Tuesday, July 7, 2026

2:30 PM - 4:00 PM

Room BE.0.08

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Details

Participants need to bring their own laptop for this workshop. Participants should install R and RStudio on their personal computers in advance. Both are free and can be installed online. 1. Download R from: https://cran.us.r-project.org 2. Click on the download link for your operating system: Windows, Linux, or macOS. 3. Install R, keeping the default installation settings. 4. Download RStudio Desktop from: https://posit.co/download/rstudio-desktop/ 5. Install RStudio, keeping the default installation settings. 6. Open RStudio to make sure the installation was successful. For participants who encounter difficulties, this guide may be helpful and includes a video tutorial: https://medium.com/@GalarnykMichael/install-r-and-rstudio-on-windows-5f503f708027 Having R and RStudio installed in advance will save time during the workshop and allow us to focus on the theoretical introduction and practical exercise. The use of single nucleotide polymorphism (SNP) markers has become central in conservation practices for its ability to address a broad scope of ecological and evolutionary questions. However, genotype datasets, especially when derived from eDNA, contain undetected errors and missing data, which can significantly bias downstream analyses and conservation decisions. This 1.5-hour interactive workshop will introduce participants to an applied and adaptable pipeline for SNP and sample filtering and recapture identification based on triplicate samples, designed for diverse purposes in conservation biology. Participants will learn about the sources, identification, and mitigation of genotyping errors and missing data, understand their consequences, and implement stepwise filtering procedures to improve genotypes reliability. The workshop is structured around a four-step pipeline: (1) SNP filtering by missing data, (2) SNP error-rate estimation and filtering using triplicate samples, (3) sample filtering by missing data, and (4) detection and filtering of recaptured individuals. This will be demonstrated using a real dataset from a conservation case study on the Asiatic wild ass (Equus hemionus) population in the Negev Highlands, Israel. We will examine how threshold choices and pipeline order shape final datasets and downstream inferences. Through guided hands-on exercises in R, attendees will run the pipeline, visualize each step’s results, and discuss appropriate threshold selection to their own datasets. Emphasis will be given to the importance of quality control in genotype-based analyses used for evidence-based conservation management, and on how repeated samples can be used for this purpose. The workshop is suitable for students, researchers, and other practitioners in molecular ecology, conservation genetics, and wildlife management, and does not require advanced programming experience. Participants will gain practical tools and conceptual understanding to improve the robustness of their genotype datasets, enabling reliable interpretation of processes that inform conservation decisions, using an approach transferable across taxa and laboratory platforms.

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Organiser