Quantifying stand structural complexity in woodland and dry sclerophyll forest, South-Eastern Australia

In this thesis I present and test a methodology for developing a stand scale index of structural complexity. If properly designed such an index can act as a summary variable for a larger set of stand structural attributes, providing a means of ranking stands in terms of their structural complexity, and by association, their biodiversity and vegetation condition. This type of index can also facilitate the use of alternative policy instruments for biodiversity conservation, such as mitigation banking, auctions and offsets, that rely on a common currency – the index value – that can be compared or traded between sites. My intention was to establish a clear and documentable methodology for developing a stand scale index of structural complexity, and to test this methodology using data from real stands.¶ ..

The effect of gap size on growth and species composition of 15-year-old regrowth in mixed blackbutt forests

In north-eastern New South Wales (NSW) the Regional Forest Agreement process has transferred more than 400 000 ha of state forests to national park, and restricted silviculture to 'single tree selection' and a light form of 'Australian group selection'. While these silvicultural systems are theoretically well suited to ecologically sustainable forest management, there is concern that in their current form they are not achieving adequate regeneration or optimising the growth of that regeneration. This is of particular concern for mixed-species blackbutt forest, for which there is no quantitative research concerning the growth and composition of regeneration within group - selection gaps. We address this issue by: (1) quantifying the effect of gap size, and other gap characteristics including distance from gap edge, on the growth of regeneration; and (2) assessing the effect of gap size on the composition of regeneration. We use the answers to these questions to recommend a gap size for group selection silviculture in mixed-species blackbutt forests in north-eastern NSW. We measured attributes describing the growth and composition of regeneration in nine circular group-selection gaps in mixedspecies blackbutt forest near Coffs Harbour and Wauchope. These gaps contained 14.5-15.5-y-old regeneration and provided three replicates of small (0.27-0.3 ha), medium (0.45-0.67 ha) and large (0.93-0.97 ha) gaps. ANOVA testing indicated significantly (P < 0.05) lower height, diameter and volume growth of dominant blackbutt stems up to five metres from gap edge. Outside this zone growth remained fairly constant, indicating dominant blackbutt trees were susceptible to suppression only in close proximity to gap edges. Multiple regression analysis confirmed the relatively short distance from gap edges over which suppression occurred, with distance to closest gap edge explaining a small proportion of the variation in the models fitted for tree- and plot-level growth. The origin of blackbutt regeneration within gaps was a significant effect in tree-level growth models, with planted stems having increased diameter and volume growth compared with stems regenerated from natural seedfall. Gap size had no significant effect on the composition of regeneration. We conclude that for the range of gaps tested, 1 -ha gaps are optimal for growth because they minimise the proportion of gap within 5 m of the retained forest edge, without altering composition. Larger gaps have also been shown to have operational and economic benefits compared with smaller gaps

The conservation value of oil palm plantation estates, smallholdings and logged peat swamp forest for birds.

The expansion of industrial oil palm cultivation threatens tropical biodiversity globally, especially in developing countries. Driven by plans to generate economic revenue, large-scale plantations are emerging in Southeast Asia, Africa and Brazilian Amazon. However, the ecological impacts of the sector are poorly studied with respect to oil palm management system, and recommended conservation measures are based on limited data. We studied avifauna in oil palm landscapes in Peninsular Malaysia under different management systems (large plantation estates versus smallholdings) and age classes (uniform age versus mixed-age stands). We sampled 41 large plantation estates and 14 smallholdings, as well as 20 sites in an extensively logged peat swamp forest, the type of natural forest prior to conversion to oil palms. Compared with logged peat swamp forest, our results showed that forest conversion to oil palm cultivation may have eliminated 48–60% of bird species. We also found: (i) plantation estates and smallholdings supported similar bird assemblages but the latter supported significantly more species (P = 0.007); and (ii) despite reduced species richness in oil palm landscapes, we found high abundance of some individual bird species in specific types of stands including some forest, migratory, and wetland species. Conversion of natural forest to oil palm landscapes should not occur in the future through clearing of primary or secondary native forests. To complement conventional conservation approaches (e.g. the establishment of protected areas) in palm oil-producing countries, existing plantation estates and smallholdings should be managed in ways to promote improved conservation outcomes, although oil palm landscapes maintained a fraction of the original forest biodiversity. Managing habitat heterogeneity at both a local and a landscape-level is highly recommended in oil palm landscapes to maintain and/or enhance avian biodiversity

The influence of agricultural system, stand structural complexity and landscape context on foraging birds in oil palm landscapes

Functional diversity, an important element of avian biodiversity, can be examined by quantifying foraging guild composition. Understanding the ecological processes that underpin functional diversity of birds in oil palm Elaeis guineensis landscapes is important because different foraging guilds are likely to be influenced in different ways by land use practices. We surveyed birds at 55 sites within oil palm landscapes and at 20 sites within logged peat swamp forest, recording 208 species belonging to 19 foraging guilds. Oil palm landscapes supported a lower abundance of insectivorous, granivorous and omnivorous birds than did logged peat swamp forest despite the latter being severely degraded due to intensive timber extraction. However, abundances of other groups of foraging birds, such as raptors and wetland taxa, were higher in oil palm landscapes than logged peat swamp forest. Frugivorous species were more abundant in smallholdings than plantation estates, probably because of the presence of native trees. Foraging guild diversity was explained by stand-level attributes such as stand age, vegetation cover, epiphyte persistence and canopy cover. However, each foraging guild exhibited unique responses to different oil palm management regimes and stand-level attributes. Only arboreal omnivores and terrestrial frugivores were affected by the proximity of nearby natural forest. This diversity of responses implies that the occurrence of particular avian foraging guilds may not be a suitable ecological indicator of best-practice palm oil production. Our study also suggests that multiple conservation measures will be needed in oil palm landscapes irrespective of management regimes, including: (1) the maintenance of ground layer vegetation cover; (2) the pruning of oil palm canopy to permit light penetration to the ground layer; (3) re-vegetation of parts of oil palm landscapes with native trees; and (4) retention of natural and/or secondary forest patches within the boundaries of plantations

Contribution of illegal hunting, culling of pest species, road accidents and feral dogs to biodiversity loss in established oil-palm landscapes

Context: Understanding the ecological impacts of the palm-oil industry on native fauna requires information on anthropogenic threats that may cause species decline or local extinction. Aim: The main aim of the study was to assess wildlife deaths caused by illegal hunting, road accidents and introduced predators in established oil-palm landscapes in Peninsular Malaysia. Methods: Between April and October 2009, we interviewed 362 oil-palm workers at 36 sites, including large industrial estates and semi-traditional smallholdings. Key results: Our results showed that (1) illegal hunting by oil-palm workers in different oil-palm management systems was not statistically significant (P = 0.097), (2) native fauna were more often destroyed as pests in smallholdings than in conventional and eco-friendly plantation estates (P = 0.005), (3) non-local poachers conducted illegal activity more often in smallholdings than in conventional and eco-friendly plantation estates (P = 0.011), (4) road accidents were reported to kill more native fauna in conventional plantation estates than in smallholdings and eco-friendly plantation estates (P < 0.001) and (5) feral dogs were reported as killing more native fauna in eco-friendly plantation estates than in conventional plantation estates and smallholdings (P = 0.034). Conclusion: In addition to the conversion of native forest to oil-palm monocultures, various other anthropogenic threats can have a substantial effect on wildlife in oil-palm landscapes. Implications: To improve the conservation value of oil-palm landscapes, we recommend that palm-oil stakeholders should implement anti-poaching patrols, organise conservation programs to educate workers, reduce vehicle speeds on roads within oil-palm landscapes, and control local populations of feral dogs

New Methods for ALK Status Diagnosis in Non–Small-Cell Lung Cancer: An Improved ALK Immunohistochemical Assay and a New, Brightfield, Dual ALK IHC–In Situ Hybridization Assay

Introduction:The demonstration of anaplastic lymphoma kinase (ALK) positivity in non–small-cell lung cancer (NSCLC) has been hindered by the technical complexity and interpretative challenges of fluorescence in situ hybridization methods for detection of ALK gene rearrangement and by the inadequate sensitivity of existing immunohistochemistry (IHC) methods for ALK protein detection. In this study, we sought to increase the sensitivity of ALK IHC detection and to develop a brightfield assay for concurrent detection of ALK protein expression and ALK gene rearrangement.Methods:We developed a horseradish peroxidase–based IHC detection system using the novel, nonendogenous hapten 3-hydroxy-2-quinoxaline (HQ) and tyramide. We also developed a dual gene protein ALK assay combining a brightfield break-apart in situ hybridization ALK assay with another sensitive IHC method using the novel, nonendogenous hapten 5-nitro-3-pyrazole. We examined the sensitivity and accuracy of these methods using surgically resected NSCLC cases examined with ALK fluorescence in situ hybridization.Results:The new HQ-tyramide IHC detection system offered readily interpretable staining with substantially greater sensitivity than conventional ALK IHC, and produced heterogeneous and homogeneous patterns of ALK protein staining among ALK-positive NSCLC surgical cases. The new 5-nitro-3-pyrazole–based IHC detection system was similar in ALK detection sensitivity to the HQ-tyramide IHC system and was compatible with the brightfield in situ hybridization assay.Conclusion:The new HQ-tyramide IHC reagent system allows more sensitive assessment of ALK protein status in NSCLC cases. The new ALK gene-protein assay allows the concurrent visualization of ALK gene and ALK protein status in single cells, allowing more accurate ALK status determination even in heterogeneous specimens

A Methodology for Modelling Canopy Structure: An Exploratory Analysis in the Tall Wet Eucalypt Forests of Southern Tasmania

A ground-based methodology is presented for spatially modelling forest canopy structure. Field measurements and allometric relationships are used to predict the profiles of free-growing tree crowns on the basis of stem diameter at breast height (dbh). These profiles are incorporated into three-dimensional canopy models using AutoCAD™ technical drawing software and field data describing the genus, dbh and relative positions of all trees greater than 10 cm dbh; critically, our models account for the effects of competition for light between neighbouring crowns. By horizontally partitioning the models, the presence of distinct strata and the dominant genera associated with each stratum can be identified. Our methodology is applicable to other forest ecosystems as a research tool for investigating changes in vertical structure, and for calibrating remote sensing technologies in order to map and monitor canopy structural variation across forested landscapes

Environmental and management factors controlling the potentially invasive native species Violet Kunzea (Kunzea parvifolia)

Violet Kunzea (Kunzea parvifolia), a native shrub of eastern Australia, is reputed to form dense thickets in areas that have undergone significant landscape modification, and has been listed as an invasive native species for which clearing is permitted under the Native Vegetation Act 2003 (NSW). We quantified factors controlling its abundance in 81 sites within the Braidwood region of NSW, on the basis of 36 strata reflecting soil landscape, topographic position, aspect and canopy cover. Within each study site 34 variables describing environmental, disturbance, management and vegetation attributes were measured using a transect sampling technique and landowner surveys. An analysis of these data indicated that, in the sites we surveyed, Violet Kunzea is a common shrub present at relatively high mean levels of cover (44%), with no preferred topographic position or aspect. There were no significant associations between management activities such as slashing or grazing, and the cover of Violet Kunzea. Multiple regression modelling indicated that overstorey cover was the key variable explaining variation in the cover of Violet Kunzea, with an increase in cover of the shrub as overstorey cover declined. We conclude that a reduction in overstorey cover results in an increase in Violet Kunzea abundance as competition is removed, and the subsequent suppression of overstorey regeneration sets up a feedback loop facilitating the further expansion of Violet Kunzea and the contraction of overstorey cover. Approaches to the management of this species will therefore require long-term commitments to conserve and restore overstorey cover

The distance to structural complement (DiSCo) approach for expressing forest structure described by Aerial Photograph Interpretation data sets

At the landscape-level Aerial Photograph Interpretation (API) is one of the oldest and most common tools for mapping forest structure. The variety of attributes available for API classifications can produce 100s of different patch types as a basis for mapping landscape mosaics. However, these maps are often difficult to interpret or use for monitoring the impacts of management and natural disturbance. In this study, we demonstrate an approach for quantifying the landscape forest structure described by API data sets. For this purpose we utilised a forest dataset comprising 1197 field plots and API mapping of crown structural characteristics for 773,280. ha of State Forest in Victoria, Australia. Our approach involved: (i) stratification of the landscape into distinct forest communities; (ii) construction of stand-level structural complexity indices for each forest community; (iii) use of stand-level indices of structural complexity to classify API typing into distinct canopy structural classes; (iv) calculation of the distance from each point within a landscape grid to achieve a full complement of canopy structural classes within each forest community. We term our methodology the distance to structural complement (DiSCo) approach, because it identifies the minimum distance to achieve a full complement of structural units within the landscape. We demonstrate the use of these values in mapping landscape structure and their potential for monitoring and modelling the effects of disturbance at this scale, including impacts on heterogeneity, connectivity, individual faunal species and particular forest communities