Preface
B. Shapiro* and M. Hofreiter
Chapter 1: Setting Up An Ancient DNA Laboratory
T. L. Fulton*
Chapter 2: A Phenol-Chloroform Protocol for Extracting DNA from Ancient Samples
R. Barnett* and G. Larson
Chapter 3: DNA Extraction of Ancient Animal Hard Tissue Samples via Adsorption to Silica Particles
N. Rohland*
Chapter 4: --Case Study: Recovery of ancient nuclear DNA from Toe Pads of the Extinct Passenger Pigeon
T. L. Fulton*, S. M. Wagner and B. Shapiro
Chapter 5: Extraction of DNA from Paleofeces
M. Kuch and H. Poinar*
Chapter 6: DNA Extraction from Keratin and Chitin
P. F. Campos, M. T. P. Gilbert*
Chapter 7: Case Study: Ancient sloth DNA Recovered from Hairs Preserved in Paleofeces
A.A. Clack*, R.D.E. MacPhee, H.N. Poinar
Chapter 8: Ancient DNA Extraction from Soils and Sediments
J. Haile*
Chapter 9: DNA Extraction from Fossil Eggshell
C. L. Oskam and M. Bunce*
Chapter 10: Ancient DNA Extraction from Plants
L. Kistler*
Chapter 11: DNA Extraction from Formalin-fixed Material
P. F. Campos, M. T. P. Gilbert*
Chapter 12: Case Study: Ancient DNA recovered from Pleistocene-age Remains of a Florida Armadillo
B. Letts and B. Shapiro*
Chapter 13: Non-destructive DNA Extraction from Museum Specimens
M. Hofreiter*
Chapter 14: Case Study: Using a Non-destructive DNA Extraction Method to Generate mtDNA Sequences from Historical Chimpanzee Specimens
E. Mohandesan, S. Prost, M. Hofreiter*
Chapter 15: PCR Amplification, Cloning and Sequencing of Ancient DNA
T. L. Fulton* and M. Stiller
Chapter 16: Quantitative Real-time PCR in aDNA Research
M. Bunce*, C. L. Oskam, M. E. Allentoft
Chapter 17: Multiplex PCR Amplification of Ancient DNA
M. Stiller*, T. L. Fulton
Chapter 18: Preparation of Next-generation Sequencing Libraries from Damaged DNA
A. W. Briggs*, P. Heyn
Chapter 19: Generating Barcoded Libraries for Multiplex High-throughput Sequencing
M. Knapp*, M. Stiller, M. Meyer
Chapter 20: Case Study: Targeted high-throughput Sequencing of Mitochondrial Genomes from Extinct Cave Bears via Direct Multiplex PCR Sequencing (DMPS)
M. Stiller*
Chapter 21: Target Enrichment via DNA Hybridization Capture
S. Horn*
Chapter 22: Case Study: Enrichment of Ancient Mitochondrial DNA by Hybridization Capture
S. Horn*
Chapter 23: Analysis of High-throughput Ancient DNA Sequencing Data
M. Kircher*
Chapter 24: Phylogenetic Analysis of Ancient DNA using BEASTS. Y. W. Ho*
