Introduction to Ancient Metagenomics


James A Fellows Yates and Christina Warinner


March 4, 2025


Ancient metagenomics applies cutting-edge metagenomic methods to the degraded DNA content of archaeological and palaeontological specimens. The rapidly growing field is currently uncovering a wealth of novel information for both human and natural history, from identifying the causes of devastating pandemics such as the Black Death, to revealing how past ecosystems changed in response to long-term climatic and anthropogenic change, to reconstructing the microbiomes of extinct human relatives. However, as the field grows, the techniques, methods, and workflows used to analyse such data are rapidly changing and improving.

In this book we will go through the main steps of ancient metagenomic bioinformatic workflows, familiarising students with the command line, demonstrating how to process next-generation-sequencing (NGS) data, and showing how to perform de novo metagenomic assembly. Focusing on host-associated ancient metagenomics, the book consists of a combination of theory and hands-on exercises, allowing readers to become familiar with the types of questions and data researchers work with.

By the end of the textbook, readers will have an understanding of how to effectively carry out the major bioinformatic components of an ancient metagenomic project in an open and transparent manner.


If you export the PDF or ePub versions of this book, some sections maybe excluded (such as videos, and embedded slide decks). Always refer to this website in doubt.


The PDF/ePub version of the book is currently still under construction, and is likely misformatted and missing much of the content. It is not recommended for use.

All material was originally developed for the SPAAM Summer School: Introduction to Ancient Metagenomics