by Pbo, Svante
Racism, 202
Radioactive phosphorus, 144–146
Radovčić, Jakov, 130, 132–135, 137–138
Rasilla, Marco de la, 136–137
“Reasons to Believe” ministry, 221
Recombination, 186
Reich, David, 173, 182, 242(fig.)
background, 170
comparing Neanderthal, African, and Chinese genomes, 177
comparing Neanderthal, African, and European genomes, 174–176
Denisova Cave remains, 241, 246–247
evidence of Neanderthal-modern human gene flow, 190, 192–193, 251
mapping modern genomes, 187
Newcomb Cleveland Prize, 224–225
publishing the findings, 217–218
Repetitive DNA sequences, 118
Replacement crowd, 213, 253
leaky replacement, 248
magnitude of Neanderthal contribution to, 201–202
MHC gene variability, 224
movement and technological development, 208
origins and movement, 198–199
Reproduction. See Interbreeding; Offspring; Sexual reproduction
Restriction enzymes, 149
Ribosomal RNA gene, 101–102, 104
RNA splicing, 112
Rogers, Jane, 161–162
Rosas, Antonio, 137
Ross, Hugh, 221
Rothberg, Jonathan, 109, 111–112, 117–120, 122, 161
Rubin, Edward M., 124, 184, 216
contamination of data, 126–127, 150, 155
Denisova Cave remains, 233–234, 239, 241
ending the collaboration, 128
friction with, 113–115
Neanderthal bacterial library, 121–122
preliminary results, 116
pyrosequencing, 109–111
Rudan, Pavao, 133–135, 138, 139(fig.)
San genome, 185, 188, 242–243
Sanger, Fred, 107
Sanger Institute, 161–162
Sanger sequencing method, 107–108, 110
Sarich, Vincent, 95
Schaffner, Walter, 36, 38
Schmitz, Ralf, 1, 17–18, 73, 123–124, 135–136
Science magazine, 18, 21, 115
Denisova Cave findings, 236
dinosaur DNA, 59–60
DNA from animal droppings, 105
MHC gene variability, 224
Neanderthal genome paper, 164–165, 216–218
Oetzi the Ice Man, 70
out-of-Africa model, 94
plant DNA, 56
potential contamination of data set, 150
pyrosequencing, 110
Rubin’s cloning paper, 122
Second-generation sequencing, 108
Serre, David, 95–97, 114
Sex chromosomes, 179–181, 243
Sexual orientation, 36–37, 88–89
Sexual reproduction
biological obstacles to, 172–173
chromosome genealogy, 185–186
comparing Neanderthal and modern human genomes, 182–183
Denisovans, 248
determining human origins, 42
genome analysis of modern humans and apes, 219
mtDNA contribution to modern humans, 96
social dominance patterns, 19
sperm motility, 211–212
See also Interbreeding
Shunkov, Michael, 232–233, 250
Side fractions, 144–146
Silica extraction method, 55
Simons, Kai, 85
Single nucleotide polymorphism (SNP), 102–103, 173–177, 183, 187, 191, 243–244
Single-copy genes, 103–104, 118
Skin, genetic changes in, 212–213
Slatkin, Montgomery “Monty,” 154, 191, 242(fig.)
background, 171
comparing Denisova and modern genomes, 245
Denisova Cave remains, 241
Denisovan genome findings, 247
evidence of Neanderthal-modern human gene flow, 195
Sloths, 63–65, 65(fig.), 66–67, 105
Social development, 206–207
Soft tissue samples, 67
Solexa company, 161–162
Sperm cells, 19–20, 60
Sperm motility, 211–212
Staatlische Museen zu Berlin, 28–29, 38–39
Stasi (East German secret police), 39
Stenzel, Udo, 147(fig.), 162, 169
AAAS conference, 165–166
comparing Denisova and Neanderthal genomes, 243–244
Denisova Cave remains, 241–242
evidence of Neanderthal-modern human gene flow, 166
mapping DNA, 153–155, 181, 208
patent controversy, 202–203
Stetter, Karl, 46
Stock, Günter, 134
Stone, Anne, 15–18
Stoneking, Mark, 15–17, 19, 88–91, 247
Stringer, Chris, 20, 190
Super-old DNAs, 57–58
Sykes, Bryan, 70
Taxonomy, 49, 237
Technology, changes over millennia, 208
Termite data, 57–58
Theory of mind, 205–206
Thomas, Kelley, 42
Thomas, Richard, 44
Thylacinus cynocephalus, 38–40, 44–45, 64, 66
Tomasello, Mike, 83–85, 205–206
Tool culture, 197–198, 250
Translocated human mtDNA, 60
Transplantation antigens, 24, 51, 223–224
Tree sloths, 63–65, 65(fig.), 66
Tribal groups, genetic diversity in,
44
Trinkaus, Erik, 95, 97, 190, 220–221
Turkana Boy, 4
23andMe, 203
UC Irvine, 56–57
Uhlén, Mathias, 107–109
Uracil, 5–6
Venter, Craig, 111, 118, 192–193
Verna, Christine, 138
Vigilant, Linda, 41, 88–91, 163–164, 201
Villablanca, Francis, 42
Vindija Cave and remains, 77(fig.), 175
cannibalized remains, 131–132, 131(fig.)
cave-bear and human bones, 76–77, 99–101
contamination of cave-bear DNA, 97
evidence of Neanderthal-modern human gene flow, 194
increasing the proportion of Neanderthal DNA, 146–151
Mezmaiskaya Cave Neanderthal remains, 79
obstacles to accessing the specimens, 129–130, 132–133, 137
Viola, Bence, 231, 233, 235, 240–241
Vjesnik newspaper, 138
von Willebrand factor gene (vWF), 102, 106
Wall, Jeffrey, 150, 155–156, 160
Ward, Ryk, 44, 71
Weapons, 198
White, Tim, 130–131
Wild, Barbara, 36–37
Willerslev, Eske, 215, 239
Wilson, Allan, 13–15, 19–20, 34–35, 37–38, 40–41, 51, 88, 94–95, 188
Wired magazine, 128
Wolpoff, Milford, 21, 190, 220
Woodward, Scott, 58–60
World Congress of Genetics (Berlin), 164
World War II, 49, 81–83
X chromosome data, 99, 179–181, 243
X-Woman Consortium, 241–243, 245–246
Y chromosome data, 179–181, 243
Yeast, 58
Yoruba, 188
Young-earth creationists, 221
Zahn, Laura, 165, 224–225
Zhai, Weiwei, 191
Zischler, Hans, 59
Zoology, 49–50
{1} R. L. Cann, Mark Stoneking, and Allan C. Wilson, “Mitochondrial DNA and human evolution,” Nature 325, 31–36 (1987).
{2} M. Krings et al., “Neandertal DNA sequences and the origin of modern humans,” Cell 90, 19–30 (1997).
{3} S. Pääbo, Über den Nachweis von DNA in altägyptischen Mumien,” Das Altertum 30, 213–218 (1984).
{4} S. Pääbo, “Preservation of DNA in ancient Egyptian mummies,” Journal of Archaeological Sciences 12, 411–417 (1985).
/>
{5} S. Pääbo, “Molecular cloning of ancient Egyptian mummy DNA,” Nature 314, 644–645 (1985).
{6} S. Pääbo and A. C. Wilson, “Polymerase chain reaction reveals cloning artefacts,” Nature 334, 387–388 (1988).
{7} R. L. Cann, Mark Stoneking, and A. C. Wilson, “Mitochondrial DNA and human evolution,” Nature 325, 31–36 (1987).
{8} W. K. Thomas, S. Pääbo, and F. X. Villablanca, “Spatial and temporal continuity of kangaroo-rat populations shown by sequencing mitochondrial-DNA from museum specimens,” Journal of Molecular Evolution 31, 101–112 (1990).
{9} J. M. Diamond, “Old dead rats are valuable,” Nature 347, 334–335 (1990).
{10} S. Pääbo, J. A. Gifford, and A. C. Wilson, “Mitochondrial-DNA sequences from a 7,000-year-old brain,” Nucleic Acids Research 16, 9775–9787 (1988).
{11} R. H. Thomas et al., “DNA phylogeny of the extinct marsupial wolf,” Nature 340, 465–467 (1989).
{12} S. Pääbo, “Ancient DNA—Extraction, characterization, molecular-cloning, and enzymatic amplification,” Proceedings of the National Academy of Sciences USA 86, 1939–1943 (1989).
{13} S. Pääbo, R. G. Higuchi, and A. C. Wilson, “Ancient DNA and the polymerase chain reaction,” Journal of Biological Chemistry 264, 9709–9712 (1989).
{14} G. Del Pozzo and J. Guardiola, “Mummy DNA fragment identified,” Nature 339, 431–432 (1989).
{15} S. Pääbo, R. G. Higuchi, and A. C. Wilson, “Ancient DNA and the polymerase chain reaction,” Journal of Biological Chemistry 264, 9709–9712 (1989).
{16} T. Lindahl, “Recovery of antediluvian DNA,” Nature 365, 700 (1993).
{17} E. Hagelberg and J. B. Clegg, “Isolation and characterization of DNA from archaeological bone,” Proceedings of the Royal Society B 244:1309, 45–50 (1991).
{18} M. Höss and S. Pääbo, “DNA extraction from Pleistocene bones by a silica-based purification method,” Nucleic Acids Research 21:16, 3913–3914 (1993).
{19} M. Höss and S. Pääbo, “Mammoth DNA sequences,” Nature 370, 333 (1994); Erika Hagelberg et al., “DNA from ancient mammoth bones,” Nature 370, 333–334 (1994).
{20} M. Höss et al., “Excrement analysis by PCR,” Nature 359, 199 (1992).
{21} E. M. Golenberg et al., “Chloroplast DNA sequence from a Miocene Magnolia species,” Nature 344, 656–658 (1990).
{22} S. Pääbo and A. C. Wilson, “Miocene DNA sequences—a dream come true?” Current Biology 1, 45–46 (1991).
{23} A. Sidow et al., “Bacterial DNA in Clarkia fossils,” Philosophical Transactions of the Royal Society B 333, 429–433 (1991).
{24} R. DeSalle et al., “DNA sequences from a fossil termite in Oligo-Miocene amber and their phylogenetic implications,” Science 257, 1933–1936 (1992).
{25} R. J. Cano et al., “Enzymatic amplification and nucleotide sequencing of DNA from 120–135-million-year-old weevil,” Nature 363, 536–538 (1993).
{26} H. N. Poinar et al., “DNA from an extinct plant,” Nature 363, 677 (1993).
{27} T. Lindahl, “Instability and decay of the primary structure of DNA,” Nature 362, 709–715 (1993).
{28} S. R. Woodward, N. J. Weyand, and M. Bunnell, “DNA sequence from Cretaceous Period bone fragments,” Science 266, 1229–1232 (1994).
{29} H. Zischler et al., “Detecting dinosaur DNA,” Science 268, 1192–1193 (1995).
{30} H. Prichard, Through the Heart of Patagonia (New York: D. Appleton and Company, 1902).
{31} M. Höss et al., “Molecular phylogeny of the extinct ground sloth Mylodon darwinii,” Proceedings of the National Academy of Sciences USA 93, 181–185 (1996).
{32} O. Handt et al., “Molecular genetic analyses of the Tyrolean Ice Man,” Science 264, 1775–1778 (1994).
{33} O. Handt et al., “The retrieval of ancient human DNA sequences,” American Journal of Human Genetics 59:2, 368–376 (1996).
{34} In fact, even at this writing, several groups are using the PCR to study mtDNA from human archaeological remains without describing clearly how they distinguish contaminating DNA sequences from endogenous ones. Some of the sequences they determine are almost certainly correct, but others are almost equally certainly incorrect.
{35} I. V. Ovchinnikov et al., “Molecular analysis of Neanderthal DNA from the northern Caucasus,” Nature 404, 490–493 (2000).
{36} M. Krings et al., “A view of Neandertal genetic diversity,” Nature Genetics 26, 144–146 (2000).
{37} H. Kaessmann et al., “DNA sequence variation in a non-coding region of low recombination on the human X chromosome,” Nature Genetics 22, 78–81 (1999); H. Kaessmann, V. Wiebe, and S. Pääbo, “Extensive nuclear DNA sequence diversity among chimpanzees,” Science 286, 1159–1162 (1999); H. Kaessmann et al., “Great ape DNA sequences reveal a reduced diversity and an expansion in humans,” Nature Genetics 27, 155–156 (2001).
{38} D. Serre et al., “No evidence of Neandertal mtDNA contribution to early modern humans,” PLoS Biology 2, 313–217 (2004).
{39} M. Currat and L. Excoffier, “Modern humans did not admix with Neandertals during their range expansion into Europe,” PLoS Biology 2, 2264–2274 (2004).
{40} A. D. Greenwood et al., “Nuclear DNA sequences from Late Pleistocene megafauna,” Molecular Biology and Evolution 16, 1466–1473 (1999).
{41} H. N. Poinar et al., “Molecular coproscopy: Dung and diet of the extinct ground sloth Nothrotheriops shastensis,” Science 281, 402–406 (1998).
{42} S. Vasan et al., “An agent cleaving glucose-derived protein cross-links in vitro and in vivo,” Nature 382, 275–278 (1996).
{43} H. Poinar et al., “Nuclear gene sequences from a Late Pleistocene sloth coprolite,” Current Biology 13, 1150–1152 (2003).
{44} J. P. Noonan et al., “Genomic sequencing of Pleistocene cave bears,” Science 309, 597–600 (2005).
{45} M. Stiller et al., “Patterns of nucleotide misincorporations during enzymatic amplification and direct large-scale sequencing of ancient DNA,” Proceedings of the National Academy of Sciences USA 103, 13578–13584 (2006).
{46} H. Poinar et al., “Metagenomics to paleogenomics: Large-scale sequencing of mammoth DNA,” Science 311, 392–394 (2006).
{47} See note 5 above.
{48} J. P. Noonan et al., “Sequencing and analysis of Neandertal genomic DNA,” Science 314, 1113–1118 (2006); R. E. Green et al., “Analysis of one million base pairs of Neanderthal DNA,” Nature 444, 330–336 (2006).
{49} After our Nature publication, we learned that it should more appropriately be called Vi-33.16, according to a more recent numbering system.
{50} R. W. Schmitz et al., “The Neandertal type site revisited: Interdisciplinary investigations of skeletal remains from the Neander Valley, Germany,” Proceedings of the National Academy of Sciences USA 99, 13342–13347 (2002).
{51} A. W. Briggs et al., “Patterns of damage in genomic DNA sequences from a Neandertal,” Proceedings of the National Academy of Sciences USA 104, 14616–14621 (2007).
{52} T. Maricic and Svante Pääbo, “Optimization of 454 sequencing library preparation from small amounts of DNA permits sequence determination of both DNA strands,” BioTechniques 46, 5157 (2009).
{53} J. D. Wall and Sung K. Kim, “Inconsistencies in Neandertal genomic DNA sequences,” PLoS Genetics 10:175 (2007).
{54} A. W. Briggs et al., “Patterns of damage in genomic DNA sequences from a Neandertal,” Proceedings of the National Academy of Sciences USA 104, 14616–14621 (2007).
{55} R. E. Green et al., “The Neandertal genome and ancient DNA authenticity,” EMBO Journal 28, 2494–2503 (2009).
{56} R. E. Green et al., “A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing,” Cell 134, 416–426 (2008).
{57} N. Patterson et al., “Genetic evidence for complex speciation of humans and chimpanzees,” Nature 441, 1103–1108 (2006).
{58} M. Tomasello, Origins of Human Communication (Cambridge, MA: MIT Press).
{59}
R. E. Green et al., “A draft sequence of the Neandertal genome,” Science 328, 710–722 (2010).
{60} My translation.
{61} L. Abi-Rached et al., “The shaping of modern human immune systems by multiregional admixture with archaic humans,” Science 334, 89–94 (2011).
{62} J. Krause et al., “Neanderthals in central Asia and Siberia,” Nature 449, 902–904 (2007).
{63} J. Krause et al., “The complete mtDNA of an unknown hominin from Southern Siberia,” Nature 464, 894–897 (2010).
{64} D. Reich et al., “Genetic history of an archaic hominin group from Denisova Cave in Siberia,” Nature 468, 1053–1060 (2010).
{65} S. Sankararaman et al., “The date of interbreeding between Neandertals and modern humans,” PLoS Genetics 8:1002947 (2012).
{66} M. Meyer, “A high coverage genome sequence from an archaic Denisovan individual,” Science 338, 222–226 (2012).
{67} W. Enard, et al., “Molecular evolution of FOXP2, a gene involved in speech and language,” Nature 418, 869–872 (2002).
{68} W. Enard et al. “A humanized version of Foxp2 affects cortico-basal ganglia circuits in mice,” Cell 137, 961–971 (2009).
{69} J. Krause et al., “The derived FOXP2 variant of modern humans was shared with Neandertals,” Current Biology 17, 1908–1912 (2007).
