Improving the detection of rare native fish species in environmental DNA metabarcoding surveys

The presence of threatened or endangered species often strongly influences management and conservation decisions. Within the Murray–Darling Basin (MDB), Australia, the presence of threatened native fish affects the management and allocation of water resources. These decisions are currently based on traditional fisheries data and a predictive MaxEnt model. However, it is important to verify the model's predictive power given the implication it may have, but this requires methods with a high detection sensitivity for rare species. Although the use of environmental DNA (eDNA) metabarcoding achieves a higher detection sensitivity compared with traditional methods, earlier surveys in the MDB have shown that the highly abundant and invasive common carp (Cyprinus carpio) can reduce detection probabilities for rare species. Consequently, a polymerase chain reaction (PCR) blocking primer designed to block the amplification of carp eDNA could increase the detection probabilities for rare native species while simultaneously reducing the required sampling effort and survey costs. Although PCR blocking primers are often used in ancient DNA and dietary studies, no aquatic eDNA metabarcoding study to date has evaluated the potential benefits of using PCR blocking primers. A laboratory and field‐based pilot study was used to address this knowledge gap and assess the impact of a blocking primer on the detection probabilities of native species and the minimum sampling effort required. Results showed that the inclusion of the blocking primer increased the detection probabilities for native species by 10–20% and reduced the minimum required sampling effort by 25–50%. These findings provide important insights into possible methods for optimizing eDNA metabarcoding surveys for the detection of rare aquatic species

Does mesocosm validation of environmental DNA methods translate to natural environment monitoring applications? A case study detecting a high-profile invader; the red eared slider turtle, Trachemys scripta elegans, in Australia

Environmental DNA (eDNA) surveys have gained popularity as a highly sensitive detection tool that generally outperform traditional detection techniques. eDNA surveys can provide a cost-effective means to identify species’ distributions and recent incursions, informing the control or containment of invasive species. The red-eared slider turtle, Trachemys scripta elegans, is one of the world’s most invasive species and is listed as a priority pest species for management in Australia. In this study, we validate two eDNA assays to detect this invasive turtle in Australia. We demonstrate high sensitivity in a laboratory setting and perfect detection rates in mesocosms for one of these eDNA assays but show that this does not translate to high detection rates in urban waterbodies at sites of known occupancy. In fact, our results suggest eDNA surveys provide sub-optimal performance compared to traditional detection methods for T.s. elegans. We suggest the capacity for eDNA surveys to provide a highly sensitive detection tool must be evaluated in natural environments on a species-by-species basis to understand any limitations and to avoid high error rates from eDNA surveys leading to wasted resources or inappropriate management decisions. For management of T.s. elegans in Australia, clearly defining the utility of certain eDNA based approaches to detect T.s. elegans and their incursions is vital for effective management of this pest species.</p

Food from faeces:Evaluating the efficacy of scat DNA metabarcoding in dietary analyses

Scat DNA metabarcoding is increasingly being used to track the feeding ecology of elusive wildlife species. This approach has greatly increased the resolution and detection success of prey items contained in scats when compared with other classical methods. However, there have been few studies that have systematically tested the applicability and reliability of this approach to study the diet of large felids species in the wild. Here we assessed the effectiveness of this approach in the cheetah Acinonyx jubatus. We tested how scat degradation, meal size, prey species consumed and feeding day (the day a particular prey was consumed) influenced prey DNA detection success in captive cheetahs. We demonstrated that it is possible to obtain diet information from 60-day old scats using genetic approaches, but the efficiency decreased over time. Probability of species-identification was highest for food items consumed one day prior to scat collection and the probability of being able to identify the species consumed increased with the proportion of the prey consumed. Detection success varied among prey species but not by individual cheetah. Identification of prey species using DNA detection methods from a single consumption event worked for samples collected between 8 and 72 hours post-feeding. Our approach confirms the utility of genetic approaches to identify prey species in scats and highlight the need to account for the systematic bias in results to control for possible scat degradation, feeding day, meal size and prey species consumed especially in the wild-collected scats

Ruling out Stellar Companions and Resolving the Innermost Regions of Transitional Disks with the Keck Interferometer

With the Keck Interferometer, we have studied at 2 um the innermost regions of several nearby, young, dust depleted "transitional" disks. Our observations target five of the six clearest cases of transitional disks in the Taurus/Auriga star-forming region (DM Tau, GM Aur, LkCa 15, UX Tau A, and RY Tau) to explore the possibility that the depletion of optically thick dust from the inner disks is caused by stellar companions rather than the more typical planet-formation hypothesis. At the 99.7% confidence level, the observed visibilities exclude binaries with flux ratios of at least 0.05 and separations ranging from 2.5 to 30 mas (0.35 - 4 AU) over >= 94% of the area covered by our measurements. All targets but DM Tau show near-infrared excess in their SED higher than our companion flux ratio detection limits. While a companion has previously been detected in the candidate transitional disk system CoKu Tau/4, we can exclude similar mass companions as the typical origin for the clearing of inner dust in transitional disks and of the near-infrared excess emission. Unlike CoKu Tau/4, all our targets show some evidence of accretion. We find that all but one of the targets are clearly spatially resolved, and UX Tau A is marginally resolved. Our data is consistent with hot material on small scales (0.1 AU) inside of and separated from the cooler outer disk, consistent with the recent SED modeling. These observations support the notion that some transitional disks have radial gaps in their optically thick material, which could be an indication for planet formation in the habitable zone (~ a few AU) of a protoplanetary disk.Comment: 36 pages, 7 figures. Accepted for publication in Ap

Monitoring riverine fish communities through eDNA metabarcoding:Determining optimal sampling strategies along an altitudinal and biodiversity gradient

Monitoring aquatic biodiversity through DNA extracted from environmental samples (eDNA) combined with high-throughput sequencing, commonly referred to as eDNA metabarcoding, is increasing in popularity within the scientific community. However, sampling strategies, laboratory protocols and analytical pipelines can influence the results of eDNA metabarcoding surveys. While the impact of laboratory protocols and analytical pipelines have been extensively studied, the importance of sampling strategies on eDNA metabarcoding surveys has not received the same attention. To avoid underestimating local biodiversity, adequate sampling strategies (i.e. sampling intensity and spatial sampling replication) need to be implemented. This study evaluated the impact of sampling strategies along an altitudinal and biodiversity gradient in the upper section of the Murrumbidgee River (Murray-Darling Basin, Australia). An eDNA metabarcoding survey was used to determine the local fish biodiversity and evaluate the influence of sampling intensity and spatial sampling replication on the biodiversity estimates. The results show that optimal eDNA sampling strategies varied between sites and indicate that river morphology, species richness and species abundance affect the optimal sampling intensity and spatial sampling replication needed to accurately assess the fish biodiversity. While the generality of the patterns will need to be confirmed through future studies, these findings provide a basis to guide future eDNA metabarcoding surveys in river systems

Small population size and extremely low levels of genetic diversity in island populations of the platypus, Ornithorhynchus anatinus

Genetic diversity generally underpins population resilience and persistence. Reductions in population size and absence of gene flow can lead to reductions in genetic diversity, reproductive fitness, and a limited ability to adapt to environmental change increasing the risk of extinction. Island populations are typically small and isolated, and as a result, inbreeding and reduced genetic diversity elevate their extinction risk. Two island populations of the platypus, Ornithorhynchus anatinus, exist; a naturally occurring population on King Island in Bass Strait and a recently introduced population on Kangaroo Island off the coast of South Australia. Here we assessed the genetic diversity within these two island populations and contrasted these patterns with genetic diversity estimates in areas from which the populations are likely to have been founded. On Kangaroo Island, we also modeled live capture data to determine estimates of population size. Levels of genetic diversity in King Island platypuses are perilously low, with eight of 13 microsatellite loci fixed, likely reflecting their small population size and prolonged isolation. Estimates of heterozygosity detected by microsatellites (H(E)= 0.032) are among the lowest level of genetic diversity recorded by this method in a naturally outbreeding vertebrate population. In contrast, estimates of genetic diversity on Kangaroo Island are somewhat higher. However, estimates of small population size and the limited founders combined with genetic isolation are likely to lead to further losses of genetic diversity through time for the Kangaroo Island platypus population. Implications for the future of these and similarly isolated or genetically depauperate populations are discussed

Speckle Imaging of Gamma2 Velorum: The Inner Wind Possibly Resolved

Accurately quantifying the rates dM/dt at which massive stars lose mass is essential to any understanding of their evolution. All dM/dt estimates to date assume wind clumping factors; not allowing for clumping leads to overestimates of dM/dt and underestimates of lifetimes and masses when these stars explode as supernovae. Mid-IR spectroscopy suggested that the wind of the nearest Wolf-Rayet star, Gamma2 Vel, is resolved with a Full Width at 10 per cent intensity of 0.5 arcsec, or 171 AU at the 342 pc distance of the star. As the Zorro speckle imager on Gemini-South is capable of 0.02 arcsec resolution, we have used it to image Gamma2 Vel at two orbital phases (0.30 and 0.44) with two narrowband and two intermediate-band filters in an attempt to resolve its wind. Our observations demonstrate that the wind of Gamma2 Vel may be resolved as a 0.07 arcsec westward elongation through an 832 nm filter at orbital phase 0.3 . If confirmed, this is the smallest scale (24 AU) at which a WR star wind asymmetry has been directly imaged. Similar imaging at multiple phases is needed to determine if the asymmetry is due to stochastic wind clumping, co-rotating interaction regions or colliding-wind, cone-shaped shocks.Comment: 7 pages, 4 Figures, in press in MNRA

Spitzer Observations of Long-term Infrared Variability among Young Stellar Objects in Chamaeleon I

Infrared variability is common among young stellar objects, with surveys finding daily to weekly fluctuations of a few tenths of a magnitude. Space-based observations can produce highly sampled infrared light curves, but are often limited to total baselines of about 1 month due to the orientation of the spacecraft. Here we present observations of the Chameleon I cluster, whose low declination makes it observable by the Spitzer Space Telescope over a 200-day period. We observe 30 young stellar objects with a daily cadence to better sample variability on timescales of months. We find that such variability is common, occurring in ~80% of the detected cluster members. The change in [3.6]–[4.5] color over 200 days for many of the sources falls between that expected for extinction and fluctuations in disk emission. With our high cadence and long baseline we can derive power spectral density curves covering two orders of magnitude in frequency and find significant power at low frequencies, up to the boundaries of our 200-day survey. Such long timescales are difficult to explain with variations driven by the interaction between the disk and stellar magnetic field, which has a dynamical timescale of days to weeks. The most likely explanation is either structural or temperature fluctuations spread throughout the inner ~0.5 au of the disk, suggesting that the intrinsic dust structure is highly dynamic