A nuclear DNA phylogeny of the woolly mammoth (Mammuthus primigenius)

Molecular Phylogenetics and Evolution

Volumn 40, Issue 2, 2006, Pages 620-627

  Capelli, Cristian ^a   MacPhee, Ross D E ^b   Roca, Alfred L ^c   Brisighelli, Francesca ^a   Georgiadis, Nicholas ^e   O'Brien, Stephen J ^d   Greenwood, Alex D ^b,f,g  

^a CATHOLIC UNIVERSITY   (Italy)

^b DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

^c SAIC FREDERICK INC   (United States)

^d NATIONAL CANCER INSTITUTE   (United States)

^e MPALA RESEARCH CENTRE   (Kenya)

^f INSTITUTE OF EPIDEMIOLOGY   (Germany)

^g TECHNICAL UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ANIMAL; ARTICLE; CELL NUCLEUS; ELEPHANT; FOSSIL; GENETIC VARIABILITY; GENETICS; PHYLOGENY;

ANIMALS; CELL NUCLEUS; DNA; ELEPHANTS; FOSSILS; PHYLOGENY; VARIATION (GENETICS);

MAMMUTHUS PRIMIGENIUS;

EID: 33745870162     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2006.03.015     Document Type: Article

References (30)

1. Binladen J., Wiuf C., Gilbert M.T., Bunce M., Barnett R., Larson G., Greenwood A.D., Haile J., Ho S.Y., Hansen A.J., and Willerslev E. Assessing the fidelity of ancient DNA sequences amplified from nuclear genes. Genetics 172 (2006) 733-741
2. Clement M., Posada D., and Crandall K.A. TCS: a computer program to estimate gene genealogies. Mol. Ecol. 9 (2000) 1657-1659
3. Debruyne R., Barriel V., and Tassy P. Mitochondrial cytochrome b of the Lyakhov mammoth (Proboscidea, Mammalia): new data and phylogenetic analyses of Elephantidae. Mol. Phylogenet. Evol. 26 3 (2003) 421-434
4. Eggert L.S., Rasner C.A., and Woodruff D.S. The evolution and phylogeography of the African elephant inferred from mitochondrial DNA sequence and nuclear microsatellite markers. Proc. R. Soc. Lond. B Biol. Sci. 269 (2002) 1993-2006
5. Georgiadis N., Bischof L., et al. Structure and history of African elephant populations: I. Eastern and southern Africa. J. Hered. 85 (1994) 100-104
6. Greenwood A.D. Mammoth biology: biomolecules, phylogeny, Numts, nuclear DNA, and the biology of an extinct species. Anc. Biomol. 3 (2001) 255-266
7. Greenwood A.D., and Pääbo S. Nuclear insertion sequences of mitochondrial DNA predominate in hair but not in blood of elephants. Mol. Ecol. 8 (1999) 133-137
8. Greenwood A.D., Capelli C., Possnert G., and Pääbo S. Nuclear DNA sequences from late Pleistocene megafauna. Mol. Biol. Evol. 16 (1999) 1466-1473
9. Greenwood A.D., Lee F., Capelli C., Desalle R., Tikhonov A.N., Marx P.A., and MacPhee R.D.E. Evolution of endogenous retrovirus-like elements of the woolly mammoth (Mammuthus primigenius) and its relatives. Mol. Biol. Evol. 18 (2001) 840-847
10. Kishino H., and Hasegawa M. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea. J. Mol. Evol. 29 (1989) 170-179
11. Krause J., Dear P.H., Pollack J.L., Slatkin M., Spriggs H., Barnes I., Lister A.M., Ebersberger I., Paabo S., and Hofreiter M. Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae. Nature 439 (2006) 724-727
12. Lyons L.A., Laughlin T.F., Copeland N.G., Jenkins N.A., Womack J.E., and O'Brien S.J. Comparative anchor tagged sequences (CATS) for integrative mapping of mammalian genomes. Nat. Genet. 15 (1997) 47-56
13. Maglio V.J. Origin and evolution of the Elephantidae. Trans. Am. Phil. Soc. Philad., New Series 63 (1973) 1-149
14. Nikaido M., Nishihara H., Hukumoto Y., and Okada N. Ancient SINEs from African endemic mammals. Mol. Biol. Evol. 20 4 (2003) 522-527
15. Noro M., Masuda R., Dubrovo I.A., Yoshida M.C., and 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 3 (1998) 314-326
16. O'hUigin C., Satta Y., Takahata N., and Klein J. Contribution of homoplasy and of ancestral polymorphism to the evolution of genes in anthropoid primates. Mol. Biol. Evol. 19 (2002) 1501-1513
17. Ozawa T., Hayashi S., and Mikhelson V.M. Phylogenetic position of mammoth and Steller's sea cow within Tethytheria demonstrated by mitochondrial DNA sequences. J. Mol. Evol. 44 4 (1997) 406-413
18. Poinar H., Kuch M., McDonald G., Martin P., and Pääbo S. Nuclear gene sequences from a late Pleistocene sloth coprolite. Curr. Biol. 13 (2003) 1150-1152
19. Poinar H.N., Schwarz C., Qi J., Shapiro B., Macphee R.D., Buigues B., Tikhonov A., Huson D.H., Tomsho L.P., Auch A., Rampp M., Miller W., and Schuster S.C. Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. Science 311 (2006) 392-394
20. Posada D., and Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics 14 9 (1998) 817-818
21. Roca A.L., Georgiadis N., Pecon-Slattery J., and O'Brien S.J. Genetic evidence for two species of elephant in Africa. Science 293 (2001) 1473-1477
22. Roca A.L., Georgiadis N., and O'Brien S.J. Cytonuclear genomic dissociation in African elephant species. Nat. Genet. 37 1 (2005) 96-100
23. Rogaev E.I., Moliaka Y.K., Malyarchuk B.A., Kondrashov F.A., Derenko M.V., Chumakov I., and Grigorenko A.P. Complete mitochondrial genome and phylogeny of Pleistocene mammoth Mammuthus primigenius. PLoS Biol. 4 3 (2006) e73
24. Satta Y., Klein J., and Takahata N. DNA archives and our nearest relative: the trichotomy problem revisited. Mol. Phylogenet. Evol. 14 (2000) 259-275
25. Springer M., Murphy W., Eizirik E., and O'Brien S.J. In: Rose K., and Archibald J.D. (Eds). The Rise of Placental Mammals: Origins and Relationships of the Major Extant Clades (2005), Johns Hopkins Univ. Press, Baltimore 37-49
26. Swofford, D.L., 2002. PAUP*: Phylogenetic Analysis Using Parsimony (* and Other Methods). Version 4.0b10. Sunderland, Massachusetts, Sinauer.
27. Thalmann O., Hebler J., Poinar H.N., Pääbo S., and Vigilant L. Unreliable mtDNA data due to nuclear insertions: a cautionary tale from analysis of humans and other great apes. Mol. Ecol. 13 (2004) 321-335
28. Thompson J.D., Gibson T.J., et al. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25 (1997) 4876-4882
29. Vignaud P., Duringer P., Mackaye H.T., Likius A., Blondel C., Boisserie J.R., De Bonis L., Eisenmann V., Etienne M.E., Geraads D., Guy F., Lehmann T., Lihoreau F., Lopez-Martinez N., Mourer-Chauvire C., Otero O., Rage J.C., Schuster M., Viriot L., Zazzo A., and Brunet M. Geology and palaeontology of the Upper Miocene Toros-Menalla hominid locality, Chad. Nature 418 (2002) 152-155
30. Yang H., Golenberg E.M., and Shoshani J. Phylogenetic resolution within the Elephantidae using fossil DNA sequence from the American mastodon (Mammut americanum) as an outgroup. Proc. Natl. Acad. Sci. USA 93 3 (1996) 1190-1194