Protist Diversity and Metabolic Strategy in Freshwater Lakes Are Shaped by Trophic State and Watershed Land Use on a Continental Scale

Scripts associated with the article

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Garner RE, Kraemer SA, Onana VE, Huot Y, Gregory-Eaves I, Walsh DA. 2022. Protist Diversity and Metabolic Strategy in Freshwater Lakes Are Shaped by Trophic State and Watershed Land Use on a Continental Scale. mSystems 7, e00316-22. https://doi.org/10.1128/msystems.00316-22.

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Scripts

• 00_ena_template_reads.R Format European Nucleotide Archive (ENA) read submission template.
• 00_ena_template_samples.R Format ENA sample submission template.
• 00_palettes.R Define palettes for figures.
• 00a_saline_lakes.R Identify saline lakes.
• 00b_medians.R Replace missing LakePulse environmental data with ecozone medians.
• 01_infer_asvs/
  • 00_workflow.txt Overview of workflow for 18S rRNA gene ASV inference.
  • 01_rename_fastq.R Modify raw fastq file names.
  • 02_create_sample_list.R Create list of samples.
  • 03_cutadapt.sh Trim primers and sequencing adapters in Cutadapt.
  • 04_dada2.R Run DADA2 pipeline on Cutadapt-trimmed reads.
• 02_curate_protists/
  • 01_format_asvs.R Join ASV (sequence and taxonomy) data.
  • 02_remove_spurious_asvs.R Remove spurious sequences.
  • 03_align_asvs.txt Align ASVs to Silva reference database in SINA.
  • 04_trim_pos.R Trim remaining primer sequence positions.
  • 05_trim_primers.R Remove remaining primer sequences.
  • 06_identify_protists.R Identify ASV data assigned to protists.
  • 07_curate_samples.R Curate samples.
• 03_trophic_functions.R Assign trophic functional diversity.
• 04_identity_pr2/
  • 01_insilico_pcr.txt Perform in silico PCR with primer set on PR2 to extract 18S rRNA gene V7 region fragment.
  • 02_primer_lengths.R Assess PR2 18S rRNA gene V7 region fragment lengths.
  • 03_blastn_asvs_pr2v7.txt BLAST ASVs against PR2_V7 database to get sequence identity with top hit.
  • 04_percentidentity.R Assess sequence identities between ASVs and PR2 references.
• 05_metadata.R Curate lake environmental metadata.
• 06_phylogeny.R Plot phylogenetic tree for protist ASVs.
• 07_phylodissim.R Create phylogenetic dissimilarity matrices (weighted, unweighted, generalized UniFrac).
• 08_incidence.R Assess ASV taxonomic composition and incidence across lakes.
• 09_alphadiversity.R Perform alpha-diversity analyses.
• 10_rarefaction/
  • 01_rarefaction_landscape.R Compute ASV rarefaction across the landscape (all lakes).
  • 02_plot_rarefaction_landscape.R Plot ASV rarefaction curve (landscape).
  • 03_rarefaction_lakes.R Compute ASV rarefaction curves by lake.
  • 04_plot_rarefaction_lakes.R Plot ASV rarefaction curves (all lakes).
• 11_accumulation.R Plot ASV accumulation curve.
• 12_map.R Plot sampling sites on map of Canada with ecozones.
• 13_ordinations.R Perform ordinations (PCA, PCoA).
• 14_lcbd.R Evaluate local contributions to beta-diversity (LCBD).
• 15_gdm/
  • 01_gdm_bray.R Create site-pairs for generalized dissimilarity modelling (GDM).
  • 01_gdm_genunifrac.R Create site-pairs for generalized dissimilarity modelling (GDM).
  • 01_gdm_trophic.R Create site-pairs for generalized dissimilarity modelling (GDM).
  • 03_gdm_permtest/ Compute GDMs using permuted variable selection.
  • 04_gdm_results.R Summarize and visualize GDM results.
• 16_betadisper_pcoa12.R Compute spatial medians within the first two dimensions of the ordination space.
• 17_radial_plots.R Plot diversity and environmental data radial bar plots.
• 18_geographic_ranges.R Calculate geographic distances for the study.
• 19_env_pca.R Perform ordinations of environmental data.
• 20_env_histograms.R Plot environmental data distributions.