The Little Book of Smiley Plots

A collection of ancient DNA patterns and their causes

Preface

A key part of any ancient DNA project is to show that the DNA is exactly that - that the DNA is ancient, rather than from modern contamination.

A key authentication method is to show the presence of elevated C to T deamination patterns (and the complementary G to A) at the end of DNA molecules - known as damage patterns - originally reported by (Briggs et al. 2007).

These patterns can be plotted in what have been colloquially known as ’Smiley Plots. However, there can be a wide range of smiley plots, some which show valid ancient DNA, and others that do not - either due to not actually having true ancient DNA but also from laboratory and/or bioinformatic artifacts.

This book aims to act as a reference guide to interpreting ancient DNA damage plots, providing a wide range of example ‘smiley plots’, with descriptions of what the describe and what can cause them. As an added bit of fun, each type of ‘smiley plot’ comes with a artistic interpretation of the line shape contributed by members of the ancient DNA community.

Briggs, Adrian W, Udo Stenzel, Philip L F Johnson, Richard E Green, Janet Kelso, Kay Prüfer, Matthias Meyer, et al. 2007. “Patterns of Damage in Genomic DNA Sequences from a Neandertal.” Proceedings of the National Academy of Sciences of the United States of America 104 (37): 14616–21. https://doi.org/10.1073/pnas.0704665104.