School of BioSciences - Research Publications
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ItemUnbiased population heterozygosity estimates from genome-wide sequence data(WILEY, 2021-10)Abstract Heterozygosity is a metric of genetic variability frequently used to inform the management of threatened taxa. Estimating observed and expected heterozygosities from genome‐wide sequence data has become increasingly common, and these estimates are often derived directly from genotypes at single nucleotide polymorphism (SNP) markers. While many SNP markers can provide precise estimates of genetic processes, the results of ‘downstream’ analysis with these markers may depend heavily on ‘upstream’ filtering decisions. Here we explore the downstream consequences of sample size, rare allele filtering, missing data thresholds and known population structure on estimates of observed and expected heterozygosity using two reduced‐representation sequencing datasets, one from the mosquito Aedes aegypti (ddRADseq) and the other from a threatened grasshopper, Keyacris scurra (DArTseq). We show that estimates based on polymorphic markers only (i.e. SNP heterozygosity) are always biased by global sample size (N), with smaller N producing larger estimates. By contrast, results are unbiased by sample size when calculations consider monomorphic as well as polymorphic sequence information (i.e. genome‐wide or autosomal heterozygosity). SNP heterozygosity is also biased when differentiated populations are analysed together while autosomal heterozygosity remains unbiased. We also show that when nucleotide sites with missing genotypes are included, observed and expected heterozygosity estimates diverge in proportion to the amount of missing data permitted at each site. We make three recommendations for estimating genome‐wide heterozygosity: (a) autosomal heterozygosity should be reported instead of (or in addition to) SNP heterozygosity; (b) sites with any missing data should be omitted and (c) populations should be analysed in independent runs. This should facilitate comparisons within and across studies and between observed and expected measures of heterozygosity.
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ItemThe power of eDNA sampling to investigate the impact of Australian mega-fires on platypus occupancy(Elsevier, 2023-10-01)Fire plays an important role in many ecosystems, but megafires are increasing the area burnt in forested regions globally. The 2019–2020 megafires in south-eastern Australia were unprecedented with respect to area burnt and the spatial extent of high-severity fire. Yet, there is limited knowledge regarding the impact of these megafires on biodiversity, especially aquatic fauna. Here we investigate the impact of the 2019–2020 megafires on the distribution of a semi-aquatic monotreme thought to be in decline: the platypus, Ornithorhynchus anatinus. We leveraged extensive pre-fire environmental DNA (eDNA) sampling and coupled this with additional sampling at two timepoints post-fire, to conduct a Before-After-Control-Impact (BACI) study. We used site occupancy-detection modelling to estimate platypus occupancy across fire affected and non-fire affected sites over time as well as the interaction between occupancy, high rainfall, and fire severity. We detected a negative effect of fire presence on platypus occupancy in both post-fire time periods. Platypus occupancy was also predicted to be lower at sites that experienced high rainfall post-fire and were situated within watersheds that had a large proportion burnt at high-severity. With area burnt and the extent of high-severity fire increasing globally, and predictions of more extreme rainfall events in south-eastern Australia in the future, the impact of fire on aquatic fauna requires greater consideration in post-fire assessments and biodiversity management more generally. The use of eDNA sampling and detection methods in a BACI framework provides a promising means to fill these knowledge gaps but does require pre-emptive sampling.
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ItemEvaluating predator control using two non-invasive population metrics: a camera trap activity index and density estimation from scat genotyping(CSIRO Publishing, 2023)Context: Invasive mammalian predators are a threat to biodiversity and agriculture globally, yet management outcomes for lethal predator control remain difficult to monitor and evaluate. Understanding whether changes in activity indices correspond to true changes in population density will help inform effective monitoring and management programs. Aims: The aim of this study was to evaluate the effect of poison baiting on invasive red fox (Vulpes vulpes) populations using two alternative population metrics: fox activity from camera trap surveys and density estimation from scat genetic analysis. Methods: We conducted before–after control–impact studies in two regions of semi-arid Australia (Wimmera and Mallee) by monitoring paired non-treatment and treatment sites during unbaited and baited periods. We estimated the effects of poison baiting on: (1) a monthly fox activity index, derived from an array of 10 off-road camera traps per site; and (2) fox density. To estimate density, we collected fox scats along 14-km transects, identified individuals using polymorphic microsatellite DNA markers and fitted spatially explicit capture–recapture models. Key results: Fox activity remained consistently low at all sites except the Mallee non-treatment. The top-ranked models of fox activity and density contained an interaction between treatment and period, with an interactive and additive effect of region, respectively. However, there was little evidence that baiting reduced fox activity or density. In the unbaited period, fox densities ranged from 0.69 (95% CI: 0.47–1.0) to 1.06 (95% CI: 0.74–1.51) foxes km−2 and were similar across regions. Conclusions: Camera traps have the potential to provide continuous index-based measures of fox populations but may not record sufficient observations to detect change. Indices can also be confounded by variations in animal behaviour. Scat genetic analysis is a viable option for providing direct estimates of population change at specific snapshots in time; however, this approach is considerably more expensive, and large sample sizes may be required if genotyping success is low. Implications: Our study presents a rare example of multiple concurrent – and non-invasive – monitoring techniques to evaluate the effectiveness of predator control. We highlight the value of rigorous study designs and high-quality density information for designing predator management and monitoring programs.
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ItemGenetic sampling and an activity index indicate contrasting outcomes of lethal control for an invasive predator(WILEY, 2022-08)ABSTRACT Invasive mammalian predators are implicated in the ongoing decline of a suite of fauna and continue to be a major cause of human–wildlife conflict globally. Lethal control of invasive predators is a common management strategy; however, the use of activity indices to measure management effectiveness is problematic. Non‐invasive genetic sampling may be a viable alternative approach to monitoring as individual animals can be identified, allowing for direct estimation of population density through newly developed spatially explicit capture–recapture techniques. Here we compare inferences derived from a basic activity index (number of scats per survey) and genetic sampling of scats within a before–after control–impact design to evaluate the effectiveness of a lethal control programme targeting red foxes (Vulpes vulpes) in south‐eastern Australia. The activity index was highly variable through time and suggested the baiting programme reduced fox activity on the treatment transect relative to changes on the non‐treatment transect. In contrast, genetic sampling and spatially explicit capture–recapture analysis suggested fox density varied little throughout the study, with any changes unable to be attributed to the baiting programme. Additionally, genetic sampling confirmed many individuals persisted through 7 months of baiting. These contrasting results may be partially explained by changes in scat detectability due to seasonal changes in behaviour and the disproportionate contribution of some individuals to scat counts. Our pre‐baiting density estimate of 0.28 foxes km2 (95% CI: 0.22–0.38) was lower than expected given the high productivity, abundant prey species and lack of larger predators in the study region. Our results highlight the need for cautious interpretation of activity indices and demonstrates the value of incorporating recent methodological and statistical advances when evaluating lethal control programmes.
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ItemAn environmental DNA approach to informing restoration of the functionally extinct oyster, Ostrea angasi(WILEY, 2022-11)Abstract The success of oyster reef restoration can be enhanced by data on the distribution of remnant populations to inform the selection of suitable restoration locations. A quantitative polymerase chain reaction‐based environmental DNA (eDNA) assay was designed to provide distribution data for the oyster, Ostrea angasi, whose reefs are functionally extinct in Port Phillip Bay, Australia. Ostrea angasi eDNA accumulation and decay was measured in aquaria containing oysters in low and high densities, prior to testing the efficacy of the eDNA approach for detection of oysters at 15 field sites. Ostrea angasi eDNA accumulated significantly faster in aquaria where more individuals were present, while eDNA became undetectable 2–6 days after oysters were removed in low‐density treatments. The eDNA samples were successful at detecting O. angasi in the field when taken in close proximity of an oyster population. Increasing the sample number and volume could maximize oyster detection, demonstrating the potential of eDNA to identify suitable sites for the restoration of functionally extinct marine ecosystems.
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ItemConservation genetics as a management tool: The five best-supported paradigms to assist the management of threatened species(NATL ACAD SCIENCES, 2022-01-04)About 50 y ago, Crow and Kimura [An Introduction to Population Genetics Theory (1970)] and Ohta and Kimura [Genet. Res. 22, 201-204 (1973)] laid the foundations of conservation genetics by predicting the relationship between population size and genetic marker diversity. This work sparked an enormous research effort investigating the importance of population dynamics, in particular small population size, for population mean performance, population viability, and evolutionary potential. In light of a recent perspective [J. C. Teixeira, C. D. Huber, Proc. Natl. Acad. Sci. U.S.A. 118, 10 (2021)] that challenges some fundamental assumptions in conservation genetics, it is timely to summarize what the field has achieved, what robust patterns have emerged, and worthwhile future research directions. We consider theory and methodological breakthroughs that have helped management, and we outline some fundamental and applied challenges for conservation genetics.
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ItemAlcohol keeps eDNA at the party longer(Pensoft Publishers, 2021-03-04)For a typical eDNA water study, water will be filtered on site, before prompt transfer to a laboratory for DNA extraction and required scientific analysis. In a setting where transport is quick and available, this is a straightforward process. However, many of our studies can occur in remote Australia where sample preservation presents many logistical challenges. Typically, we advise clients to store eDNA water filters after sampling below 4 °C to ensure minimal DNA degradation. For many clients however, field studies often occur in an isolated setting without adequate refrigeration facilities, and as such present challenges for this process. Rather than compromise on sample integrity, EnviroDNA conducted a pilot study into the use of alternate preservation methods on our most commonly used 0.22 mm Sterivex filters. With help from our friendly neighbourhood goldfish tank, our standard 4 °C protocol was compared to a variety of conditions including filled ethanol filters, flushed ethanol filters, lysis buffer and silica bead storage conditions at both 4 °C and room temperature. The study, conducted at various time points over 14-days, used qPCR to quantify the amount of DNA extracted from the filter. Our results revealed that storage within or using flushed ethanol, allowed the samples to be stored for longer time intervals at room temperature, with similar, or in some cases, improved DNA elutions. This protocol optimisation has allowed us to offer an alternate sample storage protocol for clients, expanding the availability and accessibility of eDNA biodiversity assessments around Australia.
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ItemShifting paradigms in restoration of the world's coral reefs(Wiley, 2017-09-01)Many ecosystems around the world are rapidly deteriorating due to both local and global pressures, and perhaps none so precipitously as coral reefs. Management of coral reefs through maintenance (e.g., marine‐protected areas, catchment management to improve water quality), restoration, as well as global and national governmental agreements to reduce greenhouse gas emissions (e.g., the 2015 Paris Agreement) is critical for the persistence of coral reefs. Despite these initiatives, the health and abundance of corals reefs are rapidly declining and other solutions will soon be required. We have recently discussed options for using assisted evolution (i.e., selective breeding, assisted gene flow, conditioning or epigenetic programming, and the manipulation of the coral microbiome) as a means to enhance environmental stress tolerance of corals and the success of coral reef restoration efforts. The 2014–2016 global coral bleaching event has sharpened the focus on such interventionist approaches. We highlight the necessity for consideration of alternative (e.g., hybrid) ecosystem states, discuss traits of resilient corals and coral reef ecosystems, and propose a decision tree for incorporating assisted evolution into restoration initiatives to enhance climate resilience of coral reefs.
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