Neanderthal Man

by Pbo, Svante

  Advance praise for

  Neanderthal Man

  “It is a rare thing to read about an important development in science by its principal innovator, written in the spirit and style in which the research unfolded. Neanderthal Man is a dispatch from the front, and if you want to learn how real science is really done, I suggest you read it.”

  —EDWARD O. WILSON,

  University Research Professor, Emeritus, HarVARD UNIVERSITY

  “Problem by problem, solution by solution, Pääbo’s gripping account of the discovery of our relationship with Neanderthals brilliantly conveys the thrill and reality of today’s big science and the excitement of a major breakthrough.”

  —RICHARD WRANGHAM

  Professor of Biological Anthropology, Harvard University, and

  author of Catching Fire: How Cooking Made Us Human

  “Svante Pääbo’s Neanderthal Man is the incredible personal story of one man’s quest for our human origins using the latest genome sequence tools. Pääbo takes us through his exciting journey to first extract DNA from ancient bones then sequence it to give us the first real glance at our human ancestors, and ultimately shows that early humans and Neanderthals interbred to produce modern humans. This is science at its best and reinforces that contained in each of our genomes is the history of humanity.”

  —J. CRAIG VENTER,

  Chairman and President, J. Craig Venter Institute

  Copyright © 2014 by Svante Pääbo

  Published by Basic Books,

  A Member of the Perseus Books Group

  All rights reserved. No part of this book may be reproduced in any manner whatsoever without written permission except in the case of brief quotations embodied in critical articles and reviews. For information, address Basic Books, 250 West 57th Street, 15th Floor, New York, NY 10107-1307.

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  Designed by Jack Lenzo

  Library of Congress Cataloging-in-Publication Data

  Pääbo, Svante.

  Neanderthal man : in search of lost genomes / Svante Paabo.

  pages cm

  Includes bibliographical references and index.

  ISBN 978-0-465-08068-7 (e-book) 1. Neanderthals. 2. Human population genetics. 3. Genome analysis. I. Title.

  GN285.P33 2014

  569.9’86--dc23

  2013041877

  10 9 8 7 6 5 4 3 2 1

  To Linda, Rune, and Freja

  Contents

  _______________

  Advance praise for Neanderthal Man

  Copyright

  Dedication

  Contents

  Preface

  Chapter 1 Neanderthal ex Machina

  Chapter 2 Mummies and Molecules

  Chapter 3 Amplifying the Past

  Chapter 4 Dinosaurs in the Lab

  Chapter 5 Human Frustrations

  Chapter 6 A Croatian Connection

  Chapter 7 A New Home

  Chapter 8 Multiregional Controversies

  Chapter 9 Nuclear Tests

  Chapter 10 Going Nuclear

  Chapter 11 Starting the Genome Project

  Chapter 12 Hard Bones

  Chapter 13 The Devil in the Details

  Chapter 14 Mapping the Genome

  Chapter 15 From Bones to Genome

  Chapter 16 Gene Flow?

  Chapter 17 First Insights

  Chapter 18 Gene Flow!

  Chapter 19 The Replacement Crowd

  Chapter 20 Human Essence?

  Chapter 21 Publishing the Genome

  Chapter 22 A Very Unusual Finger

  Chapter 23 A Neanderthal Relative

  Postscript

  About the Author

  Index

  Preface

  _____________

  The idea to write this book was first suggested to me by John Brockman. Without his initiative and encouragement, I would never have taken the time to write a manuscript much longer than the short scientific articles I am used to authoring. Once I got started, however, I enjoyed the process. Thank you for making this happen!

  Many people have helped me by reading the text and suggesting improvements. First of all I thank my wife, Linda Vigilant, who in addition was always supportive of the endeavor, even if it meant me being away from the family. Sarah Lippincot, Carol Rowney, Christine Arden, and, above all, Tom Kelleher at Basic Books were excellent editors. I hope I have learned from them. Carl Hannestad, Kerstin Lexander, Viola Mittag, and others read parts or all of the text and gave helpful suggestions. Souken Danjo provided hospitality in Saikouji for some of the time I needed to withdraw from the world.

  I recount events as I remember them. But I suspect that I may have mixed up or conflated a few specifics here and there—for example, regarding various meetings in and trips to Berlin, to 454 Life Sciences, and so on. Obviously, too, I recount events from my own subjective perspective, trying to give credit (and its opposite) where in my opinion it is due. I am aware that this perspective is not the only way one can view such events. In order not to burden the text with too many names and details, I have refrained from mentioning many persons who were nevertheless important. I apologize to everyone who feels unduly ignored!

  Chapter 1

  Neanderthal ex Machina

  __________________________________

  Late one night in 1996, just as I had dozed off in bed, my phone rang. The caller was Matthias Krings, a graduate student in my laboratory at the Zoological Institute of the University of Munich. All he said was, “It’s not human.”

  “I’m coming,” I mumbled, threw on some clothes, and drove across town to the lab. That afternoon, Matthias had started our DNA sequencing machines, feeding them fragments of DNA he had extracted and amplified from a small piece of a Neanderthal arm bone held at the Rheinisches Landesmuseum in Bonn. Years of mostly disappointing results had taught me to keep my expectation low. In all probability, whatever we had extracted was bacterial or human DNA that had infiltrated the bone sometime in the 140 years since it had been unearthed. But on the phone, Matthias had sounded excited. Could he have retrieved genetic material from a Neanderthal? It seemed too much to hope for.

  In the lab, I found Matthias along with Ralf Schmitz, a young archaeologist who had helped us get permission to remove the small section of arm bone from the Neanderthal fossil stored in Bonn. They could hardly control their delight as they showed me the string of A’s, C’s, G’s, and T’s coming out of one of the sequencers. Neither they nor I had ever seen anything like it before.

  What to the uninitiated may seem a random sequence of four letters is in fact shorthand for the chemical structure of DNA, the genetic material stored in almost every cell in the body. The two strands of the famous double helix of DNA are made up of units containing the nucleotides adenine, thymine, guanine, and cytosine, abbreviated A, T, G, and C. The order in which these nucleotides occur makes up the genetic information necessary to form our body and support its functions. The particular piece of DNA we were looking at was part of the mitochondrial genome—mtDNA, for short—that is transmitted in the egg cells of all mothers to their children. Several hundred copies of it are stored in the mitochondria, tiny structures in the cells, and it specifies information necessary for these structures to fulfill their function of producing energy. Each of us carries only one type of mtDNA, which comprises a mere 0.0005 percent of our genome. Since we carry in each cell many thousands o
f copies of just the one type, it is particularly easy to study, unlike the rest of our DNA—a mere two copies of which are stored in the cell nucleus, one from our mother and one from our father. By 1996, mtDNA sequences had been studied in thousands of humans from around the world. These sequences would typically be compared to the first determined human mtDNA sequence, and this common reference sequence, in turn, could be used to compile a list of which differences were seen at which positions. What excited us was that the sequence we had determined from the Neanderthal bone contained changes that had not been seen in any of those thousands of humans. I could hardly believe that what we were looking at was real.

  As I always am when faced with an exciting or unexpected result, I was soon plagued by doubts. I looked for any possibility that what we saw could be wrong. Perhaps someone had used glue produced from cow hide to treat the bones at some point, and we were seeing mtDNA from a cow. No: we immediately checked cow mtDNA (which others had already sequenced) and found that it was very different. This new mtDNA sequence was clearly close to the human sequences, yet it was slightly different from all of them. I began to believe that this was, indeed, the first piece of DNA ever extracted and sequenced from an extinct form of human.

  We opened a bottle of champagne kept in a fridge in the lab’s coffee room. We knew that, if what we were seeing was really Neanderthal DNA, enormous possibilities had opened up. It might one day be possible to compare whole genes, or any specific gene, in Neanderthals to the corresponding genes in people alive today. As I walked back home through a dark and quiet Munich (I’d had too much champagne to drive), I could hardly believe what had happened. Back in bed, I couldn’t sleep. I kept thinking about Neanderthals, and about the specimen whose mtDNA it seemed we had just captured.

  In 1856, three years before the publication of Darwin’s The Origin of Species, workers clearing out a small cave in a quarry in Neander Valley, about seven miles east of Düsseldorf, uncovered the top of a skull and some bones they thought had come from a bear. But within a few years the remains were identified as those of an extinct, perhaps ancestral, form of human. This was the first time that such remains had been described, and the finding shook the world of naturalists. Over the years, research has continued on those bones and many more like them since found, seeking to discern who the Neanderthals were, how they lived, why they disappeared some 30,000 years ago, how our modern ancestors interacted with them over thousands of years of coexistence in Europe, and whether they were friend or foe, our forebears, or simply our long-lost cousins (see Figure 1.1). Tantalizing hints of behaviors familiar to us, such as care of the injured, ritualistic burial, and maybe even the production of music, emerged from archaeological sites, telling us that the Neanderthals were much more like us than is any living ape. How alike? Whether they could speak, whether they were a dead-end branch of the hominin family tree, or whether some of their genes are hidden in us today are all questions that have become an integral part of paleoanthropology, the academic discipline that can be said to have started with the discovery of those bones in Neander Valley, from which we now seemed able to extract genetic information.

  Figure 1.1. A reconstructed Neanderthal skeleton (left) and a present-day human skeleton (right). Credit: Ken Mowbray, Blaine Maley, Ian Tattersall, Gary Sawyer, American Museum of Natural History.

  As interesting as these questions were in themselves, it seemed to me that the Neanderthal bone fragment held the promise of an even larger prize. Neanderthals are the closest extinct relative of contemporary humans. If we could study their DNA, we would undoubtedly find that their genes were very similar to ours. Some years earlier, my group had sequenced a large number of DNA fragments from the chimpanzee genome and had shown that in DNA sequences we shared with the chimpanzees, only a bit over 1 percent of the nucleotides differed. Clearly, the Neanderthals must be much closer to us than that. But—and this is what was immensely exciting—among the few differences one would expect to find in the Neanderthal genome, there must be those that set us apart from all earlier forms of human forerunners: not just from the Neanderthals but also from Turkana Boy, who lived some 1.6 million years ago; Lucy, some 3.2 million years ago; and Peking Man, more than half a million years ago. Those few differences must form the biological foundations of the radically new direction our lineage took with the emergence of modern humans: the advent of rapidly developing technology, of art in a form we today immediately recognize as art, and maybe of language and culture as we now know it. If we could study Neanderthal DNA, all this would be within our grasp. Wrapped in such dreams (or delusions of grandeur), I finally drifted off to sleep as the sun rose.

  The next day Matthias and I both arrived late at the lab. After checking the DNA sequence from the night before to make sure we had not made any mistakes, we sat down and planned what to do next. It was one thing to get the sequence of one little piece of mtDNA that looked interesting from the Neanderthal fossil, but it would be quite another to convince ourselves, let alone the rest of the world, that it was mtDNA from an individual who lived (in this particular case) some 40,000 years ago. My own work over the previous twelve years made our next step fairly clear. First, we needed to repeat the experiment—not just the last step but all the steps, beginning with a new piece of the bone in order to show that the sequence we had obtained was not some fluke derived from a badly damaged and modified modern mtDNA molecule in the bone. Second, we needed to extend the sequence of mtDNA we had obtained by retrieving overlapping DNA fragments from the bone extract. This would enable us to reconstruct a longer mtDNA sequence, with which we could begin to estimate just how different the mtDNA of Neanderthals was from that of humans today. And then a third step was necessary. I myself had often suggested that extraordinary claims about DNA sequences from ancient bones require extraordinary evidence—namely, repetition of the results in another lab, an unusual step in a typically competitive scientific field. The claim that we had retrieved Neanderthal DNA would certainly be considered extraordinary. To exclude unknown sources of error in our lab, we needed to share some of the precious bone material with an independent lab and hope that it could manage to repeat our result. All of this I discussed with Matthias and Ralf. We laid out plans for the work and swore one another to absolute secrecy outside our research groups. We wanted no attention until we were sure that what we had was the real thing.

  Matthias got to work at once. Having spent almost three years on mostly fruitless attempts to extract DNA from Egyptian mummies, he was energized by the prospect of success. Ralf seemed frustrated over having to return to Bonn, where he could do nothing but eagerly await word of our results. I tried to concentrate on my other projects, but it was hard to take my mind off what Matthias was doing.

  What Matthias needed to do was not all that easy. We were dealing, after all, with something other than the intact and pristine DNA that comes from a blood sample drawn from a living person. The neat and tidy double-­stranded, helical DNA molecule in the textbooks—with its nucleotides A, T, G, and C, attached in complementary pairs (adenine with thymine, guanine with cytosine) to the two sugar-phosphate backbones—is not a static chemical structure when stored in the nuclei and mitochondria of our cells. Rather, DNA continually suffers chemical damage, which is recognized and repaired by intricate mechanisms. In addition, DNA molecules are extremely long. Each of the twenty-three pairs of chromosomes in the nucleus comprises one enormous DNA molecule; the total length of one set of twenty-three chromosomes adds up to about 3.2 billion nucleotide pairs. Since the nucleus has two copies of the genome (each copy stored on one set of twenty-three chromosomes, of which we inherit one from our mother and one from our father), it contains about 6.4 billion nucleotide pairs. By comparison, the mitochondrial DNA is tiny, with a little over 16,500 nucleotide pairs; but given that the mtDNA we had was ancient, the challenge involved in sequencing it was great.

  The most common type of damage that occurs spontaneously in DNA molecules, whether nuclea
r DNA or mtDNA, is the loss of a chemical component—an amino group—from the cytosine nucleotide (C), turning it into a nucleotide that does not naturally occur in DNA called uracil, abbreviated U. There are enzyme systems in the cells that remove these U’s and replace them with the correct nucleotide, C. The discarded U’s end up as cellular garbage, and from analyses of damaged nucleotides excreted in our urine it has been calculated that about ten thousand C’s per cell morph into U’s each day, only to be removed and then replaced. And this is just one of several types of chemical assaults our genome suffers. For example, nucleotides are lost, creating empty sites that quickly lead to breakage of the strands in the DNA molecules. Working against this are enzymes that fill in such missing nucleotides before a break can occur. If a break does occur, other enzymes join the DNA molecules back together. In fact, the genomes in our cells would not remain intact for even an hour if these repair systems were not there to maintain them.

  These repair systems, of course, require energy to work. When we die, we stop breathing; the cells in our body then run out of oxygen, and as a consequence their energy runs out. This stops the repair of DNA, and various sorts of damage rapidly accumulate. In addition to the spontaneous chemical damage that continually occurs in living cells, there are forms of damage that occur after death, once the cells start to decompose. One of the crucial functions of living cells is to maintain compartments where enzymes and other substances are kept separate from one another. Some of these compartments contain enzymes that can cut DNA strands and are necessary for certain types of repair. Other compartments contain enzymes that break down DNA from various microorganisms that the cell may encounter and engulf. Once an organism dies and runs out of energy, the compartment membranes deteriorate, and these enzymes leak out and begin degrading DNA in an uncontrolled way. Within hours and sometimes days after death, the DNA strands in our body are cut into smaller and smaller pieces, while various other forms of damage accumulate. At the same time, bacteria that live in our intestines and lungs start growing uncontrollably when our body fails to maintain the barriers that normally contain them. Together these processes will eventually dissolve the genetic information stored in our DNA—the information that once allowed our body to form, be maintained, and function. When that process is complete, the last trace of our biological uniqueness is gone. In a sense, our physical death is then complete.