Dataset DOI: 10.5061/dryad.4mw6m90rf

Description of the data and file structure

This archive contains data and R scripts needed to reproduce the results in the paper:

“Gut microbiome communities vary across translocated populations of the Seychelles warbler”

All variable names in these data should be self-explanatory, but please don't hesitate to send an email to the corresponding author if anything is unclear.

Files and variables

File: SampleProcessing.R

Description: This R script contains the code necessary to reproduce all initial pre-processing steps using outputs from QIIMEII (e.g. decontamination, sample filtering, extraction repeatability tests). The outputs from this code (Filtered ASV, taxonomy and metadata files) are used in all downstream analysis.

Note that this uses the entire warbler gut microbiome dataset and is further filtered in the cross island analysis script to only comparable years/seasons.

File: CrossIslandAnalysis.R

Description: This R script contains the code necessary to reproduce analyses of translocated and source populations (sampled in comparable seasons). It uses the filtered ASV, taxonomy, and metadata files generated in SampleProcessing.R

File: Metadata.csv

Description: This file contains the sample metadata and is used as input to SampleProcessing.R

Variables

• sample.idrows: Unique identifier for each faecal sample (appears as row names in R)
• sample.id: Unique identifier for each faecal sample
• BirdID: Unique identifier for each bird
• TubeNumber: Tube number for each faecal sample given at the time of sampling
• OriginalSampleIDUnique: Unique tube number for sequenced faecal samples- (suffix "R" means a repeat extraction of the same sample was sequenced, suffix "b" refers to the second time a sample was sequenced to assess repeatability within and across sequencing runs, suffix "PRO" refers to a repeat extraction of the same sample with the PRO version of the Qiagen DNeasy PowerSoil kit- note that PRO extractions are for a pilot study and not used in this analysis)
• FieldPeriodID: Unique identifier for the field period sample was taken in (164 = major17 Cousin, 166= minor18 Cousin, 167= major18 Cousin, 169=minor19 on Cousine, 171= minor19 Cousin, 173= major19 Cousin, 174= minor20 Cousin, 175 and 176= major21 Cousin, 177=minor22 Cousin, 178=major22, 179= major22 on Denis, 183= major22 on Fregate, 187= major 2023 on Aride)
• Season: Major or minor breeding season
• SequencingRun: sequencing run for that sample
• CatchID: Unique identifier for catch
• OccasionID: Unique identifier for data associated with catch
• BTO: Unique BTO ring number for each Bird
• FieldRing: Unique colour ring combination for each Bird
• CatchTerritoryID: Territory ID where bird was caught/sampled (note not necessarily breed group territory).
• SampleDate: date faecal sample was taken
• SampleYear: year faecal sample was taken
• FreezerDate: date faecal sample was frozen at -80 degrees
• TimeAt4Degrees: number of days faecal sample stored at 4 degrees C prior to freezing.
• SampleType: Sample type (Control or Faecal)
• SampleType4Way: Sample type in further detail. Collection control; Extraction control (blank swab) or PCR negative (water control in PCR); Positive control (mock community); Faecal sample.
• ExtractionDate: date of DNA extraction from faecal sample
• Qubit: Concentration (ng/μl) of DNA extracted from sample. NA values indicate concentrations too low to read.
• Island: island from which sample was derived (CN= Cousin, AR= Aride, FR= Fregate, CE= Cousine, DS= Denis)
• SexEstimate: sex of bird (1= male, 0= female)
• SampleTime: time of day bird was caught/sampled
• MinutesSinceSunrise: time bird was caught as minutes since sunrise (06:00 am)
• Ageclass: ageclass of bird (FL= fledgling, OFL= old fledgling, SA= Sub-adult, A= adults)- microbiome mature in OFL onwards
• EyeColour: yecolour of bird (G= grey, LB= light brown, RB= red brown).

File: ASV_table.csv

Description: This file contains the raw abundances of Amplicon Sequence Variants (ASV) inferred for each faecal sample using QIIMEII. This ASV table is used to generate phyloseq objects and is used as input to SampleProcessing.R. The paired-end sequences for each sample used to generate the table have been deposited with the ENA under the study accession numbers PRJEB45408 (samples taken in 2017 and 2018) and PRJEB47095 (samples taken in 2019 and 2020), PRJEB67634 (samples taken in 2021 and 2022) and PRJEB81863 (all samples from translocated populations).

File: Taxonomy.csv

Description: This file contains the taxonomy (kingdom, phylum, class, order, family, genus, species) of ASVs in ASV_table.csv. The corresponding Amplicon Sequence Variant ID is given in the column "ASVID". It was generated as part of the QIIMEII pipeline. This file is used to generate phyloseq objects and is used as input to SampleProcessing.R. An empty cell is given when an ASV can't be accurately assigned a taxonomy at the taxonomic level defined by the column header.

File: tree.nwk

Description:  ASV rooted tree file generated as part of the QIIMEII pipeline and is used as input to SampleProcessing.R and CrossIslandAnalysis.R

File: FilteredASVTable.csv

Description: A filtered ASV table generated using the SampleProcessing.R script (following decontam etc...) which is used in all downstream analysis in the CrossIslandAnalysis.R script. Variables are the same as those found in the non-filtered ASV table.

File: FilteredMetadata.csv

Description:  A filtered metadata table generated using the SampleProcessing.R script (following decontam etc...) which is used in all downstream analysis in the CrossIslandAnalysis.R script. Variables are the same as those found in the non-filtered Metadata.csv file.

File: FilteredTaxonomyTable.csv

Description: A filtered taxonomy table generated using the SampleProcessing.R script (following decontam etc...) which is used in all downstream analysis in the CrossIslandAnalysis.R script.  Variables are the same as those found in the non-filtered taxonomy table.

File: CatchDuplicatesSorted.csv

Description: A csv file defining which sample to keep in analyses when there are duplicate samples from the same catch (decision made based on sample source). File is used in CrossIslandAnalysis.R script to filter catch duplicates to avoid pseudoreplication.

Variables:

• sample.idrows: Unique identifier for each faecal sample (appears as row names in R)
• sample.id: Unique identifier for each faecal sample
• TubeNumber: Tube number for each faecal sample given at the time of sampling
• CatchID: Unique identifier for catch
• SampleReads: The number of sequencing reads generated for that sample
• CatchDupKeep: whether to include the catch duplicate in downstream analysis (Y) or not (N)

Code/software

#SampleProcessing.R

This R script contains the code necessary to reproduce all initial pre-processing steps using outputs from QIIMEII (e.g. decontamination, sample filtering, extraction repeatability tests). The outputs from this code (Filtered ASV, taxonomy and metadata files) are used in all downstream analysis. Packages/versions are detailed in the methods section of the published paper.

Note that this uses the entire warbler gut microbiome dataset and will be further filtered in the cross island analysis to only comparable years/seasons.

#CrossIslandAnalysis.R

This R script contains the code necessary to reproduce analyses of translocated and source populations (sampled in comparable seasons). It uses the filtered ASV, taxonomy and metadata files generated in SampleProcessing.R. Packages/versions are detailed in the methods section of the published paper.

Access information

Other publicly accessible locations of the data:

The paired-end sequences for each sample have been deposited with the European Nucleotide Archive under the study accession numbers PRJEB45408 (samples taken in 2017 and 2018) and PRJEB47095 (samples taken in 2019 and 2020), PRJEB67634 (samples taken in 2021 and 2022) and PRJEB81863 (all samples from translocated populations).