Phylogeny of the Carnivora (Mammalia): Congruence vs Incompatibility among Multiple Data Sets

Molecular Phylogenetics and Evolution

Volumn 9, Issue 3, 1998, Pages 414-426

  Flynn, John J ^a   Nedbal, Michael A ^a  

^a FIELD MUSEUM OF NATURAL HISTORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME B; PREALBUMIN; RIBOSOME RNA; RNA, RIBOSOMAL, 12S;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; CARNIVORA; CLASSIFICATION; GENETICS; HUMAN; INTRON; MAMMAL; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PHYLOGENY; STATISTICAL MODEL;

ANIMALS; CARNIVORA; CYTOCHROME B GROUP; EVOLUTION, MOLECULAR; HUMANS; INTRONS; LIKELIHOOD FUNCTIONS; MAMMALS; MODELS, GENETIC; MODELS, STATISTICAL; MOLECULAR SEQUENCE DATA; PHYLOGENY; PREALBUMIN; RNA, RIBOSOMAL;

EID: 0032087257     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1006/mpev.1998.0504     Document Type: Article

References (67)

1. Arnason U., Bodin K., Gullberg A., Ledje C., Mouchaty S. A molecular view of pinniped relationships with particular emphasis on the true seals. J. Mol. Evol. 40:1995;78-85.
2. Arnason U., Ledje C. The use of highly repetitive DNA for resolving cetacean and pinniped phylogenies. Mammal Phylogeny, Placentals. 1993;Springer-Verlag, New York. p. 74-80.
3. Arnason U., Widegren B. Pinniped phylogeny enlightened by molecular hybridizations using highly repetitive DNA. Mol. Biol. Evol. 3:1986;356-365.
4. Berta A., Ray C. E., Wyss A. R. Skeleton of the oldest known pinnipedEnaliarctos mealsi. Science. 244:1989;60-62.
5. Bremer K. The limits of amino-acid sequence data in angiosperm phylogenetic reconstruction. Evolution. 42:1988;795-803.
6. Bugge J. The cephalic arterial system in carnivores, with special reference to the systematic classification. Acta Anat. 101:1978;45-61.
7. Bull J. J., Huelsenbeck J. P., Cunningham C. W., Swofford D. L., Waddell P. J. Partitioning and combining data in phylogenetic analysis. Syst. Biol. 42:1993;384-397.
8. Cunningham C. W. Can three incongruence tests predict when data should be combined. Mol. Biol. Evol. 14:1997;733-740.
9. de Queiroz A. For consensus (sometimes). Syst. Biol. 42:1993;368-372.
10. de Queiroz A., Donoghue M. J., Kim J. Separate versus combined analysis of phylogenetic evidence. Annu. Rev. Ecol. Syst. 26:1995;657-681.
11. Dragoo J. W., Honeycutt R. L. Systematics of mustelid-like carnivores. J. Mamm. 78:1997;426-443.
12. Farris J. S., Källersjö M., Kluge A. G., Bult C. Constructing a significance test for incongruence. Syst. Biol. 44:1995;570-572.
13. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 39:1985;783-791.
14. Felsenstein J. PHYLIP: Phylogeny Inference Package. 1993;Univ. of WashingtonDepartment of Genetics, Seattle.
15. Felsenstein J., Churchill G. A. A Hidden Markov Model approach to variation among sites in rate of evolution. Mol. Biol. Evol. 13:1996;93-104.
16. Flynn J. J. Carnivoran phylogeny and rates of evolution: morphological, taxic, and molecular. Gittleman J. L. Carnivore Behavior, Ecology, and Evolution. 1996;542-581 Cornell Univ. Press, New York.
17. Flynn J. J., Neff N. A., Tedford R. H. Phylogeny of the Carnivora. Benton M. The Phylogeny and Classification of the Tetrapods. Mammals. 1988;73-116 Clarendon Press, Oxford.
18. Gilbert, D. G. 1995, SeqPup, a biological sequence editor and analysis program for multiple computer systems, ftp://iubio.bio.indiana.edu/molbio/seqpup/.
19. Goldman N. Simple diagnostic statistical tests of models for DNA substitution. J. Mol. Evol. 37:1993;650-661.
20. Goldman D., Giri P. R., O'Brien S. J. Molecular genetic-distance estimates among the Ursidae as indicated by one- and two-dimensional protein electrophoresis. Evolution. 43:1989;282-295.
21. Gutell R. R., Weiser B., Woese C. R., Noller H. F. Comparative anatomy of 16-S-like ribosomal RNA. Prog. Nucleic Acid Res. Mol. 32:1985;155-216.
22. Hickson R. E., Simon C., Cooper A., Spicer G. S., Sullivan J., Penny D. Conserved sequence motifs, alignment, and secondary structure for the third domain of animal 12S rRNA. Mol. Biol. Evol. 13:1996;150-169.
23. Hillis D. M., Bull J. J. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst. Biol. 42:1993;182-192.
24. Hunt R. M. Evolution of the aeluroid Carnivora: Significance of auditory structure in the nimravid catDinictis. Am. Mus. Novitates. 2886:1987;1-74.
25. Hunt R. M. Evolution of the aeluroid Carnivora: Significance of the ventral promontorial process of the petrosal, and the origin of basicranial patterns in the living families. Am. Mus. Novitates. 2930:1989;1-32.
26. Hunt R. M. Evolution of the aeluroid Carnivora: Viverrid affinities of the Miocene carnivoranHerpestides. Am. Mus. Novitates. 3023:1991;1-34.
27. Hunt R. M., Barnes L. G. Basicranial evidence for ursid affinity of the oldest pinnipeds. Proc. San Diego Soc. Nat. Hist. 29:1994;57-67.
28. Irwin D. M., Kocher T. D., Wilson A. C. Evolution of the cytochromeb. J. Mol. Evol. 32:1991;128-144.
29. Janczewski D. N., Modi W. S., Stephens J. C., O'Brien S. J. Molecular evolution of mitochondrial 12S RNA and cytochromeb. Mol. Biol. Evol. 12:1995;90-707.
30. Kishino H., Hasegawa M. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order of Hominoidea. J. Mol. Evol. 29:1989;170-179.
31. Larson A. The comparison of morphological and molecular data in phylogenetic systematics. Schierwater B., Streit B., Wagner G. P., DeSalle R. Molecular Ecology and Evolution: Approaches and Applications. 1994;371-390 Birkhäuser Verlag, Basel.
32. Ledje C., Arnason U. Phylogenetic analyses of complete cytochromeb. J. Mol. Evol. 42:1996a;135-144.
33. Ledje C., Arnason U. Phylogenetic relationships within caniform carnivores based on analyses of the mitochondrial 12S rRNA gene. J. Mol. Evol. 43:1996b;641-649.
34. Lento G. M., Hickson R. E., Chambers G. K., Penny D. Use of spectral analysis to test hypotheses on the origin of pinnipeds. Mol. Biol. Evol. 12:1995;28-52.
35. Lockhart P. J., Larkum A. W. D., Steel M. A., Waddell P. J., Penny D. Evolution of chlorophyll and bacteriochlorophyll: The problem of invariant sites in sequence analysis. Proc. Natl. Acad. Sci. USA. 93:1996;1930-1934.
36. Mason-Gamer R. J., Kellogg E. A. Testing for phylogenetic conflict among molecular data sets in the tribe Triticeae (Gramineae). Syst. Biol. 45:1996;524-545.
37. Masuda R., Yoshida M. C., Shinyashiki F., Bando G. Molecular phylogenetic status of the iriomote catFelis iriomotensis, Zool. Sci. 11:1994;597-604.
38. Mickevich M. F., Farris J. S. The implications of congruence inMenidia. Syst. Zool. 30:1981;351-370.
39. Miyamoto M. M., Goodman M. Biomolecular systematics of eutherian mammals: Phylogenetic patterns and classification. Syst. Zool. 35:1986;230-240.
40. O'Brien S. J., Nash W. G., Wildt D. E., Bush M. E., Benveniste R. E. A molecular solution to the riddle of the giant panda's phylogeny. Nature. 317:1985;140-144.
41. Rodrigo A. G., Kelly-Borges M., Bergquist P. R., Bergquist P. L. A randomization test of the null hypothesis that two cladograms are sample estimates of a parametric phylogenetic tree. N. Z. J. Bot. 31:1993;257-268.
42. Sambrook J., Fritsch E. F., Maniatis T. Molecular Cloning: A Laboratory Manual. 1989;Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
43. Sarich V. M. Pinniped origins and the rate of evolution of carnivore albumins. Syst. Zool. 18:1969;286-295.
44. Sarich V. M. The giant panda is a bear. Nature. 245:1973;218-220.
45. Slattery J. P., O'Brien S. J. Molecular phylogeny of the red panda (Ailurus fulgens. J. Hered. 86:1995;413-422.
46. Sullivan J. Combining data with different distributions of among-site rate variation. Syst. Biol. 45:1996;375-380.
47. Sullivan J., Holsinger K. E., Simon C. Among-site rate variation and phylogenetic analysis of 12S rRNA data in sigmodontine rodents. Mol. Biol. Evol. 12:1995;988-1001.
48. Swofford D. L. PAUP: Phylogenetic Analysis Using Parsimony. 1993;Illinois Natural History Survey, Champaign.
49. Swofford D. L. PAUP*: Phylogenetic Analysis Using Parsimony. 1997;Sinauer, Sunderland.
50. Talbot S. L., Shields G. F. Phylogeny of the bears (Ursidae) inferred from complete sequences of three mitochondrial genes. GenBank. 1995.
51. Tedford R. H. Relationships of pinnipeds to other carnivores (Mammalia). Syst. Zool. 25:1976;363-374.
52. Templeton A. R. Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and the apes. Evolution. 37:1983;221-244.
53. Tsuzuki T., Mita S., Maeda S., Araki S., Shimada K. Structure of the human prealbumin gene. J. Biol. Chem. 260:1985;12224-12227.
54. Véron G. La position systématique deCryptoprocta ferox. Mammalia. 59:1995;551-582.
55. Véron G., Catzeflis F. M. Phylogenetic relationships of the endemic Malagasy carnivoreCryptoprocta ferox. J. Mammal. Evol. 1:1993;169-185.
56. Vrana P. B., Milinkovitch M. C., Powell J. R., Wheeler W. C. Higher level relationships of the arctoid Carnivora based on sequence data and "total evidence" Mol. Phylogenet. Evol. 3:1994;47-58.
57. Wang X. New cranial material ofSimocyonAilurus. J. Vert. Paleontol. 17:1997;184-198.
58. Wayne R. K., Benveniste R. E., Janczewski D. N., O'Brien S. J. Molecular and biochemical evolution of the Carnivora. Gittleman J. L. Carnivore Behavior, Ecology, and Evolution. 1989;465-535 Cornell Univ. Press, New York.
59. Werdelin L., Solounias N. The Hyaenidae: Taxonomy, systematics and evolution. Fossils Strata. 30:1991;1-104.
60. Wolsan M. Phylogeny and classification of early European Mustelida (Mammalia: Carnivora). Acta Theriol. 38:1993;345-384.
61. Wozencraft W. C. The phylogeny of the recent Carnivora. Gittleman J. L. Carnivore Behavior, Ecology, and Evolution. 1989;495-535 Cornell Univ. Press, New York.
62. Wozencraft W. C. Order Carnivora. Wilson D. E., Reeder D. M. Mammal Species of the World: A Taxonomic and Geographic Reference. 1993;279-348 Smithsonian Institution Press, Washington.
63. Wyss A. R. The walrus auditory region and the monophyly of pinnipeds. Am. Mus. Novitates. 2871:1987;1-31.
64. Wyss A. R. Evidence from flipper structure for a single origin of pinnipeds. Nature. 334:1988;427-428.
65. Wyss A. R. Flippers and pinniped phylogeny: Has the problem of convergence been overrated. Mar. Mamm. Sci. 5:1989;343-360.
66. Wyss A. R., Flynn J. J. A phylogenetic analysis and definition of the Carnivora. Szalay F., Novacek M., McKenna M. Mammal Phylogeny: Placentals. 1993;32-52 Springer-Verlag, New York.
67. Zhang Y.-P., Ryder O. A. Mitochondrial DNA sequence evolution in the Arctoidea. Proc. Natl. Acad. Sci. USA. 90:1993;9557-9561.