paleoELA

Scripts associated with the manuscript

---

Garner RE, Taranu ZE, Higgins SN, Paterson MJ, Gregory-Eaves I, Walsh DA. Eutrophication and warming drive algal community shifts in synchronized time series of experimental lakes.

---

scripts/

• infer_asvs/
  • 00-workflow_18s.txt Overview of workflow for 18S rRNA amplicon sequence variant (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.
  • 05-read_tracking.R Track read loss through the ASV table creation pipeline.
• 00-clean_pr2.R Clean and dereplicate Protist Ribosomal Reference database (PR2) v. 5.0.0 eukaryotic taxonomy.
• 00-ena_read_manifest.R Generate European Nucleotide Archive (ENA) read manifest files.
• 00-ena_sample_template.R Populate template for ENA sample submission.
• 00-00-ena_webin_reads.sh Submit read manifest files via ENA Webin Client.
• 00-palettes.R Define palettes for figures.
• 00a-dating.R Consolidate sediment dating information.
• 00b_map.R Map region and lakes.
• 02-curate_asvs.R Curate ASV dataset.
• 03a-taxcuration.R Retain ASVs assigned to protists and fungi.
• 03b-alignment_tree.txt Align ASVs to Silva reference database in SINA.
• 03d-trophic_function.R Linked functional assignments to ASVs by taxon.
• 03e-sediment_data.R Parse sediment ASV metadata including sediment intervals and age-dates.
• 04-stratigraphy.R Evaluate sediment ASV assemblage taxonomic, functional, and sequence composition.
• 05-pca.R Perform principal component analyses on sediment ASV assemblages.
• 07-algae.R Assess algal taxonomic composition of sediment samples.
• 07-nasvs_nseqs_taxonomy.R Assess sediment taxonomic group ASV/sequence compositions.
• 08-ela_env_data.R Define functions to summarize Experimental Lakes Area (ELA) environmental data.
• 08a-ela_climate_data.R Summarize ELA climate data.
• 08d-ela_chemistry_data.R Summarize ELA nutrient data.
• 09-eccc_climate.R Summarize Environment Canada historical climate data.
• 09-ela_phytoplankton_data.R Format ELA algal monitoring data.
• 10-ela_phytoplankton_biomass.R Summarize ELA algal biomass data.
• 10-ela_phytoplankton_species.R Summarize ELA algal species cell count, density, and biomass data.
• 11-ela_monitoring.R Consolidate ELA monitoring data.
• 12-pca_phytoplankton.R Perform principal component analyses on monitoring assemblages.
• 18-rv.R Calculat RV multivariate correlations between monitoring and sediment assemblages.
• 21-gam_devexpl_plots.R Plot generalized additive model (GAM) results.
• 21-gam_functions_phytoplankton.R Define functions to compute GAMs on monitoring assemblages.
• 21-gam_functions_seddna.R Define functions to compute GAMs on sediment assemblages.
• 21a-gam_phytoplankton.R Compute GAMs on monitoring assemblages.
• 21b-gam_seddna.R Compute GAMs on sediment assemblages.
• 21c-gam_seddna_monitor.R Compute GAMs on sediment assemblages truncated to monitoring time frames.
• 23-plot_nutriclim.R Plot nutrient and air temperature trends.
• 24-pc_loadings.R Extract top principal component taxon loadings.
• 25-ela_taxonomy_plots.R Plot algal community time series.
• 26-pc1.R Plot first principal component axis.