by Pbo, Svante
Postscript
__________________
Three years later, as I write this, we still do not know what happened to the other part of the finger bone that Anatoly sent to Berkeley. Perhaps one day it can be used for dating so that we will know when the Denisova girl lived.
Anatoly and his team have continued to unearth amazing bones in Denisova Cave. They have found another huge molar that contains Denisovan DNA. They have also found a toe bone that turned out to come from a Neanderthal.
David Reich and his postdoc Sriram Sankararaman have used genetic models to date the admixture between Neanderthals and modern humans to sometime between 40,000 and 90,000 years ago.{65} This shows that actual interbreeding between Neanderthals and modern humans has caused the extra similarity between the Neanderthal genome and the genomes of people in Europe and Asia, not the more complicated scenario of ancient substructure in Africa that we also considered in 2010.
Matthias Meyer, something of a technical wizard in our lab, has developed new and amazingly sensitive methods to extract DNA and make libraries. This has allowed us to use the tiny leftover fragments of the Denisova finger bone to sequence its genome to a total coverage of 30-fold.{66} Recently, we have followed up by sequencing the Neanderthal genome from the toe bone found in Denisova Cave to 50-fold coverage. These ancient genomes are now of higher accuracy than most genomes determined from people living today.
When we compare the Neanderthal genome to the genome of the Denisovan girl, we see that she carried a component in her genome from a hominin that diverged from the human lineage earlier than Neanderthals and Denisovans. We also see that Denisovans mixed with Neanderthals, and that they contributed small amounts of DNA not only to people in Melanesia but also to people who live on mainland Asia today. These were subtle signals of past mixing that we could not see in 2010, when we worked with genomes of lower quality. The picture that emerges is that there was plenty of mixing among several types of humans in the late Pleistocene, but mostly of small proportions.
Together with new data from the 1,000 Genomes Project, these two archaic genomes of high quality now allow us to create a near-complete catalog of sites in the genome where all people today are different from Neanderthals and Denisovans as well as from the apes. This catalog contains 31,389 single nucleotide changes and 125 insertions and deletions of a few nucleotides. Of these, 96 change amino acids in proteins, and perhaps 3,000 affect sequences that regulate how genes are turned on and off. There are surely some nucleotide differences, particularly in repetitive parts of the genome, that we have missed, but it is clear that the genetic “recipe” for making a modern human is not very long. The next big challenge is to find out what the consequences of these changes are.
George Church, a brilliant technical innovator at Harvard University, has suggested that scientists should use our catalog to modify a human cell back to the ancestral state and then use that cell to recreate or “clone” a Neanderthal. In fact, already when we announced that we had completed the Neanderthal genome sequencing at the AAAS meeting in 2009, George was quoted by the New York Times as saying that “a Neanderthal could be brought to life with present technology for about $30 million.” He added that if someone were eager to supply the financing, he “might go along with it.” To his credit, he acknowledged that there are ethical problems with such a project, but suggested that to avoid those, one could use not a human cell but a chimpanzee cell!
This, as well as later statements to the same effect, I write off as George’s tendency to be provocative. Nevertheless, they point to a dilemma. How do we study traits specific to humans—for example, language or aspects of intelligence—when for both technical and ethical reasons we cannot do what George suggests? The way forward is, on the one hand, the introduction of human and Neanderthal genetic variants into the genomes of human and apes cells that can then be used not to clone individuals but to study their physiology in a plastic dish in the laboratory and, on the other hand, the introduction of such variants into laboratory mice. Our laboratory in Leipzig has already taken the first steps in that direction. In 2002, we found that the protein made from a gene called FOXP2, which Tony Monaco’s group in Oxford, England, had shown to be involved in language ability in humans, differed at two amino-acid positions from the same protein in apes and almost all other mammals.{67} Encouraged by the fact that the mouse FOXP2 protein is very similar to the FOXP2 protein of the chimpanzee, we decided to introduce the two human changes into the mouse genome. It took several years of hard work by a talented student, then postdoc, then group leader in our lab, Wolfgang Enard, until the first mice that made the human version of the FOXP2 protein were born. The results greatly exceeded my expectations. The peeps the pups produced at about two weeks of age when removed from the nest differed subtly but significantly from those of their non-humanized littermates, supporting the idea that these changes have something to do with vocal communication. This finding has led to much more work showing that the two changes affect how neurons extend outgrowths to contact other neurons and how they process signals in parts of the brain that have to do with motor learning.{68} At the moment, we are collaborating with George Church to put these changes into human cells that can be differentiated to neurons in the test tube.
Although the two changes in FOXP2 are actually shared with Neanderthals and Denisovans, {69} these experiments nevertheless point to how, in the future, we may sort out which changes are crucial for what makes modern humans special. One can imagine putting such changes into cell lines, and into mice, alone and in different combinations, in order to “humanize” and “neanderthalize” biochemical pathways or intracellular structures, and then to study their effects. One day, we may then be able to understand what set the replacement crowd apart from their archaic contemporaries, and why, of all the primates, modern humans spread to all corners of the world and reshaped, both intentionally and unintentionally, the environment on a global scale. I am convinced that parts of the answers to this question, perhaps the greatest one in human history, lies hidden in the ancient genomes we have sequenced.
About the Author
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Svante Pääbo is the director of the Department of Genetics at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. He has been featured in the New York Times, Newsweek, National Geographic, and The Economist, as well as on NPR, PBS, and the BBC. In 2009, Time named him one of the 100 Most Influential People in the World. Pääbo lives in Leipzig.
Index
________________
Academy of Achievement, 163
Adenovirus, 24
Africa
Denisovan data, 244–245
gene flow through, 192
impact of Neanderthal DNA findings, 222–223
replacement crowd, 198–200
See also Out-of-Africa hypothesis
Africans, modern
exchanges with Europeans, 187–188
mapping the Neanderthal genome, 155
MHC gene variability, 224
mtDNA comparisons with ancient DNA, 12
Neanderthal nucleotide matches, 183
San genome, 185–188
SNPs as indication of interbreeding, 173–177
AIDS, 36
Akademgorodok, Siberia, 232–236
Allelic surfing, 194, 199
Almas (snow men), 235
Alu elements, 33–34
Amber, DNA preservation in, 57–58, 61, 105
American Association for the Advancement of Science (AAAS), 165–166, 176, 224–225
American Museum of Natural
History, 57–58
Amino group loss, 5–8, 113
Amino-acid preservation, 78
Amplification of DNA
limitations of ancient samples, 46
Native American remains, 71
Oetzi, the Ice Man, 69–70
PCR process, 8–12
PCR process on mummy a
nd
thylacine samples, 39–40
Anasazi, 131
Ancestors. See Common ancestors
Ancestral allele, 156–158, 181, 243
Ancestry testing, 202–203
Animal droppings, DNA in, 56, 105–107
Antediluvian DNA, 58–59
Apes, 89–90
cognitive development, 85–86, 205–207
comparing Neanderthal, modern human and ape genomes, 182
genome analysis of modern humans and, 219
nuclear DNA variation, 92
See also Chimpanzees; Gorillas
Asia
ancient Native American DNA sequences, 44
Middle East origins scenario, 189
replacement crowd, 199
Asians, modern
comparing, Neanderthal, African, and Chinese genomes, 177
Denisovans’ contribution to the Asian genome, 245, 247, 251–252
mapping Neanderthal gene flow, 194–195
MHC gene variability, 224
mtDNA comparisons with ancient DNA, 12
multiregional model of human origins, 20–21
reaction to Neanderthal DNA findings, 222–223
Aurignacian culture, 198
Autrum, Hansjochem, 50
Bacteria, mtDNA in, 59
Bacterial cloning, 25, 109–111, 114–115, 121–122, 128
Bacterial DNA, 57, 146–151, 153
Behaviors and rituals, 3
Bentley, David, 161–162
Bergström, Sune, 184
Berlin-Brandenburg Academy of
Sciences and Humanities, 134–135, 138
Blank extract, 51, 54
Bodmer, Walter, 82
Boesch, Christophe, 83–84, 89–90
Bonobos, 94, 212
Bougainville, 245–247
Brajković, Dejana, 130, 132
Brain size, 219
Briggs, Adrian, 147(fig.), 171, 228, 239–242
AAAS conference, 166
background, 114–115
comparing Denisova and modern genomes, 246
454 process, 117, 119
increasing Neanderthal DNA proportions, 148
increasing sequencing efficiency, 122
Brigham Young University, Utah, 58–60
Broad Institute, 164–165, 171
Bronze Age humans, 52, 76
Burbano, Hernan, 147(fig.)
Bustamante, Carlos, 249
California Polytechnic State
University, 58
Cannibalism, 131–132
Cano, Raul, 58
Carmel mountains, Israel, 197
Cartilage, DNA remains in, 30, 30(fig.), 54–55
Cavalli-Sforza, Luca, 93
Cave-bear bones, 76–78, 97, 99–101, 103–104, 109–113
Cell journal, 18–21, 79, 165
Cetus Corporation, 40–41
Chimpanzees, 89–90, 183
ancestral and derived alleles, 176
cognitive development, 207
common ancestor of humans and, 93(fig.), 169
comparing human genome and chimpanzee genome, 4
comparing Neanderthal, modern human and ape genomes, 182
competition for reproduction,
212
genetic variation, 79, 93–94
reconstructing the ancestral
genome, 169
reference for Neanderthal genome mapping, 155–156
See also Apes; Gorillas
Chinese genome
comparing, Neanderthal, African, and Chinese genomes, 177
Denisovan SNPs, 244
mapping gene flow, 194–195
Neanderthal nucleotide matches, 183
sequencing modern genomes, 185–186, 189
Chromosome 17 inversion, 166–167
Church, George, 252–253
Clean room procedures, 52–57, 87–88, 87(fig.)
Clegg, J.B., 55
Cloning
bacterial cloning, 25, 109–111, 114–115, 121–122, 128
bringing a Neanderthal to life, 252
Cetus Corporation processes, 40
Croatian Neanderthal samples, 78–79
independent verification, 14–18
mammoth remains, 101–103
mummy DNA, 32–35
Native American remains, 71
Oetzi, the Ice Man, 69–70
PCR process, 8–12
quagga DNA, 34, 40–41
reconstruction of Neanderthal mtDNA, 11(fig.)
thylacine data, 44–45
transplantation antigens, 24
See also Polymerase chain reaction
Cognitive development, 205–207
Cold Spring Harbor Laboratory, 37–38, 43–44, 116, 120, 219
Common ancestors
Denisova mtDNA data, 229
Denisovans and Neanderthals, 243–244, 247–248
fossil data, 95
humans and chimpanzees, 169–171, 182
humans and great apes, 93(fig.),
94
Mitochondrial Eve, 13(fig.), 14–15, 88
modern humans and Neanderthals, 72–73, 78, 91
separation of humans and chimpanzees, 169–171
sloths, 66–67
using the chimpanzee as reference for Neanderthal genome mapping, 155–156
Wilson’s research, 41
Comrie, Bernard, 83–84
Consensus nucleotide, 10
Conservation genetics, 56
Contamination
as obstacle to Neanderthal genome mapping, 155–156
bacterial cloning versus 454 process, 150–151
clean room procedures, 52–57, 87–88, 87(fig.)
collecting El Sidrón bones, 137
Denisova Cave remains, 230–231, 239
importance of eliminating, 15–17, 50–51
inconsistencies with human reference genome, 124–127
isolating experiments and samples, 52–56
isolating nuclear DNA in cave bears and mammoths, 112–113
mapping the Neanderthal genome, 156–158
mechanisms of, 64–65
multiregional theory, 95–97
mummy samples, 51–52
Contamination (continued)
Native American remains, 44, 67–68
nuclear DNA extraction from mammoths, 101
nuclear genome of the Neanderthal, 160
Oetzi, the Ice Man, 69–71
PCR process, 8–12
putative dinosaur DNA, 59–60
sex chromosome data, 179–181
Convergent evolution, 45, 64–66
Coop, Graham, 124, 155
Copper Age remains, 68–71
Coprolites. See Animal droppings, DNA in
Creationism, 221
Criteria of authenticity, 51–52
Croatian Academy of Sciences and Arts, 77, 130, 132–135, 138, 139(fig.), 179
Dabney, Jesse, 147(fig.)
Darwin, Charles, 63
Das Altertum journal, 32
David, Charles, 47, 50
Deamination (of nucleotides), 7,
154
Denisova Cave remains
comparing Denisova and modern genomes, 244–245
comparing Denisova and Neanderthal genomes, 233, 243–244
comparing Neanderthal mtDNA sequences with Denisova sequences, 228–231
publishing the findings, 235–236, 245–249
sequencing the nuclear genome, 238–242
tooth, 235, 236(fig.)
Derevianko, Anatoly, 227–228, 228(fig.), 231–233, 235, 238–239, 242(fig.), 244, 250
Derived allele, 156–158, 176, 181,
243
Diamond, Jared, 43
Dinosaur, DNA extraction from, 58–60, 111
DNA amplification. See Amplification of DNA
DNA extraction
cannibalized remains, 132
Denisovan girl, 251
Egyptian mummies, 27–32
> improving efficiency, 143–151
initial studies of ancient materials, 26–27
silica extraction method, 55
Solexa technique, 161
Vindija bone samples, 139–141
See also Polymerase chain reaction
DNA sequencing
chimpanzee genome, 4
Denisova Cave remains, 236–237
determining human origins, 41–43
humans and apes, 94
information derived from, 25
initial results, 1
kangaroo rats, 42–43
mapping convergent evolution, 66
Neanderthal genome mapping project, 118, 122–123
preserved Native American skeletons, 43–44
pyrosequencing, 107–108, 111–115
Sanger method, 107–108, 110
technical intricacies of DNA retrieval, 45–46
Egg cells, 19–20
Egholm, Michael, 111, 114, 118–119, 122–124, 146, 149, 160–161, 163
Egyptology, 23–25
El Sidrón, Spain, 136–137
Elephants, nuclear DNA extraction from, 101–103
Enard, Wolfgang, 253
Endangered species, 56
Enhancers, 38
Errors in mapping, 154
Eskimo remains, 215
Ethical concerns, 252–253
European Bioinformatics Institute, Cambridge, England, 218
European Molecular Biology Organization, 135
Europeans, modern
Africans’ exchanges with, 187–188
comparing Neanderthal data with modern genome, 181
determining Neanderthals’ contribution to the modern genome, 171–173
genetic variation, 92–93
human reference genome and present-day human genome, 185–188
mapping gene flow, 192–195
mapping modern genomes, 188
mapping the Neanderthal genome, 155
MHC gene variability, 224
mtDNA comparisons with ancient DNA, 12
multiregional model of human origins, 20–21
Neanderthal mtDNA in, 96–97
out-of-Africa model of human origins, 19
reaction to Neanderthal DNA findings, 222–223
replacement crowd, 199
SNPs as indication of interbreeding, 173–177
studying modern and ancient Egyptians, 25–26
See also Africans, modern; Asians, modern; Modern humans
Evans, Tom, 148
Evolutionary anthropology, 83–84
