Mitogenomic analyses of caniform relationships

Molecular Phylogenetics and Evolution

Volumn 45, Issue 3, 2007, Pages 863-874

  Arnason, Ulfur ^a   Gullberg, Anette ^a   Janke, Axel ^a   Kullberg, Morgan ^a  

^a LUND UNIVERSITY   (Sweden)

Author keywords

Arctoidea; Carnivora; Cynoidea; Mitogenomics; Molecular phylogeny; Musteloidea; Pinnipedia; The wolf dog split and basal human divergences; Ursidae

Indexed keywords

ANIMAL; ARTICLE; CARNIVORA; CLASSIFICATION; GENETICS; HUMAN; MITOCHONDRIAL GENOME; MOLECULAR EVOLUTION; PHYLOGENY;

ANIMALS; CARNIVORA; EVOLUTION, MOLECULAR; GENOME, MITOCHONDRIAL; HUMANS; PHYLOGENY;

AILURIDAE; AILUROPODA MELANOLEUCA; AILURUS FULGENS; CANIFORMIA; CANIS FAMILIARIS; CARNIVORA; FELIFORMIA; MEPHITIDAE; MUSTELIDAE; PINNIPEDIA; PROCYON; PROCYONIDAE; URSIDAE;

EID: 36049030256     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2007.06.019     Document Type: Article

References (80)

1. Abascal F., Zardoya R., and Posada D. ProtTest: selection of the best-fit models of protein evolution. Bioinformatics 7 (2005) 2104-2105
2. Adachi J., and Hasegawa M. MOLPHY v. 2.3. Comput. Sci. Monogr. 28 (1996) 1
3. Akaike H. A new look at the statistical model identification. IEEE Trans. Autom. Contr. 19 (1974) 716-723
4. Arnason U. Comparative chromosome studies in Pinnipedia. Hereditas 76 (1974) 179-226
5. Arnason U. The relationship between the four principal pinniped karyotypes. Hereditas 87 (1977) 227-242
6. Arnason U., and Widegren B. Pinniped phylogeny enlightened by molecular hybridizations using highly repetitive DNA. Mol. Biol. Evol. 3 (1986) 356-365
7. Arnason U., Gullberg A., and Widegren B. The complete nucleotide sequence of the mitochondrial DNA of the fin whale. J. Mol. Evol. 33 (1991) 556-568
8. Arnason U., and Johnsson E. The complete mitochondrial DNA sequence of the harbor seal, Phoca vitulina. J. Mol. Evol. 34 (1992) 493-505
9. Arnason U., and Ledje C. The use of highly repetitive DNA for resolving cetacean and pinniped phylogenies. In: Szalay F.S., Novacek M.J., and McKenna M.C. (Eds). Mammal Phylogeny, Placentals (1993), Springer-Verlag 74-80
10. Arnason U., Bodin K., Gullberg A., Ledje C., and Mouchaty S. A molecular view of pinniped relationships with particular emphasis on the true seals. J. Mol. Evol. 40 (1995) 78-85
11. Arnason U., Xu X., and Gullberg A. Comparison between the complete mitochondrial DNA sequences of human and the common chimpanzee. J. Mol. Evol. 42 (1996) 145-152
12. Arnason U., Gullberg A., Janke A., and Xu X. Pattern and timing of evolutionary divergences among hominoids based on analyses of complete mtDNAs. J. Mol. Evol. 43 (1996) 650-661
13. Arnason U., Gullberg A., and Janke A. Molecular timing of primate divergences as estimated by two nonprimate calibration points. J. Mol. Evol. 47 (1998) 718-727
14. Arnason U., Gullberg A., Gretarsdottir S., Ursing B., and Janke A. The mitochondrial genome of the sperm whale and a new molecular reference for estimating eutherian divergence dates. J. Mol. Evol. 50 (2000) 569-578
15. Arnason U., Adegoke J.A., Bodin K., Born E.W., Esa Y.B., Gullberg A., Nilsson M., Short R.V., Xu X., and Janke A. Mammalian mitogenomic relationships and the root of the eutherian tree. Proc. Natl. Acad. Sci. USA 99 (2002) 8151-8156
16. Arnason U., and Janke A. Mitogenomic analyses of eutherian relationships. Cytogenet. Genome Res. 96 (2002) 20-32
17. Arnason U., Gullberg A., Janke A., Kullberg M., Lehman N., Petrov E.A., and Väinolä R. Pinniped phylogeny and a new hypothesis for their origin and dispersal. Mol. Phylogenet. Evol. 41 (2006) 345-354
18. Baskin J.A. Mustelidae. In: Janis C.M., Scott K.M., and Jacobs L.L. (Eds). Evolution of Tertiary Mammals of North America vol. 1 (1998), Cambridge University Press, Cambridge 152-173
19. Berta A., and Wyss A.R. Pinniped phylogeny. Proc. San Diego Soc. Nat. Hist. 29 (1994) 33-56
20. Bininda-Emonds O.R.P., and Russell A.P. A morphological perspective on the phylogenetic relationships of the extant phocid seals. (Mammalia: Carnivora: Phocidae). Bonner Zool. Monogr. 41 (1996) 1-256
21. Bininda-Emonds O.R.P., Gittleman J.L., and Purvis A. Building large trees by combining phylogenetic information: a complete phylogeny of the extant Carnivora (Mammalia). Biol. Rev. 74 (1999) 143-175
22. Braunitzer G., and Hofmann O. Les hémoglobines des pandas. CR Soc. Biol. 181 (1987) 116-121
23. Bryant H.N., Russell A.P., and Fitch W.D. Phylogenetic relationships within the extant Mustelidae (Carnivora): appraisal of the cladistic status of the Simpsonian subfamilies. Zool. J. Linn. Soc. 108 (1993) 301-334
24. Cao Y., Janke A., Waddell P.J., Westerman M., Takenaka O., Murata S., Okada N., Paabo S., and Hasegawa M. Conflict among individual mitochondrialproteins in resolving the phylogeny of eutherian orders. J. Mol. Evol. 47 (1998) 307-322
25. Davis C.S., Delisle I., Stirling I., Siniff D.B., and Strobeck C. A phylogeny of extant Phocidae inferred from complete mitochondrial DNA coding regions. Mol. Phylogenet. Evol. 33 (2004) 363-377
26. de Jong W.W., and Goodman M. Mammalian phylogeny studied by sequence analysis of the eye lens protein alpha-crystallin. Z. Säugetierk 5 (1982) 257-276
27. Delisle I., and Strobeck C. A phylogeny of the Caniformia (order Carnivora) based on 12 complete protein-coding mitochondrial genes. Mol. Phylogenet. Evol. 37 (2005) 192-201
28. Deméré T.A. The family Odobenidae: a phylogenetic analysis of fossil and living taxa. Proc. San Diego Soc. Nat. Hist. 29 (1994) 99-123
29. Dragoo J.W., and Honeycutt R.L. Systematics of mustelid-like carnivores. J. Mammal. 78 (1997) 426-443
30. Felsenstein J. Phylogenetic Inference Programs (PHYLIP) (1993), University of Washington and University Herbarium, University of California, Seattle
31. Flynn J.J., and Galiano H. Phylogeny of early Tertiary Carnivora, with a description of a new species of Protictis from the Middle Eocene of northwestern Wyoming. Am. Mus. Novit. 2725 (1982) 1-64
32. Flynn J.J., Neff N.A., and Tedford R.H. Phylogeny of the Carnivora. In: Benton M. (Ed). The Phylogeny and Classification of the Tetrapods, Mammals vol. 2 (1988), Clarendon Press, Oxford 73-116
33. Flynn J.J., Nedbal M.A., Dragoo J.W., and Honeycutt R.L. Whence the red panda?. Mol. Phylogenet. Evol. 17 (2000) 190-199
34. Flynn J.J., Finarelli J.A., Zehr S., Hsu J., and Nedbal M.A. Molecular phylogeny of the Carnivora (Mammalia): assessing the impact of increased sampling on resolving enigmatic relationships. Syst. Biol. 54 (2005) 317-337
35. Flynn J.J., and Wesley-Hunt G.D. Carnivora. In: Rose K.D., and Archibald D. (Eds). The Rise of Placental Mammals: Origins and Relationships of the Major Extant Clades (2005), The Johns Hopkins University Press 175-198
36. Fulton T.L., and Strobeck C. Molecular phylogeny of the Arctoidea (Carnivora): effect of missing data on supertree and supermatrix analyses of multiple data sets. Mol. Phylogenet. Evol. 41 (2006) 165-181
37. Guindon S., and Gascuel S. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52 (2003) 696-704
38. Huelsenbeck J.P., and Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17 (2001) 754-755
39. Hunt Jr. R.M., and Tedford R.T. Phylogenetic relationships within the aeluroid Carnivora and implications of their temporal and geographic distribution. In: Szalay F.S., Novacek M.J., and McKenna M.C. (Eds). Mammal Phylogeny, Placentals (1993), Springer-Verlag 53-73
40. Ingman M., Kaessmann H., Pääbo S., and Gyllensten U. Mitochondrial genome variation and the origin of modern humans. Nature 408 (2000) 708-713
41. Jansen E., Fronval T., Rack F., and Channell J.E.T. Pliocene-Pleistocene ice rafting history and cyclicity in the Nordic Seas during the last 3.5 Myr. Paleoceanography 15 (2000) 709-721
42. Kohno, N., 1993. Have the pinnipeds been derived from the ursids? Abstracts of the Annual Meeting of the Palaeontological Society of Japan (Jan. 29-30, Tsukuba), p. 79.
43. Koretsky I., and Sanders A.E. Paleontology of the late Oligocene Ashley and Chandler Bridge formations of South Carolina, 1: paleogene pinniped remains; the oldest known seal (Carnivora: Phocidae). Smithsonian Contrib. Paleobiol. 93 (2002) 179-183
44. Lanave C., Preparata G., Saccone C., and Serio G. A new method for calculating evolutionary substitution rates. J. Mol. Evol. 20 (1984) 86-93
45. Ledje C., and Arnason U. Phylogenetic analyses of complete cytochrome b sequences of the order Carnivora with particular emphasis on the Caniformia. J. Mol. Evol. 42 (1996) 135-144
46. Ledje C., and Arnason U. Phylogenetic relationships within caniform carnivores based on the analyses of the mitochondrial 12S rRNA gene. J. Mol. Evol. 43 (1996) 641-649
47. Leone C.A., and Wiens A.L. Comparative serology of carnivores. J. Mammal. 37 (1956) 11-23
48. Linnaeus, C., 1758. Systema Naturae. Holmiae [Stockholm], Laurentii Salvii.
49. McKenna M.C., and Bell S.K. Classification of Mammals Above the Species Level (1997), Columbia University Press, New York
50. Miyamoto M.M., and Goodman M. Biomolecular systematics of eutherian mammals: phylogenetic patterns and classification. Syst. Zool. 35 (1986) 230-240
51. O'Brien S.J., Nash W.G., Wildt D.E., Bush M.E., and Benveniste R.E. A molecular solution to the riddle of the giant panda's phylogeny. Nature 317 (1985) 140-144
52. Posada D., and Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
53. Rambaut, A., 1996. Se-Alv2.0a11: sequence alignment editor. Available from: .
54. Sanderson J. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol. Biol. Evol. 19 (2002) 101-109
55. Sarich V.M. Pinniped origins and the rate of evolution of carnivore albumins. Syst. Zool. 18 (1969) 286-295
56. Sarich V.M. Pinniped phylogeny. Syst. Zool. 18 (1969) 416-422
57. Sarich V.M. The giant panda is a bear. Nature 245 (1973) 218-220
58. Sarich V.M., and Wilson A.C. Immunological time scale for human evolution. Science 158 (1967) 1200-1203
59. Sato J.J., Hosoda T., Wolsan M., Tsuchiya K., Yamamoto M., and Suzuki H. Phylogenetic relationships and divergence times among mustelids (Mammalia: Carnivora) based on nucleotide sequences of the nuclear interphotoreceptor retinoid binding protein and mitochondrial cytochrome b genes. Zool. Sci. 20 (2003) 243-264
60. Sato J.J., Hosoda T., Wolsan M., and Suzuki H. Molecular phylogeny of arctoids (Mammalia: Carnivora) with emphasis on phylogenetic and taxonomic positions of the ferret-badgers and skunks. Zool. Sci. 21 (2004) 111-118
61. Sato J.J., Wolsan M., Suzuki H., Hosoda T., Yamaguchi Y., Hiyama K., Kobayashi M., and Minami S. Evidence from nuclear DNA sequences sheds light on the phylogenetic relationships of Pinnipedia: single origin with affinity to Musteloidea. Zool. Sci. 23 (2006) 125-146
62. Scheffer V.B. Seals, Sea Lions and Walruses (1958), Stanford University Press, California
63. Schmidt H.A., Strimmer K., Vingron M., and von Haeseler A. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18 (2002) 502-504
64. Senut B., Pickford M., Gommery D., Mein P., Cheboi K., and Coppens Y. First hominid from the Miocene (Lukeino Formation, Kenya). CR Acad. Sci. Paris, Sciences de la Terre et des Planètes 332 (2001) 137-144
65. Stone K.D., and Cook J.A. Molecular evolution of the Holarctic martens (genus Martes, Mammalia: Carnivora: Mustelidae). Mol. Phylogenet. Evol. 24 (2002) 169-179
66. Swofford, D.L., 2002. PAUP*, Version 4, Sinauer Associates, Sunderland, Massachusetts.
67. Tian Y., Nie W.H., Wang J.H., Yang Y.F., and Yang F.T. Comparative chromosome painting shows the red panda (Ailurus fulgens) has a highly conserved karyotype. Acta Genet. Sinica 29 (2002) 124-127
68. Vigilant L., Stoneking M., Harpending H., Hawkes K., and Wilson A.C. African populations and the evolution of human mitochondrial DNA. Science 253 (1991) 1503-1507
69. Wesley-Hunt G.D., and Flynn J.J. Phylogeny of the Carnivora: basal relationships among the carnivoramorphans, and assessment of the position of "Miacoidea" relative to Carnivora. J. Syst. Paleontol. 3 (2005) 1-28
70. Wolsan M. Phylogeny and classification of early European Mustelida (Mammalia: Carnivora). Acta Theriol. 38 (1993) 345-384
71. Wolsan M., and Lange-Badré B. An arctomorph carnivoran skull from the Phosphorites du Quercy and the origin of procyonids. Acta Palaeontol. Pol. 41 (1996) 277-298
72. Wolsan M. Oldest mephitine cranium and its implications for the origin of skunks. Acta Palaeontol. Pol. 44 (1999) 223-230
73. Wozencraft W.C. The phylogeny of the recent Carnivora. In: Gittleman J.L. (Ed). Carnivore behavior, ecology, and evolution (1989), Cornell University Press 495-535
74. Wurster D.H., and Benirschke K. Comparative cytogenetic studies in the order Carnivora. Chromosoma 24 (1968) 336-382
75. Wyss A.R. The walrus auditory region and the monophyly of pinnipeds. Am. Mus. Novit. 2871 (1987) 1-13
76. Wyss A.R., and Flynn J.J. A phylogenetic analysis and definition of the Carnivora. In: Szalay F.S., Novacek M.J., and McKenna M.C. (Eds). Mammal Phylogeny 2, Placentals (1993), Springer-Verlag, New York, Berlin, Heidelberg 32-52
77. Xu X., Janke A., and Arnason U. The complete mitochondrial DNA sequence of the greater Indian rhinoceros, Rhinoceros unicornis, and the phylogenetic relationship among Carnivora, Perissodactyla and Artiodactyla (+Cetacea). Mol. Biol. Evol. 13 (1996) 1167-1173
78. Yang Z. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39 (1994) 306-314
79. Yu L., Li Q.W., Ryder O.A., and Zhang Y.P. Phylogeny of the bears (Ursidae) based on nuclear and mitochondrial genes. Mol. Phylogenet. Evol. 32 (2004) 480-494
80. Yu L., and Zhang Y.P. Phylogeny of the caniform carnivora: evidence from multiple genes. Genetica 127 (2006) 65-79