Ancient DNA: methods and protocols / ed. by B.Shapiro, M.Hofreiter. - New York: Humana Press: Springer, 2012. - xii, 247 p.: ill. - (Methods in molecular biology; 840) (Springer protocols). - Incl. bibl. ref. - Ind.: p.243-247. - ISBN 978-1-61779-515-2; ISSN 1064-3745  Место хранения:   056 | Институт химической биологии и фундаментальной медицины CO РАН | Новосибирск| Библиотека

Оглавление / Contents

Preface ......................................................... v Contributors ................................................... xi 1 Setting Up an Ancient DNA Laboratory ......................... 1 Tara L. Fulton 2 A Phenol-Chloroform Protocol for Extracting DNA from Ancient Samples ............................................. 13 Ross Barnett and Greger Larson 3 DNA Extraction of Ancient Animal Hard Tissue Samples via Adsorption to Silica Particles .............................. 21 Nadin Rohland 4 Case Study: Recovery of Ancient Nuclear DNA from Toe Pads of the Extinct Passenger Pigeon ............................. 29 Tara L. Fulton, Stephen M. Wagner, and Beth Shapiro 5 Extraction of DNA from Paleofeces ........................... 37 Melanie Kuch and Hendrik Poinar 6 DNA Extraction from Keratin and Chitin ...................... 43 Paula F. Campos and Thomas M.P. Gilbert 7 Case Study: Ancient Sloth DNA Recovered from Hairs Preserved in Paleofeces ..................................... 51 Andrew A. Clack, Ross D.E. MacPhee, and Hendrik N. Poinar 8 Ancient DNA Extraction from Soils and Sediments ............. 57 James Haile 9 DNA Extraction from Fossil Eggshell ......................... 65 Charlotte L. Oskam and Michael Bunce 10 Ancient DNA Extraction from Plants .......................... 71 Logan Kistler 11 DNA Extraction from Formalin-Fixed Material ................. 81 Paula F. Campos and Thomas M.P. Gilbert 12 Case Study: Ancient DNA Recovered from Pleistocene-Age Remains of a Florida Armadillo .............................. 87 Brandon Letts and Beth Shapiro 13 Nondestructive DNA Extraction from Museum Specimens ......... 93 Michael Hojreiter 14 Case Study: Using a Nondestructive DNA Extraction Method to Generate mtDNA Sequences from Historical Chimpanzee Specimens .................................................. 101 Elmira Mohandesan, Stefan Prost, and Michael Hojreiter 15 PCR Amplification, Cloning, and Sequencing of Ancient DNA ........................................................ 111 Tara L. Fulton and Mathias Stiller 16 Quantitative Real-Time PCR in aDNA Research ................ 121 Michael Bunce, Charlotte L. Oskam, and Morten E. Allentoft 17 Multiplex PCR Amplification of Ancient DNA ................. 133 Mathias Stiller and Tara L. Fulton 18 Preparation of Next-Generation Sequencing Libraries from Damaged DNA ................................................ 143 Adrian W. Brings and Patricia Heyn 19 Generating Barcoded Libraries for Multiplex High- Throughput Sequencing ...................................... 155 Michael Knapp, Mathias Stiller, and Matthias Meyer 20 Case Study: Targeted high-Throughput Sequencing of Mitochondrial Genomes from Extinct Cave Bears via Direct Multiplex PCR Sequencing (DMPS) ............................ 171 Mathias Stiller 21 Target Enrichment via DNA Hybridization Capture ............ 177 Susanne Horn 22 Case Study: Enrichment of Ancient Mitochondrial DNA by Hybridization Capture ................................... 189 Susanne Horn 23 Analysis of High-Throughput Ancient DNA Sequencing Data .... 197 Martin Kircher 24 Phylogenetic Analysis of Ancient DNA using BEAST ........... 229 Simon Y.W. Ho Index ......................................................... 243