Data and Software

OUR DATA

We participate in the open science movement and strive to make our scientific research and its dissemination accessible to all.

ONLINE COURSES

“Introduction to Ancient Metagenomics”, 2022 SPAAM Summer School, 40 hours of instruction and practicals. Co-sponsored by the Werner Siemens Foundation, the Max Planck-Harvard Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), the Max Planck Institute for Evolutionary Anthropology (MPI-EVA) and the Jena School of Microbial Communication (JSMC) of Friedrich Schiller University (FSU).

LABORATORY PROTOCOLS

Graphical Overview of Sampling Procedures

Graphical Overview of Laboratory Procedures

A-Z of ancient DNA protocols for shotgun Illumina Next Generation Sequencing: compilation of 12 complete bench protocols for each step of ancient DNA laboratory procedures:

  • Minimally-invasive sampling of pars petrosa (os temporale) for ancient DNA extraction
  • Tooth sampling from the inner pulp chamber for ancient DNA extraction
  • Dental calculus field sampling protocol (Sabin version; recommended for intact dentitions)
  • Dental calculus field sampling protocol (Warinner version; recommended for loose teeth)
  • Ancient DNA extraction from skeletal material
  • Ancient DNA extraction from dental calculus
  • Library adapter preparation for dual-index double-stranded DNA Illumina sequencing
  • Non-UDG treated double-stranded ancient DNA library preparation for Illumina sequencing
  • Half-UDG treated double-stranded ancient DNA library preparation for Illumina sequencing
  • Full-UDG treated double-stranded ancient DNA library preparation for Illumina sequencing
  • Illumina double-stranded DNA dual indexing for ancient DNA
  • Library amplification and pooling for Illumina sequencing

Modern DNA protocols for shotgun Illumina Next Generation sequencing

Ancient Protein Extraction from Skeletal Material Protocol, dx.doi.org/10.17504/protocols.io.7vwhn7e

We are in the process of making more of our protocols available on protocols.io. Visit our group page: https://www.protocols.io/groups/warinnergroup and https://www.protocols.io/groups/mpishh-archaeogenetics

DATA ANALYSIS PIPELINES AND TOOLS

We have developed or contributed to the development of the following pipelines and tools:

nf-core / taxprofiler, an analysis pipeline for taxonomic classification and profiling of shotgun metagenomic data that allows for in-parallel taxonomic identification of reads or taxonomic abundance estimation with multiple classification and profiling tools against multiple databases.

cuperdec, tool for characterizing ancient microbiome preservation published in Fellows Yates et al. 2021. Download cuperdec R package.

PyDamage, pipeline for authenticating ancient DNA contains published in Borry et al. 2021

CoproID, pipeline for determining the host species of paleofeces published in Borry et al. 2020

SourcePredict, tool for estimating metagenome source published in Borry 2019

AncientMetagenomeDir, a community-curated directory of ancient metagenomes published in Fellows Yates et al. 2021a

sam2lca, a tool for assigning lowest common ancestor taxonomy to aligned DNA sequences in sam, bam, or cram files, published in Borry et al. 2022

nf-core / funcscan, a pipeline for screening of functional components and natural products from assembled contigs

SPAAM, Standards, Precautions and Advances in Ancient Metagenomics, a community of researchers focusing on ancient metagenomics

Cookiecutter opinionated bioinformatics project structure, a structure generator for organizing metagenomics projects for git repositories

nf-core/eager, a reproducible, portable, and efficient ancient genome analysis toolkit published in Fellows Yates et al. 2021b

Learn more about how you can integrate Nextflow and nf-core into your ancient environmental eDNA workflows: https://www.nextflow.io/blog/2024/nextflow-nf-core-ancient-env-dna.html

We are in the process of making more of our tools and pipelines available in GitHub. Check back soon!

DATASETS

Below you can find links to the raw data used in our publications.

ETHNOGRAPHIC DATASETS

Open-access database of thousands of photos, videos, and interviews made in partnership with mobile pastoralists in Mongolia about their dairying practices, traditions, and way of life. This database was produced as part of the DAIRYCULTURES and Heirloom Microbes projects.
Publication: https://www.journals.uchicago.edu/doi/pdf/10.1086/716065
Ethnographic database: https://dairycultures.org/ethnographic_data/

GENETIC DATASETS

Metagenomic dental calculus datasets of 102 archaeological humans from Oceania and Island Southeast Asia in Velsko et al. 2024
Publication: https://doi.org/10.1101/2023.10.18.563027
Code: https://github.com/ivelsko/pacific_calculus (DOI: 10.5281/zenodo.13903784)
Data: https://www.ebi.ac.uk/ena/browser/view/PRJEB61887

Metagenomic dental calculus datasets of 12 Neanderthals, 34 ancient humans, and 19 present-day humans in Klapper et al. 2023
Publication: https://doi.org/10.1126/science.adf5300
Code: https://github.com/paleobiotechnology/EMN001_Paleofuran
Data: https://www.ebi.ac.uk/ena/browser/view/PRJEB55583

Metagenomic dental calculus datasets of 75 archaeological humans from Middenbeemster, Netherlands in Velkso et al. 2022
Publication: https://doi.org/10.1093/pnasnexus/pgac148
Code: https://github.com/ivelsko/smoking_calculus/
Data: https://www.ebi.ac.uk/ena/browser/view/PRJEB52394

Genomic datasets of 33 archaeological humans from prehistoric Nepal in Liu et al. 2022
Publication: https://doi.org/10.1038/s41467-022-28827-2
Data: https://www.ebi.ac.uk/ena/browser/view/PRJEB41752

18 genomic datasets from archaeological human dentine and petrous bone from Bronze Age Dzungaria and the Tarim Basin in Zhang et al. 2021
Publication: https://doi.org/10.1038/s41586-021-04052-7
Data: https://www.ebi.ac.uk/ena/browser/view/PRJEB46875

124 metagenomic dental calculus datasets from primates, Neanderthals, and humans in Fellows Yates et al. 2021
Publication: https://www.pnas.org/content/118/20/e2021655118
Code: https://github.com/jfy133/Hominid_Calculus_Microbiome_Evolution; DOI: 10.5281/zenodo.3740493
Data: https://www.ebi.ac.uk/ena/browser/view/PRJEB34569

214 metagenomic and human genome capture data from archaeological human dentine and petrous bone from Mongolia in Jeong et al. 2020
Publication: https://www.cell.com/cell/pdf/S0092-8674(20)31321-0.pdf
Data: https://www.ebi.ac.uk/ena/data/view/PRJEB35748; https://edmond.mpdl.mpg.de/imeji/collection/2ZJSw35ZTTa18jEo

20 paleofeces and archaeological sediment metagenomes, published in Borry et al. 2020
Publication: https://peerj.com/articles/9001/
Data: https://www.ebi.ac.uk/ena/data/view/PRJEB33577; https://www.ebi.ac.uk/ena/data/view/PRJEB35362

33 dental calculus metagenomes 6 individual from Medieval England and Spain and 19th century St. Helena, published in Fagernäs et al. 2020
Publication: https://www.sciencedirect.com/science/article/pii/S0305440320300571
Data: https://www.ncbi.nlm.nih.gov/bioproject/PRJEB35483

43 historic and 10 modern metagenomic datasets from dental calculus published in Velsko et al. 2019
Publication (OA): https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-019-0717-3
Data (historic): https://www.ebi.ac.uk/ena/data/view/PRJEB30331
Data (modern): https://www.ebi.ac.uk/ena/data/view/PRJEB31185

Genome-wide human genetic data from 22 Late Bronze Age individuals from Khovsgol, Mongolia published in Jeong et al. 2018
Publication (OA): https://www.pnas.org/content/pnas/early/2018/10/31/1813608115.full.pdf
Data: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA429081/

48 metagenomic and human genome capture data from archaeological human dentin and calculus samples published in Ziesemer et al. 2018
Publication (OA): https://onlinelibrary.wiley.com/doi/full/10.1002/ajpa.23763
Data: https://www.ebi.ac.uk/ena/data/view/PRJEB25624

Whole human genome data from 7 ancient individuals (1600-6000 BP) from the Lake Titicaca region of Peru published in Lindo et al. 2018
Publication (OA): http://advances.sciencemag.org/content/4/11/eaau4921
Data: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA470966

122 metagenomic datasets from archaeological human dental calculus and dentin samples published in Mann et al. 2018
Publication (OA): https://www.nature.com/articles/s41598-018-28091-9
Data: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA445215

30 metagenomic and Salmonella enterica capture datasets published in Vågene et al. 2018
Publication: https://www.nature.com/articles/s41559-017-0446-6
Data: https://www.ebi.ac.uk/ena/data/view/PRJEB23438

15 mitochondrial genomes from ancient Mexico and Central America published in Morales-Arce et al. 2017
Publication (OA): https://www.nature.com/articles/s41598-017-18356-0
Data: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA360145

Whole human genome datasets from 8 ancient individuals (1250-3150 BP) from the Himalayan Annapurna Conservation Area (ACA) in Nepal published in Jeong et al. 2016
Publication (OA): https://www.pnas.org/content/pnas/early/2016/06/16/1520844113.full.pdf
Data: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA299403

29 human metagenomic and mitochondrial capture datasets from archaeological and modern dental calculus and dentin published in Ozga et al. 2015
Publication (OA): https://onlinelibrary.wiley.com/doi/epdf/10.1002/ajpa.22960
Data: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA293758

Human gut microbiome data from 116 metagenomic and 58 16S rRNA gene datasets from Oklahoma, USA published in Sankaranarayanan et al. 2015
Publication (OA): https://www.cell.com/current-biology/fulltext/S0960-9822(15)01354-8
Data: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA268964; https://www.ebi.ac.uk/ena/data/view/PRJEB13619

Human oral microbiome data from 116 shotgun and 16S rRNA gene datasets from archaeological and modern dental calculus published in Ziesemer et al. 2015
Publication (OA): https://www.nature.com/articles/srep16498
Data: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA278036

Human gut microbiome data from 116 shotgun and 79 16S rRNA gene datasets from Peru published in Tito et al. 2015
Publication (OA): https://www.nature.com/articles/ncomms7505
Data: https://www.ncbi.nlm.nih.gov/bioproject/268964; https://www.ebi.ac.uk/ena/data/view/PRJEB13051

Human oral microbiome data from metagenomic and 16S rRNA gene datasets published in Warinner et al. 2014 (Nat Genet)
Publication (OA): https://www.nature.com/articles/ng.2906
Data: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA216965

Human oral microbiome data from 16S rRNA gene datasets from 2 archaeological individuals and 3 environmental control samples from Swift Water Place, Alaska
Publication: Google Books link; Publisher link
Data: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA474746

Human oral microbiome data from 16S rRNA gene datasets from 5 archaeological individuals from the Yale New Haven Hospital cemetery
Publication (OA): https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0219279
Data: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA505811

PROTEOMIC DATASETS

Dental calculus proteomes from 45 individuals from 6000 BCE to 500 CE the North and South Caucasus, published in Scott et al. 2022.
Publication (OA): https://www.nature.com/articles/s41559-022-01701-6
Data: https://www.ebi.ac.uk/pride/archive/projects/PDX027728

Dental calculus proteomes from 7 individuals from the Middle Bronze Age site of Xiaohe in the Tarim Basin (ca. 2000-1700 BCE), published in Zhang et al. 2021.
Publication: https://www.nature.com/articles/s41586-021-04052-7
Data: https://www.ebi.ac.uk/pride/archive/projects/PXD027706

Dental calculus proteomes of 14 individuals from Late Bronze Age Megiddo and Early Iron Age Tel Erani, published in Scott et al. 2020
Publication: https://www.pnas.org/content/early/2020/12/16/2014956117
Data: https://www.ebi.ac.uk/pride/archive/projects/PXD021498

Dental calculus proteomes from 32 individuals from ancient Mongolia, published in Wilkin et al. 2020
Publication: https://www.nature.com/articles/s41559-020-1120-y
Data: https://www.ebi.ac.uk/pride/archive/projects/PXD014730; https://www.ebi.ac.uk/pride/archive/projects/PXD014730

27 dental calculus proteomes 6 individual from Medieval England and Spain and 19th century St. Helena, published in Fagernäs et al. 2020
Publication: https://www.sciencedirect.com/science/article/pii/S0305440320300571
Data: https://www.ebi.ac.uk/pride/archive/projects/PXD015817

Dental calculus proteomes from 14 victims of the Great Irish Famine, published in Geber et al. 2020
Publication: https://www.pnas.org/content/116/39/19380.short
Data: http://doi.org/10.6019/PXD015002

Dental calculus proteomes from 9 Late Bronze Age individuals from Khovsgol, Mongolia, published in Jeong et al. 2018
Publication (OA): https://www.pnas.org/content/pnas/early/2018/10/31/1813608115.full.pdf
Data: https://www.ebi.ac.uk/pride/archive/projects/PXD008217

Dental calculus proteomes from 100 archaeological and 14 modern individuals published in Hendy et al. 2018 and Velsko et al. 2019
Publication (OA): https://royalsocietypublishing.org/doi/full/10.1098/rspb.2018.0977; https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-019-0717-3
Data: https://www.ebi.ac.uk/pride/archive/projects/PXD009603

Dental calculus proteomes from 98 archaeological individuals published in Warinner et al. 2014 (Sci Rep)
Publication (OA): https://www.nature.com/articles/srep07104
Data: see https://www.ebi.ac.uk/pride/archive/projects/PXD009603

Dental calculus proteomes from 4 medieval and 2 modern humans and 4 dentin proteomes from medieval humans published in Warinner et al. 2014 (Nat Genet)
Publication: https://www.nature.com/articles/ng.2906
Data: http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD000412