Students use dead wood (saproxylic) fungi occurrence data from New Jersey, USA collected by students and faculty of Kean University to learn the basics of community ecology. Simple NMDS ordination and Jaccard index is performed using R.
The assignment is developed for one laboratory session of 2.5 hours.The module was taught to sophomore students majoring in biology, with only basic knowledge of ecology and statistics. An additional laboratory session of 2.5 hours (can be assigned to be completed online at home) would be required prior to this module if students are unfamiliar with R. Please see the instructors notes for more details.
This module can be used in ecology classes to demonstrate basic community analysis, or compliment the course material letting students to explore one of the forest habitats, dead wood, and its decomposers - saproxylic fungi. It can be also used in beginners bioinformatics or biostatistics classes to introduce basics of ordination in R.
In this activity, students will:
- Discuss quantitative methods used in community ecology. Presentation slides are provided to guide this discussion.
- Use basics of statistical software R.
- Familiarize with the global biodiversity portals such as inaturalist.org or gbif.org and methods of storage and open sharing of data.
- Use open biodiversity dataset to perform NMDS ordination analysis in R (package vegan).
- Compare and contrast dead wood fungal communities in different types of forests (hardwood vs softwood).
Software used was: R / R-Studio; packages: dplyr and vegan.
In this module, a modified version of an openly published dataset is used. Full dataset can accessed at gbif.org:
Shumskaya M, Zambell C, Mishra S, Bell E, Blue S, Yearwood-Marut J, Marut W, Vindas-Cruz A, Jennings A, Hylton N, Burghardt J (2019). Survey of saproxylic fungi across parks of New Jersey. Kean University. Occurrence dataset https://doi.org/10.15468/ngpb5m
What is included in this module:
1. PowerPoint slides to introduce the activity. Slides contain a simple in-class exercise on Jaccard similarity calculation and free-hand ordination.
2. Student's handout to distribute in class.
3. Instructor's notes. Contains recommendations for instructors. Sample student answers are provided in a separated file.
4. Two scripts in R: one to distribute to students who will have to do some editing for the script to work, and one for instructors with completed commands to serve as an example of a working script.
5. The dataset csv file.
- deadwood.csv(CSV | 16 KB)
- NMDS_TeachingModule_KeanU_saproxylicFungi_instructor.R(R | 8 KB)
- NMDS_TeachingModule_KeanU_saproxylicFungi_instructorsNotes.docx(DOCX | 26 KB)
- NMDS_TeachingModule_KeanU_saproxylicFungi_sampleAnswer.docx(DOCX | 103 KB)
- NMDS_TeachingModule_KeanU_saproxylicFungi_Slides.pptx(PPTX | 3 MB)
- NMDS_TeachingModule_KeanU_saproxylicFungi_studentHandout.docx(DOCX | 27 KB)
- NMDS_TeachingModule_KeanU_saproxylicFungi_students.R(R | 8 KB)
- License terms
Cite this work
Researchers should cite this work as follows:
- Shumskaya, M., Zambell, C. (2019). NMDS to Study Dead Wood Fungi Communities in Parks of New Jersey. NEON Faculty Mentoring Network, QUBES Educational Resources. doi:10.25334/A2ME-QH70
Version 1.0 was prepared as a part of 2019 NEON FMN.