Data from: Amplicon pyrosequencing late Pleistocene permafrost: the removal of putative contaminant sequences and small-scale reproducibility

• Main Authors: Porter, Teresita M., Golding, G. Brian, King, Christine, Froese, Duane, Zazula, Grant, Poinar, Hendrik N.
• Format: Dataset
• Language: unknown
• Published: Data Archiving and Networked Services (DANS) 2020
• Subjects: Life sciences; medicine and health care; reproducibility; Barcoding; ancient DNA; amplicon pyrosequencing; Beringia; contamination; geo; envir; Yukon; permafrost
• Online Access: https://doi.org/10.5061/dryad.4m7d1

DNA sequencing of ancient permafrost samples can be used to reconstruct past plant, animal and bacterial communities. In this study, we assess the small-scale reproducibility of taxonomic composition obtained from sequencing four molecular markers (mitochondrial 12S ribosomal DNA (rDNA), prokaryote 16S rDNA, mitochondrial cox1 and chloroplast trnL intron) from two soil cores sampled 10 cm apart. In addition, sequenced control reactions were used to produce a contaminant library that was used to filter similar sequences from sample libraries. Contaminant filtering resulted in the removal of 1% of reads or 0.3% of operational taxonomic units. We found similar richness, overlap, abundance and taxonomic diversity from the 12S, 16S and trnL markers from each soil core. Jaccard dissimilarity across the two soil cores was highest for metazoan taxa detected by the 12S and cox1 markers. Taxonomic community distances were similar for each marker across the two soil cores when the chi-squared metric was used; however, the 12S and cox1 markers did not cluster well when the Goodall similarity metric was used. A comparison of plant macrofossil vs. read abundance corroborates previous work that suggests eastern Beringia was dominated by grasses and forbs during cold stages of the Pleistocene, a habitat that is restricted to isolated sites in the present-day Yukon. DRYAD_dataflowExcel spreadsheet showing a sample dataflow.finalOTUseedsFasta formatted text files with the seed sequence for each OTU used in the study.perlScriptsPerl scripts used in the study.readidLineageMapTab delimited text files containing the readID for each OTU seed, taxonomic lineage, and OTU abundance.barcodePrimerFilesText files containing the barcodes and primers used in the study.Rscripts[R] scripts used in the study.