Ancient DNA evidence for the loss of a highly divergent brown bear clade during historical times

Molecular Ecology

Volumn 17, Issue 8, 2008, Pages 1962-1970

  Calvignac, Sebastien ^a   Hughes, Sandrine ^a   Tougard, Christelle ^b   Michaux, Jacques ^c   Thevenot, Michel ^d   Philippe, Michel ^e   Hamdine, Watik ^f   Hänni, Catherine ^a  

^a UNIVERSITÉ LYON 1   (France)

^b UNIVERSITÉ DE BOURGOGNE   (France)

^c INSTITUT DES SCIENCES DE L EVOLUTION   (France)

^d PSL RESEARCH UNIVERSITY   (France)

^e Centre de Conservation et d'Etude des Collections   (France)

^f Fédération des Pourvoieries du Québec   (Canada)

Author keywords

Ancient DNA; Brown bear; Holocene; mtDNA; North Africa; Phylogeography

Indexed keywords

URSUS ARCTOS;

EID: 42049118539     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2008.03631.x     Document Type: Article

References (53)

1. Auboire G, Gillon P (1995) Fossil bears bones from Takouatz Guerrissène (Djurdjura, Algeria). Nouvelles Archives du Muséum National d'Histoire Naturelle de Lyon, 19 45.
2. Avise JC (2000) Phylogeography: The History and Formation of Species. Harvard University Press, Boston, Massachusetts.
3. Barnes I, Matheus P, Shapiro B, Jensen D, Cooper A (2002) Dynamics of Pleistocene population extinctions in Beringian brown bears. Science, 295, 2267 2270.
4. Blyth E (1841) Letter from Edward Blyth. Proceedings of the Zoological Society of London 9.
5. Bourguignat J (1867) Ursus nouveau. Imprimerie de Mme Veuve Bouchard-Huzard, Paris, France.
6. Brandli L, Handley LJ, Vogel P, Perrin N (2005) Evolutionary history of the greater white-toothed shrew (Crocidura russula) inferred from analysis of mtDNA, Y, and X chromosome markers. Molecular Phylogenetics and Evolution, 37, 832 844.
7. Cheylan G (1990) Endémisme et spéciation chez les mammifères méditerranéens. Vie et Milieu, 40, 137 143.
8. Delisle I, Strobeck C (2002) Conserved primers for rapid sequencing of the complete mitochondrial genome from carnivores, applied to three species of bears. Molecular Biology and Evolution, 19, 357 361.
9. Dobson M, Wright A (2000) Faunal relationships and zoogeographical affinities of mammals in north-west Africa. Journal of Biogeography, 27, 417 424.
10. Emerson BC, Hewitt GM (2005) Phylogeography. Current Biology, 15, R367 R371.
11. Galtier N, Gouy M, Gautier C (1996) seaview and phylo_win: two graphic tools for sequence alignment and molecular phylogeny. Computer Applications in the Biosciences, 12, 543 548.
12. Gilbert MT, Hansen AJ, Willerslev E et al 2003) Characterization of genetic miscoding lesions caused by postmortem damage. American Journal of Human Genetics, 72, 48 61.
13. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology, 52, 696 704.
14. Guindon S, Lethiec F, Duroux P, Gascuel O (2005) PHYML Online - a web server for fast maximum likelihood - based phylogenetic inference. Nucleic Acids Research, 33, w557 559.
15. Hamdine W, Thevenot M, Michaux J (1998) Recent history of the brown bear in the Maghreb. Comptes Rendus de l'Academie des Sciences, Serie III-Sciences de la Vie, 321, 565 570.
16. Hänni C, Laudet V, Stehelin D, Taberlet P (1994) Tracking the origins of the cave bear (Ursus spelaeus) by mitochondrial DNA sequencing. Proceedings of the National Academy of Sciences, USA, 91, 12336 12340.
17. Hänni C, Brousseau T, Laudet V, Stehelin D (1995) Isopropanol precipitation removes PCR inhibitors from ancient bone extracts. Nucleic Acids Research, 23, 881 882.
18. Hansen A, Willerslev E, Wiuf C, Mourier T, Arctander P (2001) Statistical evidence for miscoding lesions in ancient DNA templates. Molecular Biology and Evolution, 18, 262 265.
19. Hofreiter M, Jaenicke V, Serre D, Haeseler Av A, Paabo S (2001a) DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA. Nucleic Acids Research, 29, 4793 4799.
20. Hofreiter M, Serre D, Poinar HN, Kuch M, Paabo S (2001b) Ancient DNA. Nature Reviews Genetics, 2, 353 359.
21. Hofreiter M, Serre D, Rohland N et al 2004) Lack of phylogeography in European mammals before the last glaciation. Proceedings of the National Academy of Sciences, USA, 101, 12963 12968.
22. IUCN (1996) http://www.redlist.org/search/details.php?species=22825.
23. Kohn M, Knauer F, Stoffella A, Schroder W, Paabo S (1995) Conservation genetics of the European brown bear - a study using excremental PCR of nuclear and mitochondrial sequences. Molecular Ecology, 4, 95 103.
24. Kurten B (1965) The Carnivora of the Palestine caves. Acta Zoologica Fennica 107.
25. Leonard JA, Wayne RK, Cooper A (2000) Population genetics of ice age brown bears. Proceedings of the National Academy of Sciences, USA, 97, 1651 1654.
26. Loreille O, Orlando L, Patou-Mathis M et al 2001) Ancient DNA analysis reveals divergence of the cave bear, Ursus spelaeus, and brown bear, Ursus arctos, lineages. Current Biology, 11, 200 203.
27. Marshall HD, Ritland K (2002) Genetic diversity and differentiation of Kermode bear populations. Molecular Ecology, 11, 685 697.
28. Masuda R, Murata K, Aiurzaniin A, Yoshida MC (1998) Phylogenetic status of brown bears Ursus arctos of Asia: a preliminary result inferred from mitochondrial DNA control region sequences. Hereditas, 128, 277 280.
29. Matheus P, Burns J, Weinstock J, Hofreiter M (2004) Pleistocene brown bears in the mid-continent of North America. Science, 306, 1150.
30. Matsuhashi T, Masuda R, Mano T, Yoshida MC (1999) Microevolution of the mitochondrial DNA control region in the Japanese brown bear (Ursus arctos) population. Molecular Biology and Evolution, 16, 676 684.
31. Michaux JR, Magnanou E, Paradis E, Nieberding C, Libois R (2003) Mitochondrial phylogeography of the woodmouse (Apodemus sylvaticus) in the Western Palearctic region. Molecular Ecology, 12, 685 697.
32. Miller CR, Waits LP (2003) The history of effective population size and genetic diversity in the yellowstone grizzly (Ursus arctos): implications for conservation. Proceedings of the National Academy of Sciences, USA, 100, 4334 4339.
33. Nylander JAA (2004) mrmodeltest 2.0. Program distributed by the author. Evolutionary Biology Centre, Uppsala University, Sweden.
34. Orlando L, Bonjean D, Bocherens H et al 2002) Ancient DNA and the population genetics of cave bears (Ursus spelaeus) through space and time. Molecular Biology and Evolution, 19, 1920 1933.
35. Paetkau D, Shields GF, Strobeck C (1998a) Gene flow between insular, coastal and interior populations of brown bears in Alaska. Molecular Ecology, 7, 1283 1292.
36. Paetkau D, Waits LP, Clarkson PL et al 1998b) Variation in genetic diversity across the range of North American brown bears. Conservation Biology, 12, 418 429.
37. Posada D, Crandall KA (1998) modeltest: testing the model of DNA substitution. Bioinformatics, 14, 817 818.
38. Rambaut A, Drummond A (2003) tracer v1.2, p. Available from URL: http://evolve.zoo.ox.ac.uk/.
39. Randi E, Gentile L, Boscagli G, Huber D, Roth HU (1994) Mitochondrial DNA sequence divergence among some west European brown bear (Ursus arctos L.) populations. Lessons for conservation. Heredity, 73 (5 480 489.
40. Ronquist F, Huelsenbeck JP (2003) mrbayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572 1574.
41. Shimodaira H, Hasegawa M (1999) Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Molecular Biology and Evolution, 16, 1114 1116.
42. Smith CI, Chamberlain AT, Riley MS, Stringer C, Collins MJ (2003) The thermal history of human fossils and the likelihood of successful DNA amplification. Journal of Human Evolution, 45, 203 217.
43. Sommer R, Benecke N (2005) The recolonization of Europe by brown bears Ursus arctos Linnaeus, 1758 after the last glacial maximum. Mammal Review, 2, 156 164.
44. Sorensen OJ (1990) The brown bear in Europe in the mid 1980s. Aquilo Series Zoology, 27, 3 16.
45. Stone KD, Cook JA (2000) Phylogeography of black bears (Ursus americanus) of the Pacific Northwest. Canadian Journal of Zoology, 78, 1218 1223.
46. Stuart AJ, Kosintsev PA, Higham TF, Lister AM (2004) Pleistocence to Holocene extinction dynamics in giant deer and woolly mammoth. Nature, 431, 684 689.
47. Swofford DL (2000) Paup* Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4. Sinauer & Associates, Sunderland, Massachusetts.
48. Taberlet P, Bouvet J (1992) Génétique de l'Ours brun des Pyrénées (Ursus arctos): premiers résultats. Comptes Rendus de l'Académie des Sciences Paris, Série III, 314, 15 21.
49. Taberlet P, Bouvet J (1994) Mitochondrial DNA polymorphism, phylogeography, and conservation genetics of the brown bear Ursus arctos in Europe. Proceedings of the Royal Society B: Biological Sciences, 255, 195 200.
50. Talbot SL, Shields GF (1996) Phylogeography of brown bears (Ursus arctos) of Alaska and paraphyly within the Ursidae. Molecular Phylogenetics and Evolution, 5, 477 494.
51. Vilà C, Amorim IR, Leonard JA et al 1999) Mitochondrial DNA phylogeography and population history of the grey wolf Canis lupus. Molecular Ecology, 8, 2089 2103.
52. Waits L, Talbot SL, Ward RH, Shields GF (1998) Mitochondrial DNA phylogeography of the north American brown bear and implications for conservation. Conservation Biology, 12, 408 417.
53. Waits L, Paetkau D, Strobeck C Compiled by C. Servheen, H. Herrero and B. Peyton and the IUCN/SSC Bear and Polar Bear Specialist Groups (1999) Genetics of the Bears of the World. In : Bears: Status Survey and Conservation Action Plan (eds Servheen C, Herrero S Peyton B pp. 25 32. IUCN, Gland, Switzerland.