How to quantify factors degrading DNA in the environment and predict degradation for effective sampling design

Extra-organismal DNA (eoDNA) from material left behind by organisms (non-invasive DNA: e.g., faeces, hair) or from environmental samples (eDNA: e.g., water, soil) is a valuable source of genetic information. However, the relatively low quality and quantity of eoDNA, which can be further degraded by environmental factors, results in reduced amplification and sequencing success. This is often compensated for through cost- and time-intensive replications of genotyping/sequencing procedures. Therefore, system- and site-specific quantifications of environmental degradation are needed to maximize sampling efficiency (e.g., fewer replicates, shorter sampling durations), and to improve species detection and abundance estimates. Using ten environmentally diverse bat roosts as a case study, we developed a robust modelling pipeline to quantify the environmental factors degrading eoDNA, predict eoDNA quality, and estimate sampling-site-specific ideal exposure duration. Maximum humidity was the stro..., From the corresponding publication: How to quantify factors degrading DNA in the environment and predict degradation for effective sampling design
Sampling
We collected bat droppings at ten lesser horseshoe bat (Rhinolophus hipposideros) maternity roosts in Thuringia (Germany) between 2015-2019 (Jan et al., 2019; Lehnen et al., 2021). We sampled each roost twice a year: once in June and once in August, i.e., before and after offspring were born. We spread sheets of newspaper under the main hanging sites, and returned after 9-13 days to collect newly deposited droppings (Puechmaille & Petit, 2007). Here, we refer to such a sampling event of 9-13 days within a roost as a “roost-visit” (RV). We only retained the 25 RVs where both roost temperature (°C) and relative humidity (%, hereafter “humidity”) were recorded with iButtons (Maxim Integrated Products, 2015 ) logging every 30 to 180 minutes inside the roost. The microclimate of the roosts varied greatly, including hot and dry attics,..., How to execute the modeling pipeline R-Script introduced in: \"How to quantify factors degrading DNA in the environment and predict degradation for effective sampling design\"
1. Before executing make sure that the following is available (code was only tested on  Windows 10 64 Bit machine and Ubuntu 20.04, see also R_sessionInfo....txt files):
- R Studio 1.4.1717
- R 4.1 (cran.r-project.org/bin/windows/base/old/4.1.0/)
2. Make sure you have downloaded and extracted the pipeline onto the machine and location you want to execute the code from.
3. Double-click on the R-project file (eoDNAQuantificationandSimulation.Rproj) to open it with R-Studio
4. R Studio should open and show that the project is loaded top right corner of R-Studio
5. The project was created using the package renv to make sure that the right versions of packages are loaded within R.
   You can check the locked package versions are loaded when clicking on \"Packages\" in R Studio. You should see all packages with a column \"Ve...