Abstracts
Résumé
Après deux décennies de découvertes et de controverses, la paléogénétique semble, sinon avoir atteint l’âge de raison, du moins avoir délaissé les frasques de son impétueuse jeunesse. Si ses principes théoriques ont été à peine affinés en quinze ans, sa pratique opérationnelle a, elle, rapidement évolué, en bénéficiant de l’explosion méthodologique de la biologie moléculaire. C’est véritablement avec l’avènement de la méthode d’amplification de l’ADN par PCR que ce champ d’étude a pris son essor. Dès 1989, les travaux se multipliaient en s’intéressant à des groupes biologiques animaux et végétaux variés : espèces récemment éradiquées par l’homme (ratites), représentants disparus de la période glaciaire (mammouth laineux) ou, encore, espèces domestiques (cochon) définirent les entités qui restent aujourd’hui les cibles favorites de ces études. Les champs d’application se sont également multipliés, afin de mieux cerner l’évolution des espèces, des populations et des génomes : génétique des populations, phylogénie d’espèces, domestication, migration de populations, paléopathologie, paléogénomique et évolution moléculaire s’offrent désormais à une discipline décidément en plein essor.
Summary
Twenty years after the advent of ancient DNA studies, this discipline seems to have reached the maturity formerly lacking to the fulfilment of its objectives. In its early development paleogenetics, as it is now acknowledged, had to cope with very limited data due to the technical limitations of molecular biology. It led to phylogenetic assumptions often limited in their scope and sometimes non-focused or even spurious results that cast the reluctance of the scientific community. This time seems now over and huge amounts of sequences have become available which overcome the former limitations and bridge the gap between paleogenetics, genomics and population biology. The recent studies over the charismatic woolly mammoth (independent sequencing of the whole mitochondrial genome and of millions of base pairs of the nuclear genome) exemplify the growing accuracy of ancient DNA studies thanks to new molecular approaches. From the earliest publications up to now, the number of mammoth nucleotides was multiplied by 100,000. Likewise, populational approaches of ice-age taxa provide new historical scenarios about the diversification and extinction of the Pleistocene megafauna on the one hand, and about the processes of domestication of animal and vegetal species by Man on the other. They also shed light on the differential structure of molecular diversity between short-term populational research (below 2 My) and long-term (over 2 My) phylogenetic approaches. All those results confirm the growing importance of paleogenetics among the evolutionary biology disciplines
Appendices
Références
- 1. Pääbo S. Molecular cloning of ancient Egyptian mummy DNA. Nature 1985 ; 314 : 644-5.
- 2. Higuchi RG, Bowman B, Freiberger M, et al. DNA sequences from the quagga, an extinct member of the horse family. Nature1984 ; 312 : 282-4.
- 3. Golenberg EM, Giannasi DE, Clegg MT, et al. Chloroplast DNA sequence from a Miocene Magnolia species. Nature 1990 ; 344 : 656-8.
- 4. Cano RJ, Poinar HN, Pieniazek NJ, et al. Amplification and sequencing of DNA from a 120-135-million-year-old weevil. Nature 1993 ; 363 : 536-8.
- 5. Woodward SR, Weyand NJ, Bunnel M. DNA sequence from cretaceous period bone fragments. Science 1994 ; 266 : 1229-32.
- 6. Gutierrez G, Marin A. 1998. The most ancient DNA recovered from an amber-preserved specimen may not be as ancient as it seems. Mol Biol Evol 15 : 926-9.
- 7. Austin JJ, Ross AJ, Smith AB, et al. 1997. Problems of reproducibility : does geologically ancient DNA survive in amber-preserved insects ? Proc R Soc B 1997 ; 264 : 467-74
- 8. Hedges SB, Schweitzer MH. Detecting dinosaur DNA. Science 1995 ; 268 : 1191-2
- 9. Austin JJ, Smith AB, Thomas RH. 1997. Palaeontology in a molecular world : the search for authentic ancient DNA. TREE 12 : 303-306
- 10. Willerslev E et Cooper A. Ancient DNA. Proc R Soc B 2005 ; 272 : 3-16.
- 11. Hagelberg E, Thomas MG, Cook Jr CE, et al. DNA from ancient mammoth bones. Nature 1994 ; 370 : 333-4.
- 12. Ozawa T, Hayashi S, Mikhelson VM. Phylogenetic position of mammoth and Steller’s sea cow within Tethytheria demonstrated by mitochondrial DNA sequences. J Mol Evol1997 ; 44 : 406-13.
- 13. Noro M, Masuda R, Dubrovo IA, et al. Molecular phylogenetic inference of the woolly mammoth Mammuthus primigenius, based on complete sequences of mitochondrial cytochrome b and 12S ribosomal genes. J Mol Evol 1998 ; 46 : 314-26.
- 14. Derenko M, Malyarchuk B, Shields GFG. Mitochondrial cytochrome b sequence from a 33000 year-old woolly mammoth (Mammuthus primigenius). Ancient Biomolecules 1997 ; 1 : 149-53.
- 15. Barriel V, Thuet E, Tassy P. Molecular phylogeny of Elephantidae. Extreme divergence of the extant forest african elephant. CR Acad Sci Paris Ser III 1999 ; 322 : 447-54.
- 16. Debruyne R, Barriel V, Tassy P. Mitochondrial cytochrome b of Lyakhov mammoth (Proboscidea, Mammalia) : new data and phylogenetic analyses of Elephantidae. Mol Phylogenet Evol 2003 ; 26 : 421-34.
- 17. Krause J, Dear PH, Pollack JL, et al. Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae. Nature 2006 ; 439 : 724-7.
- 18. Pineau P, Henry M, Suspène R, et al. PCR amplification from all Metazoan species with a universal primer set from nuclear gene HIST2H4. Mol Biol Evol 2004 ; 22 : 582-8.
- 19. Krajewski C, Buckley L, Westerman M. 1997. DNA phylogeny of the marsupial wolf resolved. Proc R Soc B 264 : 911-7.
- 20. Poinar HN, Schwarz C, Qi J, Shapiro B, et al. Metagenomics to paleogenomics : large-scale sequencing of mammoth DNA. Science 2006 ; 311 : 392-4.
- 21. Cooper A, Mourer-Chauviré C, Chambers GK, et al. Independent origins of New Zealand moas and kiwis. Proc Natl Acad Sci USA 1992 ; 89 : 8741-4.
- 22. Cooper A, Lalueza-Fox C, Anderson S, et al. Complete mitochondrial genome sequences of two extinct moas clarify ratite evolution. Nature 2001 ; 409 : 704-7.
- 23. Shapiro B, Drummond AJ, Rambaut A, et al. Rise and fall of the Beringian steppe bison. Science 2004 ; 306 : 1561-5.
- 24. Barnes I, Matheus P, Shapiro B, et al. Dynamics of pleistocene population extinctions in Beringian brown bears. Science 2002 ; 295 : 2267-70.
- 25. Lambert DM, Ritchie PA, Millar CD, et al. Rates of evolution in ancient DNA from Adélie Penguins. Science 2002 ; 295 : 2270-3
- 26. Baker AJ, Huynen LJ, Haddrath O, et al. Reconstructing the tempo and mode of evolution in an extinct clade of birds with ancient DNA : the giant moas of New Zealand. Proc Natl Acad Sci USA 2005 ; 102 : 8257-62.
- 27. Larson G, Dobney K, Albarella, et al. Worlwide phylogeography of wild boar reveals multiple centers of pig domestication. Science2005 ; 307 : 1618-21.
- 28. Weinstock J, Willerslev E, Sher A et al. Evolution, systematics, and phylogeography of pleistocene horses in the New World : a molecular perspective. PLoS Biol 2005 ; 3 : e241.
- 29. Ho SYW, Phillips MJ, Cooper A, Drummond AJ. Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Mol Biol Evol 2005 ; 22 : 1561-8.
- 30. Jaenicke-Després V, Buckler ES, Smith BD, et al. Early allelic selection in maize as revealed by ancient DNA. Science 2003 ; 302 : 1206-8.
- 31. Penny D. Evolutionary biology : relativity for molecular clocks. Nature 2005 ; 436 : 183-4.
- 32. Excoffier L. Ce que nous dit la généalogie des gènes. La Recherche 1997 ; 302 : 82-9.