Data for Soil nematode functional diversity, successional patterns, and indicator taxa associated with vertebrate decomposition - Nematode_data_master_LTAYLOR_Soil nematode functional diversity during vertebrate decomposition

This is the master complied nematode data file that includes all sampling sites and dates. The first column contains the taxon name. The second column contains the functional group designation associated with each taxon (B1, B2, B2, etc.). All remaining columns are data files sorted by study date, soil depth (core or interface), and location (cage = underneath beavers, or control). Values are total abundance (per 100 cm3) for each taxon in the sample. NOTE: Data is not in order by study date. This is the master file that is used to generate Figure 2 (abundance and alpha diversity boxplots), Figures 3 and 6 (beta diversity, including stacked bar graphs and the Faunal Profile), Figure 4 (RDA), and Figures 5 and 7 (heatmaps). All calculations for alpha diversity (Shannon diversity) and the faunal profile can be found detailed in manuscript reference [56], Keenan et al. (2018) https://doi.org/10.1371/journal.pone.0208845. All boxplots and faunal profile diagrams were constructed using base R, and code can be found in the supplementary file entitled: Rcode_ LTAYLOR_Soil nematode functional diversity during vertebrate decomposition. Beta diversity (stacked bar graphs) are based upon individual taxon means calculated for each sampling date that are expressed as a percentage of total sample. Data is presented according to associated metadata (cp class or trophic class). Stacked bar graphs were constructed using base R and the R packages “ggplot2” and “RColorBrewer”. Code can be found in the supplementary file entitled: Rcode_ LTAYLOR_Soil nematode functional diversity during vertebrate decomposition. Beta diversity (RDA) are calculated from a data matrix constructed by transposing the master data file such that columns contain individual taxa, and rows contain individual samples. RDA graphs were constructed using the R package “vegan”, and R code can be found in the supplementary file entitled: Rcode_ LTAYLOR_Soil nematode functional diversity during vertebrate decomposition. Heatmaps are based upon individual taxon means calculated for each sampling date. Bacterial-feeding and fungal-feeding taxon means were additionally square-root transformed. The data matrix was constructed such that columns contain sampling dates, and rows contain individual taxa. Heatmaps were constructed using the R package “pheatmap”, and R code can be found in the supplementary file entitled: Rcode_ LTAYLOR_Soil nematode functional diversity during vertebrate decomposition.

vertebrate decomposition
nematode
hotspots
succession

Taylor, Lois S. (Depositor)
Taylor, Lois S. (Creator)
DeBruyn, Jennifer (Creator)
Bernard, Ernest (Creator)

2017-03-17