A browsable record of the published ancient-metagenomic literature on eukaryotes — where it was sampled, when it was published, and how it was analysed. Filter the corpus and the map, bar charts, and counts redraw against the same publication-level logic used in the project's R figures.
Ancient metagenomic analysis of eukaryotes, particularly through shotgun sequencing, began gaining traction around 2016, marking a significant shift in how researchers study past ecosystems and evolutionary processes. Unlike microbial and viral ancient DNA studies, which have a longer history, the recovery and analysis of ancient eukaryotic DNA from complex environmental and archaeological samples remain a relatively new and rapidly developing field. This research area is expanding into diverse applications, including the reconstruction of past biodiversity, tracking the evolution of parasites and symbionts, understanding ancient food webs, and shedding light on human–animal–plant interactions over time. With continued advancements in sequencing technology and bioinformatics, ancient eukaryotic metagenomics is poised to reveal deeper insights into past life and environmental changes.
Here, we have compiled all publications that have analyzed ancient metagenomic data (excluding metabarcoding data) with a focus on the eukaryotic fraction (link to the spreadsheet). This list builds upon and expands the existing literature collected in the Inventory of ancient environmental DNA from sedimentary archives: locations, methods, and target taxa (doi:10.5281/zenodo.6847521). Our updated compilation not only includes the most recent publications but also broadens the scope to include environmental sources beyond sediments.
We define ancient environmental samples as those containing genetic material from more than one unknown organism, which can include sources such as coprolites, stalagmites, and sedimentary deposits. Additionally, we have enriched the dataset with details on analytical methodologies, including databases used, sequencing strategies (shotgun sequencing vs. capture enrichment), and the bioinformatic tools applied for trimming, quality control, mapping, and authentication of ancient DNA sequences. It is important to note that studies employing capture enrichment may also include shotgun-sequenced data, but not vice versa.
Our aim is for this resource to be continuously updated and valuable to the research community. The complete list is available here; if you find errors or missing publications, feel free to leave comments in the Google Sheet. Below, we provide a visual summary of where studies have been conducted worldwide, the annual publication trends, and the proportion of studies employing the two main analytical strategies.
Each marker is one sampled site. Colour and symbol are switchable; the Okabe–Ito palette matches the project's published figures.
Counts are distinct publications (by DOI), matching the R script — a multi-site study counts once.
How many publications used each reference target and each read mapper, within the current filter.
Holi is a bioinformatic pipeline for ancient metagenomic data. It integrates tools for processing raw sequence reads, taxonomic classification, authenticity assessment, and visualisation, aimed at researchers working with ancient eDNA (aeDNA) and especially the eukaryotic fraction. With a focus on the challenges of ancient metagenomics — low-quality, damaged DNA — Holi attempts accurate taxonomic identification through a competitive setup, authentication of ancient DNA damage patterns, and genome/reference-wide statistics for reporting.
The dataset behind this page is the compilation described at the top of this page. It is a living resource — contribute corrections or additions in the Google Sheet, then load the updated export here with the button above.
To regenerate the original static figures in R:
git clone https://github.com/miwipe/Holi.git # open sedaDNA_litterature.Rproj, then run generate_figures.R