Ancient DNA: Methods and Protocols (Hardcover, 2012)

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 BEAST S. Y. W. Ho 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 BEAST S. Y. W. Ho 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