The utility of the incongruence length difference test

Systematic Biology

Volumn 51, Issue 4, 2002, Pages 625-637

  Barker, F Keith ^a   Lutzoni, François M ^b  

^a DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

^b DUKE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DNA SEQUENCE; PHYLOGENY;

PHYLOGENY; SEQUENCE ANALYSIS, DNA;

EID: 0036699888     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/10635150290102302     Document Type: Article

References (46)

1. Archie, J. W. 1996. Measures of homoplasy. Pages 153-188 in Homoplasy: The recurrence of similarity in evolution (M. J. Sanderson and L. Hufford, eds.). Academic Press, San Diego, CA.
2. Archie, J. W., and J. Felsenstein. 1993. The number of evolutionary steps on random and minimum length trees for random evolutionary data. Theor. Popul. Biol. 43:52-79.
3. Barrett, M., M. J. Donoghue, and E. Sober. 1991. Against consensus. Syst. Zool. 40:486-493.
4. Brower, A. V. Z., R. Desalle, and A. Vogler. 1996. Gene trees, species trees, and systematics: A cladistic perspective. Annu. Rev. Ecol. Syst. 27:423-450.
5. 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.
6. Carbone, I., J. B. Anderson, and L. M. Kohn. 1999. Patterns of descent in clonal lineages and their multilocus fingerprints are resolved with combined gene genealogies. Evolution 53:11-21.
7. Chippindale, P. T., and J. J. Wiens. 1994. Weighting, partitioning, and combining characters in phylogenetic analysis. Syst. Biol. 43:278-287.
8. Colless, D. H. 1980. Congruence between morphometric and allozyme data for Menidia species: A reappraisal. Syst. Zool. 29:288-299.
9. Cunningham, C. W. 1997a. Can three incongruence tests predict when data should be combined? Mol. Biol. Evol. 14:733-740.
10. Cunningham, C. W. 1997b. Is congruence between data partitions a reliable predictor of phylogenetic accuracy? Empirically testing an iterative procedure for choosing among phylogenetic methods. Syst. Biol. 46:464-478.
11. Darlu, P., and G. Lecointre. 2002. When does the incongruence length difference test fail? Mol. Biol. Evol. 19:432-437.
12. Desalle, R., and A. V. Z. Brower. 1997. Process partitions, congruence, and the independence of characters: Inferring relationships among closely related Hawaiian Drosophila from multiple gene regions. Syst. Biol. 46:751-764.
13. Dolphin, K., R. Belshaw, C. D. L. Orme, and D. L. J. Quicke. 2000. Noise and incongruence: Interpreting results of the incongruence length difference test. Mol. Phylogenet. Evol. 17:401-406.
14. Dowton, M., and A. D. Austin. 2002. Increased incongruence does not necessarily indicate increased phylogenetic accuracy-The behavior of the ILD test in mixed-model analyses. Syst. Biol. 51:19-31.
15. Farris, J. S., M. KaÌllersjoÌ, A. G. Kluge, and C. Bult. 1995a. Constructing a significance test for incongruence. Syst. Biol. 44:570-572.
16. Farris, J. S., M. KaÌllersjoÌ, A. G. Kluge, and C. Bult. 1995b. Testing significance of incongruence. Cladistics 10:315-319.
17. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17:368-376.
18. Geiser, D. M., J. I. Pitt, and J. W. Taylor. 1998. Cryptic speciation and recombination in the aflatoxin producing fungus Aspergillus flavus. Proc. Natl. Acad. Sci. USA 95:388-393.
19. Giribet, G., G. D. Edgecombe, and W. C. Wheeler. 2001. Arthropod phylogeny based on eight molecular loci and morphology. Nature 413:157-161.
20. Graham, S. W., J. R. Kohn, B. R. Morton, J. E. Eckenwalder, and S. C. H. Barrett. 1998. Phylogenetic congruence and discordance among one morphological and three molecular data sets from Pontederiaceae. Syst. Biol. 47:545-567.
21. Hasegawa, M., H. Kishino, and T. Yano. 1985. Dating the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22:160-174.
22. Huelsenbeck, J. P., and J. J. Bull. 1996. A likelihood ratio test to detect conflicting phylogenetic signal. Syst. Biol. 45:92-98.
23. Jukes, T. H., and C. R. Cantor. 1969. Evolution of protein molecules. Pages 21-132 in Mammalian protein metabolism (H. N. Munro, ed.). Academic Press, New York.
24. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.
25. Kluge, A. G., and A. J. Wolf. 1993. Cladistics: What's in a word? Cladistics 9:183-199.
26. Koufopanou, V., A. Burt, and J. W. Taylor. 1997. Concordance of gene genealogies reveals reproductive isolation in the pathogenic fungus Coccidioides immitis. Proc. Natl. Acad. Sci. USA 94:5478-5482.
27. Lutzoni, F. M. 1997. Phylogeny of lichen- and non-lichen-forming omphalinoid mushrooms and the utility of testing for combinability among multiple data sets. Syst. Biol. 46:373-406.
28. Lutzoni, F. M., and R. Vilgalys. 1995. Integration of morphological and molecular data sets in estimating fungal phylogenies. Can. J. Bot. 73:S649-S659.
29. Maddison, W. P., and D. R. Maddison. 1999. MacClade: Analysis of phylogeny and character evolution, version 3.08. Sinauer, Sunderland, Massachusetts.
30. Mason-Gamer, R. J., and E. A. Kellogg. 1996. Testing for phylogenetic conflict among molecular data sets in the tribe Triticeae (Gramineae). Syst. Biol. 45:524-545.
31. Mickevich, M. F., and M. S. Johnson. 1976. Congruence between morphological and allozyme data in evolutionary inference and character evolution. Syst. Zool. 25:260-270.
32. Nixon, K. C., and J. M. Carpenter. 1996. On simultaneous analysis. Cladistics 12:221-241.
33. Rambaut, A., and N. C. Grassly. 1997. Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13:235-238.
34. Reed, R. D., and F. A. H. Sperling. 1999. Interaction of process partitions in phylogenetic analysis: An example from the swallowtail butterfly genus Papilio. Mol. Biol. Evol. 16:286-297.
35. Rodrigo, A. G., M. Kelly-Borges, P. R. Bergquist, and P. L. Bergquist. 1993. A randomisation test of the null hypothesis that two cladograms are sample estimates of a parametric phylogenetic tree. N.Z.J. Bot. 31:257-268.
36. Stanger-Hall, I. K., and C. W. Cunningham. 1998. Support for a monophyletic Lemuriformes: Overcoming incongruence between data partitions. Mol. Biol. Evol. 15:1572-1577.
37. Sullivan, J. 1996. Combining data with different distributions of among-site variation. Syst. Biol. 45:375-380.
38. Swofford, D. L. 1998. PAUP*: Phylogenetic analysis using parsimony (*and other methods), version 4.0. Sinauer, Sunderland, Massachusetts.
39. Templeton, A. R. 1983. Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the humans and apes. Evolution 37:221-244.
40. Vidal, N., and G. Lecointre. 1998. Weighting and congruence: A case study based on three mitochondrial genes in vipers. Mol. Phylogenet. Evol. 9:366-374.
41. Wenzel, J. W., and M. E. Siddall. 1999. Noise. Cladistics 15:51-64.
42. Wilgenbusch, J., and K. de Quieroz. 2000. Phylogenetic relationships among the phrynosomatid sand lizards inferred from mitochondrial DNA sequences generated by heterogeneous evolutionary processes. Syst. Biol. 49:592-612.
43. Yang, Z. 1993. Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol. Biol. Evol. 10:1396-1401.
44. Yang, Z. 1996. Maximum-likelihood models for combined analyses of multiple sequence data. J. Mol. Evol. 42:587-596.
45. Yang, Z. 2000. Phylogenetic analysis by maximum likelihood (PAML), version 3.0c. Univ. College, London.
46. Yoder, A. D., J. A. Irwin, and B. A. Payseur. 2001. Failure of the ILD to determine data combinability for slow loris phylogeny. Syst. Biol. 50:408-424.