by Pbo, Svante
Evolutionary biology, 42–43, 63–65
Evolutionary models. See Multiregional hypothesis of human origins; Out-of-Africa hypothesis
Excoffier, Laurent, 98, 193–194, 199
Extinct mammals, 9–10, 52
clean room procedures, 87–88
DNA extraction from bone samples, 55
ground sloth, 63–67
See also Cave-bear bones; Mammoth remains; Quagga DNA; Thylacinus cynocephalus
Fluorescence in mummies, 27–28, 30, 105–106
Forensic science, 67
454 Life Sciences, 109, 111–114, 116–120, 122–124, 126–127, 134–135, 140, 144, 153, 159–163
FOXP2 gene, 252–253
Fu, Qiaomei, 147(fig.), 228–231, 233
Fuhlrott, Johann Carl, 129
Fundamentalist Christians, 221
Gannon, Frank, 135
Gay rights, 36–37
Gee, Henry, 236, 238
Gene flow
chromosome 17 evidence, 166
comparing Neanderthal, African, and European genomes, 174
Gene flow (continued)
Denisovans, 242, 246–247, 249
searching present-day genomes, 191–195
Trinkaus critique of findings, 220–221
Genetic diversity in North American tribal groups, 44
Genetic variation
among Neanderthals, 79
determining Neanderthals’ contribution to the modern genome, 171–173
evidence of Neanderthal-modern human gene flow, 166
mapping the Neanderthal genome, 156
out-of-Africa hypothesis, 91–94
social implications of Neanderthal gene flow findings, 200
Gorillas
common ancestor with humans and chimpanzees, 94
competition for reproduction, 212
genetic variation, 79
See also Apes; Chimpanzees
Gorjanovic-Kramberger, Dragutin, 76
Green, Richard E. “Ed,” 115, 159–160, 169
AAAS conference, 165–166
background, 111–112
common ancestors of Neanderthal and San, 186
comparing Neanderthal, modern human and ape genomes, 181–182
comparing Neanderthal and human reference genome, 124–125
data-handling programs, 162–163
Denisova genome, 243
estimating DNA contamination, 179–181
evidence of Neanderthal-modern human gene flow, 166–167, 191–192
454 process, 117, 119
mapping the DNA, 153–158
Newcomb Cleveland Prize, 224–225
patent controversy, 203
publishing the findings, 217–218, 220
transplantation antigens, 224
Greenwood, Alex, 99–101, 173
Ground sloths, 63–65, 65(fig.), 66–67, 105
Grunert, Stephan, 31–32
Gušić, Ivan “Johnny,” 138, 139(fig.)
Hagelberg, Erika, 55
Hair, Eskimo, 215
Handt, Oliva, 52, 53(fig.), 54–55, 67–70
Hawks, John, 220
Heinze, Anja, 147(fig.)
Herak, Milan, 130
Prichard, Hesketh, 63
Heterozygous position, 102–104
Higuchi, Russell, 34, 40–41, 51
Hofreiter, Michael, 113
Holthoer, Rostislav, 24–25, 27–29, 31, 38–39, 227
Homo altaiensis, 238
Homo erectus, 229
Homo heidelbergensis, 229, 238
Höss, Matthias, 52, 53(fig.), 54–55, 65, 101, 140
Hublin, Jean-Jacques, 90, 197
Human Diversity Panel, 246
Human evolutionary history, 43–44, 52
Human genome, 33, 38
Human Genome Project, 107
Human origins hypotheses, 41–42. See also Middle East scenario; Multiregional hypothesis of human origins; Out-of-Africa hypothesis
Human reference genome
as template for Neanderthal
sequences, 118
indicating contamination of Neanderthal sequences, 124–127
mapping gene flow, 192–195
mapping the Neanderthal genome, 153–155
reconstructing Neanderthal mtDNA, 160
sequencing modern genomes, 185–188
Hybrid molecules, 45–46, 60
Ice Man remains, 68–71
Illumina company, 161–164, 166, 169, 176, 181
Imitation as human behavior, 206
Immune system, 24
Incomplete lineage sorting, 247
Independent verification, 14–18
Insect DNA, 57–58
Interbreeding
comparing Neanderthal and
modern human genomes, 182–183
creationist view of, 221–222
Denisovan-Neanderthal interaction, 242–243, 251–252
mapping the five modern
genomes, 188–195
Neanderthal-modern human link, 96–97
replacement crowd, 198–199
SNPs as indicators of, 173–177
See also Sexual reproduction
Jäckle, Herbert, 47, 50, 120–121
Jeffreys, Alec, 25
Jeune Afrique magazine, 222
Johnson, Philip, 154, 166, 171, 181
Journal of Archaeological Science, 32
Journal of Molecular Evolution, 43
Jumping PCR, 46, 69–70
Kaessmann, Henrik, 91–94, 108–109
Kaiser Wilhelm Society, 81–82
Kangaroo rats, 42–43, 43(fig.)
Kelso, Janet, 147(fig.), 153–154, 209–213
Kilger, Christian, 202–203
Kim, Sung, 150, 160
Kircher, Martin, 147(fig.), 162, 165–166, 202–203, 209–213, 239, 245
Klein, Richard, 190
Knauer, Felix, 56
Krapina Cave collection, 76–77, 132–133
Krause, Johannes, 147(fig.)
access to Vindija Cave remains, 133–134
background, 129–130
comparing Neanderthal mtDNA sequences with Denisova sequences, 229–233
DNA from Vindija Cave remains, 136–141
454 process, 117, 119
Okladnikov Cave remains, 227
publishing the findings, 218
pyrosequencing, 114
sequencing the nuclear genome, 238–240
toasts, 234–235
Krings, Matthias, 1, 8–12, 16, 18, 21, 74–76, 78–79
Kučan, Željko, 138, 139(fig.)
Kudaravalli, Sridhar, 124
Lachmann, Michael, 170
Lalueza-Fox, Carles, 137
Lander, Eric, 164–166
Language development, 207, 252–253
Language groups, sampling for genetic diversity, 93
Larhammar, Dan, 34
Lawrence Berkeley National Laboratory, 109–110, 113–115, 121–122
Leaky replacement, 248
Learning as human behavior, 206–207
Lenardic, Jadranka, 130
Lewin, Benjamin, 18
Limestone caves, 76–78
Lindahl, Tomas, 18, 39–40, 51–52, 58, 76
Lucy, 4
Magnolia latahensis, 56–57
Maillard reaction, 106
Major histocompatibility complex (MHC), 223–224
Malez, Mirko, 76–77, 130–131
Mammoth remains
nuclear DNA extraction, 101–103, 111–113
pyrosequencing, 115
SNPs, 173
tracing evolutionary history, 55–56
“Marco Polo Neanderthals”, 183
Maričić, Tomislav “Tomi,” 137–138, 144–146, 147(fig.), 166, 179
Marsupials. See Thylacinus cynocephalus
Matzke, Nicholas J., 221
Max Planck Society, 81–90, 120–121, 155, 202–203
McLean, Corey, 219–220
Melanesia, 24
5, 247, 249–252
Mengele, Josef, 81–82
Methyl groups, 148
Meyer, Matthias, 147(fig.), 251
Mezmaiskaya Cave, Russia, 78–79, 136
Middle East scenario, 189–191, 195, 197–200
Migration, 41–42, 183
Mitochondria, 59–60
Mitochondrial DNA (mtDNA), 1–2,
4
BYU data, 59
Croatian samples, 78–79
Denisova Cave remains, 228–231, 240–244
determining Neanderthals’ contribution to the modern genome, 172
genetic variation among various Neanderthals, 95–97
human-ape link, 99
in animal droppings, 105–107
independent verification, 14–18
inheritance mechanism, 19–20
kangaroo rats, 42–43
limitations on view of genetic history, 19–20
Mitochondrial Eve, 14
multiregional model, 91
mutations, 12–14
Mylodon darwinii, 65
Native American remains, 71
Neanderthal type specimen and other Neanderthal specimens, 75–76
Neanderthal-modern human link, 96–98
nuclear DNA from mammoth bones, 101–103
Oetzi, the Ice Man, 69–70
Okladnikov Cave bone fragment, 228
PCR process, 8–12
quagga DNA, 34
reconstruction of Neanderthal mtDNA, 11(fig.), 159–168
SNPs as indicators of interbreeding, 174
tracing a common ancestor, 13(fig.)
Mitochondrial Eve, 13(fig.), 14–15, 88
Modern humans
cataloging genetic changes after Neanderthal-modern human separation, 209–213
cloning mummy DNA, 33
cognitive development, 205–207
common ancestor of apes and, 93(fig.)
Denisova tooth morphology, 241
Denisovan genome and, 242
Denisovans, Neanderthals, and, 243–244, 247–248
genome analysis of apes and, 219
Middle East scenario, 197–198
mtDNA comparisons with ancient DNA, 10, 12
mtDNA variation, 75–76
potential for Neanderthal offspring, 200–203
replacement crowd, 198–200
technical development, 208
See also Asians, modern; Europeans, modern
Molar, Neanderthal, 235, 236(fig.), 240–242, 245
Molecular clock, 66
Monaco, Tony, 252–253
Monogamy, 212
Morphological features, 66, 240–241, 245
Mullikin, Jim, 173–174, 183
Mullis, Kary, 8, 37, 39–40
Multiregional hypothesis of human origins, 20–21, 91–98, 188–189, 220
Mummies
blue fluorescence in, 27–28, 30, 105–106
cartilage samples, 54–55
contamination of DNA data, 51–52
DNA extraction and cloning, 25–35
DNA survival and decay, 7
Native American remains, 68, 71
Oetzi the Ice Man, 68–71
PCR process, 37–40
Mutations
cataloging genetic changes after Neanderthal-modern human separation, 209–213
derived alleles, 157
mapping convergent evolution,
66
Neanderthal contributions to modern European genome, 166–167
Neanderthal interbreeding with early modern humans, 192
obstacle to reconstructing genetic history, 12–14
putative dinosaur DNA, 59–60
studying nuclear DNA variation, 92–93
Myers, Gene, 111
Mylodon darwinii, 63–65, 65(fig.)
Native Americans
cannibalism, 131
Native Americans (continued)
comparing modern genome with, 68, 71
Denisovan genome and, 245
DNA data from preserved skeletons, 43–44
Nature Genetics journal, 79, 94
Nature magazine, 18, 51–52
contamination of data, 127, 150–151, 157–158, 160
Denisova Cave findings, 236–238, 242, 248–249
DNA in amber, 58
DNA retrieval from animal droppings, 56
454 paper, 122
human-chimpanzee joining and separation, 170
mammoth data, 55
Mezmaiskaya Cave Neanderthal remains, 78–79
Neanderthal genome paper, 164–165
quagga data, 34–35, 41
Siberian Neanderthal data, 228
thylacine data, 45
Nazi Germany, 81–83
Neander Valley, Germany, 2–3, 135–136
Neanderthal Genome Analysis Consortium, 175, 241. See also Neanderthal genome project
Neanderthal genome project
analyzing the results, 179–184
cataloging genetic changes after Neanderthal-modern human separation, 209–213
clean room procedures, 87–88
collaboration efforts, 134–135
contamination of data, 95–97
Denisovan mapping, 251–253
determining Neanderthals’ contribution to the modern genome, 171–173
El Sidrón bones, 136–137
European and African connections to Neanderthal genome, 176–177
explaining cognitive and technological development, 208–209
funding, 120–121
human reference genome and present-day human genome, 185–187
Illumina data, 164–166
inconsistencies with human reference genome, 124–127
interbreeding question, 182–183
mapping the genome, 153–158, 164–167
Mezmaiskaya Cave bones, 136
Middle East scenario, 189–191
minimizing bacterial DNA, 146–151
minimizing DNA loss in sampling, 143–146
mtDNA reconstruction, 159–160
mtDNA variation, 75–76
multiregional-continuity model of human origins, 91
Neander Valley bones, 135–136
Neanderthal interbreeding with early modern humans, 190–195
obtaining bone samples, 72–75, 129–134
obtaining Vindija bones, 137–141
people and processes, 117–119, 121–123, 169–171
publication of findings, 215–225
SNP analysis, 173–177
technical improvements,
127–128
Neanderthals
explaining differences between modern humans and, 208
first discovered remains and early research, 2–3
New England Biolabs, 148
Newcomb Cleveland Prize, 224–225
Nielsen, Rasmus, 191–192
Noonan, Jim, 124, 127
Nordborg, Magnus, 96
N-phenacylthiazolium bromide (PTB), 106
Nuclear DNA
animal droppings, 106–107
cave-bear bones, 99–101, 103–104, 109–113
Denisova Cave remains, 231, 239––240
dinosaur DNA, 60
mammoth bones, 101–103, 111–113
misplaced mitochondrial fragments, 59
Nuclear genome
Denisova Cave remains, 233, 238, 241–242
determining Neanderthals’ contribution to the modern genome, 98–99, 172
human-ape link, 94, 99
multiregional and out-of-Africa models of human origins,
91–92
SNPs as indicators of interbreeding, 174
Nucleotides, 1–2
Nuu-Chah-Nulth (First Nations group), 44
Nyrén, Pål, 107–109
Oetzi, the Ice Man, 68–71
Oetztal, Austria, 68–71
Offspring
chromosome genealogy, 185–187
determining Neanderthals’ contribution
to the modern genome, 172–173, 182–183
evidence of Neanderthal-modern human gene flow, 98–99, 189, 200–203
primates’ competition for reproduction, 212
SNPs as indicators of interbreeding, 173–177
social dominance and gene flow, 193–194
taxonomic classifications, 237–238
See also Interbreeding; Sexual reproduction
Okladnikov Cave, Siberia, 227
Old-earth creationists, 221
1,000 Genomes Project, 209–210, 252
Out-of-Africa hypothesis, 15, 19–21, 34, 88, 91, 188–189, 237
Owen, Richard, 63
Papuans, 183, 185–186, 188–189, 194–195, 242–247
Parham, Peter, 223–224
Patents, 202–203
Patterson, Nick, 173
background, 170–171
comparing Denisova and modern genomes, 244–246
comparing Neanderthal, African, and Chinese genomes, 177
comparing Neanderthal, African, and European genomes, 174
Denisova Cave remains, 241, 243, 246
evidence of Neanderthal-modern human gene flow, 190
mapping modern genomes, 187
Paunović, Maja, 77–78, 130
PCR. See Polymerase chain reaction
Peking Man, 4, 20
Penile spine deletion, 219
Permafrost remains, 102–104, 115, 215, 239
Pettersson, Per, 23–24, 26, 34
Plants, DNA sequencing of, 56–58
Playboy magazine, 222
Poinar, George, 58
Poinar, Hendrik, 58, 105–106, 115, 239
Pointing as human behavior, 205–206
Polymerase chain reaction (PCR), 8–12
automation of, 40
contamination of samples, 50–56
criteria of authenticity, 51–52
dubious results, 61
importance of, 37
improving efficiency of, 144–145
independent verification, 14–16
inhibiting nuclear DNA extraction, 100–101
jumping PCR, 46, 69–70
Oetzi, the Ice Man, 69–70
reconstruction of Neanderthal mtDNA, 11(fig.)
technical intricacies of DNA retrieval, 45–46
technological advances, 109, 143
thylacine data, 39–40, 44–45
Population geneticists, 169–170
Population split, 187
Possnert, Göran, 31
Primorac, Dragan, 135
Pritchard, Jonathan, 124
Proceedings of the National Academy of Sciences, 45, 115
Proteins, genetic changes in, 210–213
Prüfer, Kay, 147(fig.), 149
Ptak, Susan, 127, 170
PTB. See N-phenacylthiazolium bromide (PTB)
Pyrosequencing (company), 108–109
Pyrosequencing (process), 107–108, 111–116
Quagga DNA, 34, 40–41
