In extensively modified landscapes, how the matrix is managed determines many conservation outcomes. Recent publications revise popular conceptions of a homogeneous and static matrix, yet we still lack an adequate conceptual model of the matrix. Here, we identify three core effects that influence patch-dependent species, through impacts associated with movement and dispersal, resource availability, and the abiotic environment. These core effects are modified by five 'dimensions': spatial and temporal variation in matrix quality; spatial scale; temporal scale of matrix variation; and adaptation. The conceptual domain of the matrix, defined as three core effects and their interaction with these five dimensions, provides a much-needed framework to underpin management of fragmented landscapes and highlights new research priorities.

The management of landscapes for biological conservation and ecologically sustainable natural resource use are crucial global issues. Research for over two decades has resulted in a large literature, yet there is little consensus on the applicability or even the existence of general principles or broad considerations that could guide landscape conservation. We assess six major themes in the ecology and conservation of landscapes. We identify 13 important issues that need to be considered in developing approaches to landscape conservation. They include recognizing the importance of landscape mosaics (including the integration of terrestrial and aquatic areas), recognizing interactions between vegetation cover and vegetation configuration, using an appropriate landscape conceptual model, maintaining the capacity to recover from disturbance and managing landscapes in an adaptive framework. These considerations are influenced by landscape context, species assemblages and management goals and do not translate directly into on-the-ground management guidelines but they should be recognized by researchers and resource managers when developing guidelines for specific cases. Two crucial overarching issues are: (i) a clearly articulated vision for landscape conservation and (ii) quantifiable objectives that offer unambiguous signposts for measuring progress.

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Environmental disturbance underpins the dynamics and diversity of many of the ecosystems of the world, yet its influence on the patterns and distribution of genetic diversity is poorly appreciated. We argue here that disturbance history may be the major driver that shapes patterns of genetic diversity in many natural populations. We outline how disturbance influences genetic diversity through changes in both selective processes and demographically driven, selectively neutral processes. Our review highlights the opportunities and challenges presented by genetic approaches, such as landscape genomics, for better understanding and predicting the demographic and evolutionary responses of natural populations to disturbance. Developing this understanding is now critical because disturbance regimes are changing rapidly in a human-modified world.

Land clearing depletes and fragments habitat, resulting in the loss of biodiversity. Corridors of native vegetation can ameliorate the impacts of land clearing by reducing isolation of remnant vegetation. However the effectiveness of linear remnants as corridors or connecting habitat is influenced by remnant size and condition. In central New South Wales, Australia, 84–95% of native vegetation has been cleared, with remnants occurring as isolated reserves and interconnecting strips beside roads and paddocks. Do the linear remnants provide connectivity throughout the landscape for reptile populations? In three 100‐km2 agricultural locations, I classified all remnants into one of 10 “landscape elements” based on shape, management, and vegetation. I used generalized linear models and permutation tests to examine differences in reptile abundance among landscape elements. Only two blind snakes were captured in paddocks, suggesting that the matrix between remnants is virtually devoid of reptiles. Remnant shape had a strong effect, with fewer species in linear remnants than in square reserves. Five species were significantly less abundant (two of these species were absent) in linear remnants. Three species had significantly lower abundance in grazed linear remnants, and one species had lower numbers on roadsides. In contrast, five species were more abundant on roadsides, with one skink tripling in number. Limited evidence suggested that food specialization, body size, and range size were not correlated with species declines. However, allozyme electrophoresis results indicated that two declining species had stronger isolation‐by‐distance effects than two widespread species, implying that the decliners had weaker dispersal powers or smaller effective population sizes. Comparisons with the reptile fauna from an uncleared landscape suggested that two species may be locally extinct and that three other species had inflated population sizes in the farming locations. In addition to substantially altering the reptile community, the cumulative impact of remnant management was to increase fragmentation beyond that expected from the distribution of remnant vegetation alone. At two locations, 22% of remnant vegetation was suitable for the Nobbi dragon Amphibolurus nobbi, and the suitable remnants were subdivided into an additional 2–4 fragments. Extensive landscape restoration is now needed to help arrest reptile declines from highly cleared agricultural landscapes.

The topics of succession and post-disturbance ecosystem recovery have a long and convoluted history. There is extensive redundancy within this body of theory, which has resulted in confusion, and the links among theories have not been adequately drawn. This review aims to distil the unique ideas from the array of theory related to ecosystem change in response to disturbance. This will help to reduce redundancy, and improve communication and understanding between researchers. We first outline the broad range of concepts that have developed over the past century to describe community change in response to disturbance. The body of work spans overlapping succession concepts presented by Clements in 1916, Egler in 1954, and Connell and Slatyer in 1977. Other theories describing community change include state and transition models, biological legacy theory, and the application of functional traits to predict responses to disturbance. Second, we identify areas of overlap of these theories, in addition to highlighting the conceptual and taxonomic limitations of each. In aligning each of these theories with one another, the limited scope and relative inflexibility of some theories becomes apparent, and redundancy becomes explicit. We identify a set of unique concepts to describe the range of mechanisms driving ecosystem responses to disturbance. We present a schematic model of our proposed synthesis which brings together the range of unique mechanisms that were identified in our review. The model describes five main mechanisms of transition away from a post-disturbance community: (i) pulse events with rapid state shifts; (ii) stochastic community drift; (iii) facilitation; (iv) competition; and (v) the influence of the initial composition of a post-disturbance community. In addition, stabilising processes such as biological legacies, inhibition or continuing disturbance may prevent a transition between community types. Integrating these six mechanisms with the functional trait approach is likely to improve the predictive capacity of disturbance theory. Finally, we complement our discussion of theory with a case study which emphasises that many post-disturbance theories apply simultaneously to the same ecosystem. Using the well-studied mountain ash (Eucalyptus regnans) forests of south-eastern Australia, we illustrate phenomena that align with six of the theories described in our model of rationalised disturbance theory. We encourage further work to improve our schematic model, increase coverage of disturbance-related theory, and to show how the model may link to, or integrate with, other domains of ecological theory.

Wildlife diseases pose an increasing threat to biodiversity and are a major management challenge. A striking example of this threat is the emergence of chytridiomycosis. Despite diagnosis of chytridiomycosis as an important driver of global amphibian declines 15 years ago, researchers have yet to devise effective large-scale management responses other than biosecurity measures to mitigate disease spread and the establishment of disease-free captive assurance colonies prior to or during disease outbreaks. We examined the development of management actions that can be implemented after an epidemic in surviving populations. We developed a conceptual framework with clear interventions to guide experimental management and applied research so that further extinctions of amphibian species threatened by chytridiomycosis might be prevented. Within our framework, there are 2 management approaches: reducing Batrachochytrium dendrobatidis (the fungus that causes chytridiomycosis) in the environment or on amphibians and increasing the capacity of populations to persist despite increased mortality from disease. The latter approach emphasizes that mitigation does not necessarily need to focus on reducing disease-associated mortality. We propose promising management actions that can be implemented and tested based on current knowledge and that include habitat manipulation, antifungal treatments, animal translocation, bioaugmentation, head starting, and selection for resistance. Case studies where these strategies are being implemented will demonstrate their potential to save critically endangered species.

Species with strong preferences for early or late successional stages after fire may be extinction prone under current fire regimes. However, the extent of specialisation to time since fire is poorly understood, and, for reptiles, succession models for predicting responses are in the development phase. In this study we tested predictions of a reptile succession model, and identified species that may be fire specialists. Reptiles were sampled in five burnt and unburnt mallee Eucalyptus woodlands, Australia. Two, 400 m transects within each burn treatment were sampled using 11 pairs of pitfall-traps that were opened for five weeks over two summers. A habitat accommodation model of succession that was previously developed for mallee reptiles correctly predicted the observed responses of three of 16 common reptile species. A further four species showed non-significant trends in the predicted direction. However, eight other species showed unexpected responses. One species showed a strong interaction between burn age and location, requiring a two-dimensional successional model in contrast with the usual linear models explaining reptile responses to fire. One third of common species were not affected by fire and so may not have increased risks of extinction due to the fire suppression/incineration cycle. However, approximately half to two-thirds of common reptiles did have a fire response, so the risk of deterministic extinction in small fragments may be substantial. Further model development is needed to better predict fire responses and to assist the design of fire mosaics that can accommodate early and late successional fire specialists.