Conserving biodiversity in human-dominated landscapes requires protecting networks of ecological reserves and managing the intervening matrix to maintain the potential for species to move among them. This dissertation provides original insights towards (1) identifying areas for protection in reserves that are critical to maintain biodiversity and (2) assessing the potential for species' movements among habitat patches in a reserve network. I develop and test methods that will facilitate conservation planning to promote viable, resilient populations through time. The first part of this dissertation tests and develops reserve selection strategies that protect either a single focal species in a dynamic landscape or multiple interacting species in a static landscape. Using a simulation model of boreal forest dynamics, I test the effectiveness of static and dynamic reserves to maintain spatial habitat requirements of a focal species, American Marten (Martes americana). Dynamic reserves improved upon static reserves but re-locating reserves was constrained by fragmentation of the matrix. Management of the spatial and temporal distribution of land-uses in the matrix will therefore be essential to retain options for re-locating reserves in the future. Additionally, to include essential consumer-resource interactions into reserve selection, a new algorithm is presented for American marten and its two primary prey species. The inclusion of their interaction had the benefit t of producing spatially aggregated reserves based on functional species requirements. The second part of this dissertation evaluates and synthesizes the network-theoretic approach to quantify connectivity among habitat patches or reserves embedded within spatially heterogeneous landscapes. I conduct a sensitivity analysis of network-theoretic connectivity analyses that derive least-cost movement behavior from the underlying cost surface which describes the relative ecological costs of dispersing through different landcover types. Landscape structure is shown to aff ect how sensitive least-cost graph connectivity assessments are to the quality (relative cost values) of landcover types. I develop a conceptual framework to classify network connectivity statistics based on the component of habitat connectivity that they quantify and the level within the network to which they can be applied. Together, the combination of reserve design and network connectivity analyses provide complementary insights to inform spatial planning decisions for conservation.

Conserving biodiversity in human-dominated landscapes requires protecting networks of ecological reserves and managing the intervening matrix to maintain the potential for species to move among them. This dissertation provides original insights towards (1) identifying areas for protection in reserves that are critical to maintain biodiversity and (2) assessing the potential for species' movements among habitat patches in a reserve network. I develop and test methods that will facilitate conservation planning to promote viable, resilient populations through time. The first part of this dissertation tests and develops reserve selection strategies that protect either a single focal species in a dynamic landscape or multiple interacting species in a static landscape. Using a simulation model of boreal forest dynamics, I test the effectiveness of static and dynamic reserves to maintain spatial habitat requirements of a focal species, American Marten (Martes americana). Dynamic reserves improved upon static reserves but re-locating reserves was constrained by fragmentation of the matrix. Management of the spatial and temporal distribution of land-uses in the matrix will therefore be essential to retain options for re-locating reserves in the future. Additionally, to include essential consumer-resource interactions into reserve selection, a new algorithm is presented for American marten and its two primary prey species. The inclusion of their interaction had the benefit t of producing spatially aggregated reserves based on functional species requirements. The second part of this dissertation evaluates and synthesizes the network-theoretic approach to quantify connectivity among habitat patches or reserves embedded within spatially heterogeneous landscapes. I conduct a sensitivity analysis of network-theoretic connectivity analyses that derive least-cost movement behavior from the underlying cost surface which describes the relative ecological costs of dispersing through different landcover types. Landscape structure is shown to aff ect how sensitive least-cost graph connectivity assessments are to the quality (relative cost values) of landcover types. I develop a conceptual framework to classify network connectivity statistics based on the component of habitat connectivity that they quantify and the level within the network to which they can be applied. Together, the combination of reserve design and network connectivity analyses provide complementary insights to inform spatial planning decisions for conservation.

Chronic anthropogenic disturbance has left many marine systems at risk of degrading into undesirable states. In many cases, ecosystem shifts are triggered by catastrophic disturbance events that are beyond the control of local management, such as coral bleaching or cyclones. Recognition of this risk has instigated what has been referred to as a new paradigm for marine stewardship; managing areas with the explicit goal of maintaining ecosystem resilience. Despite this, there has been little synthetic influence of resilience theory on marine conservation planning. This thesis focuses on how to make good decisions regarding the selection of marine protected areas (MPAs), in the face of catastrophic disturbance events and for the conservation of highly dynamic marine systems. Large-scale catastrophic events, although rare, lie generally beyond the control of local management and can prevent marine reserves from achieving biodiversity outcomes. In Chapter 2, I formulate a new conservation planning problem that aims to minimize the probability of missing marine conservation targets as result of catastrophic events. To illustrate this approach, I address the problem of minimizing the impact of large scale coral bleaching events on a reserve system for the Great Barrier Reef, Australia. By explicitly considering the threat of catastrophic bleaching as part of the reserve design problem, it was possible to substantially improve the likely persistence of coral reefs within reserve networks, for a negligible increase in reserve cost. The results also demonstrate that simply aiming to protect the reefs at lowest risk of catastrophic bleaching does not necessarily lead to the best conservation outcomes. It is thought that recovery of marine habitats from uncontrollable disturbance may be faster in marine reserves than in unprotected habitats. But which marine habitats should be protected, those areas at greatest risk or those at least risk? In Chapter 3, I define this problem mathematically for two alternate conservation objectives and determine under which conditions each of the different protection strategies are optimal. With regard to the risk of uncontrollable disturbance, the optimal protection strategy depends on both the conservation objective and the expected rate of habitat recovery inside and outside protected areas. I illustrate this decision making with an example of cyclone disturbance of coral reefs on Australia’s Great Barrier Reef. An adequate consideration of risk can indicate surprising routes to conservation success. The resilience of coral reef systems is closely linked to the presence of grazing herbivores. Although herbivore populations are generally protected through permanent static reserves, the benefits of protection are dynamic in both time and space. Periodically moving protection between reefs allows access to the greatest potential benefits of reservation and can help address social reluctance to permanently close areas. Using analytic methods to solve a theoretical case study, I demonstrate that periodically rotating protection around a reef system can lead to greater average reef resilience than under static protection, but only if the overall level of reservation is high enough or the rotation does not include all reefs in the system. The past ten years have seen increasing enthusiasm for MPAs as a tool for pelagic conservation. However, numerous criticisms have been levelled against the use of place-based management in such a dynamic environment. Evidence, tools and information to address these criticisms and establish the feasibility and relevance of pelagic MPAs are dispersed across the conservation, oceanography and fisheries management literature. In Chapter 5, I review this information and present a synthetic framework for systematic planning of pelagic MPAs. Although many of the lessons learned so far about MPA design in coastal systems can be transferred to pelagic systems, there are some fundamental differences and new challenges involved in the conservation of patchy and highly dynamic resources. These challenges are very much at the leading edge of new conservation science and are likely to stimulate solutions with impact far beyond the design of pelagic MPAs.