Evolution and phylogeny of old world deer

Molecular Phylogenetics and Evolution

Volumn 33, Issue 3, 2004, Pages 880-895

  Pitra, Christian ^a   Fickel, Joerns ^a   Meijaard, Erik ^b   Groves, Colin P ^c  

^a LEIBNIZ INSTITUTE FOR ZOO AND WILDLIFE RESEARCH   (Germany)

^b JAMES COOK UNIVERSITY   (Australia)

^c AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

Author keywords

Cervinae; Cytochrome b; Evolution; Molecular clock; Molecular systematics; Speciation

Indexed keywords

CYTOCHROME B; DNA; MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; CALIBRATION; DEER; DNA SEQUENCE; EVOLUTION; FOSSIL; GENETIC VARIABILITY; GENETICS; METABOLISM; MOLECULAR EVOLUTION; PHYLOGENY; SPECIES DIFFERENCE; TIME;

ANIMALS; CALIBRATION; CYTOCHROMES B; DEER; DNA; DNA, MITOCHONDRIAL; EVOLUTION; EVOLUTION, MOLECULAR; FOSSILS; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; TIME FACTORS; VARIATION (GENETICS);

CERVIDAE; CERVINAE; CERVUS; CERVUS ELAPHUS; DAMA; MUNTIACUS MUNTJAK; MYA;

EID: 7444264024     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ympev.2004.07.013     Document Type: Article

References (85)

1. U. Arnason, J.A. Adegoke, K. Bodin, E.W. Born, Y.B. Esa, A. Gullberg, M. Nilsson, R.V. Short, X. Xu, and A. Janke Mammalian mitogenomic relationships and the root of the eutherian tree Proc. Natl. Acad. Sci. USA 99 2002 8151 8156
2. J.C. Avise, and C.J. Glenn Proposal for a standardized temporal scheme of biological classification for extant species Proc. Natl. Acad. Sci. USA 96 1999 7358 7363
3. B. Azanza Sur la nature des appendices frontaux des cervidés (Artiodactyla, Mammalia) du Miocêne inférieur et moyen. Remarques sur leur systématique et leur phylogénie C. R. Acad. Sci. Paris II 316 1993 1163 1169
4. B. Azanza, and E. Menendez Los ciervos fósiles del éogeno español Paleontol. Evol. 23 1990 75 82
5. A. Bachofen-Echt Die fossilen Geweihe von Cervus elaphus and ihre Beziehungen zu den lebenden Formen Paleontol. Zeit. 21 1939 68 76
6. J. Beninde Der Merkmalswert des Hirschgeweihs für die paläntologische Systematik der Gattung Cervus Paleontol. Zeit. 19 1937 52 56
7. V. Brooke On the classification of the Cervidae, with a synopsis of the existing species Proc. Zool. Soc. Lond. 1878 1878 883 928
8. G.A. Bubenik, and A.B. Bubenik Horns, Proghorns, and Antlers: Evolution, Morphology, Physiology and Social Significance 1990 Springer New York
9. J. Burger, W. Rosendahl, O. Loreille, H. Hemmer, T. Eriksson, A. Götherström, J. Hiller, M.J. Collins, T. Wess, and K.W. Alt Molecular phylogeny of the extinct cave lion Panthera leo spelaea Mol. Phylogenet. Evol. 30 2004 841 849
10. J. Castresana Cytochrome b phylogeny and the taxonomy of great apes and mammals Mol. Biol. Evol. 18 2001 465 471
11. M.A. Cronin Mitochondrial-DNA phylogeny of deer (Cervidae) J. Mammal. 72 1991 553 566
12. M.A. Cronin, R. Stuart, B.J. Pierson, and J.C. Patton Kappa-casein gene phylogeny of higher ruminants (Pecora, Artiodactyla) Mol. Phylogenet. Evol. 6 1996 295 311
13. S. Comincini, M. Sironi, C. Bandi, C. Giunta, M. Rubini, and F. Fontana RAPD analysis of systematic relationships among the Cervidae Heredity 76 1996 215 221
14. C.E. Cook, Y. Wang, and G. Sensabaugh A mitochondrial control region and cytochrome b phylogeny of sika deer (Cervus nippon) and report of tandem repeats in the control region Mol. Phylogenet. Evol. 12 1999 47 56
15. A. Cooper, and H.N. Poinar Ancient DNA: do it right or not at all Science 289 2000 1139
16. C. Darwin The Descent of Man, and Selection in Relation to Sex second ed. 1871 Murray London
17. G. Di Stefano, and C. Petronio Systematics and evolution of the Eurasian Plio-Pleistocene tribe Cervini (Artiodactyla, Mammalia) Geol. Romana 36 2002 311 334
18. J.M. Dolan A deer of many lands: a guide to the subspecies of Red Deer Cervus elaphus L. Zoonooz 62 10 1988 4 34
19. E. Douzery, and E. Randi The mitochondrial control region of Cervidae: evolutionary patterns and phylogenetic content Mol. Biol. Evol. 14 1997 1154 1166
20. J.R. Ellerman, and T.C.S. Morrison-Scott Checklist of Palaearctic and Indian Mammals, 1758 to 1947 1951 British Museum (Natural History) Trustees London
21. D.J. Emlen Costs and the diversification of exaggerated animal structures Science 291 2001 1534 1536
22. J. Felsenstein Confidence limits on phylogenies: an approach using the bootstrap Evolution 39 1985 783 791
23. J. Felsenstein Phylogenies from molecular sequences: inference and reliability Annu. Rev. Genet. 22 1988 521 565
24. J. Felsenstein PHYLIP: Phylogeny Inference Package 1993 University of Washington Seattle, WA
25. Flerov, K.K., 1952. Fauna of USSR: Mammals. 2. Musk Deer and Deer. Moscow, Leningrad: Academy of Sciences of USSR (English translation for National Science Foundation, Washington, DC, and Israel Program for Scientific Translations)
26. V. Geist Horn-like structures as rank symbols, guards and weapons Nature 220 1968 813 814
27. V. Geist On speciation in Ice Age mammals, with special reference to cervids and caprids Can. J. Zool. 65 1987 1067 1084
28. Geist, V., 1998. Deer of the World, Their Evolution, Behavior, and Ecology: Stackpole Books
29. A.W. Gentry The Miocene differentiation of Old World Pecora (Mammalia) Hist. Biol. 7 1994 115 158
30. P.M. Giao, D. Tuoc, V.V. Dung, E.D. Wikramanayake, G. Amato, P. Arctander, and J.R. MacKinnon Description of Muntiacus truongsonensis, a new species of muntjac (Artiodactyla: Muntiacidae) from Central Vietnam, and implications for conservation Anim. Conserv. 1 1998 61 68
31. F.H. Giles The riddle of Cervus schomburgki J. SIAM Soc. (Nat. Hist. Suppl.) 11 1937 1 34
32. M. Goodman, C.A. Porter, J. Czelusniak, S.L. Page, H. Schneider, J. Shoshani, G. Gunnell, and C.P. Groves Toward a phylogenetic classification of primates based on DNA evidence complemented by fossil evidence Mol. Phylogenet. Evol. 9 1998 585 598
33. S.J. Gould The origin and function of bizarre structures: Antler size and skull size in the Irish elk, Megaloceros giganteus Evolution 8 1974 191 200
34. C.P. Groves A note on the systematic position of the Muntjac (Artiodactyla, Cervidae) Z. Saugetierk 39 1974 369 372
35. C.P. Groves Time and taxonomy Ludus Vitalis 9 15 2001 91 96
36. C.P. Groves Primate Taxonomy 2001 Smithsonian Institution Press Washington, DC
37. C.P. Groves Taxonomy of ungulates of the Indian subcontinent J. Bombay Nat. Hist. Soc. 100 2003 341 362
38. C.P. Groves, and P. Grubb Relationships of living deer C.M. Wemmer Biology and Management of the Cervidae 1987 Smithsonian Inst. Press Washington, DC
39. C.P. Groves, and P. Grubb Muntiacidae G.A. Bubenik A.B. Bubenik Horns, Pronghorns and Antlers Horns, Proghorns, and Antlers: Evolution, Morphology, Physiology and Social Significance 1990 Springer New York
40. P. Grubb Order Artyodactyla D.E. Wilson D.M. Reeder Mammal Species of the World. A Taxonomic and Geographic Reference second ed. 1993 Smithsonian University Press Washington, DC
41. D. Han Preliminary study of the fossils of the order Artiodactyla from the ancient fossil locality of Lufeng: Renlixue Xuebao Acta Anthropol. Sinica 4 1985 4 54
42. P.H. Harvey, R.M. May, and S. Nee Phylogenies without fossils Evolution 48 1994 523 529
43. A. Hassanin, and E.J.P. Douzery Molecular and morphological phylogenies of ruminants, and the alternative position of the Moschidae Syst. Biol. 52 2003 206 228
44. B.R. Holland, D. Penny, and M.D. Hendy Outgroup misplacement and phylogenetic inaccuracy under a molecular clock-a simulation study Syst. Biol. 52 2003 229 238
45. J.P. Huelsenbeck, and F. Ronquist MRBAYES: Bayesian inference of phylogenetic trees Bioinformatics 17 2001 754 755
46. J.P. Huelsenbeck, B. Larget, R.E. Miller, and F. Ronquist Potential applications and pitfalls of Bayesian inference of phylogeny Syst. Biol. 51 2002 673 688
47. R.C. Hulbert Jr. Taxonomic evolution in North American Neogene horses (subfamily Equinae): the rise and fall of an adaptive radiation Paleobiology 19 1993 216 234
48. C.M. Janis, and K.M. Scott The interrelationships of higher ruminant families with special reference on the members of the Cervoidea Am. Mus. Novit. 2893 1987 1 85
49. G.C. Johns, and J.C. Avise A comparative summary of genetic distances in the vertebrates from the mitochondrial cytochrome b Mol. Biol. Evol. 15 1998 1481 1490
50. T.D. Kocher, W.K. Thomas, A. Meyer, S.V. Edwards, S. Pääbo, F.X. Villablanca, and A.C. Wilson Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers Proc. Natl. Acad. Sci. USA 86 1989 6196 6200
51. S. Kumar, K. Tamura, and M. Nei MEGA*: Molecular Evolutionary Genetics Analysis, Version 1.02 1993 Pennsylvania State University University Park
52. R. Kuwayama, and T. Ozawa Phylogenetic relationships among european red deer, wapiti, and sika deer inferred from mitochondrial DNA sequences Mol. Phylogenet. Evol. 15 2000 115 123
53. M. Li, H.B. Tamate, F.-W. Wei, X.-M. Wang, R. Masuda, H.-L. Sheng, and N. Ohtaishi Phylogenetic relationships among deer in China derived from mitochondrial DNA cytochrome b sequence Acta Theriol. 48 2003 207 219
54. F.B. Loomis Phylogeny of the deer Am. J. Sci. 16 1928 531 542
55. J.C. Ludt, W. Schroeder, O. Rottmann, and R. Kuehn Mitochondrial DNA phylogeography of red deer (Cervus elaphus) Mol. Phylogenet. Evol. 3 2004 1064 1083
56. W.P. Maddison, and D.W. Maddison MacClade: Analysis of Phylogeny and Character Evolution, Version 3.08 1999 Sinauer Associates Sunderland, MA
57. S. Magallon, and M.J. Sanderson Absolute diversification rates in angiosperm clades Evolution 55 2001 1762 1780
58. Meijaard, E., 2003. Solving mammalian riddles. A reconstruction of the Tertiary and Quaternary distribution of mammals and their palaeoenvironments in island South-East Asia. Department of Anthropology and Archaeology, Australian National University, Canberra, Australia
59. E. Meijaard, and C.P. Groves Morphometrical relationships between South-east Asian deer (Cervidae, tribe Cervini): evolutionary and biogeographic implications J. Zool. 263 2004 179 196
60. M.M. Miyamoto, F. Kraus, and O.A. Ryder Phylogeny and evolution of antlered deer determined from mitochondrial DNA sequences Proc. Natl. Acad. Sci. USA 87 1990 6127 6131
61. Mohr, E., 1968. Haltung und Zucht des Schomburgk-Hirsches, Rucervus schomburgki Blyth, 1863. D. Zool. Garten (NF) 36, 34-57
62. E. Paradis Assessing temporal variations in diversification rates from phylogenies: estimation and hypothesis testing Proc. R. Soc. Lond. B 264 1997 1141 1147
63. C. Pitra, A.J. Hansen, D. Lieckfeldt, and P. Arctander An exceptional case of historical outbreeding in African sable antelope populations Mol. Ecol. 11 2002 1197 1208
64. R.I. Pocock The larger deer of British India. Part II J. Bombay Nat. Hist. Soc. 43 1943 553 572
65. S. Poe Sensitivity of phylogeny estimation to taxonomic sampling Syst. Biol. 47 1998 18 31
66. D. Posada, and K.A. Crandall Modeltest: testing the model of DNA substitution Bioinformatics 14 1998 817 818
67. R.O. Polziehn, and C. Strobeck A phylogenetic comparison of red deer and wapiti using mitochondrial DNA Mol. Phylogenet. Evol. 22 2002 342 356
68. E. Randi, N. Mucci, M. Pierpaoli, and E.J.P. Douzery New phylogenetic perspectives on the Cervidae (Artiodactyla) are provided by the mitochondrial cytochrome b gene Proc. R. Soc. Lond. B 265 1998 793 801
69. E. Randi, N. Mucci, F. Claro-Hergueta, A. Bonnet, and E.J.P. Douzery A mitochondrial DNA control region phylogeny of the Cervinae: speciation in Cervus and implications for conservation Anim. Conserv. 4 2001 1 11
70. F. Rodriguez, J.F. Oliver, A. Marin, and J.R. Medina The general stochastic model of nucleotide substitution J. Theor. Biol. 142 1990 485 501
71. M.J. Sanderson A nonparametric approach to estimating divergence times in the absence of rate constancy Mol. Biol. Evol. 14 1997 1218 1231
72. O. Seehausen Hybridization and adaptive radiation Trends Ecol. Evol. 19 2004 198 207
73. K. Strimmer, and A. von Haeseler Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies Mol. Biol. Evol. 13 1996 964 969
74. B. Su, Y.-X. Wang, H. Lan, W. Wang, and Y. Zhang Phylogenetic study of complete cytochrome b genes in musk deer (genus Moschus) using museum samples Mol. Phylogenet. Evol. 12 1999 241 249
75. D.L. Swofford PAUP*: phylogenetic analysis using parsimony (* and Other Methods) 2001 Sinauer Associates Sunderland, MA
76. K. Tamura, and M. Nei Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees Mol. Biol. Evol. 10 1993 512 526
77. H. Taru, and Y. Hasegawa The Plio-Pleistocene fossil mammals from the Kasumi and Tama Hills Mem. Nat. Sci. Mus. 38 2002 43 56
78. J.D. Thompson, T.J. Gibson, F. Plewniak, F. Jeanmougin, and D.G. Higgins The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Res. 15 25 1997 4876 4882
79. e Cong. Nat. Soc. Savantes, Montpellier, Sci. II, 79-91
80. I.A. Vislobokova, and A.Y. Godina Application of the structural analysis of frontal appendages for determining the systematic position of fossil higher ruminants Paleontol. J. 1993 108 123
81. E.S. Vrba, and G.B. Schaller Antelopes, Deer, and Relatives: Fossil Record, Behavioral Ecology, Systematics, and Conservation 2000 Yale University Press New Haven
82. D. Webb Evolutionary history of New World Cervidae E.S. Vrba G.B. Schaller Antelopes, Deer, and Relatives: Fossil Record, Behavioral Ecology, Systematics, and Conservation 2000 Yale University Press New Haven
83. X. Xia, and Z. Xie DAMBE: software package for data analysis in molecular biology and evolution J. Hered. 92 2001 371 373
84. X. Xia, Z. Xie, M. Salemi, L. Chen, and Y. Wang An index of substitution saturation and its application Mol. Phylogenet. Evol. 26 2002 1 7
85. D.J. Zwickl, and D.M. Hillis Increased taxon sampling greatly reduces phylogenetic error Syst. Biol. 51 2002 588 598