Introduction to Ancient DNA - SPAAM Summer School: Introduction to Ancient Metagenomics (2022)
Channel: SPAAM Community
Date: 2022-09-05

WARNING: This recording shows archaeological human skeletal remains between (Medieval Mandible, Skull from Europe and 1000 year old Peruvian Spinal Column)  00:006:45-00:16:42. They have been previously published in academic journals, and are shown here for educational purposes.

Instructors: Christina Warinner

Abstract: This lecture introduces you to ancient DNA and the enormous technological changes that have taken place since the field’s origins in 1984. Starting with the Quagga and proceeding to microbes, we discuss where ancient microbial DNA can be found in the archaeological record and examine how ancient DNA is defined by its condition, not by a fixed age. We next cover genome basics and take an in-depth look at the way DNA degrades over time. We detail the fundamentals of DNA damage, including the specific chemical processes that lead to DNA fragmentation and C to T miscoding lesions. We then demystify the DNA damage “smile plot” and explain the how the plot’s symmetry or asymmetry is related to the specific enzymes used to repair DNA during library construction. We discuss how DNA damage is and is not clock-like, how to interpret and troubleshoot DNA damage plots, and how DNA damage patters can be used to authenticate ancient samples, specific taxa, and even sequences. We cover laboratory strategies for removing or reducing damage for greater accuracy for genotype calling, and we discuss the pros and cons of single-stranded library protocols. We then take a closer look at proofreading and non-proofreading polymerases and note key steps in NGS library preparation during which enzyme selection is critical in ancient DNA studies. Finally, we examine the big picture of why DNA damage matters in ancient microbial studies, and its effects on taxonomic identification of sequences, accurate genome mapping, and metagenomic assembly.