An insider's view on bringing extinct species back to life

Could extinct species, like mammoths and passenger pigeons, be brought back to life? In How to Clone a Mammoth, Beth Shapiro, an evolutionary biologist and pioneer in ancient DNA research, addresses this intriguing question by walking readers through the astonishing and controversial process of de-extinction. From deciding which species should be restored to anticipating how revived populations might be overseen in the wild, Shapiro vividly explores the extraordinary cutting-edge science that is being used to resurrect the past. Considering de-extinction's practical benefits and ethical challenges, Shapiro argues that the overarching goal should be the revitalization and stabilization of contemporary ecosystems. Looking at the very real and compelling science behind an idea once seen as science fiction, How to Clone a Mammoth demonstrates how de-extinction will redefine conservation's future.

An insider's view on bringing extinct species back to life

Could extinct species, like mammoths and passenger pigeons, be brought back to life? The science says yes. In How to Clone a Mammoth, Beth Shapiro, evolutionary biologist and pioneer in ancient DNA research, walks readers through the astonishing and controversial process of de-extinction. From deciding which species should be restored, to sequencing their genomes, to anticipating how revived populations might be overseen in the wild, Shapiro vividly explores the extraordinary cutting-edge science that is being used--today--to resurrect the past. Journeying to far-flung Siberian locales in search of ice age bones and delving into her own research--as well as those of fellow experts such as Svante Paabo, George Church, and Craig Venter--Shapiro considers de-extinction's practical benefits and ethical challenges. Would de-extinction change the way we live? Is this really cloning? What are the costs and risks? And what is the ultimate goal?

Using DNA collected from remains as a genetic blueprint, scientists aim to engineer extinct traits--traits that evolved by natural selection over thousands of years--into living organisms. But rather than viewing de-extinction as a way to restore one particular species, Shapiro argues that the overarching goal should be the revitalization and stabilization of contemporary ecosystems. For example, elephants with genes modified to express mammoth traits could expand into the Arctic, re-establishing lost productivity to the tundra ecosystem.

Looking at the very real and compelling science behind an idea once seen as science fiction, How to Clone a Mammoth demonstrates how de-extinction will redefine conservation's future.

1. Setting Up an Ancient DNA Laboratory

Tara L. Fulton and Beth Shapiro

2. Pretreatment: Removing DNA Contamination from Ancient Bones and Teeth Using Sodium Hypochlorite and Phosphate

Petra Korlevic and Matthias Meyer

3. Pretreatment: Improving Endogenous Ancient DNA Yields Using a Simple Enzymatic Pre-Digestion Step

Hannes Schroeder, Peter de Barros Damgaard, and Morten E. Allentoft

4. Extraction of Highly Degraded DNA from Ancient Bones and Teeth

Jesse Dabney and Matthias Meyer

5. Sampling and Extraction of Ancient DNA from Sediments

Laura S. Epp, Heike H. Zimmermann, and Kathleen R. Stoof-Leichsenring

6. Extraction of Ancient DNA from Plant Remains

Nathan Wales and Logan Kistler

7. DNA Extraction from Keratin and Chitin

Paula F. Campos and M. Thomas P. Gilbert

8. Double-Stranded Library Preparation for Ancient and Other Degraded Samples

Kirstin Henneberger, Axel Barlow, and Johanna L.A. Paijmans

9. A Method for Single-Stranded Ancient DNA Library Preparation

Marie-Theres Gansauge and Matthias Meyer

10. Sequencing Library Preparation from Degraded Samples for Non-Illumina Sequencing Platforms

Renata Martins, Marie-Louise Kampmann, and Daniel W. Förster

11. Whole-Genome Capture of Ancient DNA Using Homemade Baits

Gloria Gonzalez-Fortes and Johanna L.A. Paijmans

12. Generating RNA Baits for Capture-Based Enrichment

Noah Snyder-Mackler, Tawni Voyles, and Jenny Tung

13. Hybridization Capture of Ancient DNA Using RNA Baits

André E.R. Soares

14. Application of Solid-State Capture for the Retrieval of Small-to-Medium Sized Target Loci from Ancient DNA

Johanna L.A. Paijmans, Gloria Gonzalez-Fortes, and Daniel W. Förster

15. Targeted PCR Amplification and Multiplex Sequencing of Ancient DNA for SNP Analysis

Saskia Wutke and Arne Ludwig

16. Targeted Amplification and Sequencing of Ancient Environmental and Sedimentary DNA

Ruth V. Nichols, Emily Curd, Peter D. Heintzman, and Beth Shapiro

17. Authentication and Assessment of Contamination in Ancient DNA

Gabriel Renaud, Mikkel Schubert, Susanna Sawyer, and Ludovic Orlando

18. Assembly of Ancient Mitochondrial Genomes without a Closely Related Reference Sequence

&n

When the 2020 Nobel Prize was awarded to the inventors of CRISPR, the revolutionary gene-editing tool, it underlined our amazing and apparently novel powers to alter nature. But as biologist Beth Shapiro argues in Life as We Made It, this phenomenon isn't new. Humans have been reshaping the world around us for ages, from early dogs to modern bacteria modified to pump out insulin. Indeed, she claims, reshaping nature--resetting the course of evolution, ours and others'--is the essence of what our species does.

In exploring our evolutionary and cultural history, Shapiro finds a course for the future. If we have always been changing nature to help us survive and thrive, then we need to avoid naive arguments about how we might destroy it with our meddling, and instead ask how we can meddle better.

Brilliant and insightful, Life as We Made It is an essential book for the decades to come.

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*