The environmental DNA (eDNA) method is a detection technique that is rapidly gaining credibility as a sensitive tool useful in the surveillance and monitoring of invasive and threatened species. ...Because eDNA analysis often deals with small quantities of short and degraded DNA fragments, methods that maximize eDNA recovery are required to increase detectability. In this study, we performed experiments at different stages of the eDNA analysis to show which combinations of methods give the best recovery rate for eDNA. Using Oriental weatherloach (Misgurnus anguillicaudatus) as a study species, we show that various combinations of DNA capture, preservation and extraction methods can significantly affect DNA yield. Filtration using cellulose nitrate filter paper preserved in ethanol or stored in a -20°C freezer and extracted with the Qiagen DNeasy kit outperformed other combinations in terms of cost and efficiency of DNA recovery. Our results support the recommendation to filter water samples within 24hours but if this is not possible, our results suggest that refrigeration may be a better option than freezing for short-term storage (i.e., 3-5 days). This information is useful in designing eDNA detection of low-density invasive or threatened species, where small variations in DNA recovery can signify the difference between detection success or failure.
Environmental DNA (eDNA) is increasingly used to monitor aquatic macrofauna. Typically, short mitochondrial DNA fragments are targeted because these should be relatively more abundant in the ...environment as longer fragments will break into smaller fragments over time. However, longer fragments may permit more flexible primer design and increase taxonomic resolution for eDNA metabarcoding analyses, and recent studies have shown that long mitochondrial eDNA fragments can be extracted from environmental water samples. Nuclear eDNA fragments have also been proposed as targets, but little is known about their persistence in the aquatic environment. Here we measure the abundance of mitochondrial eDNA fragments of different lengths and of short nuclear eDNA fragments, originating from captive fish in experimental tanks, and we test whether longer mitochondrial and short nuclear fragments decay faster than short mitochondrial fragments following fish removal. We show that when fish are present, shorter mitochondrial fragments are more abundant in water samples than both longer mitochondrial fragments and short nuclear eDNA fragments. However, the rate of decay following fish removal was similar for all fragment types, suggesting that the differences in abundance resulted from differences in the rates at which different fragment types were produced rather than differences in their decay rates.
Imperfect sensitivity, or imperfect detection, is a feature of all survey methods that needs to be accounted for when interpreting survey results. Detection of environmental DNA (eDNA) is ...increasingly being used to infer species distributions, yet the sensitivity of the technique has not been fully evaluated. Sensitivity, or the probability of detecting target DNA given it is present at a site, will depend on both the survey method and the concentration and dispersion of target DNA molecules at a site. We present a model to estimate target DNA concentration and dispersion at survey sites and to estimate the sensitivity of an eDNA survey method. We fitted this model to data from a species‐specific eDNA survey for Oriental weatherloach, Misgurnus anguillicaudatus, at three sites sampled in both autumn and spring. The concentration of target DNA molecules was similar at all three sites in autumn but much higher at two sites in spring. Our analysis showed the survey method had ≥95% sensitivity at sites where target DNA concentrations were ≥11 molecules per litre. We show how these data can be used to compare sampling schemes that differ in the number of field samples collected per site and number of PCR replicates per sample to achieve ≥95% sensitivity at a given target DNA concentration. These models allow researchers to quantify the sensitivity of eDNA survey methods to optimize the probability of detecting target species, and to compare DNA concentrations spatially and temporarily.
Summary
Determining the timing and location of reproductive events is critical for efficient management of species. However, methods currently used for aquatic species are costly, time intensive, ...biased and often require destructive or injurious sampling. Hence, developing a non‐invasive sampling method to accurately determine the timing and location of reproduction for aquatic species would be extremely valuable.
We conducted an experimental and field study to determine the influence of spawning, and the mass release of spermatozoa in particular, on environmental DNA (eDNA) concentrations. Using a quantitative PCR approach we monitored changes in nuclear and mitochondrial eDNA concentrations over time.
The data from the experimental study and the field survey supported our hypothesis that spawning events are characterized by higher concentrations of nuclear relative to mitochondrial eDNA. Outside of the reproductive period, we find that nuclear and mitochondrial DNA fragments are equally abundant in environmental water samples.
We have shown that changes in the relative abundance of nuclear and mitochondrial eDNA can be used to monitor spawning activity of the endangered Macquarie perch. Our method is likely to be transferrable to other aquatic species and can be particularly useful to increase our understanding of the spawning biology of cryptic, rare or threatened species as well as design and evaluate environmental management actions and determine species establishment.
Environmental DNA (eDNA) metabarcoding surveys enable rapid, noninvasive identification of taxa from trace samples with wide‐ranging applications from characterizing local biodiversity to identifying ...food‐web interactions. However, the technique is prone to error from two major sources: (a) contamination through foreign DNA entering the workflow, and (b) misidentification of DNA within the workflow. Both types of error have the potential to obscure true taxon presence or to increase taxonomic richness by incorrectly identifying taxa as present at sample sites, but multiple error sources can remain unaccounted for in metabarcoding studies. Here, we use data from an eDNA metabarcoding study designed to detect vertebrate species at waterholes in Australia's arid zone to illustrate where and how in the workflow errors can arise, and how to mitigate those errors. We detected the DNA of 36 taxa spanning 34 families, 19 orders and five vertebrate classes in water samples from waterholes, demonstrating the potential for eDNA metabarcoding surveys to provide rapid, noninvasive detection in remote locations, and to widely sample taxonomic diversity from aquatic through to terrestrial taxa. However, we initially identified 152 taxa in the samples, meaning there were many false positive detections. We identified the sources of these errors, allowing us to design a stepwise process to detect and remove error, and provide a template to minimize similar errors that are likely to arise in other metabarcoding studies. Our findings suggest eDNA metabarcoding surveys need to be carefully conducted and screened for errors to ensure their accuracy.
The determination of exoplanet properties and occurrence rates using Kepler data critically depends on our knowledge of the fundamental properties (such as temperature, radius, and mass) of the ...observed stars. We present revised stellar properties for 197,096 Kepler targets observed between Quarters 1-17 (Q1-17), which were used for the final transiting planet search run by the Kepler Mission (Data Release 25, DR25). Similar to the Q1-16 catalog by Huber et al., the classifications are based on conditioning published atmospheric parameters on a grid of Dartmouth isochrones, with significant improvements in the adopted method and over 29,000 new sources for temperatures, surface gravities, or metallicities. In addition to fundamental stellar properties, the new catalog also includes distances and extinctions, and we provide posterior samples for each stellar parameter of each star. Typical uncertainties are ∼27% in radius, ∼17% in mass, and ∼51% in density, which is somewhat smaller than previous catalogs because of the larger number of improved constraints and the inclusion of isochrone weighting when deriving stellar posterior distributions. On average, the catalog includes a significantly larger number of evolved solar-type stars, with an increase of 43.5% in the number of subgiants. We discuss the overall changes of radii and masses of Kepler targets as a function of spectral type, with a particular focus on exoplanet host stars.
Eradications of invasive species are usually expensive and difficult to conduct. Knowing when to declare an eradication successful requires distinguishing between failed detection of the target ...species due to imperfect sensitivity of the detection method and true species absence. This is difficult because the sensitivities of many detection methods are unknown.
Environmental DNA (eDNA) methods can be used to detect species by analysing DNA present in environmental samples. eDNA has been promoted as a particularly sensitive and cost‐effective way to detect species at low densities and, importantly, the sensitivity of eDNA surveys can be quantified. Nevertheless, the effort and costs involved in detecting species at extremely low densities, such as required during eradication, have not been previously calculated.
We evaluated the sensitivity of eDNA surveys in detecting the invasive European carp, Cyprinus carpio, in two lakes in Tasmania, Australia, one in which carp have been eradicated and a second in which carp are currently being eradicated. We determined the sampling effort and associated cost required to detect the species at very low density in these lakes.
While our eDNA survey detected the current low density carp population present in Lake Sorell, we show that an exponential increase in sampling effort and associated cost will be required to confidently detect the species as the population declines. Similarly, while our eDNA survey corroborated the species absence from Lake Crescent, our detection confidence was low. We quantify the survey effort and financial investment required to confidently establish eradication success in Lake Crescent.
Synthesis and applications. Estimating the environmental DNA (eDNA) survey effort and cost required to detect species at a given density will enable practitioners to make informed decisions on the feasibility of implementing such surveys. Quantifying the sensitivity of eDNA surveys will also inform the confidence practitioners should place in eDNA detection results to ensure appropriate management actions are implemented and provide a suitable stopping point at which to confidently declare eradication success.
Estimating the environmental DNA (eDNA) survey effort and cost required to detect species at a given density will enable practitioners to make informed decisions on the feasibility of implementing such surveys. Quantifying the sensitivity of eDNA surveys will also inform the confidence practitioners should place in the results of eDNA detection surveys to ensure appropriate management actions are implemented and provide a suitable stopping point at which to confidently declare eradication success.
High‐throughput sequencing of environmental DNA (i.e., eDNA metabarcoding) has become an increasingly popular method for monitoring aquatic biodiversity. At present, such analyses require ...target‐specific primers to amplify DNA barcodes from co‐occurring species, and this initial amplification can introduce biases. Understanding the performance of different primers is thus recommended prior to undertaking any metabarcoding initiative. While multiple software programs are available to evaluate metabarcoding primers, all programs have their own strengths and weaknesses. Therefore, a robust in silico workflow for the evaluation of metabarcoding primers will benefit from the use of multiple programs. Furthermore, geographic differences in species biodiversity are likely to influence the performance of metabarcoding primers and further complicate the evaluation process. Here, an in silico workflow is presented that can be used to evaluate the performance of metabarcoding primers on an ecoregion scale. This workflow was used to evaluate the performance of published and newly developed eDNA metabarcoding primers for the freshwater fish biodiversity of the Murray–Darling Basin (Australia). To validate the in silico workflow, a subset of the primers, including one newly designed primer pair, were used in metabarcoding analyses of an artificial DNA community and eDNA samples. The results show that the in silico workflow allows for a robust evaluation of metabarcoding primers and can reveal important trade‐offs that need to be considered when selecting the most suitable primer. Additionally, a new primer pair was described and validated that allows for more robust taxonomic assignments and is less influenced by primer biases compared to commonly used fish metabarcoding primers.
An in silico workflow, artificial DNA communities, and eDNA samples were used to evaluate the performance of previously published and newly developed metabarcoding primers for fishes on an ecoregion scale. The results show that the in silico workflow allows for a robust evaluation of metabarcoding primers, and the newly designed primer pair is less affected by primer biases.
Abstract
We present high-angular-resolution imaging observations of 517 host stars of TESS exoplanet candidates using the ‘Alopeke and Zorro speckle cameras at Gemini North and South. The sample ...consists mainly of bright F, G, K stars at distances of less than 500 pc. Our speckle observations span angular resolutions of ∼20 mas out to 1.″2, yielding spatial resolutions of <10–500 au for most stars, and our contrast limits can detect companion stars 5–9 mag fainter than the primary at optical wavelengths. We detect 102 close stellar companions and determine the separation, magnitude difference, mass ratio, and estimated orbital period for each system. Our observations of exoplanet host star binaries reveal that they have wider separations than field binaries, with a mean orbital semimajor axis near 100 au. Other imaging studies have suggested this dearth of very closely separated binaries in systems which host exoplanets, but incompleteness at small separations makes it difficult to disentangle unobserved companions from a true lack of companions. With our improved angular resolution and sensitivity, we confirm that this lack of close exoplanet host binaries is indeed real. We also search for a correlation between planetary orbital radii versus binary star separation; but, given the very short orbital periods of the TESS planets, we do not find any clear trend. We do note that in exoplanet systems containing binary host stars, there is an observational bias against detecting Earth-size planet transits due to transit depth dilution caused by the companion star.
The Herschel Orion Protostar Survey obtained well-sampled 1.2-870 m spectral energy distributions (SEDs) of over 300 protostars in the Orion molecular clouds, home to most of the young stellar ...objects (YSOs) in the nearest 500 pc. We plot the bolometric luminosities and temperatures for 330 Orion YSOs, 315 of which have bolometric temperatures characteristic of protostars. The histogram of the bolometric temperature is roughly flat; 29% of the protostars are in Class 0. The median luminosity decreases by a factor of four with increasing bolometric temperature; consequently, the Class 0 protostars are systematically brighter than the Class I protostars, with a median luminosity of 2.3 as opposed to 0.87 . At a given bolometric temperature, the scatter in luminosities is three orders of magnitude. Using fits to the SEDs, we analyze how the luminosities corrected for inclination and foreground reddening relate to the mass in the inner 2500 au of the best-fit model envelopes. The histogram of the envelope mass is roughly flat, while the median-corrected luminosity peaks at 15 for young envelopes and falls to 1.7 for late-stage protostars with remnant envelopes. The spread in luminosity at each envelope mass is three orders of magnitude. Envelope masses that decline exponentially with time explain the flat mass histogram and the decrease in luminosity, while the formation of a range of stellar masses explains the dispersion in luminosity.
PDF
