The Visual Display of Quantitative Information

Environmental DNA - An emerging tool in conservation for monitoring past and present biodiversity

Contrasting treatment‐specific survival using double‐robust estimators

Extraction and identification of DNA from an environmental sample has proven noteworthy recently in detecting and monitoring not only common species, but also those that are endangered, invasive, or elusive. Particular attributes of so-called environmental DNA (eDNA) analysis render it a potent tool for elucidating mechanistic insights in ecological and evolutionary processes. Foremost among these is an improved ability to explore ecosystem-level processes, the generation of quantitative indices for analyses of species, community diversity, and dynamics, and novel opportunities through the use of time-serial samples and unprecedented sensitivity for detecting rare or difficult-to-sample taxa. Although technical challenges remain, here we examine the current frontiers of eDNA, outline key aspects requiring improvement, and suggest future developments and innovations for research.

https://www.cell.com/trends/ecology-evolution/pdf/S0169-5347(14)00086-X.pdf

Environmental DNA for wildlife biology and biodiversity monitoring

Environmental DNA for wildlife biology and biodiversity monitoring (vol 29, pg 358, 2014)

Recent studies have demonstrated that detection of environmental DNA (eDNA) from aquatic vertebrates in water bodies is possible. The Burmese python, Python bivittatus, is a semi-aquatic, invasive species in Florida where its elusive nature and cryptic coloration make its detection difficult. Our goal was to develop a diagnostic PCR to detect P. bivittatus from water-borne eDNA, which could assist managers in monitoring this invasive species. First, we used captive P. bivittatus to determine whether reptilian DNA could be isolated and amplified from water samples. We also evaluated the efficacy of two DNA isolation methods and two DNA extraction kits commonly used in eDNA preparation. A fragment of the mitochondrial cytochrome b gene from P. bivittatus was detected in all water samples isolated with the sodium acetate precipitate and the QIAamp DNA Micro Kit. Next, we designed P. bivittatus-specific primers and assessed the degradation rate of eDNA in water. Our primers did not amplify DNA from closely related species, and we found that P. bivittatus DNA was consistently detectable up to 96 h. Finally, we sampled water from six field sites in south Florida. Samples from five sites, where P. bivittatus has been observed, tested positive for eDNA. The final site was negative and had no prior documented evidence of P. bivittatus. This study shows P. bivittatus eDNA can be isolated from water samples; thus, this method is a new and promising technique for the management of invasive reptiles.

/pdf/detecting-an-elusive-invasive-species-a-diagnostic-pcr-to-1s863pqgcu.pdf

Detecting an elusive invasive species: a diagnostic PCR to detect Burmese python in Florida waters and an assessment of persistence of environmental DNA

/pdf/feral-swine-impacts-on-agriculture-and-the-environment-5fi6iwyibf.pdf

Feral swine impacts on agriculture and the environment

Monitoring animal populations is an essential component of wildlife research and management. Population indices can be efficient methods for monitoring populations when more labour-intensive density- estimation procedures are impractical or invalid to apply, and many monitoring objectives can be couched in an indexing framework. Indexing procedures obtain maximal utility if they exhibit key characteristics, including being practical to apply, being sensitive to changes or differences in the target species' population, having an inherent variance formula and allowing for precision in index values, and relying on as few assumptions as possible. Additional useful characteristics include being able simultaneously to monitor multiple animal species and to describe spatial characteristics of the species monitored. Here, a paradigm is presented that promotes the characteristics that make indices most useful. Observations are made at stations located throughout the area of interest. Stations can take many forms, depending on the observations, and range from points for visual counts to tracking plots to chew cards, and many others. A wide variety of observation methods for many animal species can fit into this format. Observations are made at each station on multiple occasions for each indexing session. Geographic location data for each station are encouraged to be collected. No assumptions of independence are made among stations, nor among observation occasions. Measurements made at each station are required to be continuous or unboundedly discrete. The formula for a general index to describe population levels is presented and its variance formula is derived. Issues relevant to the application of this methodology, and indices in general, are discussed.

/pdf/indexing-principles-and-a-widely-applicable-paradigm-for-1w21jfu763.pdf

Indexing principles and a widely applicable paradigm for indexing animal populations

We conducted an extensive simulation study to compare the performance of a large group of plotless density estimators (PDEs) to obtain clarification of their relative performance in a diversity of sampling situations. The PDEs studied included well-known ones from the literature plus some extensions and modifications introduced here. The simulations cover 96 combinations of 6 spatial patterns, 4 sample sizes, and 4 population densities. We made comparisons within classes of similar estimators, and we indicate the best-performing PDEs out of the complete set studied. Over all spatial patterns, the angle-order estimator with measurements to the third- closest individual in each quadrant had the lowest relative root-mean-squared error (RRMSE), followed by the same estimation method with measurements to the second closest individual in each quadrant. Also performing well were the variable area transect, the ordered distance estimator using the third closest individual, and an extension of the Kendall-Moran estimator that searches for the second nearest neighbor and pools search areas from all sample points. Opinions and recommendations are given as to which PDEs perform well enough and are practical enough to deserve strong consideration for use in the field.

/pdf/a-comparison-of-plotless-density-estimators-using-monte-1ceojx05i3.pdf

A Comparison of Plotless Density Estimators Using Monte Carlo Simulation

Three methods of assessing relative abundance of wild canids were evaluated on a population of dingoes, Canis lupus dingo (Corbett), on a cattle station in south-westem Queensland. The tested indices relied on measurements of activity based on spoor. Two of the techniques attracted the target species to tracking stations through the use of a novel (fatty acid scent) or food-based (buried meat) attractant. The third index (activity) measured the number of dingo tracks crossing tracking stations placed at 1-km intervals along a road transect. All three indices had a high level of agreement for detecting differences in relative abundance, with correlation coefficients exceeding 0.85. When the stations were analysed in 1-km segments, the activity index proved the most sensitive, producing proportionally more positive responses than either of the other two indices irrespective of whether the tracking stations were assessed at 1-, 2-, 3- or 4-day intervals. Inconsistencies between indices existed, with the derived abundance indices not showing the anticipated reduction following population reduction. The effect of season and the interaction between dingo activity and index methodology are discussed.

Richard M. Engeman

Papers

Detecting an elusive invasive species: a diagnostic PCR to detect Burmese python in Florida waters and an assessment of persistence of environmental DNA

Feral swine impacts on agriculture and the environment

Indexing principles and a widely applicable paradigm for indexing animal populations

A Comparison of Plotless Density Estimators Using Monte Carlo Simulation

Evaluation of Three Relative Abundance Indices for Assessing Dingo Populations