Data set incongruence and the phylogeny of crocodilians

Systematic Biology

Volumn 45, Issue 4, 1996, Pages 393-414

  Poe, Steven ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

Combined analysis; Crocodilians; Incongruence; Phylogeny; Separate analysis

Indexed keywords

ALLIGATOR; ALLIGATORINAE; CROCODYLIDAE (ALL CROCODILES); CROCODYLUS; GAVIALIS; TOMISTOMA;

EID: 0030311233     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1093/sysbio/45.4.393     Document Type: Article

References (69)

1. ABACUS CONCEPTS. 1992. StatView. Abacus Concepts, Berkeley, California.
2. AGGARAWAL, R. K., K. C. MAJUMDAR, J. W. LANG, AND L. SING. 1994. Generic affinities among crocodilians as revealed by DNA fingerprinting with a Bkm-derived probe. Proc. Natl. Acad. Sci. USA 91:10601-10605.
3. BARRET, M., M. J. DONOGHUE, AND E. SOBER. 1991. Against consensus. Syst. Zool. 40:486-493.
4. BENTON, M. J. 1993. The fossil record 2. Chapman & Hall, London.
5. BENTON, M. J., AND J. CLARK. 1988. Archosaur phylogeny and the relationships of the Crocodylia. Pages 295-338 in The phylogeny and classification of the tetrapods, Volume 1. Amphibians, reptiles, birds (M. J. Benton, ed.). Systematics Association Special Volume 35A. Clarendon Press, London.
6. BRAZAITIS, P. 1973. The identification of living crocodilians. Zoologica 59:59-88.
7. BREMER, K. 1988. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42:795-803.
8. BROOKS, D. R., AND R. T. O'GRADY. 1989. Crocodilians and their helminth parasites: Macroevolutionary considerations. Am. Zool. 29:873-883.
9. BUFFETAUT, E. 1985. The place of Gavialis and Tomistoma in eusuchian evolution: A reconciliation of paleontological and biochemical data. Neues. Jahrb. Paläontol. Monatsh. 12:707-716.
10. BULL, J. J., J. P. HUELSENBECK, C. W. CUNNINGHAM, D. L. SWOFFORD, AND P. J. WADDEL. 1993. Partitioning and combining data in phylogenetic analysis. Syst. Biol. 42:384-397.
11. CHIPPINDALE, P. T., AND J. J. WIENS. 1994. Weighting, partitioning, and combining characters in phylogenetic analysis. Syst. Biol. 43:278-287.
12. CLARK, J. M. 1994. Patterns of evolution in Mesozoic Crocodyliformes. Pages 84-97 in In the shadow of the dinosaurs: Early Mesozoic tetrapods (N. C. Fraser and H. D. Sues, eds.). Cambridge Univ. Press, Cambridge, England.
13. COHEN, M. M., AND C. GANS. 1970. The chromosomes of the order Crocodilia. Cytogenetics 9:81-105.
14. CONOVER, W. J. 1971. Practical nonparametric statistics. John Wiley and Sons, New York.
15. DEEMING, D. C., AND M. W. J. FERGUSON. 1989. The mechanism of temperature dependent sex determination in crocodilians: A hypothesis. Am. Zool. 29: 973-985.
16. DENSMORE, L. D. 1983. Biochemical and immunological systematics of the order Crocodilia. Pages 397-465 in Evolutionary biology, Volume 16 (M. K. Hecht, B. Wallace, and G. H. Prance, eds.). Plenum, New York.
17. DENSMORE, L. D., AND P. S. WHITE. 1991. The systematics and evolution of the Crocodilia as suggested by restriction endonuclease analysis of mitochondrial and nuclear ribosomal DNA. Copeia 1991:602-615.
18. DE QUEIROZ, A. 1993. For consensus (sometimes). Syst. Biol. 42:368-373.
19. DONOGHUE, M. J., J. A. DOYLE, J. GAUTHIER, A. G. KLUGE, AND T. ROWE. 1989. The importance of fossils in phylogeny reconstruction. Annu. Rev. Ecol. Syst. 20:431-160.
20. DONOGHUE, M. J., R. G. OLMSTEAD, J. F. SMITH, AND J. D. PALMER. 1992. Phylogenetic relationships of Dipsacales based on rbcL sequences. Ann. Mo. Bot. Gard. 79:333-345.
21. DONOGHUE, M. J., AND M. J. SANDERSON. 1992. The suitability of molecular and morphological evidence in reconstructing plant phylogeny. Pages 340-368 in Molecular systematics in plants (P. S. Soltis, D. E. Soltis, and J. J. Doyle, eds.). Chapman and Hall, New York.
22. DUMÉRIL, A. M. C. 1806. Zoologie analytique, or methode naturelle de classification des animaux. Perroneau, Paris.
23. FARRIS, J. S. 1989. The retention index and the rescaled consistency index. Cladistics 5:417-419.
24. FARRIS, J. S., M. K. KÄLLERSJÖ, A. G. KLUGE, AND C. BULT. 1994. Testing significance of incongruence. Cladistics 10:315-319.
25. FELSENSTEIN, J. F. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791.
26. FREY, E., J. RIESS, AND S. F. TARSITANO. 1989. The axial tail musculature of recent crocodiles and its phyletic implications. Am. Zool. 29:857-862.
27. FISHER, R. A. 1954. Statistical methods for research workers, 12th edition. Oliver & Boyd, Edinburgh.
28. GATESY, J., AND G. D. AMATO. 1992. Sequence similarity of 12S ribosomal segment of mitochondrial DNAs of gharial and false gharial. Copeia 1992:241-244.
29. GATESY, J., R. DESALLE, AND W. C. WHEELER. 1993. Alignment-ambiguous nucleotide sites and the exclusion of systematic data. Mol. Phylogenet. Evol. 2: 152-157.
30. GAUTHIER , J., A. G. KLUGE, AND T. ROWE. 1988. Amniote phylogeny and the importance of fossils. Cladistics 4:105-209.
31. GREER, A. E. 1970. Evolutionary and systematic significance of crocodilian nesting habits. Nature 227: 523-524.
32. HASS, C. A., M. A. HOFFMAN, L. D. DENSMORE III, AND L. R. MAXSON. 1992. Crocodilian evolution: Insights from immunological data. Mol. Phylogenet. Evol. 1:193-201.
33. HECHT, M. K., AND B. MALONE. 1972. On the early history of the gavialid crocodilians. Herpetologica 28:281-284.
34. HENNIG, W. 1966. Phylogenetic systematic. Univ. Illinois Press, Urbana.
35. HIGGINS, D. G., A. G. BLEASBY, AND R. FUCHS. 1992. CLUSTAL V: Improved software for multiple sequence alignment. Cabios 8:189-191.
36. HILLIS, D. M. 1985. Evolutionary genetics of the Andean lizard genus Pholidobolus (Sauria: Gymnophthalmidae): Phylogeny, biogeography, and a comparison of tree construction techniques. Syst. Zool. 34:109-126.
37. HILLIS, D. M. 1987. Molecular versus morphological approaches to systematics. Annu. Rev. Ecol. Syst. 18: 23-42.
38. HILLIS, D. M. 1995. Approaches for assessing phylogenetic accuracy. Syst. Biol. 44:3-16.
39. HILLIS, D. M., AND J. P. HUELSENBECK. 1992. Signal, noise, and reliability inphylogenetic analyses. J. Hered. 83:189-195.
40. HUELSENBECK, J. P. 1994. Comparing the stratigraphic record to estimates of phylogeny. Paleobiology 20: 470-483.
41. HUELSENBECK, J. P., D. L. SWOFFORD, C. W. CUNNINGHAM, J. J. BULL, AND P. J. WADDEL. 1994. Is character weighting a panacea for the problem of data set heterogeneity in phylogenetic analysis? Syst. Biol. 43:288-291.
42. IORDANSKY, N. N. 1973. The skull of the Crocodilia. Pages 201-260 in Biology of the Reptilia, Volume 4 (C. Gans and T. Parsons, eds.). Academic Press, London.
43. KLUGE, A. G. 1989. A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Syst. Zool. 38:7-25.
44. KLUGE, A. G., AND J. S. FARRIS. 1969. Quantitative phyletics and the evolution of the anurans. Syst. Zool. 18:1-32.
45. LARSON, A. 1994. The comparison of molecular and morphological data in phylogenetic systematics. Pages 371-390 in Molecular ecology and evolution: Approaches and applications (B. Schierwater, B. Streit, G. P. Wagner, and R. DeSalle, eds.). Birkhäuser Verlag, Basel, Switzerland.
46. MADDISON, W. P., AND D. R. MADDISON. 1992. MacClade: Analysis of phylogeny and character evolution, version 3.0. Sinauer, Sunderland, Massachusetts.
47. MICKEVICK, M. F., AND J. S. FARRIS. 1981. The implications of congruence in Menidia. Syst. Zool. 30:351-370.
48. MIYAMOTO, M. M., AND W. F. FITCH. 1995. Testing species phylogenies and phylogenetic methods with congruence. Syst. Biol. 44:64-76.
49. MOOK, C. C., AND G. E. MOOK. 1940. Some problems in crocodilian nomenclature. Am. Mus. Novit. 1098: 1-10.
50. NORELL, M. A. 1988. Cladistic approaches to paleobiology as applied to the phylogeny of alligatorids. Ph.D. Thesis, Yale Univ., New Haven, Connecticut.
51. NORELL, M. A. 1989. The higher level relationships of the extant Crocodylia. J. Herpetol. 23:325-335.
52. OMLAND, K. E. 1994. Character congruence between a molecular and a morphological phylogeny for dabbling ducks (Anas). Syst. Biol. 43:369-387.
53. PATTERSON, C., D. WILLIAMS, AND C. J. HUMPHRIES. 1993. Congruence between molecular and morphological phylogenies. Annu. Rev. Ecol. Syst. 24:153-188.
54. RICE, W. R. 1989. Analyzing tables of statistical tests. Evolution 43:223-225.
55. ROMER, A. S. 1956 Osteology of the reptiles. Univ. Chicago Press, Chicago.
56. ROSS, F. D., AND G. C. MAYER. 1983. On the dorsal armor of the Crocodilia. Pages 305-331 in Advances in herpetology and evolutionary biology (A. Rhodin and K. Miyata, eds.). Museum of Comparative Zoology, Cambridge, Massachusetts.
57. SHINE, R. 1988. Parental care in reptiles. Pages 275-330 in Biology of the Reptilia, Volume 16 (C. Gans and R. Huey, eds.). Academic Press, London.
58. SHUMACHER, G. 1973. The head muscles and hyolaryngeal skeleton of turtles and crocodilians. Pages 101-199 in Biology of the Reptilia, Volume 4 (C. Gans and T. Parsons, eds.). Academic Press, London.
59. SOKAL, R. R., AND F. J. ROHLF. 1981. Biometry, 2nd edition. W. H. Freeman, New York.
60. STEEL, R. 1973. Crocodylia. Pages 1-116 in Handbuch der Palaoherpetologie 16 (O. Kuhn, ed.). Gustav Fischer Verlag, Stuttgart.
61. SWOFFORD, D. L. 1991. When are phylogeny estimates from molecular and morphological data incongruent? Pages 295-333 in Phylogenetic analysis of DNA sequences (M. M Miyamoto and J. Cracraft, eds.). Oxford Univ. Press, New York.
62. SWOFFORD, D. L. 1993. PAUP: Phylogenetic analysis using parsimony, version 3.1. Illinois Natural History Survey, Champaign.
63. TAPLIN, L. E., AND G. C. GRIGG. 1989. Historical zoogeography of the eusuchian crocodilians: A physiological perspective. Am. Zool. 29:885-901.
64. TARSITANO, S. S., E. FREY, AND J. REISS. 1989. The evolution of the Crocodilia: A conflict between morphological and biochemical data. Am. Zool. 29:843-856.
65. TEMPLETON, A. 1983. Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and the apes. Evolution 37:221-244.
66. TITUS, T. A., AND A. LARSON. 1995. A molecular phylogenetic perspective on the evolutionary radiation of the salamander family Salamandridae. Syst. Biol. 44:125-151.
67. WHEELER, W. C. 1990. Nucleic acid sequences and random outgroups. Cladistics 6:363-368.
68. WIENS, J. J., AND P. T. CHIPPINDALE. 1994. Combining and weighting characters and the prior agreement approach revisited. Syst. Biol. 43:564-566.
69. WIENS, J. J., AND T. W. REEDER. 1995. Combining data sets with different numbers of taxa for phylogenetic analysis. Syst. Biol. 44:548-558.