DOI: 10.5281/zenodo.10671862
title: Arctic-boreal bryophyte dynamics since the last glacial from ancient DNA metabarcoding

description: A total of 26 lake-sediment cores collected from 26 study sites spanning the glacial and interglacial transition are used in this study. These sites are distributed across Siberia, Beringia, and Alaska regions, with a gradient of vegetation types dominated by tundra in the northern region and transitioning to boreal forest in the southern extents. DNA samples from the sediment core were analysed with a standard sedimentary ancient DNA metabarcoding pipeline (see additional description), which resulted in a raw dataset of all DNA plant sequences, which were then filtered for Bryophytes (Bryophyte DNA dataset). The Bryophyte DNA dataset contains 120 unique ASV. Samples in the Bryophyte DNA dataset are then grouped into 1000-year time slices and are subsequently resampled to a base count of 500 read counts for each time slice. After that, a Bryophyte trait datastet is assigned to the Bryophyte DNA dataset. 

 

Input files



Excel file with all data used in the R-Script: "Bryophytes_data.xlsx"

WorldClim 2.0 dataset with mean temperatures of Warmest Quarter (https://www.worldclim.org/; Fick, S.E. and R.J. Hijmans, 2017. WorldClim 2: new 1km spatial resolution climate surfaces for global land areas. International Journal of Climatology 37 (12): 4302-4315): "wc2.1_30s_bio_10.tif"


R script



R-Script: "2025-01-14_R-Script_ arctic_boreal_bryophyte_dynamics_DNA_metabarcoding.R"


R outputs



resampled Bryophyte metabarcoding percentage dataset with ASV: "2025-01-14_bryophyta_resampled_percentages_mean_100runs_sequences.csv"

resampled Bryophyte metabarcoding percentage dataset with unique scientific names: "2025-01-14_bryophyta_resampled_percentages_mean_100runs_scientific_names.csv"

GBIF taxa occurrences with WorldClim temperature data: "2025-01-14_gbif_taxa_occurrences_seqtypes_climate.csv"


 
description: DNA samples from the sediment core were subsampled under cool and clean conditions and ancient DNA work was conducted in the paleogenetic laboratories at Alfred Wegener Institute, Potsdam, Germany. DNA was extracted in batches, each of the batches included nine samples (3-10 g sample-1) and one extraction control, using the PowerMax® Soil DNA Isolation Kit (Mo Bio Laboratories, Inc., USA). All subsequent steps were performed according to the instructions of the manufacturer Qiagen, except for the final elution volume which varied between 1.6 and 2.0 mL. PCR reactions were conducted using g and h primer targeting the vascular plant trnL P6 loop of the chloroplast genome, each modified with unique 8 bp tags differing by at least five base pairs to distinguish samples post-sequencing. After pooling the PCR samples from each sediment core into a PCR Pool, sequencing for each pool was performed by Fasteris Gensupport SA sequencing service (Switzerland) with the paired-end sequencing on a HiSeq or NextSeq Illumina platform. Raw sequences were analysed using OBITools software (version 3.0.0) against a specific plant database (SibAla_2023). The customized database SibAla_2023 has been compiled using different R packages with the following steps: (1) taxa selection from a given region (55–90°N, 50–150°E and 40–90°N, 150°E–140°W) and taxa occurrences (>10) using the Global Biodiversity Information Facility (GBIF; accessed 15-12-2022) resulting in 233 families, 1059 genera, and 4849 species. (2) GBIF occurrences were aligned with available trnL P6 loop sequence types from public databases and (3) a quality filtering of selected P6 loop sequences was applied. The SibAla_2023 database includes a total of 4939 entries, comprising 3398 plant species, 947 genera, and 223 families that collapse into 2371 unique P6 loop sequence types. Compared to GBIF occurrences, the database provides 95.7% taxonomic coverage at the family level, 89.4% at the genus level, and 70.1% at the species level.