ARCTIS — A MATLAB® toolbox for archaeological imaging spectroscopy

Imaging spectroscopy acquires imagery in hundreds or more narrow contiguous spectral bands. This offers unprecedented information for archaeological research. To extract the maximum of useful archaeological information from it, however, a number of problems have to be solved. Major problems relate to data redundancy and the visualization of the large amount of data. This makes data mining approaches necessary, as well as efficient data visualization tools. Additional problems relate to data quality. Indeed, the upwelling electromagnetic radiation is recorded in small spectral bands that are only about ten nanometers wide. The signal received by the sensor is, thus quite low compared to sensor noise and possible atmospheric perturbations. The often small, instantaneous field of view (IFOV)—essential for archaeologically relevant imaging spectrometer datasets—further limits the useful signal stemming from the ground. The combination of both effects makes radiometric smoothing techniques mandatory. The present study details the functionality of a MATLAB®-based toolbox, called ARCTIS (ARChaeological Toolbox for Imaging Spectroscopy), for filtering, enhancing, analyzing, and visualizing imaging spectrometer datasets. The toolbox addresses the above-mentioned problems. Its Graphical User Interface (GUI) is designed to allow non-experts in remote sensing to extract a wealth of information from imaging spectroscopy for archaeological research. ARCTIS will be released under creative commons license, free of charge, via website (http://luftbildarchiv.univie.ac.at)

Incorporating governance influences into social-ecological system models: a case study involving biodiversity conservation

Addressing environmental problems requires sophisticated approaches to complexity and uncertainty. Conceptual models are increasingly used to improve understanding of complex system interactions. However, cursory treatment of governance limits their analytical potential. This study included governance considerations in a social-ecological system model of biodiversity conservation in the Tasmanian Midlands (Australia). Effectiveness of engagement processes and conservation programme longevity were identified as critical governance influences. The conceptual representation of this system enabled exploration of how governance influences interact with social drivers (e.g. landholder engagement in conservation practices) to modify the effect of biophysical drivers (e.g. land use) on biodiversity outcomes. Such a methodology provides essential information for identifying and guiding governance related points of intervention

Traveltime Inversion of Vertical Radar Profiles

Traveltimes of direct arrivals in vertical radar profiles (VRPs) are tomographically inverted to estimate the earth’s electromagnetic (EM) velocity between a surface transmitter and a downhole receiver. We determine the 1D interval velocity model that best fits the first-arrival traveltimes by using a weighted, damped, least-squares inversion scheme. We assess the accuracy of the velocity model using synthetic traveltimes from a known velocity-distribution model simulating an unconfined aquifer. The inverted velocity profile closely matched the velocity profile of the input model in the synthetic examples. Using vertical radar profile data from an unconfined aquifer near Boise, Idaho, we inverted traveltimes to obtain velocity estimates at the well location. The velocity change at a depth of 2.0 m corresponds well with the measured depth to the water table of 1.95 m, and at depths between 2 and 18 m, the velocities ranged between 0.06 and 0.1 m/ns. Our estimates approximately match the velocity distribution determined from neutron-derived porosity logs at depths greater than about 2 m. An important function of inverse methods is to assess (quantitatively and qualitatively) the uncertainty of inverted velocity estimates. We note that the velocity values in the upper and lower parts of the inverted model are not as well constrained compared to those between the depths of 4 and 13 m. From the model resolution and model covariance matrices of the real-data inversion,we determine the uncertainty in our velocity model, leading to more reliable interpretations of the subsurface

Using insights from pragmatism to develop reforms that strengthen institutional competence for conserving biodiversity

The poor performance of biodiversity institutions has prompted calls for reform. Adaptive governance has been promoted as a means of supporting improved biodiversity outcomes. However, incorporating adaptive elements into biodiversity governance has been a challenge. In particular, efforts to make institutions more “adaptive” often fail to account for existing capacity and context-specific factors. Clear guidance on how to move from general, ambitious adaptive governance prescriptions to specific, context-dependent recommendations is needed. This paper demonstrates how insights from pragmatism can inform an approach for designing institutional reforms that address current shortcomings in adaptive governance approaches. This design scaffolds reform options on a platform of existing competency and institutional legacy. Informed by the results of a prior institutional diagnosis, reform development followed a three-stage process: defining plausible reform spaces; identifying reform possibilities within these spaces; and elaborating reform options. Two very different landscapes provided the case studies: (1) a highly modified agricultural landscape, where private landholders are responsible for managing biodiversity as a public good; (2) a group of national parks, where the state holds primary responsibility. The reforms in the agricultural landscape build on successful landholder and organizational efforts to self-organize and pursue innovative solutions, while those for the protected area enable greater managerial discretion and address the challenges of working across multiple government jurisdictions. This context-driven approach draws on insights from pragmatism to provide guidance on the design of institutional reforms that meet the demands of adaptive governance in a way that is both systematic and realisti

Fit-for-Purpose Institutions? An Evaluation of Biodiversity Conservation in the Agricultural Landscape of the Tasmanian Midlands, Australia

Biodiversity loss is a globally significant problem. Institutional failure to halt this loss suggests current arrangements are not fit for the purpose of conserving biodiversity. The objective of this paper is to diagnose institutional fitness for conserving biodiversity in the Tasmanian Midlands of Australia, a highly modified agricultural landscape with critically endangered biodiversity values. This paper presents and applies a novel diagnostic framework that adopts a broad view of institutional fit, drawing on concepts from adaptive governance, institutional theory, and public administration, and finds four areas of poor fit that can guide reform efforts. The first is a narrow framing of biodiversity objectives, leading to neglect of key social and ecological concerns. Second, the interplay of current arrangements fails to buffer key economic and political drivers, and compromises adaptive capacity. Third, limited government authority and embedded power relations raise questions about the effectiveness and fairness of current approaches. Finally, the reluctance of governments to devolve authority and decision-making powers to self-organizing networks constrains adaptation. This suite of fit problems constrains achievement of biodiversity conservation, particularly in dealing with landscape multifunctionality, the need to balance private landholder rights and responsibilities, and the need to consider how to respond to emerging novel and hybrid ecosystems

Visualizing probabilistic models: Intensive Principal Component Analysis

Unsupervised learning makes manifest the underlying structure of data without curated training and specific problem definitions. However, the inference of relationships between data points is frustrated by the `curse of dimensionality' in high-dimensions. Inspired by replica theory from statistical mechanics, we consider replicas of the system to tune the dimensionality and take the limit as the number of replicas goes to zero. The result is the intensive embedding, which is not only isometric (preserving local distances) but allows global structure to be more transparently visualized. We develop the Intensive Principal Component Analysis (InPCA) and demonstrate clear improvements in visualizations of the Ising model of magnetic spins, a neural network, and the dark energy cold dark matter ({\Lambda}CDM) model as applied to the Cosmic Microwave Background.Comment: 6 pages, 5 figure

Barcoding success as a function of phylogenetic relatedness in Viburnum, a clade of woody angiosperms

BACKGROUND: The chloroplast genes matK and rbcL have been proposed as a “core” DNA barcode for identifying plant species. Published estimates of successful species identification using these loci (70-80%) may be inflated because they may have involved comparisons among distantly related species within target genera. To assess the ability of the proposed two-locus barcode to discriminate closely related species, we carried out a hierarchically structured set of comparisons within Viburnum, a clade of woody angiosperms containing ca. 170 species (some 70 of which are currently used in horticulture). For 112 Viburnum species, we evaluated rbcL + matK, as well as the chloroplast regions rpl32-trnL, trnH-psbA, trnK, and the nuclear ribosomal internal transcribed spacer region (nrITS). RESULTS: At most, rbcL + matK could discriminate 53% of all Viburnum species, with only 18% of the comparisons having genetic distances >1%. When comparisons were progressively restricted to species within major Viburnum subclades, there was a significant decrease in both the discriminatory power and the genetic distances. trnH-psbA and nrITS show much higher levels of variation and potential discriminatory power, and their use in plant barcoding should be reconsidered. As barcoding has often been used to discriminate species within local areas, we also compared Viburnum species within two regions, Japan and Mexico and Central America. Greater success in discriminating among the Japanese species reflects the deeper evolutionary history of Viburnum in that area, as compared to the recent radiation of a single clade into the mountains of Latin America. CONCLUSIONS: We found very low levels of discrimination among closely related species of Viburnum, and low levels of variation in the proposed barcoding loci may limit success within other clades of long-lived woody plants. Inclusion of the supplementary barcodes trnH-psbA and nrITS increased discrimination rates but were often more effective alone rather than in combination with rbcL + matK. We surmise that the efficacy of barcoding in plants has often been overestimated because of the lack of comparisons among closely related species. Phylogenetic information must be incorporated to properly evaluate relatedness in assessing the utility of barcoding loci

Scenario analysis for biodiversity conservation: A social-ecological system approach in the Australian Alps

Current policy interventions are having limited success in addressing the ongoing decline in global biodiversity. In part, this is attributable to insufficient attention being paid to the social and governance processes that drive decisions and can undermine their implementation. Scenario planning that draws on social–ecological systems (SES) analysis provides a useful means to systematically explore and anticipate future uncertainties regarding the interaction between humans and biodiversity outcomes. However, the effective application of SES models has been limited by the insufficient attention given to governance influences. Understanding the influence governance attributes have on the future trajectory of SES is likely to assist choice of effective interventions, as well as needs and opportunities for governance reform. In a case study in the Australian Alps, we explore the potential of joint SES and scenario analyses to identify how governance influences landscape-scale biodiversity outcomes. Novel aspects of our application of these methods were the specification of the focal system's governance attributes according to requirements for adaptive capacity, and constraining scenarios according to the current governance settings while varying key social and biophysical drivers. This approach allowed us to identify how current governance arrangements influence landscape-scale biodiversity outcomes, and establishes a baseline from which the potential benefits of governance reform can be assessed