Carlo Pacioni

Contribution of genetics to ecological restoration

Ecological restoration of degraded ecosystems has emerged as a critical tool in the fight to reverse and ameliorate the current loss of biodiversity and ecosystem services. Approaches derived from different genetic disciplines are extending the theoretical and applied frameworks on which ecological restoration is based. We performed a search of scientific articles and identified 160 articles that employed a genetic approach within a restoration context to shed light on the links between genetics and restoration. These articles were then classified on whether they examined association between genetics and fitness or the application of genetics in demographic studies, and on the way the studies informed restoration practice. Although genetic research in restoration is rapidly growing, we found that studies could make better use of the extensive toolbox developed by applied fields in genetics. Overall, 41% of reviewed studies used genetic information to evaluate or monitor restoration, and 59% provided genetic information to guide prerestoration decision‐making processes. Reviewed studies suggest that restoration practitioners often overlook the importance of including genetic aspects within their restoration goals. Even though there is a genetic basis influencing the provision of ecosystem services, few studies explored this relationship. We provide a view of research gaps, future directions and challenges in the genetics of restoration.

Genetic diversity loss in a biodiversity hotspot: Ancient DNA quantifies genetic decline and former connectivity in a critically endangered marsupial

The extent of genetic diversity loss and former connectivity between fragmented populations are often unknown factors when studying endangered species. While genetic techniques are commonly applied in extant populations to assess temporal and spatial demographic changes, it is no substitute for directly measuring past diversity using ancient DNA (aDNA). We analysed both mitochondrial DNA (mtDNA) and nuclear microsatellite loci from 64 historical fossil and skin samples of the critically endangered Western Australian woylie (Bettongia penicillata ogilbyi), and compared them with 231 (n = 152 for mtDNA) modern samples. In modern woylie populations 15 mitochondrial control region (CR) haplotypes were identified. Interestingly, mtDNA CR data from only 29 historical samples demonstrated 15 previously unknown haplotypes and detected an extinct divergent clade. Through modelling, we estimated the loss of CR mtDNA diversity to be between 46% and 91% and estimated this to have occurred in the past 2000–4000 years in association with a dramatic population decline. In addition, we obtained near‐complete 11‐loci microsatellite profiles from 21 historical samples. In agreement with the mtDNA data, a number of ‘new’ microsatellite alleles was only detected in the historical populations despite extensive modern sampling, indicating a nuclear genetic diversity loss >20%. Calculations of genetic diversity (heterozygosity and allelic rarefaction) showed that these were significantly higher in the past and that there was a high degree of gene flow across the woylies historical range. These findings have an immediate impact on how the extant populations are managed and we recommend the implementation of an assisted migration programme to prevent further loss of genetic diversity. Our study demonstrates the value of integrating aDNA data into current‐day conservation strategies.

Hematologic characteristics of the woylie (Bettongia penicillata ogilbyi).

Abstract An accurate assessment of animal health is fundamental to disease investigation in wildlife. Blood samples (n = 609) from several populations of the endangered woylie or brush-tailed bettong (Bettongia penicillata ogilbyi), collected between March 2006 and April 2010 in Western Australia and South Australia, were used to establish hematologic reference ranges. Differences between populations, sexes, and seasons were also investigated. Significant sex differences in hematocrit, red blood cell, total white blood cell, neutrophil, lymphocyte, and eosinophil counts were evident in at least one population. Generally, males had higher hematocrit and blood cell concentrations than did females. A positive association of the erythron parameters with rainfall was also detected. The hematologic characteristics of woylie populations described in this study greatly increase knowledge of the health status in these populations. The data also represent a baseline to enable monitoring and detection of changes in the health status in these populations as well as representing a valid dataset for comparison with hematologic investigations in other macropods and marsupials.

A high prevalence of Theileria penicillata in woylies (Bettongia penicillata)

The woylie or brush-tailed bettong (Bettongia penicillata) is a medium-sized native Australian marsupial that has undergone a dramatic decline in numbers in recent years. Trypanosome parasites have been identified in the woylie but little is known about the prevalence and clinical impact of other haemoprotozoan parasites in these marsupials. In the present study, the occurrence and molecular phylogeny of a piroplasm was studied in woylies from six different sites in Western Australia (WA). Blood samples were screened by PCR at the 18S rRNA locus and 80.4% (123/153) of the blood samples were positive for piroplasm DNA. Sequence and phylogenetic analysis of 12 of these positives identified them as Theileria penicillata, and sequencing of cloned PCR products indicated that no other species of Theileria were present. Infected woylies had a lower body weight but microscopic evaluation of the blood films indicated that T. penicillata did not appear to cause red cell injury or anaemia. Further studies are required to determine the clinical significance of T. penicillata in woylies.

A virological investigation into declining woylie populations

Abstract. The woylie (Bettongia penicillata ogilbyi) is a critically endangered small Australian marsupial that is in a state of accelerated population decline for reasons that are currently unknown. The aim of the present study was to elucidate the involvement of several viral pathogens through strategic serological testing of several wild woylie populations. Testing for antibodies against the Wallal and Warrego serogroup of orbiviruses, Macropod herpesvirus 1 and Encephalomyocarditis virus in woylie sera was undertaken through virus neutralisation tests. Moreover, testing for antibodies against the the alphaviruses Ross River virus and Barmah Forest virus and the flaviviruses Kunjin virus and Murray Valley encephalitis virus was undertaken through virus neutralisation tests and ELISA mainly because of the interest in the epidemiology of these important zoonoses as it was considered unlikely to be the cause of the decline. Between 15 and 86 samples were tested for each of the four sites in south-western Australia (Balban, Keninup, Warrup and Karakamia). Results indicated no exposure to any of the viral pathogens investigated, indicating that all populations are currently naïve and may be at risk if these pathogens were to be introduced.

Assessing the economic benefits of starling detection and control to Western Australia

The common starling (Sturnus vulgaris) has a proven invasion history in many countries, and at a continental scale in North America and Australasia. In Australia, starlings are firmly established throughout the eastern states and Tasmania. Incursions of starlings into Western Australia (WA) represent a significant threat to this State’s agricultural, public amenity and biodiversity assets. We present models of starling population dynamics that incorporate environmental and control effort variability. We incorporate knowledge of starling ecology with economic data to assess the potential economic cost of starlings establishing in WA, evaluating the cost–benefits for each management scenario. We calculated starling population size will approach carrying capacity in WA within as little as 30 years if left unchecked. A population of this size could cost the WA economy up to

Predators and genetic fitness: key threatening factors for the conservation of a bettong species

43.7 million annually in 2011/2012 dollars. Over a 50 year horizon, the conservative benefit–cost ratio for ongoing detection and control at the current level of expenditure is 6.03:1. However, even under current levels of control, starling numbers are projected to increase to almost 11 million by 2061. Further improvements in the efficiency of starling detection and control and/or an increased level of expenditure on detection and control are required.

vortexR: an R package for post Vortex simulation analysis

Globally, many wildlife species are declining and an increasing number are threatened by extinction or are extinct. Active management is generally required to mitigate these trends and population viability analysis (PVA) enables different scenarios to be evaluated and informs management decisions. Based on population parameters obtained from a threatened bettong, the woylie (Bettongia penicillata ogilbyi), we developed and validated a PVA model. We identified the demographic and genetic responses to different threatening factors and developed a general framework that would facilitate similar work in other bettong species. The two main threatening processes are predation by introduced animals and its interaction with reduced fitness (e.g. due to inbreeding depression or a disease). Although predation alone can drive a decline in certain circumstances (e.g. when predation success is independent from prey population density), synergistically, predation and reduced fitness can be particularly relevant, especially for small populations. The minimum viable population size was estimated at 1000–2000 individuals. In addition, the models identified that research into age-specific mortality rates and predation rates by introduced animals should be the focus of future work. The PVA model created here provides a basis to investigate threatening processes and management strategies in woylie populations and other extant bettong species, given the ecological and physiological similarities among these threatened species.

Spatially-explicit model for assessing wild dog control strategies in Western Australia

Summary Population viability analysis is an important tool for wildlife ecologists, geneticists and managers, which is used for the assessment of extinction risks, the evaluation of threatening processes and the establishment of conservation targets. Vortex is among the leading population modelling software and the latest release includes an automated sensitivity test module. However, an equivalent automation of the post-simulation data inspection and analysis is currently missing. vortexR is an R package to automate the analysis and visualisation of outputs from the population viability modelling software Vortex. vortexR facilitates collating Vortex output files, data visualisation and basic analyses (e.g. pairwise comparisons of scenarios), as well as providing more advanced statistics, such as searching for the best regression model(s) from a list of predictors to investigate the main effect and the interaction effects of the variables of interest. This package speeds up and greatly facilitates the reproducibility and portability of post-simulation analysis results.

Augmenting the conservation value of rehabilitated wildlife by integrating genetics and population modeling in the post-rehabilitation decision process

Large predators can significantly impact livestock industries. In Australia, wild dogs (Canis lupus familiaris, Canis lupus dingo, and hybrids) cause economic losses of more than AUD