This repo contains data and R scripts for the manuscript Frankia diversity in sympatrically-occurring red alder (Alnus rubra) and Sitka alder (Alnus viridis), which is currently being submitted to the journal Trees.
Files with .shared filetypes contain OTU tables output from mothur.
The OTU of each sample is contained in OTU_listfile.csv.
For GPS information, please see gps_plots.csv.
| filename | purpose |
|---|---|
| 16S_frankia_output_.opti_mcc.shared | output from mothur required for R analyses |
| 16S_MAFFT_unique.opti_mcc.samp.shared | output from mothur required for R analyses |
| 16S_MAFFT_unique.opti_mcc.shared | output from mothur required for R analyses |
| bac_env_sample.csv | secondary matrix for 16S community aggregated by sample |
| bac_env_tree.csv | secondary matrix for 16S community aggregated by tree |
| bs_tree_nifH_clean3.jpg | revised Figure 3 |
| clade_16S_labs4.csv | clade labels for the 16S tree |
| clade_labs4.csv | clade labels for the nifH tree |
| end_trim_2_MAFFT_993.opti_mcc.shared | output from mothur required for R analyses |
| env_b_trees.csv | soil data aggregated by tree for 16S community samples |
| env_trees.csv | soil data aggregated by tree for nifH community samples |
| frankia-mothur.Rmd | R markdown |
| gg_env.csv | this was used to generate the heatmap from Figure 4, which was replaced with Table 2 during revisions |
| gps_plots.csv | these are the GPS coordinates used to generate the ggmap object |
| gps_trees_dist.csv | these are latitude and longitude coordinates for trees sampled |
| msh-frankia-alnus.Rproj | R project |
| nif_env_sample.csv | secondary matrix for nifH community aggregated by sample |
| nif_env_tree.csv | secondary matrix for nifH community aggregated by tree |
| nif_MAFFT_out-samp.opti_mcc.shared | output from mothur required for R analyses |
| OTU_listfile.csv | list file output from mothur which shows which samples cluster into which OTUs |
| overview_zoom13_2.jpeg | this is revised Figure 1 with transects and without plot-level panel insets |
| panel_zoom20_2.jpeg | this is revised Figure 1 with transects and plot-level panel insets |
| plots.csv | these are the original coordinates provided from the field crew |
| PP_specaccum_combined.jpeg | revised Figure 2 |
| RAxML_bipartitions.1.newick | tree input files |
| RAxML_bipartitions_nifH.TEST | tree input files |
| RAxML_bipartitions16S_2.newick | tree input files |
| RAxML_bipartitionsnifH_2.newick | tree input files |
| README.md | read me file |
| nifH_end_trim_2_delim.fasta | sequences in fasta format |
| soil_data.csv | raw soil data by plot |
| end_trim_2_MAFFT.phy | alignment file |