Ross B. Cunningham

Modelling the abundance of rare species: statistical models for counts with extra zeros

Abstract We consider several statistical models for the analysis of the abundance of a rare species and these are illustrated in detail with data for the abundance of Leadbeaters Possum in montane ash forests of south-eastern Australia. These data are characterised by a discrete distribution with the zero class inflated. In many statistical problems the parameters of this distribution depend on covariates, such as the number of hollow bearing trees. We advocate a conditional model which is simple to interpret and readily fitted. We show how to obtain standard errors for the parameter estimates. We also show how to estimate the mean abundance of animals at a site. The methods outlined in this paper offer a powerful framework for the study of problems having a discrete response (like abundance) with the zero class inflated.

EFFECTS OF FOREST FRAGMENTATION ON BIRD ASSEMBLAGES IN A NOVEL LANDSCAPE CONTEXT

We report findings of a large-scale study in a 100 000-ha subsection of the Tumut region in southern New South Wales, southeastern Australia. The study was designed to measure the effects of landscape context and habitat fragmentation on forest birds. The study region consisted of a forest mosaic characterized by different landscape contexts: large, continuous areas of native Eucalyptus forest, extensive stands of exotic softwood (radiata pine, Pinus radiata) plantation, and remnant patches of native Eucalyptus forest scattered throughout the extensive areas of radiata pine plantation. A set of 85 eucalypt remnants was randomly selected across several stratifying variables: four patch size classes (1-3 ha, 4-10 ha, 11-20 ha, and .20 ha), two isolation age classes (,20 years and .20 years since fragmentation), and five dominant eucalypt forest type classes. In addition to the 85 eucalypt remnants, a further 80 3-ha sites were selected for study: 40 in large, continuous areas of eucalypt forest and 40 in radiata pine stands. Point-interval counts of forest birds at the 165 sites were conducted in 1996 and 1997. Of 90 species recorded, 23.1 species (95% confidence interval, 22.0, 24.2 species), on average, were present in continuous eucalypt forest, 20.6 (19.5, 21.7) species in patch- shaped eucalypt remnants, 20.6 (19.5, 21.7) species in strip-shaped eucalypt remnants, and 16.7 (15.6, 17.8) species in radiata pine. Strong gradients in bird assemblages were found. These gradients were governed by a combination of landscape context, remnant size, and remnant shape effects, and, in the case of radiata pine sites, the extent of native forest surrounding the pine. These gradients could, in part, be explained by bird life history attributes such as foraging guild and nesting height. For example, birds more often detected in patch-shaped remnants were smaller, produced smaller clutches, were more likely to be migratory, and typically had cup nests or burrows. The results of our study showed that eucalypt fragments of all sizes and shapes have significant conservation value. This is because they contain many native species of birds, some of which are more abundant in fragments than they are in continuous eucalypt forests, and also because they increase native bird populations in nearby non-native pine plantations.

Short-term plyometric training improves running economy in highly trained middle and long distance runners.

Fifteen highly trained distance runners (&OV0312;O2max 71.1 ± 6.0 ml·min−1·kg−1, mean ± SD) were randomly assigned to a plyometric training (PLY; n = 7) or control (CON; n = 8) group. In addition to their normal training, the PLY group undertook 3 × 30 minutes PLY sessions per week for 9 weeks. Running economy (RE) was assessed during 3 × 4 minute treadmill runs (14, 16, and 18 km·h−1), followed by an incremental test to measure &OV0312;O2max. Muscle power characteristics were assessed on a portable, unidirectional ground reaction force plate. Compared with CON, PLY improved RE at 18 km·h−1 (4.1%, p = 0.02), but not at 14 or 16 km·h−1. This was accompanied by trends for increased average power during a 5-jump plyometric test (15%, p = 0.11), a shorter time to reach maximal dynamic strength during a strength quality assessment test (14%, p = 0.09), and a lower &OV0312;O2-speed slope (14%, p = 0.12) after 9 weeks of PLY. There were no significant differences in cardiorespiratory measures or &OV0312;O2max as a result of PLY. In a group of highly-trained distance runners, 9 weeks of PLY improved RE, with likely mechanisms residing in the muscle, or alternatively by improving running mechanics.

MODELING COUNT DATA OF RARE SPECIES: SOME STATISTICAL ISSUES

Most species abundance data show that a small number of species contribute the vast majority of individuals to a community. Thus, most taxa in a community are uncommon or rare. Yet such species will frequently be of ecological, conservation, or management interest. Data for uncommon or rare species will be presence/absence data or counts of abundance that contain a greater number of zero observations than would be predicted using standard, unimodal statistical distributions. Such data are generally referred to as zero-inflated data and require specialized methods for statistical analysis. Statistical approaches to modeling zero-inflated data include nonstandard mixture models; two-part, conditional models; and birth process models. In this paper, we briefly summarize two of these methods and illustrate the two-part, conditional approach to the problem of modeling count data with extra zeros. An advantage of this approach includes separate fits and separate interpretations of both components of count data;...

The conservation of arboreal marsupials in the montane ash forests of the Central Highlands of Victoria, South-East Australia: III. The habitat requirements of leadbeater's possum Gymnobelideus leadbeateri and models of the diversity and abundance of arboreal marsupials

Factors influencing the presence and abundance of leadbeaters possum Gymnobelideus leadbeateri McCoy and the diversity and abundance of other species of arboreal marsupials in montane ash forests were determined from logistic and Poisson regression analyses. The presence of G. leadbeateri was related to the number of trees with hollows and the basal area of Acacia spp. There was a positive correlation between the abundance of the animal and the number of trees with hollows, the quantity of decorticating bark and a negative correlation with the number of shrubs and the slope of the site. The diversity of arboreal marsupials was greatest on sites with a large number of trees with hollows, a high basal area of Acacia spp., a large quantity of decorticating bark and south- or east-facing sites. A model containing similar variables was developed for the abundance of arboreal marsupials. This model also produced a significant negative correlation with the number of stumps resulting from timber harvesting operations. Our findings highlight the deficiencies of current measures to conserve arboreal marsupials which are dependent on hollows in trees, when these forests are harvested by clear-felling.

Characteristics of hollow-bearing trees occupied by arboreal marsupials in the montane ash forests of the Central Highlands of Victoria, south-east Australia

Abstract A total of 1125 hollow-bearing trees was observed for the presence of arboreal marsupials in the montane ash forests of the Central Highlands of Victoria, south-east Australia. Different species of arboreal marsupials exhibited preferences for hollow-bearing trees with different characteristics. Gymnobelideus leadbeateri (Leadbeaters possum) selected short, fat trees with numerous holes and a large quantity of dense surrounding vegetation. Very large hollow-bearing trees were favoured as nest sites by Petauroides volans. Petaurus breviceps preferred trees with a large number of fissures, whereas trees favoured by Antechinus stuartii were tall and thin. Trees selected as nest sites by Trichosurus caninus were typically short and fat with few holes. Our results provide evidence of resource partitioning of hollow-bearing trees amongst arboreal marsupials. Clear-felling of montane ash forest on an 80–120-year rotation will have a highly detrimental effect on arboreal marsupials by substantially reducing the number and range of types of hollow-bearing trees required to support the complete diversity of species. The 80–120-year interval between logging operations will result in trees being harvested well before they develop characteristics which make them suitable nest sites for arboreal marsupials.

REPTILE AND ARBOREAL MARSUPIAL RESPONSE TO REPLANTED VEGETATION IN AGRICULTURAL LANDSCAPES

We report reptile and arboreal marsupial responses to vegetation planting and remnant native vegetation in agricultural landscapes in southeastern Australia. We used a hierarchical survey to select 23 landscapes that varied in the amounts of remnant native vegetation and planted native vegetation. We selected two farms within each landscape. In landscapes with plantings, we selected one farm with and one farm without plantings. We surveyed arboreal marsupials and reptiles on four sites on each farm that encompassed four vegetation types (plantings 7-20 years old, old-growth woodland, naturally occurring seedling regrowth woodland, and coppice [i.e., multistemmed] regrowth woodland). Reptiles and arboreal marsupials were less likely to occur on farms and in landscapes with comparatively large areas of plantings. Such farms and landscapes had less native vegetation, fewer paddock trees, and less woody debris within those areas of natural vegetation. The relatively large area of planting on these farms was insufficient to overcome the lack of these key structural attributes. Old-growth woodland, coppice regrowth, seedling regrowth, and planted areas had different habitat values for different reptiles and arboreal marsupials. We conclude that, although plantings may improve habitat conditions for some taxa, they may not effectively offset the negative effects of native vegetation clearing for all species, especially those reliant on old-growth woodland. Restoring suitable habitat for such species may take decades to centuries.

The abundance and development of cavities in Eucalyptus trees: a case study in the montane forests of Victoria, southeastern Australia

Abstract A study of the abundance of cavities in Eucalyptus regnans, Eucalyptus delegatensis, Eucalyptus nitens, Eucalyptus obliqua and Eucalyptus cypellocarpa is described. The investigation used a database of 2315 living and dead trees with cavities, measured on 523 sites each of 3 ha throughout the montane ash forests of the Central Highlands of Victoria, southeastern Australia. Poisson regression analysis was used to examine the relationships between the number and type of cavities and a range of attributes of trees. These analyses demonstrated that, for all species of trees, the abundance of holes, fissures and hollow branches increased with tree diameter. Log-linear analysis of contingency tables demonstrated that various combinations of cavity types typically occur. Patterns of co-occurrence of cavities changed significantly according to the diameter, height and form of trees. The application of restricted maximum likelihood estimation (REML) for examining multi-level data, enabled the relatioships between the number of cavities, tree characteristics and site parameters to be analysed The characteristics of trees that were important were height, diameter and form. Site parameter that had a significant influence on the total number of cavities in trees included slope, latitude and stand age. This highlights the range of factors, at several measured spatial scales, that may influence the development of cavities in Eucalyptus trees. Although the various relationships derived in this study were highly significant, the statistical models had limited predictive ability. Thus for any given tree the development of cavities will be influenced by site and tree attributes as well as highly stochastic episodic events that may occur during its lifetime. The key findings from the study are discussed in terms of their relevance to forest wildlife management.

The conservation of arboreal marsupials in the Montane ash forests of the central highlands of Victoria, Southeast Australia: I. Factors influencing the occupancy of trees with hollows

Abstract A total of 1125 trees with hollows on 152 sites in the montane ash forests of the Central Highlands of Victoria was observed for the presence of arboreal marsupials. One of every 3 trees was occupied by an arboreal marsupial and

A large-scale “experiment” to examine the effects of landscape context and habitat fragmentation on mammals

Abstract A large-scale “experiment” was undertaken in a 100 000 ha region of south-eastern Australia to examine the response of mammals to landscape context, habitat fragmentation and other factors. The investigation examined the presence and abundance of mammals in three broad categories of sites for which there were strong contrasts in the composition of the surrounding landscape: • Large contiguous areas of Eucalyptus forest, • Areas dominated by exotic plantation softwood Radiata Pine (Pinus radiata) trees, and • Fragments of eucalypt forest surrounded by an extensive P. radiata plantation. These sites provided the basis for assessing the effects of what we term “landscape context”. Eighty-six fragments of remnant eucalypt forest of varying size, shape, isolation age and other attributes were selected by a stratified, randomization process. Forty sites were located in large contiguous areas of Eucalyptus forest and these were matched to the sites in the remnants on the basis of forest type, geology and climatic conditions. A further 40 sites were selected in areas dominated by P. radiata trees and these also were matched to sites in the remnants and those in large contiguous areas of native forest on the basis of geology and climatic conditions. Two major surveys sampled mammals in the study. Hairtubing (a technique for detecting animals from the analysis of fur collected in a small portable bait station) was utilized at all 166 sites selected in the study. Trapping and a combination of different types of hairtubing was then employed at a subset of 58 sites. Data from these surveys was used to investigate the response of mammals to landscape context, habitat fragmentation and other attributes. A sub-theme of the study was to assess the efficacy of different methods to count mammals. There were large differences in the effectiveness of the different field techniques. The best technique (best in the sense of counting most animals) varied between species, particularly in relation to body size. Trapping and smaller-sized hairtubes were superior for small mammals such as Brown Antechinus (Antechinus stuartii) and Bush Rat (Rattus fuscipes). Large hairtubes performed best in the detection of large mammals like the Common Wombat (Vombatus ursinus), Common and Mountain Brushtail Possums (Trichosurus vulpecula and Trichosurus caninus), and Swamp Wallaby (Wallabia bicolor). W. bicolor and V. ursinus showed no response to landscape context and were detected at similar rates in the remnants, sites in large contiguous areas of native forest and sites dominated by stands of P. radiata. Trichosurus spp. were recorded significantly less often in sites dominated by P. radiata trees. Landscape context effects for R. fuscipes and A. stuartii varied depending on the field methods employed to sample mammals. However, in general, R. fuscipes and A. stuartii were recorded significantly less frequently in P. radiata sites than sites in large contiguous areas of Eucalyptus forest or fragments of remnant eucalypt forest surrounded by the softwood plantation. An important finding of our work was that although some species were extremely rare in P. radiata stands, no significant differences were identified in mammal presence and abundance between sites located in large contiguous areas of Eucalyptus forest and sites in fragments of remnant eucalypt forest surrounded by the softwood plantation. This finding suggests that either: animals from potential population sources in contiguous eucalypt forest can move through the softwood plantation and colonise the remnants, or populations residing in the fragments of remnant eucalypt forest are large enough to resist local extinction. Softwood plantations are presently being expanded in south-eastern Australia, particularly on semi-cleared farmland that supports remnant fragments of native Eucalyptus forest and woodland. Our findings indicate that remnant native forest within plantations of exotic P. radiata trees are occupied by several species of native mammals even when these fragments are surrounded by extensive, largely unsuitable plantation forests that have been established for many decades. These fragments should not be cleared during efforts to expand the softwood plantation estate. Large remnants and those with particular habitat features such as a dense cover of vegetation should have priority for exemption from clearing.