Leader of the pack: faecal pellet deposition order impacts PCR amplification in wombats

Non-invasive monitoring and reintroduction biology of the brush-tailed rock-wallaby (

Thirty-nine endangered brush-tailed rock-wallabies (Petrogale penicillata) were reintroduced to Grampians National Park, western Victoria, between 2008 and 2012. Subsequent high mortality, low breeding, and no recruitment were linked to fox predation and physical disturbance during monitoring. From 2014 to 2017, the colony was left undisturbed and monitored only by remote camera. Five adult animals were identified across this period (1 ♂ and 3 ♀s – all tagged; and one untagged female), and an average of 0.7 pouch young were birthed per tagged female per year. In 2019, camera-monitoring and non-invasive genetic monitoring (faecal) were used to identify colony members, genetic diversity, and breeding. Camera monitoring in 2019 identified the same five individuals, whereas genetic monitoring using 12 microsatellites identified eight individuals (two male and six female genotypes). Genetic diversity within the colony was moderate (expected heterozygosity (He) = 0.655, observed heterozygosity (Ho) = 0.854). Leaving the colony undisturbed after 2013 correlated with improved adult survival, increased breeding, and successful recruitment of young to the population. Recommendations for the Grampians colony include continuation of regular camera- and scat monitoring to improve our understanding of the reintroduction biology of P. penicillata and other marsupials in open, unfenced landscapes.

Square salads: exploring the diet of the southern hairy-nosed wombat (Lasiorhinus latifrons) via DNA metabarcoding

Southern hairy-nosed wombats (Lasiorhinus latifrons) are large semi-fossorial marsupials that inhabit semiarid areas of southern South Australia and southeast Western Australia. Despite their size and prominence on the landscape, little is published about diet and foraging preferences. Further, it is unclear whether this wombat species’ diet overlaps with sympatric western grey kangaroos (Macropus fuliginosus), which are locally abundant across the southern hairy-nosed wombat’s distribution. Competition for food resources may be an added stressor in Murraylands populations where kangaroos are plentiful. Here, we identified diet items and dietary overlap of southern hairy-nosed wombats and western grey kangaroos. We accomplished this by opportunistically sampling fresh faecal pellets from both species at Brookfield Conservation Park in April 2017. We performed DNA metabarcoding via Illumina next generation sequencing of the faecal DNA using the plant ITS2 gene. We identified 10 genera in the wombat diet and 20 in the diet of kangaroos; diets of both species included native and introduced genera. Eight genera were shared between both marsupials. This work highlights the capabilities of non-invasive genetic sampling in concert with DNA metabarcoding to elucidate diet and dietary overlap between species.

A fecal sequel: Testing the limits of a genetic assay for bat species identification

DNA metabarcoding assays are powerful tools for delving into the DNA in wildlife feces, giving unprecedented ability to detect species, understand natural history, and identify pathogens for a range of applications in management, conservation, and research. Next-generation sequencing technology is developing rapidly, which makes it especially important that predictability and reproducibility of DNA metabarcoding assays are explored together with the post-depositional ecology of the target taxon’s fecal DNA. Here, we defined the constraints of an assay called ‘Species from Feces’ used by government agencies, research groups, and non-governmental organizations to identify bat species from guano. We tested assay sensitivity by examining how time and humidity affect the ability to recover and successfully sequence DNA in guano, assessing whether a fecal pellet from a rare bat species could be detected in a background of feces from other bat species, and evaluating the efficacy of Species from Feces as a survey tool for bat roosts in temperate and tropical areas. We found that the assay performs well with feces over two years old in dry, cool environments, and fails by 12 months at 100% relative humidity. We also found that it reliably identifies rare DNA, has great utility for surveying roosts in temperate and tropical regions, and detects more bat species than do visual surveys. We attribute the success of Species from Feces to characteristics of the assay paired with application in taxa that are particularly well-suited for fecal DNA survival. In a time of rapid evolution of DNA metabarcoding approaches and their use with feces, this study illustrates the strengths and limitations of applied assays.

Guano exposed: Impact of aerobic conditions on bat fecal microbiota

Bats and their associated guano microbiota provide important terrestrial and subterranean ecosystem services and serve as a reservoir for a wide range of epizootic and zoonotic diseases. Unfortunately, large-scale studies of bats and their guano microbiotas are limited by the time and cost of sample collection, which requires specially trained individuals to work at night to capture bats when they are most active. Indirectly surveying bat gut microbiota through guano deposits could be a more cost-effective alternative, but it must first be established whether the postdefecation exposure to an aerobic environment has a large impact on the guano microbial community. A number of recent studies on mammalian feces have shown that the impact of aerobic exposure is highly species specific; therefore, it is difficult to predict how exposure will affect the bat guano microbiota without empirical data. In our study, we collected fresh guano samples from 24 individuals of 10 bat species that are common throughout the arid environments of the American southwest and subjected the samples to 0, 1, and 12 hr of exposure. The biodiversity decreased rapidly after the shift from an anaerobic to an aerobic environment-much faster than previously reported in mammalian species. However, the relative composition of the core guano microbiota remained stable and, using highly sensitive targeted PCR methods, we found that pathogens present in the original, non-exposed samples could still be recovered after 12 hr of exposure. These results suggest that with careful sample analysis protocols, a more efficient passive collection strategy is feasible; for example, guano could be collected on tarps placed near the roost entrance. Such passive collection methods would greatly reduce the cost of sample collection by allowing more sites or roosts to be surveyed with a fraction of trained personnel, time, and effort investments needed.

Breaking down scats: degradation of DNA from greater bilby (Macrotis lagotis) faecal pellets

Isolating DNA from scats (faeces) of threatened species is a valuable, non-invasive method for identifying individuals. To establish whether genotyping of greater bilby (Macrotis lagotis) individuals from faecal pellets collected in the field can be useful for population monitoring, an understanding of the DNA degradation rates is necessary. To determine the relationship between time and degradation of bilby faecal DNA, and assess whether a two-step elution process during extraction results in better-quality DNA, faecal pellets were collected from captive individuals, maintained under seminatural conditions, then harvested at known periods. DNA was amplified from faecal pellets with a 99% success rate and error rates of less than 5% up to 14 days after deposition. The amplification rate decreases, and the rate of allelic dropout increases with time, but DNA can still be amplified at rates above 60% and error rates below 15% at 90–180 days. We found that a second elution step was unnecessary, with more DNA amplified over a longer period using the first eluate. Viable DNA exists on bilby faecal pellets for a long period after deposition, which is useful for obtaining genetic samples for population monitoring programs and studies on population genetics.

Major Histocompatibility Complex Class II in the red-tailed phascogale (Phascogale calura)

Diversity in major histocompatibility complex (MHC) genes can be correlated with the level of immunological fitness of an individual or group of individuals. This study tested published primer sets designed to amplify fragments of the MHC Class II DAB and DBB genes to amplify the equivalent gene fragments in red-tailed phascogales (Phascogale calura). Seventeen genomic DNA samples extracted from phascogale muscle tissue were used to amplify the initial DAB and DBB fragments; however, only DAB PCR proved successful. The fragments were 172 bp in length between the primers and had a high level of identity to other known marsupial MHC Class II DAB gene sequences (89–98%), including those of the koala (Phascolarctos cinereus), Tasmanian devil (Sarcophilus harrisii), common brushtail possum (Trichosurus vulpecula) and several wallaby species. Multiple sequence alignment revealed limited variability of MHC Class II genes between the individuals, but eight individual sequences in total. Genomic DNA was subsequently extracted from three fresh red-tailed phascogale scat samples and DAB fragments successfully amplified. The technique will allow for red-tailed phascogales to be sampled non-invasively in the wild and to determine the level of MHC diversity among individuals in the population.

Species From Feces: Order-Wide Identification of Chiroptera From Guano and Other Non-Invasive Genetic Samples

Bat guano is a relatively untapped reservoir of information, having great utility as a DNA source because it is often available at roosts even when bats are not and is an easy type of sample to collect from a difficult-to-study mammalian order. Recent advances from microbial community studies in primer design, sequencing, and analysis enable fast, accurate, and cost-effective species identification. Here, we borrow from this discipline to develop an order-wide DNA mini-barcode assay (Species from Feces) based on a segment of the mitochondrial gene cytochrome c oxidase I (COI). The assay works effectively with fecal DNA and is conveniently transferable to low-cost, high-throughput Illumina MiSeq technology that also allows simultaneous pairing with other markers. Our PCR primers target a region of COI that is highly discriminatory among Chiroptera (92% species-level identification of barcoded species), and are sufficiently degenerate to allow hybridization across diverse bat taxa. We successfully validated our system with 54 bat species across both suborders. Despite abundant arthropod prey DNA in guano, our primers were highly specific to bats; no arthropod DNA was detected in thousands of feces run on Sanger and Illumina platforms. The assay is extendable to fecal pellets of unknown age as well as individual and pooled guano, to allow for individual (using singular fecal pellets) and community (using combined pellets collected from across long-term roost sites) analyses. We developed a searchable database (http://nau.edu/CEFNS/Forestry/Research/Bats/Search-Tool/) that allows users to determine the discriminatory capability of our markers for bat species of interest. Our assay has applications worldwide for examining disease impacts on vulnerable species, determining species assemblages within roosts, and assessing the presence of bat species that are vulnerable or facing extinction. The development and analytical pathways are rapid, reliable, and inexpensive, and can be applied to ecology and conservation studies of other taxa.

Improving genetic monitoring of the northern hairy-nosed wombat (Lasiorhinus krefftii)

The endangered northern hairy-nosed wombat (Lasiorhinus krefftii) has been monitored via remote sampling and genetic techniques since 2000, thus avoiding the detrimental effects on the animals of trapping and increasing the precision of abundance estimates. The currently available dinucleotide microsatellite markers used for this task are prone to stutter and other polymerase chain reaction artefacts, making allele calling difficult, and requiring costly duplication to ensure accuracy. To remedy this we have developed eight new tri- and tetranucleotide microsatellite markers that reduce the problem of stutter in DNA analysis. These new markers, along with three of the existing markers (two microsatellites and the SRY gender marker) were optimised in a single multiplex reaction that will reduce the time and cost of future northern hairy-nosed wombat hair censuses. We tested this new multiplex on 277 non-invasively collected hairs. One locus was rejected due to null-allele issues. The remaining nine microsatellite loci had two or three alleles. Genotype frequencies in the sample of detected individuals did not differ significantly from Hardy–Weinberg equilibrium and there was no evidence of linkage disequilibrium. This new multiplex provides comparable power to distinguish individuals, fewer issues with stutter artefacts and a reduced time and cost of analysis. It will be useful for future population censuses and long-term monitoring of individuals once they have been scored in previously genotyped and assigned samples.

Reliable genotyping of the koala (Phascolarctos cinereus) using DNA isolated from a single faecal pellet

The koala, an Australian icon, has been added to the threatened species list. Rationale for the listing includes proposed declines in population size, threats to populations (e.g. disease) and loss and fragmentation of habitat. There is now an urgent need to obtain accurate data to assess the status of koala populations in Australia, to ensure the long-term viability of this species. Advances in genetic techniques have enabled DNA analysis to study and inform the management of wild populations; however, sampling of individual koalas is difficult in tall, often remote, eucalypt forest. The collection of faecal pellets (scats) from the forest floor presents an opportunistic sampling strategy, where DNA can be collected without capturing or even sighting an individual. Obtaining DNA via noninvasive sampling can be used to rapidly sample a large proportion of a population; however, DNA from noninvasively collected samples is often degraded. Factors influencing DNA quality and quantity include environmental exposure, diet and methods of sample collection, storage and DNA isolation. Reduced DNA quality and quantity can introduce genotyping errors and provide inaccurate DNA profiles, reducing confidence in the ability of such data to inform management/conservation strategies. Here, we present a protocol that produces a reliable individual koala genotype from a single faecal pellet and highlight the importance of optimizing DNA isolation and analysis for the species of interest. This method could readily be adapted for genetic studies of mammals other than koalas, particularly those whose diet contains high proportions of volatile materials that are likely to induce DNA damage.

Rapid species identification of eight sympatric northern Australian macropods from faecal-pellet DNA

Context Conservation of vulnerable and endangered species requires a comprehensive understanding of their distribution and habitat requirements, so as to implement effective management strategies. Visual scat surveys are a common non-invasive method for monitoring populations. However, morphological similarity of scats among sympatric species presents a problem for accurate identification. Visual misidentifications of scats can have major impacts on the accuracy of abundance and distribution surveys of target species, wasting resources and misdirecting management and conservation actions. DNA identification of scats can overcome this issue, while simultaneously providing a rich source of genetic information for population and dietary studies. Aims We developed a simple and reliable method to identify morphologically similar macropod scats from eight sympatric species in north-eastern Australia, using polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) of a portion of the mtDNA ND2 gene. Methods We identified a short (275-bp) polymorphic region of ND2, which is easily amplifiable from degraded DNA, developed a primer set, and identified a set of three restriction endonucleases (AluI, BstNI and HphI) which, in combination, can discriminate among the eight target species. So as to test the effectiveness of this protocol, we collected 914 macropod scats from 53 sites in the north-eastern Australia. Key results In total, 406 of these scats were extracted, with 398 (98%) containing amplifiable macropod DNA. All 398 scats were subsequently identified to species by using our RFLP protocol. Sequencing of a subset of these samples confirmed the accuracy of the test. Species identification of scats by using DNA identified eight species of macropods, five of which were outside their documented distributions, one of which was ~400 km. Conclusions Our PCR–RFLP method is a simple and efficient means to identify macropod scats to species, eliminating the need for sequencing, which is costly, time-consuming and requires additional laboratory equipment. Implications The method allows for rapid and non-invasive assessment of macropod species and is particularly useful for surveying populations across multiple sites.