Ancient DNA

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(TM) 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.

Setting Up An Ancient DNA Laboratory.-A Phenol-Chloroform Protocol for Extracting DNA from Ancient Samples.-DNA Extraction of Ancient Animal Hard Tissue Samples via Adsorption to Silica Particles.-Case Study: Recovery of ancient nuclear DNA from Toe Pads of the Extinct Passenger Pigeon.-Extraction of DNA from Paleofeces.-DNA Extraction from Keratin and Chitin.-Case Study: Ancient sloth DNA Recovered from Hairs Preserved in Paleofeces.-Ancient DNA Extraction from Soils and Sediments.-DNA Extraction from Fossil Eggshell.-Ancient DNA Extraction from Plants.-DNA Extraction from Formalin-fixed Material.-Case Study: Ancient DNA recovered from Pleistocene-age Remains of a Florida Armadillo.-Non-destructive DNA Extraction from Museum Specimens.-Case Study: Using a Non-destructive DNA Extraction Method to Generate mtDNA Sequences from Historical Chimpanzee Specimens .-PCR Amplification, Cloning and Sequencing of Ancient DNA.-Quantitative Real-time PCR in aDNA Research.-Multiplex PCR Amplification of Ancient DNA.-Preparation of Next-generation Sequencing Libraries from Damaged DNA.-Generating Barcoded Libraries for Multiplex High-throughput Sequencing.-Case Study: Targeted high-throughput Sequencing of Mitochondrial Genomes from Extinct Cave Bears via Direct Multiplex PCR Sequencing (DMPS).-Target Enrichment via DNA Hybridization Capture.-Case Study: Enrichment of Ancient Mitochondrial DNA by Hybridization Capture.-Analysis of High-throughput Ancient DNA Sequencing Data.-Phylogenetic Analysis of Ancient DNA using BEAST.