Clair L. Alston

Carbon storage in the soils and vegetation of contrasting land uses in northern New South Wales, Australia

The organic carbon stock in biomass and soil profiles sampled from nearby paddocks with different land-use histories was estimated at 7 sites in the upper Liverpool Plains catchment and the Manilla district of north-western New South Wales, Australia. The distribution of soil carbon concentrations over a depth of 2 m was significantly affected by site and land use. Continuous cultivation and cropping over ≥20 years significantly depleted carbon concentrations compared with grassy woodlands in the surface 0.20 m at all sites and to a depth of 0.60 m at 3 sites. Depth of sampling (0–0.20 v. 0–1.0 m) significantly affected the differences between land uses at most sites regarding estimates of the stock of soil carbon. These results show that differences in soil carbon concentrations and stock size do not remain constant with depth between contrasting land uses. However, comparisons between land uses of the total amount of carbon stored were dominated by the number of trees per ha and the size of the trees in grassy woodlands. The implications of these results for carbon accounting are discussed.

Evaluation of the Suchey-Brooks method of age estimation in an Australian subpopulation using computed tomography of the pubic symphyseal surface.

Despite the prominent use of the Suchey-Brooks (S-B) method of age estimation in forensic anthropological practice, it is subject to intrinsic limitations, with reports of differential interpopulation error rates between geographical locations. This study assessed the accuracy of the S-B method to a contemporary adult population in Queensland, Australia and provides robust age parameters calibrated for our population. Three-dimensional surface reconstructions were generated from computed tomography scans of the pubic symphysis of male and female Caucasian individuals aged 15-70 years (n = 195) in Amira and Rapidform. Error was analyzed on the basis of bias, inaccuracy and percentage correct classification for left and right symphyseal surfaces. Application of transition analysis and Chi-square statistics demonstrated 63.9 and 69.7% correct age classification associated with the left symphyseal surface of Australian males and females, respectively, using the S-B method. Using Bayesian statistics, probability density distributions for each S-B phase were calculated, providing refined age parameters for our population. Mean inaccuracies of 6.77 (±2.76) and 8.28 (±4.41) years were reported for the left surfaces of males and females, respectively; with positive biases for younger individuals (<55 years) and negative biases in older individuals. Significant sexual dimorphism in the application of the S-B method was observed; and asymmetry in phase classification of the pubic symphysis was a frequent phenomenon. These results recommend that the S-B method should be applied with caution in medico-legal death investigations of Queensland skeletal remains and warrant further investigation of reliable age estimation techniques.

Beef carcasses with larger eye muscle areas, lower ossification scores and improved nutrition have a lower incidence of dark cutting.

This study evaluated the effect of eye muscle area (EMA), ossification, carcass weight, marbling and rib fat depth on the incidence of dark cutting (pH(u)>5.7) using routinely collected Meat Standards Australia (MSA) data. Data was obtained from 204,072 carcasses at a Western Australian processor between 2002 and 2008. Binomial data of pH(u) compliance was analysed using a logit model in a Bayesian framework. Increasing eye muscle area from 40 to 80 cm², increased pH(u) compliance by around 14% (P<0.001) in carcasses less than 350 kg. As carcass weight increased from 150 kg to 220 kg, compliance increased by 13% (P<0.001) and younger cattle with lower ossification were also 7% more compliant (P<0.001). As rib fat depth increased from 0 to 20mm, pH(u) compliance increased by around 10% (P<0.001) yet marbling had no effect on dark cutting. Increasing musculature and growth combined with good nutrition will minimise dark cutting beef in Australia.

Ontogeny of the spheno-occipital synchondrosis in a modern Queensland, Australian population using computed tomography.

Due to disparity regarding the age at which skeletal maturation of the spheno-occipital synchondrosis occurs in forensic and biological literature, this study provides recalibrated multislice computed tomography (MSCT) age standards for the Australian (Queensland) population, using a Bayesian statistical approach. The sample comprises retrospective cranial/cervical MSCT scans obtained from 448 males and 416 females aged birth to 20 years from the Skeletal Biology and Forensic Anthropology Research Osteological Database. Fusion status of the synchondrosis was scored using a modified six-stage scoring tier on an MSCT platform, with negligible observer error (κ = 0.911 ± 0.04, intraclass correlation coefficient = 0.994). Bayesian transition analysis indicates that females are most likely to transition to complete fusion at 13.1 years and males at 15.6 years. Posterior densities were derived for each morphological stage, with complete fusion of the synchondrosis attained in all Queensland males over 16.3 years of age and females aged 13.8 years and older. The results demonstrate significant sexual dimorphism in synchondrosis fusion and are suggestive of intrapopulation variation between major geographic regions in Australia. This study contributes to the growing repository of contemporary anthropological standards calibrated for the Queensland milieu to improve the efficacy of the coronial process for medicolegal death investigation. As a stand-alone age indicator, the basicranial synchondrosis may be consulted as an exclusion criterion when determining the age of majority that constitutes 17 years in Queensland forensic practice.

Extending the Bayesian mixture model to incorporate spatial information in analysing sheep CAT scan images

The purpose of CAT scanning in some animal science experiments is to provide estimates of the proportion of the tissues, fat, muscle, and bone present in an individual body, and compare some of the density characteristics. In this paper we present an extension to the hierarchical Bayesian Normal mixture model, which incorporates some of the information provided by the neighbouring pixels in a CAT scan image. This neighbour information is included in the model through the use of a Markov random field for the component allocation variable. This extended mixture model provides a more responsive fit to the local likelihood of the data than that of the independent mixture model. The effectiveness of this modelling technique is illustrated by comparing its performance with that of a Normal mixture model and a fixed boundary method in 3 examples. In these examples it is shown that the extended mixture model we propose is most useful in situations that involve only slight separation of components. The advantages of the model decline as the separation of components increases.

Bayesian mixture models in a longitudinal setting for analysing sheep CAT scan images

CAT scanning is used in longitudinal animal science experiments to assess possible changes to carcase composition induced by treatment over given time periods. A hierarchical Bayesian mixture model can be used to analyse the CAT scan data in terms of the proportion of each tissue type present in a scan. In this paper we present an extension to the hierarchical Bayesian mixture model in which estimated parameters from neighbouring CAT scans can be incorporated into the current model. These models are demonstrated using two examples.

Introducing Computed Tomography Standards for Age Estimation of Modern Australian Subadults Using Postnatal Ossification Timings of Select Cranial and Cervical Sites

Contemporary, population‐specific ossification timings of the cranium are lacking in current literature due to challenges in obtaining large repositories of documented subadult material, forcing Australian practitioners to rely on North American, arguably antiquated reference standards for age estimation. This study assessed the temporal pattern of ossification of the cranium and provides recalibrated probabilistic information for age estimation of modern Australian children. Fusion status of the occipital and frontal bones, atlas, and axis was scored using a modified two‐ to four‐tier system from cranial/cervical DICOM datasets of 585 children aged birth to 10 years. Transition analysis was applied to elucidate maximum‐likelihood estimates between consecutive fusion stages, in conjunction with Bayesian statistics to calculate credible intervals for age estimation. Results demonstrate significant sex differences in skeletal maturation (p < 0.05) and earlier timings in comparison with major literary sources, underscoring the requisite of updated standards for age estimation of modern individuals.

Statistical analysis of sheep CAT scan images using a Bayesian mixture model

CAT scanning techniques are available to provide images that can aid in the assessment of carcass traits in live sheep during the course of animal experiments. In this paper we present a Bayesian formulation of an analysis that allows us to determine the composition of a scan in terms of proportions of the image attributable to fat, muscle (lean tissue), and bone. The technique, known as finite mixture modelling, also provides information about the distributional properties of some of these components, such as fat and bone. In the case of muscle, the analysis estimates several Gaussian distributions that combine to provide an approximation to its likelihood. The model is estimated through the use of the Gibbs sampler, with the distributional properties of carcass components being obtained from the resultant Markov chains.

Effect of Broadcast Baiting on Abundance Patterns of Red Imported Fire Ants (Hymenoptera: Formicidae) and Key Local Ant Genera at Long-Term Monitoring Sites in Brisbane, Australia

ABSTRACT In 2001, the red imported fire ant (Solenopsis invicta Buren) was identified in Brisbane, Australia. An eradication program involving broadcast bait treatment with two insect growth regulators and a metabolic inhibitor began in September of that year and is currently ongoing. To gauge the impacts of these treatments on local ant populations, we examined long-term monitoring data and quantified abundance patterns of S. invicta and common local ant genera using a linear mixed-effects model. For S. invicta, presence in pitfalls reduced over time to zero on every site. Significantly higher numbers of S. invicta workers were collected on high-density polygyne sites, which took longer to disinfest compared with monogyne and lowdensity polygyne sites. For local ants, nine genus groups of the 10 most common genera analyzed either increased in abundance or showed no significant trend. Five of these genus groups were significantly less abundant at the start of monitoring on high-density polygyne sites compared with monogyne and low-density polygyne sites. The genus Pheidole significantly reduced in abundance over time, suggesting that it was affected by treatment efforts. These results demonstrate that the treatment regime used at the time successfully removed S. invicta from these sites in Brisbane, and that most local ant genera were not seriously impacted by the treatment. These results have important implications for current and future prophylactic treatment efforts, and suggest that native ants remain in treated areas to provide some biological resistance to S. invicta.

A Bayesian analysis of an agricultural field trial with three spatial dimensions

Modern technology now has the ability to generate large datasets over space and time. Such data typically exhibit high autocorrelations over all dimensions. The field trial data motivating the methods of this paper were collected to examine the behaviour of traditional cropping and to determine a cropping system which could maximise water use for grain production while minimising leakage below the crop root zone. They consist of moisture measurements made at 15 depths across 3 rows and 18 columns, in the lattice framework of an agricultural field. Bayesian conditional autoregressive (CAR) models are used to account for local site correlations. Conditional autoregressive models have not been widely used in analyses of agricultural data. This paper serves to illustrate the usefulness of these models in this field, along with the ease of implementation in WinBUGS, a freely available software package. The innovation is the fitting of separate conditional autoregressive models for each depth layer, the ‘layered CAR model’, while simultaneously estimating depth profile functions for each site treatment. Modelling interest also lay in how best to model the treatment effect depth profiles, and in the choice of neighbourhood structure for the spatial autocorrelation model. The favoured model fitted the treatment effects as splines over depth, and treated depth, the basis for the regression model, as measured with error, while fitting CAR neighbourhood models by depth layer. It is hierarchical, with separate onditional autoregressive spatial variance components at each depth, and the fixed terms which involve an errors-in-measurement model treat depth errors as interval-censored measurement error. The Bayesian framework permits transparent specification and easy comparison of the various complex models compared.