Interpreting the decline of a koala population at Marys Mount, Liverpool Plains, north-west New South Wales (2013–2016)

In the early 1990s the koala became the mascot for a revegetation program to control salinity on agricultural land around Gunnedah in New South Wales, and a snapshot of the koala’s distribution in the shire was collected at that time, mainly via a mail survey. After the success of tree plantings in the 1990s, the koala population of the Liverpool Plains became a focus of increasing local conservation efforts, as well as research to explain koala population dynamics. This included a repeat mail survey conducted in 2006, which enabled the comparison of the reported distributions to be undertaken. These two citizen science surveys had different response rates but both produced extensive datasets. By 2006, koalas were reported from a wider extent than in 1990, particularly to the north and east of the town, and in more developed agricultural areas, but with highest densities in areas with more than 25% wooded vegetation. In 1990, koalas were reported mostly from locations that were surrounded by more than 40% wooded vegetation with the core of the distribution being on the basalt hills south of the town of Gunnedah. Koalas were also reported with increased relative frequency in the town, and this formed the core of the reported sightings at that time. There were still no reports from many of the vegetated hilly margins of the shire. The observed changes in the pattern of reporting reflects the actual distribution of koalas intersected with the likelihood of observation and the willingness of people to report koalas, and also identify the areas that may be under-sampled to determine the true habitat breath of koalas in the area.

Koalas are prime candidates to study the impact of climate change because they are specialised folivores and lack any ready means of avoiding weather extremes. Koalas are widely but patchily distributed throughout eastern mainland Australia. Efforts to protect them from landscape-scale threats have been identified in the NSW 2008 Koala Recovery Plan, the 2010 NSW Priorities for biodiversity adaptation to climate change and the 2009-14 National Koala Conservation and Management Strategy. The statements in the formal strategies and recovery plans identify a number of problems, two of which we address in this paper. The first problem is that of extreme weather and the second is the change of leaf quality from rising levels of carbon dioxide. This paper capitalises on our field study in Gunnedah, in north-west NSW, which examined a 1990s success story where the local koala population benefited from the plantings of trees and shrubs to hold down the water table in the face of a rising salinity crisis. In late 2009, heatwaves killed an estimated 25% of the Gunnedah koala population. This foreshadows how increased climate variability will impact on koala populations. In 2008, chlamydiosis - a disease causing infertility - had been established as being present in the Gunnedah population. The likely spread of this disease throughout the Gunnedah koala population presents a further challenge to wildlife managers in the context of a changing climate. The potential indirect effects of global climate change - how increasing concentrations of atmospheric CO2 may reduce the availability of the nutrients in Eucalyptus foliage to koalas - is described and the implication drawn that elevated concentrations of atmospheric CO2 may threaten some populations of free-ranging koalas. The Liverpool Plains are among Australia's prime agricultural landscapes where the conservation of biodiversity occurs largely on private land. Consequently, we need to integrate climate change adaptation with rural land management and restoration practices. The research demonstrates the contribution from the cross-disciplinary links. It adds to our ability to monitor sustainable native fauna populations and threatened species by distinguishing among the multiple causes of population change, and it can also be viewed as a pilot demonstrating the value of longitudinal wild population disease monitoring.

To overcome shortcomings in discriminating Chlamydia pecorum strains infecting the koala (Phascolarctos cinereus) at the local level, we developed a novel genotyping scheme for this pathogen to inform koala management at a fine-scale subpopulation level. We applied this scheme to two geographically distinct koala populations in New South Wales, Australia: the Liverpool Plains and the Southern Highlands to South-west Sydney (SHSWS). Our method provides greater resolution than traditional multi-locus sequence typing, and can be used to monitor strain emergence, movement, and divergence across a range of fragmented habitats. Within the Liverpool Plains population, suspected recent introduction of a novel strain was confirmed by an absence of genetic diversity at the earliest sampling events and limited diversity at recent sampling events. Across the partially fragmented agricultural landscape of the Liverpool Plains, diversity within a widespread sequence type suggests that this degree of fragmentation may hinder but not prevent spread. In the SHSWS population, our results suggest movement of a strain from the south, where diverse strains exist, into a previously Chlamydia-free area in the north, indicating the risk of expansion towards an adjacent Chlamydia-negative koala population in South-west Sydney. In the south of the SHSWS where koala subpopulations appear segregated, we found evidence of divergent strain evolution. Our tool can be used to infer the risks of strain introduction across fragmented habitats in population management, particularly through practices such as wildlife corridor constructions and translocations.

In ruminants infected with Chlamydia pecorum, shorter lengths of coding tandem repeats (CTR) within two genes, the inclusion membrane protein (incA) and Type III secretor protein (ORF663), have been previously associated with pathogenic outcomes. In other chlamydial species, the presence of a chlamydial plasmid has been linked to heightened virulence, and the plasmid is not ubiquitous in C. pecorum across the koala's range. We therefore investigated these three markers: incA, ORF663 and C. pecorum plasmid, as potential indicators of virulence in two koala populations in New South Wales with differing expression of urogenital chlamydiosis; the Liverpool Plains and one across the Southern Highlands and South-west Sydney (SHSWS). We also investigated the diversity of these loci within strains characterised by the national multi-locus sequence typing (MLST) scheme. Although CTR lengths of incA and ORF663 varied across the populations, they occurred only within previously described pathogenic ranges for ruminants. This suggests a relatively short-term host-pathogen co-evolution within koalas and limits the utility of CTR lengths for incA and ORF663 as virulence markers in the species. However, in contrast to reports of evolution of C. pecorum towards lower virulence, as indicated by longer CTR lengths in ruminants and swine, CTR lengths for ORF663 appeared to be diverging towards less common shorter CTR lengths within strains recently introduced to koalas in the Liverpool Plains. We detected the plasmid across 90% and 92% of samples in the Liverpool Plains and SHSWS respectively, limiting its utility as an indicator of virulence. It would be valuable to examine the CTR lengths of these loci across koala populations nationally. Investigation of other hypervariable loci may elucidate the evolutionary trajectory of virulence in C. pecorum induced disease in koalas. Profiling of virulent strains will be important in risk assessments for strain movement to naïve or susceptible populations through translocations and wildlife corridor construction.

A 5-year Chlamydia vaccination programme could reverse disease-related koala population decline: Predictions from a mathematical model using field data

The aim of this study was to develop tools for monitoring and modelling threats to wildlife and apply these approaches to koala populations in a rapidly urbanising landscape. The study addressed problems in establishing the conservation status of a population through the examination of the direct and indirect threats to species’ persistence at the landscape scale (10000s ha). Wildlife populations are increasingly under pressure as human activities expand into natural ecosystems. In Australia, rapid population growth along the eastern seaboard is impacting heavily on regional biodiversity and threatening the persistence of many species, including the koala (Phascolarctos cinereus). Land clearing for residential developments and associated infrastructure such as roads, results in direct threats to habitat amount and species abundance; and introduces new threats associated with habitat fragmentation, vehicles, dogs and disease. Effective management of koala populations in these rapidly urbanising landscapes requires detailed regional information and monitoring tools to assess the current conservation status and trends in the population, habitat and threatening processes. This study integrated traditional ecological survey techniques with remote sensing, geographical information systems and landscape fragmentation analysis, to monitor the direct threats of habitat loss; decline in abundance; and contraction in extent of a regional koala population. The associated threats of increased mortality caused by vehicles, dogs and disease were monitored using statistical techniques applied to a long-term data set of incidental koala mortality. Spatial modelling underpinned much of this research and was integrated with satellite image processing for the delineation of potential koala habitat and to assess changes in koala numbers and distribution over time. Spatial modelling was also applied to identify, quantify, map and categorise the major causes of mortality and estimate the impacts on koala persistence. The inter-relationship between landscape configuration, forest fragmentation and the causes of koala mortality were modelled to explain the independent effects of natural and anthropogenic variables. Predictions from these models were tested using geostatistical techniques to determine their suitability for informing threatened species management decision making. The study was conducted in an area of 375km2 known as the Koala Coast, located 20km south-east of Brisbane, South East Queensland, Australia. The study contributes to an understanding of the interrelationship between the koala, the environment, and threatening processes impacting on long-term survival and species’ persistence. The monitoring and modelling tools provide: tools to assess the current condition and changes in conservation status of a koala population based on habitat change; the first regional koala population estimate utilising direct counts; the first assessment of the anthropogenic mortality rate in a regional koala population; the first comprehensive evaluation of road kill blackspots for an entire regional road network (for any wildlife species); and the first enumeration of the association between traffic volume and koala mortality. It is likely that the koala populations on the urban footprint will not be able to withstand the high rates of anthropogenic mortality in addition to natural mortality and that this will result in localised extinctions. Abundance modelling revealed that, if left unchecked, the high mortality and reduction of habitat values will result in the loss of a substantial portion (38%) of the koala population. The landscape configuration of the remaining non-urban area was found to be too small to maintain a minimum viable population of 5000 koalas and indicates that the Koala Coast population may be reaching a point where extinction of the population becomes inevitable. Consequently, immediate management action is urgently needed to implement mortality mitigation measures, improve koala habitat values and prevent any further increases in the size of the urban footprint. Long-term persistence of wildlife in rapidly urbanising landscapes is dependent on the ability to address local threats and implement conservation plans. This study provides some of the tools and approaches to better manage wildlife populations such as the koala. Land managers and planners now need to prevent the loss of koalas and koala populations; mitigate the threats affecting koala survival; reverse the declines in habitat and abundance; and monitor the success of management actions.

In the summer of 1979–80, there was a sharp decline in the koala population along Mungalalla Creek in south‐western Queensland. The decline was associated with a heatwave and drought. Live animals and carcasses were counted soon after the decline and at three subsequent periods. It was estimated that more than 63% of the population died. The drought and heatwave caused extensive leaf‐fall and/or browning of the foliage in food trees along stretches of dry creek. The proximate cause of death was thought to be a combination of malnutrition and dehydration. There was evidence, including the differential survival of koalas along the creek, of marked heterogeneity in the quality of the habitat. At sites where the trees were not affected (mainly on large permanent water‐holes) koalas had good body condition and mortality was low, whereas on stretches of dry creek (marginal habitat), koalas were in poor health (poor condition, anaemia, high tick loads) and mortality was very high. Survival of the population was not threatened because many animals survived at the permanent water‐holes. There is evidence that mortality was highest among young animals which may be excluded from optimal sites by older dominant animals. In the years after the crash, continuing drought appeared to prevent recovery of the population. It is thought that such population crashes are rare events as they are apparently caused partly by unusual climatic conditions.

How much can a koala bear? Physiological stress, movement patterns and diet of koalas (Phascolarctos cinereus) at the semi-arid edge of their distribution

Koalas are an iconic, endangered, Australian marsupial. Disease, habitat destruction, and catastrophic mega-fires have reduced koalas to remnant patches of their former range. With increased likelihood of extreme weather events and ongoing habitat clearing across Australia, koala populations are vulnerable to further declines and isolation. Small, isolated populations are considered at risk when there is increased inbreeding, erosion of genomic diversity, and loss of adaptive potential, all of which reduce their ability to respond to prevailing threats. Here, we characterized the current genomic landscape of koalas using data from The Koala Genome Survey, a joint initiative between the Australian Federal and New South Wales Governments that aimed to provide a future-proofed baseline genomic dataset across the koala's range in eastern Australia. We identified several regions of the continent where koalas have low genomic diversity and high inbreeding, as measured by runs of homozygosity. These populations included coastal sites along southeast Queensland and northern and mid-coast New South Wales, as well as southern New South Wales and Victoria. Analysis of genomic vulnerability to future climates revealed that northern koala populations were more at risk due to the extreme expected changes in this region, but that the adaptation required was minimal compared with other species. Our genomic analyses indicate that continued development, particularly linear infrastructure along coastal sites, and resultant habitat destruction are causing isolation and subsequent genomic erosion across many koala populations. Habitat protection and the formation of corridors must be employed for all koala populations to maintain current levels of diversity. For highly isolated koala populations, active management may be the only way to improve genomic diversity in the short term. If koalas are to be conserved for future generations, reversing their genomic isolation must be a priority in conservation planning.

Cryptococcosis is a fungal disease in humans and animals, caused by the Cryptococcus neoformans and Cryptococcus gattii species complexes. Clinical cryptococcosis primarily manifests as upper respiratory tract disease; however, dissemination to other organs, particularly the brain, can occur. Nasal colonisation and subclinical cryptococcosis are common in koalas (Phascolarctos cinereus) due to their shared environmental niche with Cryptococcus: Eucalyptus trees. However, for reasons that remain unclear, the prevalence of clinical disease is low in koalas. Interactions between respiratory pathogens and the nasal mycobiome are thought to play a role in the development and progression of numerous respiratory diseases. As such, this study aimed to characterise the mycobiome of the nasal vestibule in koalas with and without evidence of cryptococcal colonisation and subclinical disease via the next-generation sequencing (NGS) of the ITS1 region of the fungal internal transcribed spacer (ITS) gene. Samples were collected from 47 koalas from a population of free-ranging koalas in the Liverpool Plains, NSW, Australia, with a known history of Cryptococcus exposure and nasal colonisation. Of the 47 animals tested, 6.4% were culture-positive only, 4.3% were seropositive only, and 2.1% were culture- and seropositive. C. gattii was detected in four samples via NGS. C. neoformans was not detected via NGS. There were no significant differences in the nasal mycobiomes of Cryptococcus-positive and -negative animals; thus, we could not establish a definitive association between the mycobiome and infection outcomes. We identified a number of fungal genera that were significantly more abundant in samples from Cryptococcus-positive animals, but there was no apparent relationship between these genera and the development of cryptococcosis. This study represents the first investigation of the nasal mycobiota of wild koalas. Further studies involving koalas with clinical disease are necessary to determine the role of the nasal mycobiota in the development of cryptococcosis.

Chlamydiosis is a significant disease affecting Eastern Australian koalas (Phascolarctos cinereus), contributing to the decline of some koala populations, necessitating investigations into appropriate management strategies to address chlamydiosis in wild koala populations. The aim of this study was to investigate the effect of a Chlamydia pecorum recombinant Major Outer Membrane Protein (rMOMP) vaccine as a potential strategy for managing chlamydiosis at a population level. This study comprised a blinded, randomised placebo-controlled trial, encompassing different koala populations where chlamydiosis is having differing effects. Wild koalas were recruited into a vaccination or a placebo treatment group and followed for 12 months, with recapture and resampling at 2, 6 and 12 months post vaccination. Vaccination stimulated a significant plasma anti-MOMP IgG response and greater IL-17 and TNFα mRNA fold change from rMOMP stimulated leukocytes, however, did not boost pre-existing immune responses, from natural infection, in koalas. The observed immunological stimulation did not translate to any effect on chlamydiosis or chlamydial shedding in our study populations. These findings highlight the necessity of improving our understanding of what constitutes a protective immune response in koalas to guide the development of a more effective vaccine. This study evaluated the estimated effect of vaccination necessary to achieve management outcomes predicted by modelling studies. It is possible that vaccination has a more modest effect and could benefit koala populations with a lower disease prevalence or be useful in conjunction with additional management strategies.

External signs of disease are frequently used as indicators of disease susceptibility. However, immune profiling can be a more effective indicator to understand how host responses to infection may be shaped by host, pathogen and environmental factors. To better inform wildlife health assessment and research directions, we investigated the utility of a novel multivariate immunophenotyping approach examining innate and adaptive immune responses in differing climatic, pathogen co-infection and demographic contexts across two koala (Phascolarctos cinereus) populations in New South Wales: the Liverpool Plains (LP), and Southern Highlands to South-west Sydney (SHSWS). Relative to the comparatively healthy SHSWS, the LP had greater and more variable innate immune gene expression (IL-1β, IL-6), and KoRV transcription. During extreme heat and drought, koalas from the LP displayed upregulation of a stress pathway gene and reduced adaptive immune genes expression, haematocrit and plasma protein, suggesting the possibility of environmental impacts through multiple pathways. In those koalas, KoRV transcription status, Chlamydia pecorum infection loads, and visible urogenital inflammation were not associated with immune variation, suggesting that immune markers were more sensitive indicators of real-time impacts than observed disease outcomes.

A decline in the koala population on Phillip I , has been evident for some time. This study, in an area set apart from public access, quantifies some aspects of this decline. A triple-count technique for a closed population model, with the freedom that the probability of sighting can vary between the surveys, was used to obtain an estimate of the population within a 65-ha study area. The initial population, in June 1980, was estimated to be 117; this declined to 62 in 3.5 years, during which period 23 deaths and 24 births were recorded. The decline, which averaged 16 koalas per year, is discussed in terms of the low birth rate, of dispersal, and of the contribution of predation by dogs to the death rate.

BackgroundThe koala (Phascolarctos cinereus) is an arboreal marsupial that was historically widespread across eastern Australia until the end of the 19th century when it suffered a steep population decline. Hunting for the fur trade, habitat conversion, and disease contributed to a precipitous reduction in koala population size during the late 1800s and early 1900s. To examine the effects of these reductions in population size on koala genetic diversity, we sequenced part of the hypervariable region of mitochondrial DNA (mtDNA) in koala museum specimens collected in the 19th and 20th centuries, hypothesizing that the historical samples would exhibit greater genetic diversity.ResultsThe mtDNA haplotypes present in historical museum samples were identical to haplotypes found in modern koala populations, and no novel haplotypes were detected. Rarefaction analyses suggested that the mtDNA genetic diversity present in the museum samples was similar to that of modern koalas.ConclusionsLow mtDNA diversity may have been present in koala populations prior to recent population declines. When considering management strategies, low genetic diversity of the mtDNA hypervariable region may not indicate recent inbreeding or founder events but may reflect an older historical pattern for koalas.

We examined a long-term, repeat dataset for the koala population within Coffs Harbour Local Government Area. Analyses of these data have led to the conclusion that, following a perceived population decline in the 1980s, the koala population of Coffs Harbour has endured between 1990 and 2011 and showed no evidence of a precipitous decline during this period. Rather, the population change is best characterised as stable to slowly declining. This conclusion appears to contradict a common view of recent koala population declines on the north coast of New South Wales. There are four possible explanations for the population’s apparent stability: that conservation efforts and planning regulations have been effective; that surviving adults are persisting in existing home ranges in remnant habitat; that the broader Coffs Harbour population is operating as a ‘source and sink’ metapopulation; and/or that the standard survey methods employed are not sufficiently sensitive to detect small population changes. These findings do not mean there is no need for future conservation efforts aimed at koalas in Coffs Harbour; however, such efforts will need to better understand and account for a koala population that can be considered to be stable to slowly declining.