index.qmd

# Preface {.unnumbered}

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 [@Briggs2007-ao]. 

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.