Assessing progress in systematics with continuous jackknife function analysis

Systematic Biology

Volumn 52, Issue 1, 2003, Pages 55-65

  Miller, Jeremy A ^a,b  

^a DEPARTMENT OF PALEOBIOLOGY   (United States)

^b GEORGE WASHINGTON UNIVERSITY   (United States)

Author keywords

Accuracy; Combined data; Comparative biology; Congruence; Data visualization; Jackknife; Pseudoreplicate; Stability; Support; Total evidence

Indexed keywords

EID: 0037292583     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/10635150390132731     Document Type: Article

References (97)

1. ARCHIE, J. W. 1989a. A randomization test for phylogenetic information in systematic data. Syst. Zool. 38:239-252.
2. ARCHIE, J. W. 1989b. Homoplasy excess ratios: New indices for measuring levels of homoplasy in phylogenetic systematics and a critique of the consistency index. Syst. Zool. 38:253-269.
3. BARRETT, M., M. J. DONOGHUE, AND E. SOBER. 1991. Against consensus. Syst. Zool. 40:486-493.
4. BOND, J., AND B. OPELL. 1998. Testing adaptive radiation and key innovation hypotheses in spiders. Evolution 52:403-414.
5. BREMER, K. 1988. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42:795-803.
6. BREMER, K. 1994. Branch support and tree stability. Cladistics 10:295-304.
7. BUCKLEY, T. R., C. SIMON, P. K. FLOOK, AND B. MISOF. 2000. Secondary structure and conserved motifs of the frequently sequenced domains IV and V of the insect mitochondrial large subunit rRNA gene. Insect Mol. Biol. 9:565-580.
8. BULL, J. J., J. P. HUELSENBECK, C. W. CUNNINGHAM, D. L. SWOFFORD, AND P. J. WADDELL. 1993. Partitioning and combining data in phylogenetic analysis. Syst. Biol. 42:384-397.
9. CARPENTER, J. M. 1992. Random cladistics. Cladistics 8:147-153.
10. CARPENTER, J. M. 1996. Uninformative bootstrapping. Cladistics 12:177-181.
11. CARPENTER, J. M., P. A. GOLOBOFF, AND J. S. FARRIS. 1998. PTP is meaningless, T-PTP is contradictory: A reply to Trueman. Cladistics 14:105-116.
12. CHIPPINDALE, P. T., AND J. J. WIENS. 1994. Weighting, partitioning, and combining characters in phylogenetic analysis. Syst. Biol. 43:278-287.
13. CODDINGTON, J. A., G. HORMIGA, AND N. SCHARFF. 1997. Giant female or dwarf male spiders? Nature 285:687-688.
14. COLWELL, R. K., AND J. A. CODDINGTON. 1994. Estimating terrestrial biodiversity through extrapolation. Philos. Trans. R. Soc. Ser. B 345:101-118.
15. CUMMINGS, M. P., S. P. OTTO, AND J. WAKELEY. 1995. Sampling properties of DNA sequence data in phylogenetic analysis. Mol. Biol. Evol. 12:814-822.
16. DAVIS, J. I. 1993. Character removal as a means of assessing stability of clades. Cladistics 9:201-210.
17. DEBRY, R. W. 2001. Improving interpretation of the decay index for DNA sequence data. Syst. Biol. 50:742-752.
18. DE LAET, J., AND E. SMETS. 1999. Data decisiveness, missing entries and the DD index. Cladistics 15:25-37.
19. DE QUEIROZ, A., M. J. DONOGHUE, AND J. KIM. 1995. Separate versus combined analysis of phylogenetic evidence. Annu. Rev. Ecol. Syst. 26:657-681.
20. DUNLOP, J. A., AND M. WEBSTER. 1999. Fossil evidence, terrestrialization and arachnid phylogeny. J. Arachnol. 27:86-93.
21. EERNISSEE, D. J., AND A. G. KLUGE. 1993. Taxonomic congruence versus total evidence, and amniote phylogeny inferred from fossils, molecules, and morphology. Mol. Biol. Evol. 10:1170-1195.
22. EMERSON, G. L., C. W. KILPATRICK, B. E. MCNIFF, J. ORRENWALDER, AND M. W. ALLARD. 1999. Phylogenetic relationships of the order Insectivora based on complete 12S rRNA sequences from mitochondria. Cladistics 15:221-230.
23. FAITH, D. P. 1991. Cladistic permutation tests for monophyly and nonmonophyly. Syst. Zool. 40:336-375.
24. FAITH, D. P., AND P. S. CRANSTON. 1991. Could a cladogram this short have arisen by chance alone?: On permutation tests for cladistic structure. Cladistics 7:1-28.
25. FARRIS, J. S. 1983. The logical basis of phylogenetic analysis. Pages 7-36 In Advances in cladistics, Volume 2 (N. I. Platnick and V. A. Funk, eds.). Columbia Univ. Press, New York.
26. FARRIS, J. S. 1989. The retention index and the rescaled consistency index. Cladistics 5:417-419.
27. FARRIS, J. S. 1999. Likelihood and inconsistency. Cladistics 15:199-204.
28. FARRIS, J. S. 2001. Support weighting. Cladistics 17:389-394.
29. FARRIS, J. S., V. A. ALBERT, M. KÄLLERSJÖ, D. LIPSCOMB, AND A. G. KLUGE. 1996. Parsimony jackknifing outperforms neighbor-joining. Cladistics 12:99-124.
30. FARRIS, J. S., M. KÄLLERSJÖ, A. G. KLUGE, AND C. BULT. 1994. Permutations. Cladistics 10:65-76.
31. FELSENSTEIN, J. 1985a. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791.
32. FELSENSTEIN, J. 1985b. Phylogenies and the comparative method. Am. Nat. 125:1-15.
33. FELSENSTEIN, J. 1987. Cases in which parsimony and compatibility methods will be positively misleading. Syst. Zool. 27:401-410.
34. GLADSTEIN, D., AND W. C. WHEELER. 1996. OY. Program and documentation. American Museum of Natural History, New York.
35. GLADSTEIN, D., AND W. C. WHEELER. 2001. POY. Program and documentation. Available online at ftp://ftp.amnh.org/pub/molecular/poy/. American Museum of Natural History, New York.
36. GOLOBOFF, P. 1991a. Homoplasy and the choice among cladograms. Cladistics 7:215-232.
37. GOLOBOFF, P. 1991b. Random data, homoplasy and information. Cladistics 7:395-406.
38. GOLOBOFF, P. 1993. NONA (a bastard son of Pee-Wee), version. 2.0. Program and documentation. Available online at http://www.cladistics.com. Published by the author, Tucumán, Argentina.
39. GRISWOLD, C. E., J. A. CODDINGTON, G. HORMIGA, AND N. SCHARFF. 1998. Phylogeny of the orb-web building spiders (Araneae, Orbiculariae: Deinopoidea, Araneoidea). Zool. J. Linn. Soc. 123:1-99.
40. HENDY, M. D., AND D. PENNY. 1989. A framework for the quantitative study of evolutionary trees. Syst. Zool. 38:297-309.
41. HENNIG, W. 1965. Phylogenetic systematics. Annu. Rev. Entomol. 10:97-116.
42. HICKSON, R. E., C. SIMON, A. COOPER, G. S. SPICER, J. SULLIVAN, AND C. PENNY. 1996. Conserved sequence motifs, alignment, and secondary structure for the third domain of animal 12S rRNA. Mol. Biol. Evol. 13:150-169.
43. HICKSON, R. E., C. SIMON, AND S. W. PERREY. 2000. The performance of several multiple-sequence alignment programs in relation to secondary-structure features for an rRNA sequence. Mol. Biol. Evol. 17:530-539.
44. HILLIS, D. M. 1996. Inferring complex phylogenies. Nature 383:130-131.
45. HILLIS, D. M. 1998. Taxonomic sampling, phylogenetic accuracy, and investigator bias. Syst. Biol. 47:3-8.
46. HORMIGA, G., W. G. EBERHARD, AND J. A. CODDINGTON. 1995. Web-construction behavior in Australian Phonognatha and the phylogeny of nephiline and tetragnathid spiders (Araneae: Tetragnathidae). Aust. J. Zool. 43:313-364.
47. HORMIGA, G., N. SCHARFF, AND J. A. CODDINGTON. 2000. The phylogenetic basis of sexual size dimorphism in orb-weaving spiders (Araneae, Orbiculariae). Syst. Biol. 49:435-462.
48. HUELSENBECK, J. P. 1995. Performance of phylogenetic methods in simulation. Syst. Biol. 44:17-48.
49. HUELSENBECK, J. P., D. L. SWOFFORD, C. W. CUNNINGHAM, J. J. BULL, AND P. J. WADDELL. 1994. Is character weighting a panacea for the problem of data heterogeneity in phylogenetic analysis? Syst. Biol. 43:288-291.
50. JUKES, T. H., AND C. CANTOR. 1969. Evolution of protein molecules. Pages 21-132 in Mammalian protein metabolism (M. N. Munro, ed.). Academic Press, New York.
51. KÄLLERSJÖ, M., J. S. FARRIS, A. G. KLUGE, AND C. BULT. 1992. Skewness and permutation. Cladistics 8:275-287.
52. KJER, K. M. 1995. Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: An example of alignment and data presentation from the frogs. Mol. Phylogenet. Evol. 4:314-330.
53. KLUGE, A. G. 1989. A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Syst. Zool. 38:7-25.
54. KLUGE, A. G. 1997a. Sophisticated falsification and research cycles: Consequences for differential character weighting in phylogenetic systematics. Zool. Scripta 26:349-360.
55. KLUGE, A. G. 1997b. Testability and the refutation and corroboration of cladistic hypotheses. Cladistics 13:81-96.
56. KLUGE, A. G., AND J. S. FARRIS. 1969. Quantitative phyletics and the evolution of anurans. Syst. Zool. 18:1-32.
57. KLUGE, A. G., AND A. J. WOLF. 1993. Cladistics: What's in a word? Cladistics 9:183-199.
58. LANYON, S. M. 1985. Detecting internal inconsistencies in distance data. Syst. Zool. 34:397-403.
59. MADDISON, D. R., AND W. P. MADDISON. 2001a. Genesis: Models of character evolution, version 0.96. Available online at http://mesquiteproject.org.
60. MADDISON, W. P., AND D. R. MADDISON. 2001b. Mesquite: A modular system for evolutionary analysis, version 0.98. Available online at http://mesquiteproject.org.
61. MILLER, R. G. 1974. The jackknife - A review. Biometrika 61:1-15.
62. MIYAMOTO, M. M., AND W. M. FITCH. 1995. Testing species phylogenies and phylogenetic methods with congruence. Syst. Biol. 44:64-76.
63. MORITZ, C., AND D. M. HILLIS. 1996. Molecular systematics: Context and controversies. Pages 1-13 in Molecular systematics, 2nd edition (D. M. Hillis, C. Moritz, and B. K. Mable, eds.). Sinauer, Sunderland, Massachusetts.
64. MORRISON, D. A., AND J. T. ELLIS. 1997. Effects of nucleotide sequence alignment on phylogeny estimation: A case study of 18S rDNAs of Apicomplexa. Mol. Biol. Evol. 14:428-441.
65. MUELLER, L. D., AND F. J. AYALA. 1982. Estimation and interpretation of genetic distance in empirical studies. Genet. Res. Camb. 40:127-137.
66. NIXON, K. C. 1999. The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics 15:407-414.
67. NIXON, K. C. 2002. WinClada, version 1.00.04. Program and documentation. Available online at http://www.cladistics.com. Published by the author, Ithaca, New York.
68. NIXON, K. C., AND J. M. CARPENTER. 1996. On simultaneous analysis. Cladistics 12:221-241.
69. O'KEEFE, R. F., AND P. J. WAGNER. 2001. Inferring and testing hypotheses of cladistic character dependence by using character compatibility. Syst. Biol. 50:657-675.
70. PAGE, R. D. M. 2000. Comparative analysis of secondary structure of insect mitochondrial small subunit ribosomal RNA using maximum weighted matching. Nucleic Acids Res. 13:131-144.
71. PAGEL, M. 1994. Detecting correlated evolution on phylogenies: A general method for the comparative analysis of discrete characters. Proc. R. Soc. Lond. B 13:131-144.
72. PENNY, D., AND M. HENDY. 1986. Estimating the reliability of evolutionary trees. Mol. Biol. Evol. 3:403-417.
73. PERES-NETO, P. R., AND F. MARQUES. 2000. When are random data not random, or is the PTP test useful? Cladistics 16:420-424.
74. PIELOU, C. E. 1966. The measurement of diversity in different types of biological collections. J. Theor. Biol. 13:131-144.
75. PIELOU, C. E. 1975. Ecological diversity. Wiley & Sons, New York.
76. SANDERSON, M. J. 1989. Confidence limits on phylogenies: The bootstrap revisited. Cladistics 5:113-129.
77. SANDERSON, M. J. 1995. Objections to bootstrapping phylogenies: A critique. Syst. Biol. 44:299-320.
78. SANDERSON, M. J., AND M. J. DONOGHUE. 1989. Patterns of variation in levels of homoplasy. Evolution 43:1781-1795.
79. SCHARFF, N., AND J. A. CODDINGTON. 1997. A phylogenetic analysis of the orb-weaving spider family Araneidae (Arachnida, Araneae). Zool. J. Linn. Soc. 120:355-434.
80. SELDEN, P. A. 1993. Fossil arachnids-Recent advances and future prospects. Mem. Queensl. Mus. 33:389-400.
81. SHULTZ, J. W. 1990. Evolutionary morphology and phylogeny of Arachnida. Cladistics 6:1-38.
82. SIDDALL, M. E. 1995. Another monophyly index: Revisiting the jackknife. Cladistics 11:33-56.
83. SIDDALL, M. E. 1998. Success of parsimony in the four-taxon case: Long branch repulsion by likelihood in the Farris zone. Cladistics 14:209-220.
84. SIDDALL, M. E., AND M. F. WHITING. 1999. Long-branch abstractions. Cladistics 15:9-24.
85. SOBER, E. 1988. Reconstructing the past: Parsimony, evolution and inference. Massachusetts Institute of Technology Press, Cambridge.
86. SULLIVAN, J., AND D. L. SWOFFORD. 2001. Should we use model-based methods for phylogenetic inference when we know that assumptions about among-site rate variation and nucleotide substitution pattern are violated? Syst. Biol. 50:723-729.
87. SWOFFORD, D. L., J. L. THORNE, J. FELSENSTEIN, AND B. M. WIEGMANN. 1996. The topology-dependent permutation test for monophyly does not test for monophyly. Syst. Biol. 45:575-579.
88. SWOFFORD, D. L., P. J. WADDELL, J. P. HUELSENBECK, P. G. FOSTER, P. O. LEWIS, AND J. S. ROGERS. 2001. Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Syst. Biol. 50:525-539.
89. TITUS, T. A., AND D. R. FROST. 1996. Molecular homology assessment and phylogeny in the lizard family Opluridae (Squamata: Iguania). Mol. Phylogenet. Evol. 6:49-62.
90. TUKEY, J. W. 1977. Exploratory data analysis. Addison-Wesley, Reading, Massachusetts.
91. VANE-WRIGHT, R. I., C. J. HUMPHRIES, AND P. H. WILLIAMS. 1991. What to protect? - Systematics and the agony of choice. Biol. Conserv. 55:235-254.
92. WENZEL, J. W. 1997. When is a phylogenetic test good enough? Mém. Mus. Natl. Hist. Nat. Paris 173:31-45.
93. WENZEL, J. W., AND M. E. SIDDALL. 1999. Noise. Cladistics 15:51-64.
94. WHEELER, W. C., AND C. Y. HAYASHI. 1998. The phylogeny of the extant chelicerate orders. Cladistics 14:173-192.
95. WILKINSON, M. 1995. Coping with abundant missing entries in phylogenetic inference using parsimony. Syst. Biol. 44:501-514.
96. WOLLENBERG, K. R. AND W. R. ATCHLEY. 2000. Separation of phylogenetic and functional associations in biological sequences by using the parametric bootstrap. Proc. Natl. Acad. Sci. USA 97:3288-3291.
97. ZUJKO-MILLER, C., AND J. A. MILLER. 2002. PEST: Precision estimated by sampling traits, version 1.0. Program and documentation. Available online at http://www.gwu.edu/~spiders/pest.htm. Published by the authors, Washington, D.C.