Microbial infection of eggs was originally investigated in terms of human health only. Recently, however, it was found that it can also cause early embryo mortality in birds, mainly through trans-shell infection prior to incubation. Trans-shell infection is highly dependent upon environmental conditions, egg temperature and egg properties such as shell quality and antimicrobial defences. Microbial infection of eggs is more likely to occur in synchronously incubating species as first laid eggs can be exposed for up to several days prior to full incubation. One example of a population that seems at particular risk of egg microbial infection is New Zealand’s little blue penguin (Eudyptula minor) from Tiritiri Matangi Island. This bird lays two eggs on average three days apart, and is believed to begin full incubation only after the second egg has been laid. Both eggs are laid in particularly humid and soiled nests and contain only low levels of lysozyme, an important antimicrobial protein. The aims of this study were therefore to 1) obtain a first examination of the rates of shell and trans-shell microbial infection of chicken eggs in New Zealand and assess the effects of cleaning on those rates, 2) investigate the role of microbes in hatching failure of little blue penguin eggs and 3) investigate other factors affecting little blue penguin egg viability. This study revealed that shell infection in chicken eggs significantly increased with exposure and significantly decreased with cleaning; however, trans-shell infection was only marginally affected by exposure and cleaning. On Tiritiri Matangi Island, Hauraki Gulf, New Zealand, nest type, egg order and shell cleaning did not affect hatching success, suggesting that nest conditions and microbial infection prior to incubation were not a major cause of egg mortality in this population. Temporary abandonment during incubation, however, was very frequent in the second half of the breeding season and fatal to most eggs. These temporary abandonments seemed to be caused by resource limitations, an aspect that should be investigated in future studies.

Wind is the second largest renewable energy source after solar. It is one of the fastest growing sources of electricity in the world and currently of wind energy is installed in the United States and an additional is under construction (Office of Energy and Environment Affairs, 2011). For the growth of wind electricity, one of the most prominent environmental concerns relates to the death of birds, bats and other avian species resulting from collision with turbine blades. This thesis develops a model that provides the optimal strategy of turning the turbines off in a wind farm for certain periods to mitigate bird mortalities. We first create a single turbine optimization model for each hour on each day of a single month. We maximize the expected revenue generation and limit the expected bird mortalities to a certain level to solve for the dates and times for which the turbine should be turned off. The optimization problem is found to be part of common class of problems called Knapsack problems and through experiments we conclude that a linear programming (LP) relaxation of the problem provides a near-optimal solution. We extend the single-turbine model to a multiple-turbine model applicable to a wind farm. In this case, we solve for the percentage of wind turbines that should be turned off to limit the expected bird mortalities to a certain level. Finally, we carry out an uncertainty analysis and estimate probability distributions over the outcome of optimal strategy of turning the turbine off. We consider the Cape Wind project as a case study and limit the analysis to only one species of endangered birds called the common loon. We find that in order to save an expected number of 10 such birds in the month of March; we need to turn the turbine off for a total of 23 hours spread over specific dates and times. The average cost per bird was found to be $171.

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