Bioinformatic workflows and taxonomic reference files for ancient DNA metagenomic classification in Arctic paleoecological studies

This Zenodo archive provides reproducible bioinformatic workflows and curated taxonomic reference files for ancient DNA metagenomic classification. The workflows and reference data have been used across multiple paleoecological and ancient DNA studies, including analyses presented in “Arctic defaunation initiated a cascade of mammal–plant interaction shifts through dispersal dynamics” (bioRxiv preprint: https://doi.org/10.1101/2025.06.23.661215). The archive includes all scripts, configuration files, and taxonomic resources required to reproduce and adapt the analyses for related ancient metagenomic datasets.