Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae

Nature

Volumn 439, Issue 7077, 2006, Pages 724-727

  Krause, Johannes ^a   Dear, Paul H ^b   Pollack, Joshua L ^c   Slatkin, Montgomery ^c   Spriggs, Helen ^b   Barnes, Ian ^d   Lister, Adrian M ^d   Ebersberger, Ingo ^e   Pääbo, Svante ^a   Hofreiter, Michael ^a  

^a MAX PLANCK INSTITUTE FOR EVOLUTIONARY ANTHROPOLOGY   (Germany)

^b MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d UNIVERSITY COLLEGE LONDON   (United Kingdom)

^e HEINRICH HEINE UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BONE; DNA; ENZYMES; GENES;

MAMMOTH; MITOCHONDRIAL GENOME; PHYLOGENETIC TREE; POLYMERASE CHAIN REACTION;

BIODIVERSITY;

MITOCHONDRIAL DNA;

EVOLUTION; MAMMAL; MITOCHONDRIAL DNA;

ARTICLE; ASIAN; BONE; CELL LINEAGE; DNA DEGRADATION; DNA SEQUENCE; ELEPHANT; EVOLUTION; GENOME; MAMMOTH; MITOCHONDRIAL GENETICS; MULTIPLEX POLYMERASE CHAIN REACTION; PHYLOGENETIC TREE; PLEISTOCENE; PRIORITY JOURNAL;

EDENTATA; ELEPHANTIDAE; ELEPHAS MAXIMUS; LOXODONTA; MAMMUTHUS PRIMIGENIUS; URSUS SPELAEUS;

EID: 32544451176     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature04432     Document Type: Article

References (29)

1. Pääbo, S. et al. Genetic analyses from ancient DNA. Annu. Rev. Genet. 38, 645-679 (2004).
2. Lambert, D. M. et al. Rates of evolution in ancient DNA from Adelie penguins. Science 295, 2270-2273 (2002).
3. Cooper, A. et al. Complete mitochondrial genome sequences of two extinct moas clarify ratite evolution. Nature 409, 704-707 (2001).
4. Haddrath, O. & Baker, A. J. Complete mitochondrial DNA genome sequences of extinct birds: ratite phylogenetics and the vicariance biogeography hypothesis. Proc. R. Soc. Lond. B 268, 939-945 (2001).
5. Höss, M., Dilling, A., Currant, A. & Pääbo, S. Molecular phylogeny of the extinct ground sloth Mylodon darwinii. Proc. Natl Acad. Sci. USA 93, 181-185 (1996).
6. Loreille, O. et al. Ancient DNA analysis reveals divergence of the cave bear, Ursus spelaeus, and brown bear, Ursus arctos, lineages. Curr. Biol. 11, 200-203 (2001).
7. Yang, H., Golenberg, E. M. & Shoshani, J. Phylogenetic resolution within the Elephantidae using fossil DNA sequences from the American mastodon (Mammut americanum) as an outgroup. Proc. Natl Acad. Sci. USA 93, 1190-1194 (1996).
8. Hofreiter, M., Jaenicke, V., Serre, D., von Haeseler, A. & Pääbo, S. DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA. Nucleic Acids Res. 29, 4793-4799 (2001).
9. Bensasson, D., Zhang, D. X., Hartl, D. L. & Hewitt, G. M. Mitochondrial pseudogenes: evolution's misplaced witnesses. Trends Ecol. Evol. 16, 314-321 (2001).
10. Greenwood, A. D. & Pääbo, S. Nuclear insertion sequences of mitochondrial DNA predominate in hair but not in blood of elephants. Mol. Ecol. 8, 133-137 (1999).
11. Greenwood, A., Capelli, C., Possnert, G. & Pääbo, S. Nuclear DNA sequences from late Pleistocene megafauna. Mol. Biol. Evol. 16, 1466-1473 (1999).
12. Noro, M., Masuda, R., Dubrovo, I. A., Yoshida, M. C. & Kato, M. Molecular phylogenetic inference of the woolly mammoth Mammuthus primigenius, based on complete sequences of mitochondrial cytochrome b and 12S ribosomal RNA genes. J. Mol. Evol. 46, 314-326 (1998).
13. Thomas, M. G., Hagelberg, E., Jone, H. B., Yang, Z. & Lister, A. M. Molecular and morphological evidence on the phylogeny of the Elephantidae. Proc. R. Soc. Lond. B 267, 2493-2500 (2000).
14. Debruyne, R., Barriel, V. & Tassy, P. Mitochondrial cytochrome b of the Lyakhov mammoth (Proboscidea, Mammalia): new data and phylogenetic analyses of Elephantidae. Mol. Phylogenet. Evol. 26, 421-434 (2003).
15. Ozawa, T., Hayashi, S. & Mikhelson, V. M. Phylogenetic position of mammoth and Steller's sea cow within Tethytheria demonstrated by mitochondrial DNA sequences. J. Mol. Evol. 44, 406-413 (1997).
16. Cummings, M. P., Otto, S. P. & Wakeley; J. Sampling properties of DNA sequence data in phylogenetic analysis. Mol. Biol. Evol. 12, 814-822 (1995).
17. Shoshani, J. Understanding proboscidean evolution: a formidable task. Trends. Ecol. Evol. 13, 480-487 (1998).
18. Felsenstein, J. Inferring Phytogenies 196-221 (Sinauer Associates, Sunderland, 2004).
19. Tajima, F. Simple methods for testing the molecular evolutionary clock hypothesis. Genetics 135, 599-607 (1993).
20. Felsenstein, J. Confidence-limits on phytogenies with a molecular clock. Syst. Zool. 34, 152-161 (1985).
21. Tassy, P. in Lothagam: The Dawn of Humanity in Eastern Africa (eds Leakey, M. G. & Harris, J. M.) 331-358 (Columbia Univ. Press, New York, 2003).
22. Nei, M. in Evolutionary Perspectives and the New Genetics (eds Gershowitz, H., Rucknagel, D. L. & Tashian, R. E.) 133-147 (Alan R. Liss, New York, 1986).
23. Chen, F. C. & Li, W. H. Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees. Am. J. Hum. Genet. 68, 444-456 (2001).
24. Tajima, F. Evolutionary relationship of DNA sequences in finite populations. Genetics 105, 437-460 (1983).
25. Posada, D. & Crandall, K. A. MODELTEST: testing the model of DNA substitution. Bioinformatics 14, 817-818 (1998).
26. Swofford, D. L. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods) (Sinauer Associates, Sunderland, 2003).
27. Ronquist, F. & Huelsenbeck, J. P. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572-1574 (2003).
28. Schmidt, H. A., Strimmer, K., Vingron, M. & Haeseler, A. TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18, 502-504 (2002).
29. Hasegawa, M., Kishino, H. & Yano, T. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22, 160-174 (1985).