Abstract
Environmental DNA (eDNA) metabarcoding is becoming a core tool in ecology and conservation biology, and is being used in a growing number of education, biodiversity monitoring, and public outreach programs in which professional research scientists engage community partners in primary research. Results from eDNA analyses can engage and educate natural resource managers, students, community scientists, and naturalists, but without significant training in bioinformatics, it can be difficult for this diverse audience to interact with eDNA results. Here we present the R package ranacapa, at the core of which is a Shiny web app that helps perform exploratory biodiversity analyses and visualizations of eDNA results. The app requires a taxonomy-by-sample matrix and a simple metadata file with descriptive information about each sample. The app enables users to explore the data with interactive figures and presents results from simple community ecology analyses. We demonstrate the value of ranacapa to two groups of community partners engaging with eDNA metabarcoding results.
Highlights
The targeted amplification and sequencing of DNA that living organisms shed into their physical environment, termed “environmental DNA metabarcoding,” is revolutionizing microbiology, ecology, and conservation research (Deiner et al, 2017; Taberlet et al 2012)
As the cost of environmental DNA (eDNA) metabarcoding declines and sample collection techniques become more streamlined (e.g. Thomas et al (2018)), professional research scientists are increasingly using eDNA metabarcoding as a platform to engage a diversity of community partners, including natural resource managers, undergraduate students, and citizen scientists in primary research
As we show in the Use cases, empowering community partners to interact with the data and perform simple but insightful community ecology analyses can help make these collaborations more enriching and valuable to both parties
Summary
The targeted amplification and sequencing of DNA that living organisms shed into their physical environment, termed “environmental DNA (eDNA) metabarcoding,” is revolutionizing microbiology, ecology, and conservation research (Deiner et al, 2017; Taberlet et al 2012). We created the R package “ranacapa”, at the core of which is a Shiny web app that can be used to visualize results from eDNA sequencing studies and perform simple community ecology analyses.
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
