Scaling the benefits of agri-environment schemes for biodiversity conservation in agricultural landscapes

Agricultural expansion and intensification are major causes of biodiversity loss. To mitigate this, billions of dollars are committed by governments annually to agri-environment conservation schemes aiming to engage landholders, often at large (continental) scales, in sustainable farming practices. While some schemes have been successful in addressing the social and policy elements of farmland conservation, assessments of their effectiveness for conserving biodiversity in farming systems is lacking. Recent studies have demonstrated that the effectiveness of programs is influenced by a number of scale-dependent factors that may influence biodiversity response but remain poorly understood. Specifically, local- and landscape-scale management actions can influence biodiversity response, and hence the effectiveness of programs, but this aspect has been little explored. My research aimed to identify ways to enhance the effectiveness of agri-environmental schemes through a better understanding of scale-related management effects on herpetofauna (reptiles and amphibians); a critical and declining vertebrate group severely threatened by agricultural development. First, I summarise current knowledge of local- and landscape-scale factors influencing agri-environment scheme effectiveness for biodiversity, highlighting novel research priorities relevant to practitioners (Paper #1). I then conducted baseline herpetofaunal surveys at 325 treatment/control sites within a critically endangered remnant woodland targeted under a large-scale (>1000 km; 172,000 km2) agri-environment scheme; the Australian Government Environmental Stewardship Programme (Paper #2). This is the most extensive xii herpetofaunal survey conducted to date throughout this woodland ecosystem. I found high levels of spatial variation in species detected across the study area; with large differences in species richness between biogeographic regions but not between treatment and control sites. Second, I conducted multi-season vegetation, habitat structural and herpetofaunal surveys at each of the 325 sites to identify key habitat variables (Paper #3) and management activities (livestock grazing; Paper #4) at local levels. I found that habitat use varied over biogeographically distinct regions, suggesting schemes that consider regional differences in local habitat preferences may be more effective than schemes that ignore such variation. Furthermore, past and present livestock grazing influenced herpetofaunal populations, but in complex and varied ways that have previously been overlooked. Finally, I collected data on land-use surrounding the remnant woodland sites and its influence on reptile movement to quantify the impact of landscape modification on community structure (Paper #5) and habitat connectivity (Paper #6). Landscape modification resulted in a change in community composition and a loss of species co-occurrence, but not a loss of species. Importantly, changes in co-occurrence pattern were complex and allowed for a novel classification of species susceptibility to the threat of land modification. Additionally, I found that pasture height and crop-sowing direction influenced reptile movements within the agricultural matrix, and hence must be considered where connectivity is a goal of agri-environment investment (Paper #6). xiii Collectively, my research identifies several outcomes that strengthen the theoretical and applied opportunities for enhancing effectiveness of agri-environment schemes. These include: (1) An improved knowledge of the environmental and anthropogenic drivers of the distributions of herpetofauna (2) Incorporating ecological effects operating at different scales can help agri-environment schemes to become more effective (3) A range of management actions is required to meet the conservation requirements for herpetofauna (4) Large occupancy datasets should be collected to extend observations of ecological patterns to identify underlying ecological processes (5) Management recommendations can be adaptively integrated into existing agri-environment schemes; as well as in new schemes. Such considerations are of broad relevance for the design of large-scale conservation strategies targeting the conservation of biodiversity across agricultural landscapes

Multilevel modelling for inference of genetic regulatory networks

Time-course experiments with microarrays are often used to study dynamic biological systems and genetic regulatory networks (GRNs) that model how genes influence each other in cell-level development of organisms. The inference for GRNs provides important insights into the fundamental biological processes such as growth and is useful in disease diagnosis and genomic drug design. Due to the experimental design, multilevel data hierarchies are often present in time-course gene expression data. Most existing methods, however, ignore the dependency of the expression measurements over time and the correlation among gene expression profiles. Such independence assumptions violate regulatory interactions and can result in overlooking certain important subject effects and lead to spurious inference for regulatory networks or mechanisms. In this paper, a multilevel mixed-effects model is adopted to incorporate data hierarchies in the analysis of time-course data, where temporal and subject effects are both assumed to be random. The method starts with the clustering of genes by fitting the mixture model within the multilevel random-effects model framework using the expectation-maximization (EM) algorithm. The network of regulatory interactions is then determined by searching for regulatory control elements (activators and inhibitors) shared by the clusters of co-expressed genes, based on a time-lagged correlation coefficients measurement. The method is applied to two real time-course datasets from the budding yeast (Saccharomyces cerevisiae) genome. It is shown that the proposed method provides clusters of cell-cycle regulated genes that are supported by existing gene function annotations, and hence enables inference on regulatory interactions for the genetic network

Breaking down the barrier: dispersal across the Antarctic Polar Front

Our view of the Antarctic Polar Front (APF) as a circum-polar biogeographic barrier is changing (Chown et al. 2015). The APF marks the convergent boundary between cold Antarctic water and warmer sub-Antarctic water, and has long been considered to prevent north-south dispersal in the Southern Ocean (reviewed by Clarke et al. 2005, Fraser et al. 2012). Our multi-year survey data provides evidence that rafting organisms readily cross the APF

Joint Modeling and Registration of Cell Populations in Cohorts of High-Dimensional Flow Cytometric Data

In systems biomedicine, an experimenter encounters different potential sources of variation in data such as individual samples, multiple experimental conditions, and multi-variable network-level responses. In multiparametric cytometry, which is often used for analyzing patient samples, such issues are critical. While computational methods can identify cell populations in individual samples, without the ability to automatically match them across samples, it is difficult to compare and characterize the populations in typical experiments, such as those responding to various stimulations or distinctive of particular patients or time-points, especially when there are many samples. Joint Clustering and Matching (JCM) is a multi-level framework for simultaneous modeling and registration of populations across a cohort. JCM models every population with a robust multivariate probability distribution. Simultaneously, JCM fits a random-effects model to construct an overall batch template -- used for registering populations across samples, and classifying new samples. By tackling systems-level variation, JCM supports practical biomedical applications involving large cohorts

Scoping study

This Scoping Study was commissioned jointly by the British Library Research & Innovation Centre (BLRIC) and JISC under the management of UKOLN. The study was authored jointly by Fretwell-Downing Informatics Ltd and CERLIM (University of Central Lancashire) with specialist contributions from Geoffrey Hare (County Librarian, Essex) and Index Data of Denmark in their respective areas of public libraries and resource discovery technologies. The findings of the study are based on a consultation exercise undertaken by the partners between February and April 1997, resulting in a strong recommendation that a National Agency should be constituted. The study proposes that the Agency should act as a facilitator to ensure that scholarly resources are visible and accessible across domains and other traditional boundaries in an efficient and sustainable manner

The life history and ecology of the Pink-tailed Worm-lizard Aprasia parapulchella Kluge a review

This review synthesises research on the Pink-tailed Worm-lizard Aprasia parapukhella - a threatened species with life-history traits and habitat and dietary preferences that make it particularly vulnerable to decline. Further information on the ecology of A. parapukhella is required in order to develop effective approaches to conservation and management, particularly given the conservation status of the species. Aprasia parapukhella is a dietary specialist living in the burrows of small ants, the eggs and larvae of which it preys upon. It is late maturing (adult size probably attained in the third or fourth year of life), has a small clutch, is thought to be longlived and has specific habitat preferences. It has a strong association with landscapes that are characterised by outcroppings of lightly-embedded surface rocks.The lizard is associated with a particular suite of ant species and ground cover tending towards open native vegetation (grasses and shrubs) at most sites, but with regional differences. Although the highest densities have been recorded in areas without tree cover, the species has also been found in open-forest and woodland.The relative density of populations and the snout-vent length and weight of specimens reveal regional differences, suggesting that further analysis of the genetic status of the population across its range is warranted. There is still much to learn about the ecology of the species, in particular with respect to movement, breeding, dispersal and the relationship between lizards and ants. Further survey for new populations remains a key priority

Path dependence: an approach for framing constraints on adaptation in Australian dairy farms

Climate change is a salient issue for southern Australia, which has been identified as one of the regions most vulnerable to climate change in the world. The potential impacts of climate change on farms could be profound and may require that producers adapt their farms to a much greater degree than currently undertaken. Generally speaking, it is expected that climate change will require considerable change to agriculture, with the responsibility for this change lying squarely with producers, many of which are small family businesses. In this thesis I explored the capacity of producers to adapt their farms in the face of climate change. Underpinning this exploration was a question regarding the role, if any, for public policy to support producers with managing climate change impacts