Arctic-boreal bryophytes from sedimentary ancient DNA metabarcoding

• Main Authors: Herzschuh, Ulrike, Liu, Ying, Liu, Sisi, Stoof-Leichsenring, Kathleen, Porada, Phillip, Courtin, Jeremy, Farkas, Luca Zofia, Biskaborn, Boris K., Diekmann, Bernhard, Huang, Yongsong, Kaufman, Darrel, Melles, Martin, Meyer, Hanno, Pestryakova, Luidmila A., Wagner, Bernd, Russell, James
• Format: Other/Unknown Material
• Language: English
• Published: Zenodo 2024
• Subjects: Paleoecology; Bryophytes; metabarcoding; sediment cores; Tundra; Alaska; Beringia; Siberia
• Online Access: https://doi.org/10.5281/zenodo.10671863

A total of 26 lake-sediment cores collected from 23 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 127 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 Bryophyte DNA dataset: "2024-02-23_combined_gh_bryophytes_sequences_unique_taxanames.csv" Bryophyte ASV and taxa names: "combined_gh_datasets_table_sequences_taxanames_eco_revised.csv" Bryophyte trait dataset: "Bryophytes_GoogleSpreadsheet_data_categorial.csv" R script Script: "2024-02-23_R-Script_gh_dataset_Bryophytes.R" R outputs Bryophyte DNA dataset 1000-year time slice:"2024-02-23_combined_gh_bryophytes_unique_taxanames_1000yr_timeslices_counts.csv" Bryophyte DNA dataset 1000-year time slice, resampled 100x: "2024-02-23_combined_gh_bryophytes_resampled_percentages_mean_100runs_sequences.csv” Bryophyte DNA dataset 1000-year time slice, resampled 100x, with Bryophyte traits: "2024-02-23_combined_gh_bryophytes_traits.csv“ 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., ...