A comparison of mark-recapture distance-sampling methods applied to aerial surveys of eastern grey kangaroos

Aerial surveys of kangaroos (Macropus spp.) in Queensland are used to make economically important judgements on the levels of viable commercial harvest. Previous analysis methods for aerial kangaroo surveys have used both mark-recapture methodologies and conventional distance-sampling analyses. Conventional distance sampling has the disadvantage that detection is assumed to be perfect on the transect line, while mark-recapture methods are notoriously sensitive to problems with unmodelled heterogeneity in capture probabilities. We introduce three methodologies for combining together mark-recapture and distance-sampling data, aimed at exploiting the strengths of both methodologies and overcoming the weaknesses. Of these methods, two are based on the assumption of full independence between observers in the mark-recapture component, and this appears to introduce more bias in density estimation than it resolves through allowing uncertain trackline detection. Both of these methods give lower density estimates than conventional distance sampling, indicating a clear failure of the independence assumption. The third method, termed point independence, appears to perform very well, giving credible density estimates and good properties in terms of goodness-of-fit and percentage coefficient of variation. Estimated densities of eastern grey kangaroos range from 21 to 36 individuals km-2, with estimated coefficients of variation between 11% and 14% and estimated trackline detection probabilities primarily between 0.7 and 0.9.

Evaluating and validating abundance monitoring methods in the absence of populations of known size: review and application to a passive tracking index

Rarely is it possible to obtain absolute numbers in free-ranging populations and although various direct and indirect methods are used to estimate abundance, few are validated against populations of known size. In this paper, we apply grounding, calibration and verification methods, used to validate mathematical models, to methods of estimating relative abundance. To illustrate how this might be done, we consider and evaluate the widely applied passive tracking index (PTI) methodology. Using published data, we examine the rationality of PTI methodology, how conceptually animal activity and abundance are related and how alternative methods are subject to similar biases or produce similar abundance estimates and trends. We then attune the method against populations representing a range of densities likely to be encountered in the field. Finally, we compare PTI trends against a prediction that adjacent populations of the same species will have similar abundance values and trends in activity. We show that while PTI abundance estimates are subject to environmental and behavioural stochasticity peculiar to each species, the PTI method and associated variance estimate showed high probability of detection, high precision of abundance values and, generally, low variability between surveys, and suggest that the PTI method applied using this procedure and for these species provides a sensitive and credible index of abundance. This same or similar validation approach can and should be applied to alternative relative abundance methods in order to demonstrate their credibility and justify their use.

Effects of exposure to Bovine viral diarrhoea virus 1 on risk of bovine respiratory disease in Australian feedlot cattle

Viruses play a key role in the complex aetiology of bovine respiratory disease (BRD). Bovine viral diarrhoea virus 1 (BVDV-1) is widespread in Australia and has been shown to contribute to BRD occurrence. As part of a prospective longitudinal study on BRD, effects of exposure to BVDV-1 on risk of BRD in Australian feedlot cattle were investigated. A total of 35,160 animals were enrolled at induction (when animals were identified and characteristics recorded), held in feedlot pens with other cattle (cohorts) and monitored for occurrence of BRD over the first 50 days following induction. Biological samples collected from all animals were tested to determine which animals were persistently infected (PI) with BVDV-1. Data obtained from the Australian National Livestock Identification System database were used to determine which groups of animals that were together at the farm of origin and at 28 days prior to induction (and were enrolled in the study) contained a PI animal and hence to identify animals that had probably been exposed to a PI animal prior to induction. Multi-level Bayesian logistic regression models were fitted to estimate the effects of exposure to BVDV-1 on the risk of occurrence of BRD.Although only a total of 85 study animals (0.24%) were identified as being PI with BVDV-1, BVDV-1 was detected on quantitative polymerase chain reaction in 59% of cohorts. The PI animals were at moderately increased risk of BRD (OR 1.9; 95% credible interval 1.0-3.2). Exposure to BVDV-1 in the cohort was also associated with a moderately increased risk of BRD (OR 1.7; 95% credible interval 1.1-2.5) regardless of whether or not a PI animal was identified within the cohort. Additional analyses indicated that a single quantitative real-time PCR test is useful for distinguishing PI animals from transiently infected animals.The results of the study suggest that removal of PI animals and/or vaccination, both before feedlot entry, would reduce the impact of BVDV-1 on BRD risk in cattle in Australian feedlots. Economic assessment of these strategies under Australian conditions is required. © 2016 Elsevier B.V.