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Authors: Svante Pbo

Tags: #In Search of Lost Genomes

Neanderthal Man (47 page)

BOOK: Neanderthal Man
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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).

{4
2}
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).

BOOK: Neanderthal Man
11.48Mb size Format: txt, pdf, ePub
ads

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