This dataset of fungal communities associated with the leaves an endemic Hawaiian tree provides students opportunities to explore relationships between environmental variables and microbial community composition.
These files comprise a processed OTU table and environmental metadata for analyses described in Zimmerman and Vitousek 2012. That study uses high-throughput sequencing to quantify the members of leaf-associated fungal communities across a set of sites on the Island of Hawai’i that span large gradients of elevation and rainfall, while keeping the host species constant. Four files are included here, in addition to a Readme file that describes the content of each column in each dataset. The initial data in the name is when the data were initially saved to this format. QC stands for Quality Checked, followed by the initials of the person performing the check (in this case Naupaka B Zimmerman). Line breaks in each file are Unix line feeds (n).
These data would be most useful for a course where the students were learning about community ecology analysis techniques, including diversity metrics and ordination. The datasets are formatted to work well with the R programming language, and can be used with the ‘vegan’ package for community ecology analyses (Oksanen et al. 2017). Slides on using vegan for community ecology analyses, including the use of this dataset, can be found on Zenodo (http://doi.org/10.5281/zenodo.836943).
Jari Oksanen, F. Guillaume Blanchet, Michael Friendly, Roeland Kindt, Pierre Legendre, Dan McGlinn, Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos, M. Henry H. Stevens, Eduard Szoecs and Helene Wagner (2017). vegan: Community Ecology Package. R package version 2.4-3. https://CRAN.R-project.org/package=vegan
Naupaka Zimmerman and Gavin Simpson. (2017, August 1). naupaka/esa_intro_vegan_2016: Archived version of workshop materials. Zenodo. http://doi.org/10.5281/zenodo.836943
Naupaka Zimmerman and Peter M. Vitousek. 2012. Fungal endophyte communities reflect environmental structuring across a Hawaiian landscape. Proceedings of the National Academy of Sciences 109:13022–13027. http://doi.org/10.1073/pnas.1209872109
Contents ( Show bundle contents ) Bundle
- Presentation.html(HTML | 511 KB)
- Presentation.Rmd(RMD | 837 B )
- TIEE_microbial_communities.Rproj(RPROJ | 228 B )
- 2011-02-06_OTU_counts_and_metadata_QC_NBZ.csv(CSV | 1 MB)
- 2011-02-06_OTU_counts_per_tree_QC_NBZ.csv(CSV | 1 MB)
- 2011-02-06_site_metadata_QC_NBZ.csv(CSV | 609 B )
- 2011-02-06_tree_metadata_QC_NBZ.csv(CSV | 7 KB)
- README_metadata.txt(TXT | 3 KB)
- License terms
Cite this work
Researchers should cite this work as follows:
- Zimmerman, N. B., Vitousek, P. (2018). Biogeography of plant-associated fungi: who lives where and why?. DIG into Data FMN (2017), /groups/dig, QUBES Educational Resources. doi:10.25334/Q42X21