Access this dataset on Dryad: DOI: 10.5061/dryad.4xgxd25p8

This dataset contains the unfiltered OBITools output for the following three libraries: Mal1, Mal2, and Mal3.

Description of the data and file structure

The dataset contains:

1. Raw data files

For each library there are four identified OBITools output tables. One for each of the following reference databases: ArctBorBryo, EMBL release 143, PhyloAlps, and PhyloNorway.

Each output file is in the TSV format and named as follows: [LibraryID]_tag.ali.frm.uniq.index_swap.nb.c2.cl.[Referencelibrary]_GH_20-07-21-iden.ann.sort.tsv. Down below the list of all output files used in this dataset:

• Mal1_tag.ali.frm.uniq.index_swap.nb.c2.cl.ArctBorBryo_GH_20-07-21-iden.ann.sort.tsv
• Mal1_tag.ali.frm.uniq.index_swap.nb.c2.cl.EMBL_143_GH_20-07-21-iden.ann.sort.tsv
• Mal1_tag.ali.frm.uniq.index_swap.nb.c2.cl.PhyloAlps_GH_20-07-21-iden.ann.sort.tsv
• Mal1_tag.ali.frm.uniq.index_swap.nb.c2.cl.PhyloNorway_GH_20-07-21-iden.ann.sort.tsv
• Mal2_tag.ali.frm.uniq.index_swap.nb.c2.cl.ArctBorBryo_GH_20-07-21-iden.ann.sort.tsv
• Mal2_tag.ali.frm.uniq.index_swap.nb.c2.cl.EMBL_143_GH_20-07-21-iden.ann.sort.tsv
• Mal2_tag.ali.frm.uniq.index_swap.nb.c2.cl.PhyloAlps_GH_20-07-21-iden.ann.sort.tsv
• Mal2_tag.ali.frm.uniq.index_swap.nb.c2.cl.PhyloNorway_GH_20-07-21-iden.ann.sort.tsv
• Mal3_tag.ali.frm.uniq.index_swap.nb.c2.cl.ArctBorBryo_GH_20-07-21-iden.ann.sort.tsv
• Mal3_tag.ali.frm.uniq.index_swap.nb.c2.cl.EMBL_143_GH_20-07-21-iden.ann.sort.tsv
• Mal3_tag.ali.frm.uniq.index_swap.nb.c2.cl.PhyloAlps_GH_20-07-21-iden.ann.sort.tsv
• Mal3_tag.ali.frm.uniq.index_swap.nb.c2.cl.PhyloNorway_GH_20-07-21-iden.ann.sort.tsv

The rows contains the observed barcodes in the library. The identification information and the samples in which the barcode is observes is reported in the columns.

2. Analysis scripts and filtered Data file

"Revision_02_R_codes.zip" contains the following:

"data" folder: contains all pre-processed .csv and .tsv files derived from the raw OBITools output after quality filtering. These files are ready to be used directly with the R scripts in this package.

R scripts: used to process OBITools output and perform downstream analyses. These R codes are named as "Ataman_et_al_2025_R_codes" as both R HTML and PDF format. These include:

• Taxonomic filtering
• Jaccard index analysis
• Merging of A and B replicates
• Species accumulation curves and breakpoint analysis (Figure 2a)
• Comparison of sedDNA and vegetation data (Figure 4a, Figure 4c)
• Linear model fitting and diagnostics (Supplementary Figure 6)

All analysis was conducted in R (R Core Team, 2024). The following packages were used: tidyverse (data visualization), vegan (species accumulation curves), segmented (breakpoint analysis for accumulation curves), DHARMa (model diagnostics and residual checking).

Supplementary Data (as referenced in the manuscript)

This supplementary dataset (Supplementary_Data.xlsx) is provided in editable Excel format (.xlsx) and corresponds directly to the tables cited throughout the manuscript. It includes the processed data resulting from the filtration and analysis steps described in the Methods section.

The file contains detailed metadata, vegetation survey results, and reference information that support the main analyses presented in the paper. Contents of the file listed down below:

Contents:

Supplementary Data 1: Sequence identifications from 42 sample pairs with reference libraries and taxa categories.

Supplementary Data 2 : Similarity and richness analysis based on the number of taxa identified.

Supplementary Data 3 : Taxa assignments after merging 42 sample pairs.

Supplementary Data 4 : Vegetation surveys: 2 m survey and vegetation plots.

Supplementary Data 5 : Additional species list recorded outside of vegetation surveys but present in the catchment.

Supplementary Data 6 : Distances between sequential vegetation plots along each transect.

Supplementary Data 7 : PCR tag lookup table to demultiplex samples in sequence libraries 1 (Tag 1), 2 (Tag 2), and 3 (Tag 3). 

Version Changes

Aug 04, 2025 version files: Added Supplementary_Data.xlsx, which compiles all supplementary tables referenced in the manuscript. This includes processed taxonomic data, similarity and richness metrics, vegetation survey results, additional species lists, plot distances, and PCR tag lookup tables.

Aug 20, 2025 version changes: Changed manuscript title from “Maximizing vegetation representation of the catchment in sedimentary DNA with targeted cores in small lakes” to “Sedimentary DNA from lake depocenters maximizes detection of catchment vegetation.”