Environmental DNA methods for biosecurity and invasion biology in terrestrial ecosystems: Progress, pitfalls, and prospects

Analysis of environmental DNA (eDNA) enables indirect detection of species without the need to directly observe and sample them. For biosecurity and invasion biology, eDNA-based methods are useful to address biological invasions at all phases, from detecting arrivals to confirming eradication of past invasions. We conducted a systematic review of the literature and found that in biosecurity and invasion biology, eDNA has primarily been used to detect new incursions and monitor spread in marine and freshwater ecosystems, with much slower uptake in terrestrial ecosystems, reflecting a broader trend common to the usage of eDNA tools. In terrestrial ecosystems, eDNA research has mostly focussed on the use of eDNA metabarcoding to characterise biodiversity, rather than targeting biosecurity threats or non-native populations. We discuss how eDNA-based methods are being applied to terrestrial ecosystems for biosecurity and managing non-native populations at each phase of the invasion continuum: transport, introduction, establishment, and spread; across different management options: containment, control, and eradication; and for detecting the impact of non-native organisms. Finally, we address some of the current technical issues and caveats of eDNA-based methods, particularly for terrestrial ecosystems, and how these might be solved. As eDNA-based methods improve, they will play an increasingly important role in the early detection and adaptive management of biological invasions, and the implementation of effective biosecurity controls.

Species-specific SNP arrays for non-invasive genetic monitoring of a vulnerable bat

Genetic tagging from scats is one of the minimally invasive sampling (MIS) monitoring approaches commonly used to guide management decisions and evaluate conservation efforts. Microsatellite markers have traditionally been used but are prone to genotyping errors. Here, we present a novel method for individual identification in the Threatened ghost bat Macroderma gigas using custom-designed Single Nucleotide Polymorphism (SNP) arrays on the MassARRAY system. We identified 611 informative SNPs from DArTseq data from which three SNP panels (44-50 SNPs per panel) were designed. We applied SNP genotyping and molecular sexing to 209 M. gigas scats collected from seven caves in the Pilbara, Western Australia, employing a two-step genotyping protocol and identifying unique genotypes using a custom-made R package, ScatMatch. Following data cleaning, the average amplification rate was 0.90 ± 0.01 and SNP genotyping errors were low (allelic dropout 0.003 ± 0.000) allowing clustering of scats based on one or fewer allelic mismatches. We identified 19 unique bats (9 confirmed/likely males and 10 confirmed/likely females) from a maternity and multiple transitory roosts, with two male bats detected using roosts, 9 km and 47 m apart. The accuracy of our SNP panels enabled a high level of confidence in the identification of individual bats. Targeted SNP genotyping is a valuable tool for monitoring and tracking of non-model species through a minimally invasive sampling approach.

Environmental detection of Fasciola hepatica by loop-mediated isothermal amplification

Fasciola hepatica, commonly referred to as liver flukes, is a substantial zoonotic parasitic disease of humans and livestock globally. While infection is readily controlled by anthelmintics, namely triclabendazole, the heavy reliance on triclabendazole has resulted in drug resistance appearing worldwide. Due to drug resistance, it is imperative to adopt an integrated parasite management program to preserve the efficacy of currently available anthelmintics. A integrated liver fluke management plan would benefit from a simple rapid, field-deployable diagnostic for detection of F. hepatica in environment and the host. Therefore, a rapid DNA test using loop-mediated isothermal amplification was developed and optimised for the detection of F. hepatica from faecal and water samples to enable the detection of parasites both within the host and from the environment. The assay presented here is fast, with amplification in ≤20 min, and highly sensitive, with a detection limit of 5 × 10^-4 ng/µL. The workflow presented here provides a time to result of ≤60 min without requiring a commercial kit for the extraction of DNA from faecal and water samples, and pending further validation from field-samples, could potentially be used to enable real-time decision making to mitigate parasite prevalence on a farming property and with no requirement for sample transportation.

The Australian Roadkill Reporting Project-Applying Integrated Professional Research and Citizen Science to Monitor and Mitigate Roadkill in Australia

Simple Summary

Australia has no database of national roadkill. The current research project fills that knowledge gap by developing a roadkill reporting application that enables professional and citizen scientists to record photographs of roadkill with location, time and date. This embodies the concept of ‘One Welfare’ as it affects humans, animals and the environment. Uploaded to a website, these data can identify roadkill hotspots, tabulate species of animals killed and potentially be used for ecological studies of roadkill numbers, species distribution, population trends, animal behaviour and disease. Initial results indicate that mammal roadkill mostly occurs at night and that of birds and reptiles during daytime. Mammals make up three-quarters of the roadkill recorded and this includes endangered species. Two examples of roadkill hotspots are shown in Queensland and Tasmania. These will enable further research to suggest how roadkill mitigation measures may be optimally employed.

Abstract

Australia has no national roadkill monitoring scheme. To address this gap in knowledge, a roadkill reporting application (app) was developed to allow members of the public to join professional researchers in gathering Australian data. The app is used to photograph roadkill and simultaneously records the GPS location, time and date. These data are uploaded immediately to a website for data management. To illustrate the capacity to facilitate cost-effective mitigation measures the article focuses on two roadkill hotspots—in Queensland and Tasmania. In total, 1609 reports were gathered in the first three months of the project. They include data on mammals (n = 1203, 75%), birds (n = 125, 7.8%), reptiles (n = 79, 4.9%), amphibians (n = 4, 0.025%), unidentified (n = 189, 11.8%) and unserviceable ones (n = 9). A significant finding is variance in the distribution of mammals and birds at different times of day. These findings reflect diurnal variation in the activity levels of different species and underline the need for data on a targeted species to be collected at appropriate times of day. By continuing to facilitate roadkill monitoring, it is anticipated that the data generated by the app will directly increase knowledge of roadkill numbers and hotspots. Indirectly, it will provide value-added information on animal behaviour, disease and population dynamics as well as for species distribution mapping.

DNA barcoding for identification of fish species from freshwater in Enugu and Anambra States of Nigeria

Within Enugu and Anambra States, Nigeria, identification of fishes has been based on morphological traits and do not account for existing biodiversity. For DNA barcoding, assessment of biodiversity, conservation and fishery management, 44 fish sampled from Enugu and Anambra States were isolated, amplified and sequenced with mitochondrial cytochrome oxidase subunit I (COI). Twenty groups clustering at 100% bootstrap value including monophyletic ones were identified. The phylogenetic diversity (PD) ranged from 0.0397 (Synodontis obesus) to 0.2147 (Parachanna obscura). The highest percentage of genetic distance based on Kimura 2-parameter was 37.00 ± 0.0400. Intergeneric distances ranged from 15.8000 to 37.0000%. Congeneric distances were 6.9000 ± 0.0140–28.1000 ± 0.0380, with Synodontis as the existing synonymous genus. Confamilial distances in percentage were 16.0000 ± 0.0140 and 25.7000 ± 0.0300. Forty-two haplotypes and haplotype diversity of 0.9990 ± 0.0003 were detected. Nucleotide diversity was 0.7372, while Fu and Li’s D* test statistic was 2.1743 (P < 0.02). Tajima’s D was 0.2424 (P > 0.10) and nucleotide frequencies were C (17.70%), T (29.40%), A (24.82%), G (18.04%) and A + T (54.22%). Transitional mutations were more than transversions. Twenty species (99–100%) were identified with the e-value, maximum coverage and bit-score of 1e−43, 99–100 and 185–1194, respectively. Seventeen genera and 12 families were found and Clariidae (n = 14) was the most dominant among other families. The fish species resolution, diversity assessment and phylogenetic relationships were successfully obtained with the COI marker. Clariidae had the highest number of genera and families. Phylogenetic diversity analysis identified Parachanna obscura as the most evolutionarily divergent one. This study will contribute to fishery management, and conservation of freshwater fishes in Enugu and Anambra States, Nigeria.

DNA mini-barcoding of leporids using noninvasive fecal DNA samples and its significance for monitoring an invasive species

Introduced in South America at the end of the 19th century, the European hare population has expanded dramatically and now represents a risk to native Brazilian forest rabbits. Monitoring the invasive Lepus europaeus and its coexistence with native Sylvilagus brasiliensis is a challenge that can be efficiently addressed by the use of molecular tools. This work describes a set of primers useful for amplifying three mini-barcodes for the molecular identification of both invasive and native leporid species using degraded fecal DNA. In addition, tests in silico indicate that these mini-barcodes can successfully amplify the DNA sequences of a number of leporids. These mini-barcodes constitute a powerful tool for the monitoring and management of the invasive L. europaeus and the conservation of native rabbits.

The value of monitoring wildlife roadkill

The number of wildlife-vehicle collisions has an obvious value in estimating the direct effects of roads on wildlife, i.e. mortality due to vehicle collisions. Given the nature of the data—species identification and location—there is, however, much wider ecological knowledge that can be gained by monitoring wildlife roadkill. Here, we review the added value and opportunities provided by these data, through a series of case studies where such data have been instrumental in contributing to the advancement of knowledge in species distributions, population dynamics, and animal behaviour, as well as informing us about health of the species and of the environment. We propose that consistently, systematically, and extensively monitoring roadkill facilitates five critical areas of ecological study: (1) monitoring of roadkill numbers, (2) monitoring of population trends, (3) mapping of native and invasive species distributions, (4) animal behaviour, and (5) monitoring of contaminants and disease. The collection of such data also offers a valuable opportunity for members of the public to be directly involved in scientific data collection and research (citizen science). Through continuing to monitor wildlife roadkill, we can expand our knowledge across a wide range of ecological research areas, as well as facilitating investigations that aim to reduce both the direct and indirect effects of roads on wildlife populations.

Consideration of sample source for establishing reliable genetic microsatellite data from mammalian carnivore specimens held in natural history collections

Specimens from natural history collections (NHCs) are increasingly being used for genetic studies and can provide information on extinct populations, facilitate comparisons of historical and contemporary populations, produce baseline data before environmental changes, and elucidate patterns of change. Destructive sampling for DNA may be in disagreement with NHC goals of long-term care and maintenance. Differentiating quality among sample sources can direct destructive sampling to the source predicted to yield the highest quality DNA and most reliable data, potentially reducing damage to specimens, laboratory costs, and genotyping errors. We used the kit fox (Vulpes macrotis) as a model species and evaluated the quality and reliability of genetic data obtained from carnivoran specimens via three different sample sources: cranial bones, nasal bones, and toepads. We quantified variation in microsatellite amplification success and genotyping error rates and assessed the reliability of source-specific genic data. Toepads had the highest amplification success rates and lowest genotyping error rates. Shorter loci had higher amplification success and lower allelic dropout rates than longer loci. There were substantial differences in the reliability of resulting multilocus genotypes. Toepads produced the most reliable data, required the fewest replicates, and therefore, had the lowest costs to achieve reliable data. Our results demonstrate that the quality of DNA obtained from specimens varies by sample source and can inform NHCs when evaluating requests for destructive sampling. Our results suggest that prior to large-scale specimen sampling, researchers should conduct pilot studies to differentiate among source-specific data reliability, identify high performing loci, reduce costs of analyses, and minimize destructive sampling.

Evaluating effective population size and genetic diversity of a declining kit fox population using contemporary and historical specimens

Loss of genetic diversity has serious conservation consequences (e.g., loss of adaptive potential, reduced population viability), but is difficult to evaluate without developing long-term, multigenerational datasets. Alternatively, historical samples can provide insights into changes in genetic diversity and effective population size (N e). Kit foxes (Vulpes macrotis) are a species of conservation concern across much of their range. In western Utah, kit fox abundance has declined precipitously from historical levels, causing concern about population persistence. We analyzed genetic samples from museum specimens and contemporary scats to evaluate temporal changes in (a) genetic diversity and (b) N e for kit foxes in western Utah, and (c) discuss our findings with respect to population risk and conservation. The N e of kit foxes in western Utah has decreased substantially. When compared to established conservation thresholds for N e (e.g., the 50/500 rule), observed levels suggest the population may be at risk of inbreeding depression and local extinction. In contrast, we found no significant decrease in genetic diversity associated with declining N e. We detected evidence of low levels of immigration into the population and suspect genetic diversity may have been maintained by this previously undescribed gene flow from adjacent populations. Low or intermittent immigration may serve to temper the potential short-term negative consequences of low N e. We recommend that kit fox conservation efforts focus on evaluating and maintaining landscape connectivity. We demonstrate how historical specimens can provide a baseline of comparison for contemporary populations, highlighting the importance of natural history collections to conservation during a period of declining funding and support.

Estimating densities for sympatric kit foxes (Vulpes macrotis) and coyotes (Canis latrans) using noninvasive genetic sampling

Kit fox (Vulpes macrotis Merriam, 1888) populations in the Great Basin Desert have declined and are of increasing concern for managers. Increasing coyote (Canis latrans Say, 1823) abundance and subsequent intraguild interactions may be one cause for this decline. Concurrent monitoring of carnivores is challenging and therefore rarely conducted. One possible solution for monitoring elusive carnivores is using noninvasive genetic sampling. We used noninvasive genetic sampling to collect fecal DNA from kit foxes and coyotes and estimate their densities from 2013–2014 in Utah, USA. We identified individuals based on microsatellite genotypes and estimated density with multisession spatially explicit capture–recapture models. Mean kit fox density was 0.02 foxes·km−2, while coyote densities were up to four times greater (0.07–0.08 coyotes·km−2). Kit fox densities were significantly lower than densities in the 1950s but were comparable with estimates from the late 1990s, suggesting that populations may be stabilizing after a precipitous decline. Our kit fox density estimates were among the lowest documented for the species. Our coyote density estimate was the first reported in our region and revealed that despite seemingly high abundance, densities are low compared with other regions. Our results suggested that kit foxes may be able to coexist with coyotes.

A single mini-barcode test to screen for Australian mammalian predators from environmental samples

Identification of species from trace samples is now possible through the comparison of diagnostic DNA fragments against reference DNA sequence databases. DNA detection of animals from non-invasive samples, such as predator faeces (scats) that contain traces of DNA from their species of origin, has proved to be a valuable tool for the management of elusive wildlife. However, application of this approach can be limited by the availability of appropriate genetic markers. Scat DNA is often degraded, meaning that longer DNA sequences, including standard DNA barcoding markers, are difficult to recover. Instead, targeted short diagnostic markers are required to serve as diagnostic mini-barcodes. The mitochondrial genome is a useful source of such trace DNA markers because it provides good resolution at the species level and occurs in high copy numbers per cell. We developed a mini-barcode based on a short (178 bp) fragment of the conserved 12S ribosomal ribonucleic acid mitochondrial gene sequence, with the goal of discriminating amongst the scats of large mammalian predators of Australia. We tested the sensitivity and specificity of our primers and can accurately detect and discriminate amongst quolls, cats, dogs, foxes, and devils from trace DNA samples. Our approach provides a cost-effective, time-efficient, and non-invasive tool that enables identification of all 8 medium-large mammal predators in Australia, including native and introduced species, using a single test. With modification, this approach is likely to be of broad applicability elsewhere.

Detecting rare carnivores using scats: Implications for monitoring a fox incursion into Tasmania

The ability to detect the incursion of an invasive species or destroy the last individuals during an eradication program are some of the most difficult aspects of invasive species management. The presence of foxes in Tasmania is a contentious issue with recent structured monitoring efforts, involving collection of carnivore scats and testing for fox DNA, failing to detect any evidence of foxes. Understanding the likelihood that monitoring efforts would detect fox presence, given at least one is present, is therefore critical for understanding the role of scat monitoring for informing the response to an incursion. We undertook trials to estimate the probability of fox scat detection through monitoring by scat‐detector dogs and person searches and used this information to critically evaluate the power of scat monitoring efforts for detecting foxes in the Tasmanian landscape. The probability of detecting a single scat present in a 1‐km² survey unit was highest for scat‐detector dogs searches (0.053) compared with person searches (x¯≅0.015) for each 10 km of search effort. Simulation of the power of recent scat monitoring efforts undertaken in Tasmania from 2011 to 2015 suggested that single foxes would have to be present in at least 20 different locations or fox breeding groups present in at least six different locations, in order to be detected with a high level of confidence (>0.80). We have shown that highly structured detection trials can provide managers with the quantitative tools needed to make judgments about the power of large‐scale scat monitoring programs. Results suggest that a fox population, if present in Tasmania, could remain undetected by a large‐scale, structured scat monitoring program. Therefore, it is likely that other forms of surveillance, in conjunction with scat monitoring, will be necessary to demonstrate that foxes are absent from Tasmania with high confidence.

A framework for developing and validating taxon-specific primers for specimen identification from environmental DNA

Taxon-specific DNA tests are applied to many ecological and management questions, increasingly using environmental DNA (eDNA). eDNA facilitates noninvasive ecological studies but introduces additional risks of bias and error. For effective application, PCR primers must be developed for each taxon and validated in each system. We outline a nine step framework for the development and validation of taxon-specific primers for eDNA analysis in ecological studies, involving reference database construction, phylogenetic evaluation of the target gene, primer design, primer evaluation in silico, and laboratory evaluation of primer specificity, sensitivity and utility. Our framework makes possible a rigorous evaluation of likely sources of error. The first five steps can be conducted relatively rapidly and (where reference DNA sequences are available) require minimal laboratory resources, enabling assessment of primer suitability before investing in further work. Steps six to eight require more costly laboratory analyses but are essential to evaluate risks of false-positive and false-negative results, while step 9 relates to field implementation. As an example, we have developed and evaluated primers to specifically amplify part of the mitochondrial ND2 gene from Australian bandicoots. If adopted during the early stages of primer development, our framework will facilitate large-scale implementation of well-designed DNA tests to detect specific wildlife from eDNA samples. This will provide researchers and managers with an understanding of the strengths and limitations of their data and the conclusions that can be drawn from them.

Real-time PCR assay to detect brown marmorated stink bug, Halyomorpha halys (Stål), in environmental DNA

BACKGROUND

Early detection before establishment and identification of key predators are time-honored strategies towards effective eradication or control of invasive species. The brown marmorated stink bug (BMSB), Halyomorpha halys, is a recent exotic pest of several important crops in North America and Europe. Resulting widespread applications of insecticides have countered years of careful integrated pest management and are leading to the resurgence of other agricultural pests. Environmental DNA (eDNA) has been used effectively to detect aquatic invasives.

RESULTS

We developed a real-time PCR (qPCR) assay for BMSB in a conserved region of the ribosomal DNA interspacer 1 (ITS1). We validated this assay on worldwide populations of BMSB and tested its specificity and sensitivity against other US Pentatomidae species and on guano of big brown bat, Eptesicus fuscus, which we confirmed is a BMSB predator in New Jersey. We also detected BMSB DNA after rapid (and inexpensive) HotSHOT DNA extractions of soiled paper from cages briefly holding BMSB, as well as from discarded exuviae.

CONCLUSION

Given the high sensitivity of our assay to BMSB environmental DNA (eDNA) in terrestrial samples, this tool should become a cost-effective approach for using eDNA to detect terrestrial invasive species and their key predators. © 2016 Society of Chemical Industry.

The dispersion and detection patterns of mtDNA-assigned red fox Vulpes vulpes scats in Tasmania are anomalous

Models used for resource allocation in eradication programmes must be based on replicated data of known quality and have proven predictive accuracy, or they may provide a false indication of species presence and/or distribution. In the absence of data corroborating the presence of extant foxes Vulpes vulpes in Tasmania, a habitat-specific model based upon mtDNA data (Sarre et al. 2012. Journal Applied Ecology, 50, 459-468) implied that foxes were widespread. Overall, 61 of 9940 (0·6%) surveyed scats were assigned as mtDNA fox positive by the fox eradication programme (FEP). We investigated the spatiotemporal distribution of the 61 mtDNA-assigned fox scats and modelled the probability of replicating scat detection in independent surveys using detection dogs based upon empirically derived probabilities of scat detection success obtained by the FEP using imported fox scats. In a prior mainland study, fox genotypes were recurrently detected in a consecutive four-day pool of scats. In Tasmania, only three contemporaneously collected scat pairs of unknown genotype were detected by the FEP within an area corresponding to a conservatively large mainland fox home range (639 ha) in a decade. Nearest neighbour pairs were widely spaced (mean = 7·0 km; circular area = 153 km2) and generated after a mean of 281 days. The majority of assigned mtDNA positive scats were found in urban and peri-urban environments corresponding to small mainland fox home ranges (30-45 ha) that imply higher scat density and more certain replication. Using the lowest empirically determined scat detection success for dogs, the failure to replicate fox scat detection on 34 of 36 occasions in a large (639 ha) home range is highly improbable (P = 0·00001) and suggestive of Type I error. Synthesis and applications. Type I error, which may have various sources, should be considered when scat mtDNA data are few, accumulated over many years, uncorroborated by observations of extant specimens, inadequately replicated in independent surveys within an expected spatiotemporal scale and reported in geographically isolated environments unlikely to have been colonized.

Degradation and detection of fox (Vulpes vulpes) scats in Tasmania: evidence from field trials

Context The Tasmanian Government is attempting to eradicate foxes from Tasmania and carnivore-scat surveys using humans and dogs combined with DNA testing are the main methods of detection. Understanding the rate that scats degrade is a key component for estimating the power of monitoring for detecting cryptic predators and will contribute to a broader understanding of the use of scat monitoring for informing eradication programs. Aims To estimate the degradation rate of fox scats and derive an estimate of the abundance of scats available to observers monitoring for fox presence. Methods In total, 486 fresh fox scats were placed at nine sites within three bioregions in Tasmania and left to degrade for up to 126 days. Scats were observed periodically by both humans and dogs to determine when they became unrecognisable and/or undetectable. Key results Recognition of scats by humans declined faster in summer than in winter and did not vary systematically among bioregions. Median survival times of scats were 19 days in summer and 26 days in winter. Recognition of scats by dogs was higher in summer than in winter, with dogs recognising scats past the time they became unrecognisable to humans. Using estimates of scat degradation derived from human observers, the equilibrium abundance of detectable scats within a fox home range was estimated to be 179–243 scats. However, the abundance of detectable scats on linear features subject to monitoring was estimated to be 10–15 scats. Conclusions Using our estimate of the abundance of scats on linear features, the current distribution of fox scats detected in Tasmania may not be as anomalous as has been suggested by others. However, fox detection from scats will be highly dependent on deposition patterns and distribution of scats on linear features and this should be critically reassessed in Tasmania. Implications Fox scats are not expected to exhibit systematic regional differences in degradation rates that might have an impact on monitoring strategies. Estimates of the abundance of scats detectable by observers are critical for assessing the effectiveness of scat-monitoring programs. We advocate that a rigorous assessment of future scat-monitoring programs in Tasmania be undertaken to determine their power to detect foxes.

Current and future directions of DNA in wildlife forensic science

Wildlife forensic science may not have attained the profile of human identification, yet the scale of criminal activity related to wildlife is extensive by any measure. Service delivery in the arena of wildlife forensic science is often ad hoc, unco-ordinated and unregulated, yet many of those currently dedicated to wildlife conservation and the protection of endangered species are striving to ensure that the highest standards are met. The genetic markers and software used to evaluate data in wildlife forensic science are more varied than those in human forensic identification and are rarely standardised between species. The time and resources required to characterise and validate each genetic maker is considerable and in some cases prohibitive. Further, issues are regularly encountered in the construction of allelic databases and allelic ladders; essential in human identification studies, but also applicable to wildlife criminal investigations. Accreditation and certification are essential in human identification and are currently being strived for in the forensic wildlife community. Examples are provided as to how best practice can be demonstrated in all areas of wildlife crime analysis and ensure that this field of forensic science gains and maintains the respect it deserves. This review is aimed at those conducting human identification to illustrate how research concepts in wildlife forensic science can be used in the criminal justice system, as well as describing the real importance of this type of forensic analysis.

Evidence of rapid population decline of the eastern quoll (Dasyurus viverrinus) in Tasmania

Australia’s mammalian fauna has suffered unparalleled extinctions and declines in recent history. Tasmania has remained largely unaffected by these losses; however, marsupial dynamics are changing rapidly and new threats are emerging. Once abundant throughout south-eastern Australia, the eastern quoll (Dasyurus viverrinus) survives only in Tasmania. Until recently, it was considered widespread and common, but it may be undergoing a rapid and severe decline. The aim of this study was to quantify changes in eastern quoll populations over recent years. Data were compiled from statewide spotlight surveys, repeated historic trapping surveys and bycatch records from non-target trapping surveys. Spotlight surveys from 150 sites across Tasmania revealed a 52% reduction in the number of eastern quoll sightings over the 10 years to 2009. Declines of 61–100% were observed in trapping surveys at three study sites compared with trapping conducted 18–31 years earlier. A reduction in trap success was recorded in five of six non-target surveys, with declines of 51–100% over 1–12 years. These results suggest that the eastern quoll can no longer be presumed secure in Tasmania. Urgent management action may be needed to ensure the future conservation of the species in its last remaining stronghold.

Allocating sex in road-killed possums using PCR

Road-killed animals are a readily available but often overlooked source of specimens and data. Determining the sex of road-killed possums is often difficult due to the severe damage carcasses sustain on impact with vehicles. Consequently, valuable information is lost. To assess the potential application of genetic techniques to address this problem, tissue biopsies (n = 47) taken from road-killed possums were sexed via PCR, through the simultaneous use of W- (G6PD) and Y-linked (SRY) primers. Comparisons with animals of known sex were used to validate the accuracy of this method, with 100% (n = 19) of samples correctly identified in a blind test. This methodology can provide researchers with valuable, additional data for road-kill studies where assigning sex in the field is not possible.

Assessment of risks to non-target species from an encapsulated toxin in a bait proposed for control of feral cats

Context The CURIOSITY® bait is the name coined for a variation of the existing sausage-style cat bait, ERADICAT®. The latter is used under experimental permit in Western Australia for research associated with cat control. The CURIOSITY bait differs from ERADICAT by providing a pH-buffered (less acidic) medium and has been proposed to reduce the risk to non-target species by encapsulating a toxin in a pellet. We trialled a prototype pellet proposed for encapsulation of 1080 and/or alternative toxins, with delivery proposed through the CURIOSITY bait. Aim Our aim was to determine whether the pellet was consumed by non-target native species from south-west of Western Australia. Methods Trials involved use of a non-toxic biomarker, Rhodamine B, encapsulated within the pellet and inserted into the CURIOSITY® bait. Uptake of the encapsulated biomarker was assessed in captive trials for the target species, the feral cat (Felis catus) and two non-target species of varanid lizard, Rosenberg’s goanna (Varanus rosenbergi) and Gould’s goanna (V. gouldii) and the non-target mammal species chuditch (Dasyurus geoffroii) and southern brown bandicoot (Isoodon obesulus). Uptake of the encapsulated biomarker was also assessed in field trials for a range of native species. Key results Captive trials demonstrated feral cats will consume the CURIOSITY bait and pellet. However, results from captive and field trials indicated several non-target species also consumed the bait and pellet. We also found the pellet itself was not sufficiently robust for use in a bait. As with previously reported studies, we found Rhodamine B to be an effective biomarker for use in cats. We also developed a technique whereby Rhodamine B can be used as a biomarker in reptiles. However, its use as a biomarker in other mammalian species was confounded by what appeared to be background, or pre-existing, levels of fluorescence, or banding, in their whiskers. Conclusion The prototype pellet is unsuitable in its current form for use with the CURIOSITY bait. We caution that the CURIOSITY bait has non-target issues in south-west of Western Australia and any proposed variations to this bait, or the ERADICAT® bait, need to be rigorously assessed for their potential risk to non-target species and assessed for the level of uptake by cats, irrespective of their suitability/unsuitability as a medium for delivery of an encapsulated toxin. We believe the threat to biodiversity-conservation values from unmitigated feral-cat predation of native fauna poses a significant and real threat and we recommend urgent investment of resources to address the issue of cat predation in a coordinated and collaborative manner within Australia and New Zealand.

Current issues in species identification for forensic science and the validity of using the cytochrome oxidase I (COI) gene

Species identification techniques commonly utilized in Australian Forensic Science laboratories are gel immunodifussion antigen antibody reactions and hair comparison analysis. Both of these techniques have significant limitations and should be considered indicative opinion based tests. The Barcode of Life Initiative aims to sequence a section of DNA (~648 base pairs) for the Cytochrome Oxidase I mitochondrial gene (COI) in all living species on Earth, with the data generated being uploaded to the Barcode of Life Database (BOLD) which can then be used for species identification. The COI gene therefore offers forensics scientists an opportunity to use the marker to analyze unknown samples and compare sequences generated in BOLD. Once sequences from enough species are on the database, it is anticipated that routine identification of an unknown species may be possible. However, most forensic laboratories are not yet suited to this type of analysis and do not have the expertise to fully interpret the implications of matches and non matches involving a poorly sampled taxa (for example where there are cryptic species) and in providing the required opinion evidence. Currently, the use of BOLD is limited by the number of relevant species held in the database and the quality assurance and regulation of sequences that are there. In this paper, the COI methodology and BOLD are tested on a selection of introduced and Australian mammals in a forensic environment as the first step necessary in the implementation of this approach in the Australian context. Our data indicates that the COI methodology performs well on distinct species but needs further exploration when identifying more closely related species. It is evident from our study that changes will be required to implement DNA based wildlife forensics using the BOLD approach for forensic applications and recommendations are made for the future adoption of this technology into forensic laboratories.

Comparison of methods to detect rare and cryptic species: a case study using the red fox (Vulpes vulpes)

Choosing the appropriate method to detect and monitor wildlife species is difficult if the species is rare or cryptic in appearance or behaviour. We evaluated the effectiveness of the following four methods for detecting red foxes (Vulpes vulpes) on the basis of equivalent person hours in a rural landscape in temperate Australia: camera traps, hair traps (using morphology and DNA from hair follicles), scats from bait stations (using DNA derived from the scats) and spotlighting. We also evaluated whether individual foxes could be identified using remote collection of their tissues. Genetic analysis of hair samples was the least efficient method of detection among the methods employed because of the paucity of samples obtained and the lack of follicles on sampled hairs. Scat detection was somewhat more efficient. Scats were deposited at 17% of bait stations and 80% of scats were amplified with a fox-specific marker, although only 31% of confirmed fox scats could be fully genotyped at all six microsatellite loci. Camera trapping and spotlighting were the most efficient methods of detecting fox presence in the landscape. Spotlighting success varied seasonally, with fox detections peaking in autumn (80% of spotlighting transects) and being lowest in winter (29% of transects). Cameras detected foxes at 51% of stations; however, there was limited seasonality in detection, and success rates varied with camera design. Log-linear models confirmed these trends. Our results showed that the appropriate technique for detecting foxes varies depending on the time of the year. It is suggested that wildlife managers should consider both seasonal effects and species biology when attempting to detect rare or elusive species.

High possum mortality on urban roads: implications for the population viability of the common brushtail and the common ringtail possum

Animal–vehicle collisions impact wildlife populations and in the northern suburbs of Sydney, both the common brushtail possum (Trichosurus vulpecula) and the common ringtail possum (Pseudocheirus peregrinus) are killed in large numbers. Over a two-year period almost 600 road-killed possums were observed from 217 road surveys covering over 7800 km, equating to 5.45 possums per week over the 36-km study area. Surveys were conducted along roads where the environment ranged from low-rise suburban to continuous sclerophyll forest. Significantly more ringtail possums were observed as road-kill, outnumbering brushtail possums by almost three to one. No sex bias was found amongst road-killed ringtail possums; however, seasonal trends and weight fluctuations were significant, with both males and females being at their lowest weights during the autumn breeding season. For brushtail possums a bias towards young males was observed. Sex and weight of road-killed brushtail possums were comparable to live-trap data from a previous study in the same location. In areas of such high possum mortality, wildlife managers may need to take action to mitigate possum road-kill.

Genetics in conservation and wildlife management: a revolution since Caughley

In his 1994 review of conservation biology, Graeme Caughley questioned the central role for genetics in that discipline. His central theme was that there was no known case of genetic malfunction leading to the extinction of a population or species, and that driving forces such as overkill, habitat fragmentation and introduced predators as well as environmental and demographic stochasticity of small populations should be considered ahead of genetics in the debate about extinction prevention. At the time, only indirect and theoretical evidence existed for genetic contributions to the declines of wildlife and most of the debate revolved around the impact of genetic variation on fitness and long-term persistence. In addition, the application of DNA technologies to the study of wildlife was in its infancy. Though this was not Caughley’s intention, many within wildlife management took his criticisms of genetic aspects of species decline as the cue to dismiss this branch of science as of minor relevance to conservation biology. Since Caughley’s critique, there has been a revolution in genetic technologies for non-model organisms with the arrival of highly informative hypervariable DNA markers. Perhaps even more importantly, developments in DNA and gene technologies have provided the opportunity to study fundamental life-history traits such as disease resistance in more direct ways than previously possible. In concert with these tools, conservation geneticists have risen to Caughley’s challenge and demonstrated unambiguously a clear role for genetic analysis in conservation biology. Despite these impressive advances, there remains an important gap between the genetic approaches available and their uptake by managers. Bridging this gap will greatly increase the capacity of wildlife managers to generate the data necessary for sound management.

Evaluating exotic predator control programs using non-invasive genetic tagging

Carnivorous predators are difficult to detect using conventional survey methods, especially at low levels of abundance. The introduced red fox (Vulpes vulpes) in Australia is monitored to determine the effectiveness of control programs, but assessing population parameters such as abundance and recruitment is difficult. We carried out a feasibility study to determine the effectiveness of using faecal DNA analysis methods to identify individual foxes and to assess abundance before and after lethal control. Fox faeces were collected in two sampling periods over four separate transects, and genotyped at five microsatellite loci. Two transects were subject to lethal control between collection periods. DNA was extracted from 170 fox faeces and, in total, 54 unique genotypes were identified. Fifteen biopsy genotypes from 30 foxes killed during lethal control were detected among the faecal genotypes. Overall, a similar number of genotypes were detected in both sampling periods. The number of individuals sampled in both periods was low (n = 6) and new individuals (n = 24) were detected in the second collection period. We were also able to detect animals that avoided lethal control, and movement of individuals between transects. The ability to identify individual foxes using these DNA techniques highlighted the shortcomings of the sample design, in particular the spatial scale and distances between transects. This study shows that non-invasive DNA sampling can provide valuable insight into pre and post fox abundance in relation to lethal control, individual behaviour and movement, as well as sample design. The information gained from this study will contribute to the design of future studies and, ultimately, control strategies.