DOI: 10.5061/dryad.cc2fqz6j9
title: Data for: Ancient sedimentary DNA shows more than 5000 years of continuous beaver occupancy in Grand Teton National Park

description: Beaver-based restoration is emerging as a cost-effective conservation and
 climate adaptation strategy, but efforts are constrained by limited
 knowledge of pre-colonial beaver distribution and their long-term
 ecosystem impacts. Here, we apply sedimentary ancient DNA (sedaDNA)
 techniques to investigate the history of beaver occupancy at three lakes
 in Grand Teton National Park, Wyoming, over the last ~10 ka, as well as
 interactions with the local plant community. To investigate
 change in the vascular plant community, extracts were PCR amplified using
 barcode primers targeting the trnL P6 loop of the plant chloroplast genome
 with five replicates per DNA extract. A barcode targeting the 16S region
 of the mammalian mitochondrial genome (16SmammP007) was also amplified and
 sequenced from a subset of samples to validate beaver presence results
 from the species-species qPCR assay. trnL metabarcoding showed differing
 plant communities in the two lower-elevation lakes as compared to the
 higher elevation lakes, with mid-Holocene shifts in the plant community
 coinciding with both local beaver establishment (as indicated by
 species-specific qPCR results) and regional climatic changes trending
 towards wetter conditions. 16S metabarcoding yielded sporadic detections
 of a limited number of mammalian taxa, but confirmed beaver detection from
 the species-species qPCR assay.
description: # Data for: Ancient sedimentary DNA shows more than 5000 years of
 continuous beaver occupancy in Grand Teton National Park Dataset DOI:
 [10.5061/dryad.cc2fqz6j9](10.5061/dryad.cc2fqz6j9) ## Description of the
 data and file structure Dataset includes two Microsoft Excel files
 (SI_tableS4_trnl_rawdata.xlsx and SI_tableS5_P007_rawdata.xlsx)
 summarizing raw metabarcode sequencing data\ generated from sedimentary
 ancient DNA associated with the Ecosphere publication:  Ancient
 sedimentary DNA shows more than 5000 years of continuous beaver occupancy
 in Grand Teton National Park. 2025. D. Nevé Baker, Darren J. Larsen, Emily
 Fairfax, Amelia P. Muscott, Beth Shapiro, Sarah E. Crump. Each data file
 contains sequencing reads that have been trimmed and processed with the
 Anacapa QC pipeline
 ([https://github.com/limey-bean/Anacapa](https://github.com/limey-bean/Anacapa)), then clustered as Amplicon Sequence Variants (ASVs). Taxonomy was then assigned by aligning ASV clusters to the NCBI nr/nt databases with the Anacapa CRUX pipeline [(https://github.com/limey-bean/CRUX_Creating-Reference-libraries-Using-eXisting-tools)](https://www.zotero.org/google-docs/?PARAMS=xik_7WysRKRy1NiXgL1BXg2roZ75zaxVpVsDU1urMqKzxhMK). ASV assignments with a 60% Bayesian Confidence Cutoff were retained. SI_tableS4_trnl_rawdata.xlsx contains vascular plant sequences generated using barcode primers targeting the *trn*L P6 loop of the plant chloroplast genome.  SI_tableS5_P007_rawdata.xlsx contains sequences generated using barcode primers targeting the 16S region of the mammalian mitochondrial genome (16SmammP007). All reads assigned as human have been removed. Each file contains a metadata sheet ("metadata") and multiple data matrix sheets ("{primer}_*ASV_taxonomy_detailed*_X"),  linked to the metadata by the "sum.taxonomy" field. A more complete description of the data structure can be found at [https://github.com/limey-bean/Anacapa](https://github.com/limey-bean/Anacapa). Data files can be visualized and analyzed in R using the Ranacapa package or with the Ranacapa online shiny application ([https://shiny.eeb.ucla.edu/ranacapa/](https://shiny.eeb.ucla.edu/ranacapa/)) **Metadata fields:** sum.taxonomy: sample replicate name sum.tax.order: sample order extraction_ID: DNA extraction ID type: sample or negative lake: lake ID core_section: sediment core section ID core_depth_mid: depth of sample (cm) on core section total_depth: depth of sample (cm) for complete core batch: metabarcode lab processing batch "na" fields indicate non-applicable data fields (e.g., for negatives). **data matrix description:** {primer}_seq_number: unique sequence identifier sequence: raw sequence after trimming and merging sequenceF: forward sequence sequenceR: reverse sequence forward_{primer}_seq_number: number of sequences assigned to sequenceF reverse_{primer}_seq_number: number of sequences assigned to sequenceR merged_{primer}_seq_number: number of sequences assigned to merged sequence variable number of columns beginning with either trnl\_ (SI_tableS4_trnl_rawdata.xlsx) or X16SmammP007\_  (SI_tableS5_P007_rawdata.xlsx), indicating sample replicate name (linked to metadata via sum.taxonomy field). Values reflect the number of assigned sequences unmerged_{primer}_seq_number: number of sequences assigned to both sequenceF and sequenceR (unmerged) single_or_multiple_hit: single or multiple taxonomic assignment with BLAST end_to_end_or_local: BLAST assignment mode max_percent_id: BLAST maximum taxonomic assignment likelihood input_sequence_length: sequence length in base pairs taxonomy: BLAST taxonomic assignment at each level taxonomy_confidence: BLAST confidence at each taxonomic level accessions: NCBI accession numbers for taxonomic assignments Empty cells indicate non-applicable fields. Empty cells will be correctly ignored by the R package Ranacapa during downstream processing. ## Code/software Microsoft Excel, LibreOffice. Data files can be visualized and analyzed in R using the Ranacapa package or with the Ranacapa online shiny application ([https://shiny.eeb.ucla.edu/ranacapa/](https://shiny.eeb.ucla.edu/ranacapa/))