plots. Larger microsite area generally led to increased survival and flowering probabilities. Full disturbance led to higher proportions flowering for <i>C. nutans</i>. Watering typically had no significant effect; in one case, it had a negative impact on <i>C. acanthoides.</i></p

Effect of microsite area and type of disturbance on rosette size in fall.

<p>Panels a and b show that rosettes were larger in larger microsites for both species in the fall (darker blue indicates full disturbance, lighter bars indicate clipped areas). For <i>Carduus acanthoides,</i> rosettes are larger in fully disturbed plots.</p

Effect of microsite area on fall emergence and survival of <i>Carduus nutans</i> and <i>C. acanthoides.</i>

<p>Panels a and b show the combined emergence and survival response for <i>C. nutans</i> and <i>C. acanthoides</i> (darker blue indicates full disturbance, lighter bars indicate clipped areas). Emergence and survival are generally higher in larger microsites. For <i>C. acanthoides,</i> performance was better in fully disturbed microsites. <i>Carduus nutans</i> did better in larger clipped microsites but smaller fully disturbed microsites.</p

Logistical constraints lead to an intermediate optimum in outbreak response vaccination

<div><p>Dynamic models in disease ecology have historically evaluated vaccination strategies under the assumption that they are implemented homogeneously in space and time. However, this approach fails to formally account for operational and logistical constraints inherent in the distribution of vaccination to the population at risk. Thus, feedback between the dynamic processes of vaccine distribution and transmission might be overlooked. Here, we present a spatially explicit, stochastic Susceptible-Infected-Recovered-Vaccinated model that highlights the density-dependence and spatial constraints of various diffusive strategies of vaccination during an outbreak. The model integrates an agent-based process of disease spread with a partial differential process of vaccination deployment. We characterize the vaccination response in terms of a diffusion rate that describes the distribution of vaccination to the population at risk from a central location. This generates an explicit trade-off between slow diffusion, which concentrates effort near the central location, and fast diffusion, which spreads a fixed vaccination effort thinly over a large area. We use stochastic simulation to identify the optimum vaccination diffusion rate as a function of population density, interaction scale, transmissibility, and vaccine intensity. Our results show that, conditional on a timely response, the optimal strategy for minimizing outbreak size is to distribute vaccination resource at an intermediate rate: fast enough to outpace the epidemic, but slow enough to achieve local herd immunity. If the response is delayed, however, the optimal strategy for minimizing outbreak size changes to a rapidly diffusive distribution of vaccination effort. The latter may also result in significantly larger outbreaks, thus suggesting a benefit of allocating resources to timely outbreak detection and response.</p></div

Transition values for healthy branches (2011-2015)

All values were estimated from digitized images of individual coral colonies. Abbreviations: Coral (individual colony identifier), Total (total number of branches), Total nv (total number of healthy branches), nv_to_nv, nv_to_nh, nv_to_hy (number of healthy branches that transitioned to healthy, unhealthy or hydroid-colonized, respectively, Impact (total visible impact proportion), Size (total coral size (m)), Site, Year (imaging year)

Appendix A. The response in the number of flower heads produced to total planting density and the proportion of other species present in the Seedling Placement Experiment.

The response in the number of flower heads produced to total planting density and the proportion of other species present in the Seedling Placement Experiment

Coral size in 2011

Size (m) of every coral colony at MC 294, MC 297 and MC 344

The response of the proportion of thistles present to microsite size.

<p>Both species were more likely to flower in larger microsites (darker blue indicates full disturbance, lighter bars indicate clipped areas). For <i>C. acanthoides</i>, the effect of disturbance type is not significant. No <i>C. acanthoides</i> individuals flowered in clipped 225 cm² microsites.</p