M ETHODS IN M OLECULAR B IOLOGY

Series Editor John M. Walker School of Life and Medical Sciences University of Hertfordshire Hatfield, Hertfordshire, AL10 9AB, UK

For further volumes: http://www.springer.com/series/7651 Ancient DNA

Methods and Protocols

Second Edition

Edited by Beth Shapiro Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA Axel Barlow Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany Peter D. Heintzman Tromsø University Museum, UiT—The Arctic University of Norway, Tromsø, Norway Michael Hofreiter, Johanna L. A. Paijmans Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany André E. R. Soares Laboratório Nacional de Computação Científica, Petrópolis, RJ, Brazil Editors Beth Shapiro Axel Barlow Department of Ecology and Evolutionary Institute for Biochemistry and Biology Biology University of Potsdam University of California Santa Cruz Potsdam, Germany Santa Cruz, CA, USA Michael Hofreiter Peter D. Heintzman Institute for Biochemistry and Biology Tromsø University Museum University of Potsdam UiT—The Arctic University of Norway Potsdam, Germany Tromsø, Norway Andre´ E. R. Soares Johanna L. A. Paijmans Laborato´rio Nacional de Computac¸a˜o Cientı´fica Institute for Biochemistry and Biology Petro´polis, RJ, Brazil University of Potsdam Potsdam, Germany

ISSN 1064-3745 ISSN 1940-6029 (electronic) Methods in Molecular Biology ISBN 978-1-4939-9175-4 ISBN 978-1-4939-9176-1 (eBook) https://doi.org/10.1007/978-1-4939-9176-1

Library of Congress Control Number: 2019933331

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This Humana Press imprint is published by the registered company Springer Science+Business Media, LLC, part of Springer Nature. The registered company address is: 233 Spring Street, New York, NY 10013, U.S.A. Preface

Research in ancient DNA began during the early 1980s with the publication of short mitochondrial DNA sequence fragments from a quagga, an extinct subspecies of the plains zebra. Following this, several institutions invested resources to develop both the laboratory infrastructure and research expertise to recover trace amounts of degraded DNA from ancient samples. For many years, the field remained small, as researchers grappled with the challenges of inhibition, degradation, and contamination of ancient DNA extracts. Today’s broad application of ancient DNA as a research tool is owed to two technical innovations within the last 25 years: the invention of the polymerase chain reaction, or PCR, and the development of economical and high-throughput sequencing technologies. PCR allowed the targeted retrieval of small fragments of DNA that, in fortunate circumstances, are preserved in fossil and museum specimens. High-throughput sequencing approaches made the recovery of many millions of preserved molecules economically viable and practi- cal, which has pushed the field into the realm of genomics. These key innovations have allowed ancient DNA to become an increasingly widespread research tool, with the capacity to expand both the temporal and taxonomic breadth of questions that can be asked in ecological and evolutionary research. As we noted in the first edition of this book that was published in 2012, progress in ancient DNA research has been inherently technology driven. In our first collection of protocols, we attempted to summarize the most common approaches toward the retrieval and analysis of ancient DNA sequences. We began with guidelines for establishing an ancient DNA laboratory and described extraction protocols that had been optimized for a wide range of different substrates. We included instructions for ancient DNA-specific approaches to DNA extraction, preparing and performing PCR and genomic library preparation, and suggested analytical approaches for population genetic analyses of ancient DNA and the initial quality control of data recovered from high-throughput sequencing. Many of the protocols included in the first edition remain relevant today. However, new protocols for both ancient DNA recovery and analysis have been introduced during the time since publication, and these have expanded significantly the range of samples from which ancient DNA can be recovered. These new protocols are the focus of this second edition. We include in this second edition protocols that address the most challenging aspects of experimental work in ancient DNA: preparing ancient samples for DNA extraction, the DNA extraction itself, and transforming extracted ancient DNA molecules so that they can be sequenced on the different available sequencing platforms, which is also known as sequencing library preparation. We also include several chapters that discuss the analysis of high-throughput sequencing data recovered from ancient specimens, which, because of the degraded nature of ancient DNA and common co-extraction of contaminant DNA, has challenges that are unique compared to data recovered from modern specimens. We begin with a chapter that discusses procedures for setting up an ancient DNA laboratory and authenticating recovered ancient DNA. Next, we include two chapters that describe methods to pretreat samples prior to ancient DNA extraction, both of which lead to improvements in the relative abundance of endogenous versus contaminant DNA. We then present four chapters that describe the latest innovations in retrieving ancient DNA from organic remains and environmental samples. We include updated protocols presenting v vi Preface double-stranded and single-stranded approaches to prepare genomic libraries, and several approaches enrich ancient DNA extracts for molecular targets of interest. Finally, we include a chapter on data authenticity assessment, which is critical for all ancient DNA studies, and a chapter that includes a practical approach and troubleshooting advice for those aiming to assemble ancient genomes from next-generation sequencing data. As in the first edition, the goal of this second edition is to present these protocols in a manner that makes them easily accessible for everyday use in the lab. We hope this book will be another useful source of information for both beginning and experienced researchers hoping to add ancient DNA to their professional toolkit. We express our sincere thanks to all the authors for their willingness to share their time and their trade secrets, and to Prof. John Walker at Humana Press for giving us the opportunity to assemble this collection of protocols.

Santa Cruz, CA, USA Beth Shapiro Potsdam, Germany Axel Barlow Tromsø, Norway Peter D. Heintzman Potsdam, Germany Michael Hofreiter Potsdam, Germany Johanna L. A. Paijmans Petropolis, RJ, Brazil Andre´ E. R. Soares Contents

Preface ...... v Contributors...... ix 1 Setting Up an Ancient DNA Laboratory ...... 1 Tara L. Fulton and Beth Shapiro 2 Pretreatment: Removing DNA Contamination from Ancient Bones and Teeth Using Sodium Hypochlorite and Phosphate ...... 15 Petra Korlevic´ and Matthias Meyer 3 Pretreatment: Improving Endogenous Ancient DNA Yields Using a Simple Enzymatic Predigestion Step ...... 21 Hannes Schroeder, Peter de Barros Damgaard, and Morten E. Allentoft 4 Extraction of Highly Degraded DNA from Ancient Bones and Teeth ...... 25 Jesse Dabney and Matthias Meyer 5 Sampling and Extraction of Ancient DNA from Sediments...... 31 Laura S. Epp, Heike H. Zimmermann, and Kathleen R. Stoof-Leichsenring 6 Extraction of Ancient DNA from Plant Remains ...... 45 Nathan Wales and Logan Kistler 7 DNA Extraction from Keratin and Chitin ...... 57 Paula F. Campos and M. Thomas P. Gilbert 8 Double-Stranded Library Preparation for Ancient and Other Degraded Samples ...... 65 Kirstin Henneberger, Axel Barlow, and Johanna L. A. Paijmans 9 A Method for Single-Stranded Ancient DNA Library Preparation...... 75 Marie-Theres Gansauge and Matthias Meyer 10 Sequencing Library Preparation from Degraded Samples for Non-illumina Sequencing Platforms ...... 85 Renata F. Martins, Marie-Louise Kampmann, and Daniel W. Fo¨rster 11 Whole-Genome Capture of Ancient DNA Using Homemade Baits ...... 93 Gloria Gonza´lez Fortes and Johanna L. A. Paijmans 12 Generating RNA Baits for Capture-Based Enrichment...... 107 Noah Snyder-Mackler, Tawni Voyles, and Jenny Tung 13 Hybridization Capture of Ancient DNA Using RNA Baits ...... 121 Andre´ E. R. Soares 14 Application of Solid-State Capture for the Retrieval of Small-to-Medium Sized Target Loci from Ancient DNA ...... 129 Johanna L. A. Paijmans, Gloria Gonza´lez Fortes, and Daniel W. Fo¨rster 15 Targeted PCR Amplification and Multiplex Sequencing of Ancient DNA for SNP Analysis...... 141 Saskia Wutke and Arne Ludwig

vii viii Contents

16 Targeted Amplification and Sequencing of Ancient Environmental and Sedimentary DNA ...... 149 Ruth V. Nichols, Emily Curd, Peter D. Heintzman, and Beth Shapiro 17 Authentication and Assessment of Contamination in Ancient DNA ...... 163 Gabriel Renaud, Mikkel Schubert, Susanna Sawyer, and Ludovic Orlando 18 Assembly of Ancient Mitochondrial Genomes Without a Closely Related Reference Sequence...... 195 Christoph Hahn

Index ...... 215 Contributors

MORTEN E. ALLENTOFT  Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark AXEL BARLOW  Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany PAULA F. CAMPOS  Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark EMILY CURD  Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA JESSE DABNEY  Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK PETER DE BARROS DAMGAARD  Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark LAURA S. EPP  Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany; Department of Biology, University of Konstanz, Konstanz, Germany DANIEL W. FO¨ RSTER  Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany TARA L. FULTON  Environment and Climate Change Canada, Edmonton, AB, Canada MARIE-THERES GANSAUGE  Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany M. THOMAS P. G ILBERT  Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark GLORIA GONZA´ LEZ FORTES  Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy CHRISTOPH HAHN  Institute of Biology, University of Graz, Graz, Austria PETER D. HEINTZMAN  Tromsø University Museum, UiT—The Arctic University of Norway, Tromsø, Norway KIRSTIN HENNEBERGER  Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany MARIE-LOUISE KAMPMANN  Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany; Section of Forensic Genetics, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark LOGAN KISTLER  Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA PETRA KORLEVIC´  European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK; Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany ARNE LUDWIG  Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany RENATA F. MARTINS  Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany; Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany ix x Contributors

MATTHIAS MEYER  Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany RUTH V. NICHOLS  Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA LUDOVIC ORLANDO  Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark; Laboratoire d’Anthropobiologie Mole´culaire et d’Imagerie de Synthe`se, CNRS UMR 5288, Universite´ de Toulouse, University Paul Sabatier, Toulouse, France JOHANNA L. A. PAIJMANS  Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany GABRIEL RENAUD  Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark SUSANNA SAWYER  Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark HANNES SCHROEDER  Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark MIKKEL SCHUBERT  Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark BETH SHAPIRO  Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA NOAH SNYDER-MACKLER  Department of Evolutionary Anthropology, Duke University, Durham, NC, USA; Department of Psychology, University of Washington, Seattle, WA, USA ANDRE´ E. R. SOARES  Laboratorio Nacional de Computac¸a˜o Cientı´fica, Petropolis, RJ, Brazil KATHLEEN R. STOOF-LEICHSENRING  Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany JENNY TUNG  Department of Evolutionary Anthropology, Duke University, Durham, NC, USA TAWNI VOYLES  Department of Evolutionary Anthropology, Duke University, Durham, NC, USA NATHAN WALES  Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA; Laboratory of Molecular Anthropology and Image Synthesis, University Paul Sabatier, Toulouse, France; Department of Archaeology, University of York, York, UK SASKIA WUTKE  Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland HEIKE H. ZIMMERMANN  Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany