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Ancient DNA : methods and protocols
edited by Beth Shapiro, Michael Hofreiter.
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Table of Contents
Setting up an ancient DNA laboratory / Tara L. Fulton -- A phenol-chloroform protocol for extracting DNA from ancient samples / Ross Barnett and Greger Larson -- DNA extraction of ancient animal hard tissue samples via adsorption to silica particles / Nadin Rohland -- Case study : recovery of ancient nuclear DNA from toe pads of the extinct passenger pigeon / Tara L. Fulton, Stephen M. Wagner, and Beth Shapiro -- Extraction of DNA from paleofeces / Melanie Kuch and Hendrik Poinar -- DNA extraction from keratin and chitin / Paula F. Campos and Thomas M.P. Gilbert -- Case study : ancient sloth DNA recovered from hairs preserved in paleofeces / Andrew A. Clack, Ross D.E. MacPhee, and Hendrik N. Poinar -- Ancient DNA extraction from soils and sediments / James Haile -- DNA extraction from fossil eggshell / Charlotte L. Oskam and Michael Bunce -- Ancient DNA extraction from plants / Logan Kistler -- DNA extraction from formalin-fixed material / Paula F. Campos and Thomas M.P. Gilbert -- Case study : ancient DNA recovered from Pleistocene-age remains of a Florida armadillo / Brandon Letts and Beth Shapiro -- Nondestructive DNA extraction from museum specimens / Michael Hofreiter -- Case study : using a nondestructive DNA extraction method to generate mtDNA sequences from historical chimpanzee specimens / Elmira Mohandesan, Stefan Prost, and Michael Hofreiter -- PCR amplification, cloning, and sequencing of ancient DNA / Tara L. Fulton and Mathias Stiller -- Quantitative real-time PCR in aDNA research / Michael Bunce, Charlotte L. Oskam, and Morten E. Allentoft -- Multiplex PCR amplification of ancient DNA / Mathias Stiller and Tara L. Fulton -- Preparation of next-generation sequencing libraries from damaged DNA / Adrian W. Briggs and Patricia Heyn -- Generating barcoded libraries for multiplex high-throughput sequencing / Michael Knapp, Mathias Stiller, and Matthias Meyer -- Case study : targeted high-throughput sequencing of mitochondrial genomes from extinct cave bears via direct multiplex PCR sequencing (DMPS) / Mathias Stiller -- Target enrichment via DNA hybridization capture / Susanne Horn -- Case study : enrichment of ancient mitochondrial DNA by hybridization capture / Susanne Horn -- Analysis of high-throughput ancient DNA sequencing data / Martin Kircher -- Phylogenetic analysis of ancient DNA using BEAST / Simon Y.W. Ho.