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Biomedical Sciences - Human Genetics | Ancient DNA - Methods and Protocols

Ancient DNA

Methods and Protocols

Series: Methods in Molecular Biology, Vol. 840

Shapiro, Beth, Hofreiter, Michael (Eds.)

2012, XII, 247p. 26 illus., 12 illus. in color.

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  • Closes the gap between appropriate methodological approaches and retrieval and anylsis of ancient DNA
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Research into ancient DNA began more than 25 years ago with the publication of short mitochondrial DNA sequence fragments from the quagga, an extinct relative of the zebra. Ancient DNA research really gained momentum following the invention of PCR, which allowed millions of copies to be made of the few remaining DNA molecules preserved in fossils and museum specimens.  In Ancient DNA: Methods and Protocols expert researchers in the field describe many of the protocols that are now commonly used to study ancient DNA. These include instructions for setting up an ancient DNA laboratory, extraction protocols for a wide range of different substrates, details of laboratory techniques including PCR and NGS library preparation, and suggestions for appropriate analytical approaches to make sense of the sequences obtained. Written in the highly successful Methods in Molecular Biology™ series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls.

 

Authoritative and practical, Ancient DNA: Methods and Protocols seeks to aid scientists in the further study of ancient DNA and the methodological approaches in ancient research.

Content Level » Professional/practitioner

Keywords » NGS - PCR - Pleistocene-age DNA - ancient DNA - ancient bone - bone hydroxyl-apatite - hydroxyl-apatite crystals - mitochondrial genomes - phylogeographic patterns - soft tissue

Related subjects » Human Genetics

Table of contents 

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 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*

 

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