How to Clone a Mammoth: The Science of De-Extinction

How to Clone a Mammoth: The Science of De-Extinction

by Beth Shapiro

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Overview

How to Clone a Mammoth: The Science of De-Extinction by Beth Shapiro

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.

Product Details

ISBN-13: 9780691157054
Publisher: Princeton University Press
Publication date: 04/05/2015
Pages: 240
Sales rank: 1,193,819
Product dimensions: 6.00(w) x 9.40(h) x 1.00(d)

About the Author

Beth Shapiro is associate professor of ecology and evolutionary biology at the University of California, Santa Cruz. Her work has appeared in numerous publications, and she received a MacArthur Award in 2009.

Read an Excerpt

How to Clone a Mammoth

The Science of De-extinction


By Beth Shapiro

PRINCETON UNIVERSITY PRESS

Copyright © 2015 Princeton University Press
All rights reserved.
ISBN: 978-1-4008-6548-2



CHAPTER 1

REVERSING EXTINCTION


A few years ago, a colleague of mine practically bit my head off for getting the end date of the Cretaceous period wrong by a little bit. I was presenting an informal seminar about my research to graduate students at my university, which at the time was Penn State. My seminar was about mammoths—in particular, about when, where, and why mammoths went extinct, or at least what we've learned about the mammoth extinction by extracting bits of mammoth DNA from frozen mammoth bones. Before talking about this very recent extinction, I opened with a discussion of older and more famous extinctions. My offending slide cited the date for the end of the Cretaceous period and beginning of the Paleogene, also known as the K-Pg boundary and best known as the time of the extinction of the dinosaurs, at "around 65 million years ago." That date, I was told, was inexcusably imprecise. The K-Pg boundary occurred 65.5 ± 0.3 million years ago (at least that was the scientific consensus of the time), and I was not to be forgiven those 200,000 to 800,000 years.

While I appreciate that my fellow academics would have preferred meticulous attention to detail, I did not bring up the dinosaurs to discuss the precise timing of their demise. My goal was simply to make the point that while we think we now know why the dinosaurs went extinct so many millions of years ago, we still argue about what caused extinctions that took place within the last ten thousand years. Did the mammoths and other ice age animals go extinct because Earth's climate was suddenly too warm to support them? Or did our ancestors hunt them to death? The question remains open, perhaps because we are not particularly comfortable with the answer.

The last dinosaurs went extinct after a massive asteroid struck just off the coast of Mexico's Yucatan Peninsula. Similar cataclysmic events—major explosive volcanic eruptions or impacts of large asteroids or comets—are thought to have caused the other four mass extinctions in Earth's history. Each time, dense clouds of dust and other debris were suddenly ejected into the atmosphere, blocking out the sunlight. Without sunlight, the plants suffered and many species died. As the plant communities collapsed, so did the animals that ate the plants, and then the animals that ate the animals that ate the plants, and so on up the food chain until somewhere between 50 percent and 90 percent of all species that were alive at the time of the catastrophic event became extinct.

The mammoth extinction is different. We know of no single catastrophic event that happened within the last 10,000 years that might have caused mammoths to go extinct. Recent genetic research shows that mammoth populations probably started to decline sometime during or just after the peak of the last ice age some 20,000 years ago, as the rich arctic grasslands—often called the steppe tundra—on which they relied for food were gradually replaced by modern arctic vegetation. Mammoths were extinct in continental North America and Asia by around 8,000 years ago but survived for another few thousand years in two isolated locations in the Bering Strait: the Pribilof Islands off the western coast of Alaska, where mammoths survived until around 5,000 years ago, and Wrangel Island off the northeastern coast of Siberia, where they survived until around 3,700 years ago.

We know from the fossil record that mammoths, steppe bison, and wild horses dominated the Arctic landscape for a long time before the peak of the last ice age. In fact, they were the most abundant large mammals in the North American Arctic for most of the last 100,000 years. This was a very cold period of Earth's history and included two ice ages—one that peaked at around 80,000 years ago and another that peaked around 20,000 years ago—separated by a long cold interval. It was only after the peak of the most recent ice age that the climate really began to warm up, transitioning into the present warm interval (the Holocene epoch) by around 12,000 years ago. Because mammoths, steppe bison, and wild horses disappeared only after the Holocene had begun, it is reasonable to conclude that these species may simply have been adapted to living in a cold climate. When the world warmed up, the cold-adapted went extinct.

While this explanation is attractively simple, it has some problems. Most importantly, while we know from the fossil record that woolly mammoths lived in North America throughout at least the last 200,000 years, that period does not include only very cold intervals. In fact, around 125,000 years ago, Earth was as warm as or warmer than it is today. This was the peak of what we call the last interglacial period, which lasted from around 130,000 years ago until the beginning of the ice age around 80,000 years ago. Remains of mammoths, steppe bison, and wild horses are found in the fossil record of the last interglacial, indicating that they were able to survive despite the warmer climate. Their bones were, however, much less abundant during the interglacial than they were during the later, cold interval. According to the fossil record from the interglacial, a different community of animals dominated the warm Arctic from that which dominated when it was cold. The community of the interglacial period included giant sloths, camels, mastodons, and giant beavers: animals that were adapted to life in a warm climate.

If we look further back in time in the fossil record, a pattern begins to emerge. The Pleistocene epoch lasted from around 2.5 million years ago until around 12,000 years ago, when the Holocene epoch began. During the Pleistocene, our planet experienced at least twenty major shifts between cold, glacial intervals (ice ages) and warmer interglacial intervals. Average temperatures swung a whopping 5°–7°C with each climatic shift. Glaciers advanced or retreated, causing plants and animals to scramble (figuratively) to find suitable habitat. When the climate was cold, cold-adapted species were widespread. When it was warm, these cold-adapted species survived in isolated patches of refugial habitat, often at the edges of their former ranges. During the warm periods, warm-adapted species were widespread, and these warm-adapted species became restricted to warm refugia when it was cold. Range shifts were common during the Pleistocene, but extinctions were rare. And then, around 12,000 years ago, the climate swung from cold to warm, just as it had many times before. This time, however, cold-adapted fauna did not simply become less abundant. This time, many of them went extinct.

What was different about this most recent climate shift? The answer is not entirely clear. However, one potential explanation stands out: By the beginning of the Holocene, a new species had appeared on nearly every continent. This new species had a remarkably big brain and a capacity to transform its habitat to suit its needs, rather than seek habitats to which it was best adapted. This species was also alarmingly destructive. Wherever it went, its arrival seemed to coincide with the extinction of other, mostly large-bodied species. This species was, of course, humans.

Was it our fault that mammoths and other ice age animals went extinct? Interestingly, there is strong evidence that climate, and not humans, may have triggered the declines toward extinction. Humans and mammoths lived together in the arctic regions of Europe and Asia for many thousands of years during the last of the Pleistocene ice ages. The archaeological record shows that humans did hunt mammoths during this time, but since mammoths survived until much later, this hunting pressure was clearly not sufficient to drive mammoths to extinction. In North America, there is even clearer evidence that climate is to blame for diminishing mammoth populations. Humans did not arrive in North America until well after the populations of mammoths, steppe bison, and wild horses had already begun to decline toward extinction. Given this evidence, it is tempting to conclude that these extinctions were not our fault. After all, if we were not there, we could not have done it.

It is important, however, to understand the difference between declining populations and disappearing populations. Estimates of population size based on the fossil record or from genetic data can pinpoint when species began to decline from their ice age peaks but not when they actually went extinct. If we focus on disappearance rather than on decline, it is difficult to say with confidence that humans did not play a pivotal role in these extinctions. Populations of cold-adapted animals declined during every warm interval, not just during the most recent warm interval. In the past, however, these populations survived by finding and hiding out in refugial habitats, biding their time until the next cold period got under way. They probably did exactly that when the present warm interval began. This behavior, however, may have made them more vulnerable to extinction once humans were in the picture.

Ultimately, mammoths, steppe bison, and wild horses probably went extinct because of a combination of climate change, human hunting, and the disappearance of the steppe tundra. Rapid warming after the last ice age led to a decline in crucial habitat. Fewer herbivores trampling and consuming the vegetation meant that nutrients recycled more slowly, reducing the productivity of the ecosystem. To make matters worse, a new and intelligent predator appeared that was capable of zeroing in on any remaining ice-age habitat as ideal hunting grounds. Growing human populations and increasingly sophisticated human technologies further isolated these refugial populations from each other and from the resources they needed to survive. For some species, refugial populations may have held on well past the beginning of the Holocene. For example, our DNA work has shown that steppe bison survived in isolated patches in the far northern Rocky Mountains until as recently as one thousand years ago. As we learn more about the timing and pattern of these and other recent extinctions, there is little doubt that the role of humans will become increasingly clear.


THE SIXTH EXTINCTION

More than 3,700 years after the last mammoth died on Wrangel Island, we are witnessing an alarming number of contemporary extinctions, and the rate of extinction appears to be increasing. Some scientists have gone so far as to refer to the Holocene extinctions as the Sixth Extinction, suggesting that the crisis in the present day has the potential to be as destructive to Earth's biodiversity as the other five mass extinctions in our planet's history.

The word alone—extinction—frightens and intimidates us. But why should it? Extinction is part of life. It is the natural consequence of speciation and evolution. Species arise and then compete with each other for space and resources. Those that win survive. Those that lose go extinct. More than 99 percent of species that have ever lived are now extinct. Indeed, our own species' dominance is possible only because the extinction of the dinosaurs made space for mammals to diversify, and eventually we outcompeted the Neandertals.

I think people are scared of extinction for three reasons. First, we fear missed opportunities. A species that is lost is gone forever. What if that species harbored a cure for some terrible disease or was critically important in keeping our oceans clean? Once that species is gone, so is that opportunity. Second, we fear change. Extinction changes the world around us in ways that we both can and cannot anticipate. Every generation thinks of our version of the world as the authentic version of the world. Extinction makes it harder for us to recognize and feel grounded in the world we know. Third, we fear failure. We enjoy living in a rich and diverse world and feel an obligation, as the most powerful species that has ever lived on this planet, to protect this diversity from our own destructive tendencies. Yet we chop down forests and destroy habitats. We hunt and poach species even when we know they are perilously close to extinction. We build cities, highways, and dams and block migration routes between populations. We pollute the oceans, rivers, land, and air. We move around as fast as we can on airplanes, trains, and boats and introduce foreign species into previously undisturbed habitats. We fail to live up to our obligation to protect or even coexist with the other species with which we share this planet. And when we stop to think about it, it makes us feel terrible.

Extinction is much easier for us to swallow when it is clearly not our fault. Why did the mammoth go extinct? As humans, we want the answer to be something natural. Natural climate change, for example. We would prefer to learn that mammoths went extinct because they needed the grasslands of the steppe tundra to survive and that they simply starved to death as the steppe tundra disappeared after the last ice age. We would prefer not to learn that mammoths went extinct because our ancestors greedily harvested them for their meat, skins, and fur.

While some of us may not care about extinction as long as we are not personally affected, many of us find extinction unacceptable, particularly if it is our fault. Most contemporary extinctions are easy to ignore, as they have little influence on our day-to-day lives. The cumulative effect of these extinctions is, however, a future of very reduced biodiversity. This future could be one in which so many changes have occurred to the terrestrial and marine ecosystems that we, ourselves, are suddenly vulnerable to extinction. It doesn't get much more personal than that.


REVERSING EXTINCTION

It's not completely surprising that the idea of de-extinction—that we might be able to bring species that have gone extinct back to life—has attracted so much attention. If extinction is not forever, then it lets us off the hook. If we can bring species that we have driven to extinction back to life, then we can right our wrongs before it is too late. We can have a second chance, clean up our act, and restore a healthy and diverse future, before it is too late to save our own species.

While it is still not possible to bring extinct species back to life, science is making progress in this direction. In 2009, a team of Spanish and French scientists announced that a clone of an extinct Pyrenean ibex, also known as a bucardo, was born in 2003 to a mother who was a hybrid of a domestic goat and a different species of ibex. To clone the bucardo, the scientists used the same technology that had been used in 1996 to successfully clone Dolly the sheep. That technology requires living cells, so in April 1999, ten months before her death, scientists captured the last living bucardo and took a small amount of tissue from her ear. They used this tissue to create bucardo embryos. Only one of 208 embryos that were implanted into the surrogate mothers survived to be born. Unfortunately, the baby bucardo had major lung deformity and suffocated within minutes.

In 2013, Australian scientists announced that they successfully made embryos of an extinct frog—the Lazarus frog—by injecting nuclei from Lazarus frog cells that had been stored in a freezer for forty years into a donor cell from a different frog species. None of the Lazarus frog embryos survived for more than a few days, but genetic tests confirmed that these embryos did contain DNA from the extinct frog.

The Lazarus frog and bucardo projects are only two of the several de-extinction projects that are under way today. These two projects involve using frozen material that was collected prior to extinction and, consequently, are among the most promising of the existing de-extinction projects. Other de-extinction projects, including mammoth and passenger pigeon de-extinction, face more daunting challenges, of which finding well-preserved material is only one. These projects are proceeding nonetheless and, in the case of the mammoth, along several different trajectories. Akira Iritani of Japan's Kinki University is trying to clone a mammoth using frozen cells and claims that he will do so by 2016. George Church at Harvard University's Wyss Institute is working to bring the mammoth back by engineering mammoth genes into elephants. Sergey Zimov of the Russian Academy of Science's Northeast Science Station worries less about about how mammoths will be brought back than about what to do with them when it happens. He established Pleistocene Park near his home in Siberia and is preparing his park for the impending arrival of resurrected mammoths.


(Continues...)

Excerpted from How to Clone a Mammoth by Beth Shapiro. Copyright © 2015 Princeton University Press. Excerpted by permission of PRINCETON UNIVERSITY PRESS.
All rights reserved. No part of this excerpt may be reproduced or reprinted without permission in writing from the publisher.
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Table of Contents

Prologue ix

Chapter 1 Reversing Extinction 1

Chapter 2 Select a Species 17

Chapter 3 Find a Well-Preserved Specimen 51

Chapter 4 Create a Clone 73

Chapter 5 Breed Them Back 99

Chapter 6 Reconstruct the Genome 109

Chapter 7 Reconstruct Part of the Genome 125

Chapter 8 Now Create a Clone 141

Chapter 9 Make More of Them 159

Chapter 10 Set Them Free 175

Chapter 11 Should We? 189

Acknowledgments 209

Notes 211

Index 213

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