Experimental evaluation of koala scat persistence and detectability with implications for pellet-based fauna census

Establishing species distribution and population trends are basic requirements in conservation biology, yet acquiring this fundamental information is often difficult. Indirect survey methods that rely on fecal pellets (scats) can overcome some difficulties but present their own challenges. In particular, variation in scat detectability and decay rate can introduce biases. We studied how vegetation communities affect the detectability and decay rate of scats as exemplified by koalas Phascolarctos cinereus: scat detectability was highly and consistently dependent on ground layer complexity (introducing up to 16% non-detection bias); scat decay rates were highly heterogeneous within vegetation communities; exposure of scats to surface water and rain strongly accelerated scat decay rate and finally, invertebrates were found to accelerate scat decay rate markedly, but unpredictably. This last phenomenon may explain the high variability of scat decay rate within a single vegetation community. Methods to decrease biases should be evaluated when planning scat surveys, as the most appropriate method(s) will vary depending on species, scale of survey and landscape characteristics. Detectability and decay biases are both stronger in certain vegetation communities, thus their combined effect is likely to introduce substantial errors in scat surveys and this could result in inappropriate and counterproductive management decisions

Susceptibility to a sexually transmitted disease in a wild koala population shows heritable genetic variance but no inbreeding depression

The koala, one of the most iconic Australian wildlife species, is facing several concomitant threats that are driving population declines. Some threats are well known and have clear methods of prevention (e.g., habitat loss can be reduced with stronger land-clearing control), whereas others are less easily addressed. One of the major current threats to koalas is chlamydial disease, which can have major impacts on individual survival and reproduction rates and can translate into population declines. Effective management strategies for the disease in the wild are currently lacking, and to date we know little about the determinants of individual susceptibility to disease. Here we investigated the genetic basis of variation in susceptibility to chlamydia using one of the most intensively studied wild koala populations. We combined data from veterinary examinations, chlamydia testing, genetic sampling and movement monitoring. Out of our sample of 342 wild koalas, 60 were found to have chlamydia. Using genotype information on 5007 SNPs to investigate the role of genetic variation in determining disease status, we found no evidence of inbreeding depression, but a heritability of 0.11 (95%CI = 0.05 – 0.23) for the probability that koalas had chlamydia. Heritability of susceptibility to chlamydia could be relevant for future disease management, as it suggests adaptive potential for the population

A review of fauna in mine rehabilitation in Australia: current state and future directions

Restoration of degraded land has been identified as a top research priority in conservation. Fauna plays a critical role in the re-establishment of a functional ecosystem, yet fauna recolonization of restored areas is less studied than flora. We reviewed the findings of 71 publications on fauna recolonization, through the example of mining rehabilitation in the Australian continent, a global stronghold of large-scale mining.Species densities and richness were frequently lower in rehabilitated compared to undisturbed areas, even more so when only native species were considered. Amongst all criteria used to measure success, recovery of the pre-mining fauna community composition was the hardest to achieve. Introduced species were often found in rehabilitated areas but further research is needed to determine the duration of this association. Meta-analyses of the factors influencing mining rehabilitation success for fauna revealed that fauna groups recolonized heterogeneously. Recolonization was dependent on the methods used to rehabilitate and the number of years since rehabilitation. Notably, methods combining the use of fresh topsoil with the addition of seeds and seedlings were most successful for fauna recolonization, both in term of fauna density and richness.Limitations to this review included strong biases toward certain mining companies, as well as missing data, which decreased the power of meta-analysis. Available publications did not evenly represent all fauna taxa and studies were short when compared to the time needed to re-construct whole ecosystems. We consider the development of comprehensive fauna standards for assessing rehabilitation success critical. This could be the next challenge in restoration ecology

Potential 'Ecological Traps' of restored landscapes: koalas Phascolarctos cinereus re-occupy a rehabilitated mine site

With progressively increasing anthropogenic habitat disturbances, restoration of impacted landscapes is becoming a critical element of biodiversity conservation. Evaluation of success in restoration ecology rarely includes faunal components, usually only encompassing abiotic and floral components of the ecosystems. Even when fauna is explicitly included, it is usually only species presence/absence criteria that are considered. If restoration is to have a positive outcome, however, populations in restored habitats should exhibit comparable survival and reproductive rates to populations found in undisturbed surroundings. If a species recolonises restored areas but later experiences decreased fitness, restored areas could become ecological sinks or traps. We investigated this possibility in a case study of koalas Phascolarctos cinereus occupying rehabilitated mining areas on North Stradbroke Island, Australia. Our holistic approach compared rehabilitated and undisturbed areas on the basis of their vegetation characteristics, of koalas' body condition, roosting trees, diet, as well as predator index. Koalas using rehabilitated areas appeared to be able to access an adequate supply of roosting and fodder trees, were in good condition and had high reproductive output. We did not find any significant differences in predator density between rehabilitated areas and undisturbed surroundings. The results presented in this study showed there was no evidence that the post-mining rehabilitated areas constitute ecological sinks or traps. However, to reach a definitive conclusion as to whether areas rehabilitated post-mining provide at least equivalent habitat to undisturbed locations, additional research could be undertaken to assess foliar nutrient/water/toxin differences and predation risk in rehabilitated areas compared with undisturbed areas. More generally, the evaluation of whether restoration successfully produces a functional ecological community should include criteria on the fitness of faunal populations reoccupying such sites, so as to ensure functioning ecosystems, rather than ecological sinks or traps, are the outcome

The habitat and diet of koalas (Phascolarctos cinereus) in Queensland

Descriptions of koala (Phascolarctos cinereus) habitat and diet from 11 sites across Queensland are presented. Koala activity was recorded from 49 regional ecosystems across nine land zones and five bioregions. Thirty-four tree species were identified from an examination of leaf cuticle fragments in faecal pellets. Although the species were from three families and seven genera, 44% of browse species (15) belonged to the myrtaceous subgenus Symphomyrtus. Eleven of these contributed most of the koala diet across all sites. However, most species were present in minor or trace dietary elements. There was also a large number of unidentified species or dietary elements, all of which were usually present in trace amounts. The importance of these minor and trace components is not known. Diet at some sites was founded on a single eucalypt species. Here the likelihood of those sites’ browse resources being lost or degraded by stochastic events, as climate variability increases, raises questions about the persistence of the resident koala populations

Accuracy and efficiency of detection dogs: a powerful new tool for koala conservation and management

Accurate data on presence/absence and spatial distribution for fauna species is key to their conservation. Collecting such data, however, can be time consuming, laborious and costly, in particular for fauna species characterised by low densities, large home ranges, cryptic or elusive behaviour. For such species, including koalas (Phascolarctos cinereus), indicators of species presence can be a useful shortcut: faecal pellets (scats), for instance, are widely used. Scat surveys are not without their difficulties and often contain a high false negative rate. We used experimental and field-based trials to investigate the accuracy and efficiency of the first dog specifically trained for koala scats. The detection dog consistently out-performed human-only teams. Off-leash, the dog detection rate was 100%. The dog was also 19 times more efficient than current scat survey methods and 153% more accurate (the dog found koala scats where the human-only team did not). This clearly demonstrates that the use of detection dogs decreases false negatives and survey time, thus allowing for a significant improvement in the quality and quantity of data collection. Given these unequivocal results, we argue that to improve koala conservation, detection dog surveys for koala scats could in the future replace human-only teams

Data from: Fresh Is best: accurate SNP genotyping from koala scats

Maintaining genetic diversity is a crucial component in conserving threatened species. For the iconic Australian koala, there is little genetic information on wild populations that is not either skewed by biased sampling methods (e.g. sampling effort skewed towards urban areas) or of limited usefulness due to low numbers of microsatellites used. The ability to genotype DNA extracted from koala scats using next-generation sequencing technology will not only help resolve location sample bias but also improve the accuracy and scope of genetic analyses (e.g. neutral versus adaptive genetic diversity, inbreeding, and effective population size). Here we present the successful SNP genotyping (1272 SNP loci) of koala DNA extracted from scat, using a proprietary DArTseq™ protocol. We compare genotype results from two day old scat DNA and 14 day old scat DNA to a blood DNA template, to test accuracy of scat genotyping. We find that DNA from fresher scat results in fewer loci with missing information than DNA from older scat, however, 14 day old scat can still provide useful genetic information, depending on the research question. We also find that a subset of 209 conserved loci can accurately identify individual koalas, even from older scat samples. In addition, we find that DNA sequences identified from scat samples through the DArTseq™ process can provide genetic identification of koala diet species, bacterial and viral pathogens, and parasitic organisms

Inbreeding and disease avoidance in a free‐ranging koala population

Habitat destruction and fragmentation are increasing globally, forcing surviving species into small, isolated populations. Isolated populations typically experience heightened inbreeding risk and associated inbreeding depression and population decline; although individuals in these populations may mitigate these risks through inbreeding avoidance strategies. For koalas, as dietary specialists already under threat in the northern parts of their range, increased habitat fragmentation and associated inbreeding costs are of great conservation concern. Koalas are known to display passive inbreeding avoidance through sex-biased dispersal, although population isolation will reduce dispersal pathways. We tested whether free-ranging koalas display active inbreeding avoidance behaviours. We used VHF tracking data, parentage reconstruction, and veterinary examination results to test whether free-ranging female koalas avoid mating with (a) more closely related males; and (b) males infected with sexually transmitted Chlamydia pecorum. We found no evidence that female koalas avoid mating with relatively more related available mates. In fact, as the relatedness of potential mates increases, so did inbreeding events. We also found no evidence that female koalas can avoid mating with males infected with C.\ua0pecorum. The absence of active inbreeding avoidance mechanisms in koalas is concerning from a conservation perspective, as small, isolated populations may be at even higher risk of inbreeding depression than expected. At risk koala populations may require urgent conservation interventions to augment gene flow and reduce inbreeding risks. Similarly, if koalas are not avoiding mating with individuals with chlamydial disease, populations may be at higher risk from disease than anticipated, further impacting population viability