Interaction of process partitions in phylogenetic analysis: An example from the swallowtail butterfly genus Papilio

Molecular Biology and Evolution

Volumn 16, Issue 2, 1999, Pages 286-297

  Reed, Robert D ^a,b   Sperling, Felix A H ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b University of Arizona   (United States)

Author keywords

Elongation factor 1 alpha; Maximum likelihood; Papilio; Phylogeny; Process partition; Total evidence

Indexed keywords

ELONGATION FACTOR 1ALPHA;

ARTICLE; BUTTERFLY; DATA ANALYSIS; DNA SEQUENCE; GENETIC ANALYSIS; GENETIC CODE; MITOCHONDRIAL MEMBRANE; MOLECULAR EVOLUTION; MOLECULAR INTERACTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PROTEIN SYNTHESIS INHIBITION;

EURYTIDES; INSECTA; PACHLIOPTA; PAPILIO; PAPILIONIDAE;

EID: 0033066833     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a026110     Document Type: Article

References (55)

1. BROWER, A. V. Z., and R. DESALLE. 1994. Practical and theoretical considerations for choice of a DNA sequence region in insect molecular systematics, with a short review of published studies using nuclear gene regions. Ann. Entomol. Soc. Am. 87:702-716.
2. 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.
3. CATERINO, M. S., and F. A. H. SPERLING. 1999. Papilio phylogeny based on mitochondrial cytochrome oxidase I and II genes. Mol. Phylogenet. Evol. 9 (in press).
4. CHANG, J. T. 1996. Inconsistency of evolutionary tree topology reconstruction methods when substitution rates vary across characters. Math. Biosci. 134:189-215.
5. CHIPPINDALE, P. T., and J. J. WIENS. 1994. Weighting, partitioning, and combining characters in phylogenetic analysis. Syst. Biol. 43:278-287.
6. CHO, S., A. MITCHELL, J. C. REGIER, C. MITTER, R. W. POOLE, T. P. FRIEDLANDER, and S. ZHAO. 1995. A highly conserved nuclear gene for low-level phylogenetics: elongation factor1 α recovers morphology-based tree for heliothine moths. Mol. Biol. Evol. 12:650-656.
7. CLARKE, C. A., I. J. GORDON, C. R. SMITH, and R. I. VANEWRIGHT. 1991. Phylogenetic relationships of three African swallowtail butterflies, Papilio dardanus, P. phorcas and P. constantinus: new data from hybrids (Lepidoptera: Papilionidae). Syst. Entomol. 16:257-273.
8. CUNNINGHAM, C. W. 1997. 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.
9. DE QUEIROZ, A. 1993. For consensus (sometimes). Syst. Biol. 42:368-372.
10. DE QUEIROZ, A., M. J. DONOGHUE, and J. KIM. 1995. Separate versus combined analysis of phylogenetic evidence. Annu. Rev. Ecol. Syst. 26:657-681.
11. 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.
12. FANG, Q. Q., S. CHO, J. C. REGIER, C. MITTER, M. MATTHEWS, R. W. POOLE, T. P. FRIEDLANDER, and S. ZHO. 1997. A new nuclear gene for insect phylogenetics: dopa decarboxylase is informative of relationships within Heliothinae (Lepidoptera: Noctuidae). Syst. Biol. 46:269-283.
13. FARRIS, J. S., M. KÄLLERSJÖ, A. G. KLUGE, and C. BULT. 1994. Testing significance of incongruence. Cladistics 10:315-319.
14. FELSENSTEIN, J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27: 401-410.
15. FRIEDRICH, M., and D. TAUTZ. 1997. Evolution of phylogeny of the Diptera: a molecular phylogenetic analysis using 28S rDNA sequences. Syst. Biol. 46:674-698.
16. GAUT, B. S., and P. O. LEWIS. 1995. Success of maximum likelihood in the four-taxon case. Mol. Biol. Evol. 12:152-162.
17. GOODMAN, M., A. E. ROMERO-HERRERA, H. DENE, J. CZELUSNIAK, and R. E. TASHIAN. 1982 Amino acid sequence evidence on the phylogeny of primates and other eutherians. Pp. 115-191 in M. GOODMAN, ed. Macromolecular sequences in systematic and evolutionary biology. Plenum Press, New York.
18. GOUY, M., and W.-H. LI. 1989. Phylogenetic analysis based on rRNA sequences supports the archaebacterial tree rather than the eocyte tree. Nature 339:145-147.
19. HANCOCK, D. L. 1983. Classification of the Papilionidae: a phylogenetic approach. Smithersia 2:1-48.
20. HARRISON, R. G. 1989. Mitochondrial DNA as a genetic marker in population and evolutionary biology. Trends Ecol. Evol. 4:6-11.
21. HARRISON, R. G, D. A. RAND, and W. C. WHEELER. 1987. Mitochondrial DNA variation in field crickets across a narrow hybrid zone. Mol. Biol. Evol. 4:144-158.
22. HASEGAWA, M., M. KISHINO, and T. YANO. 1985. Dating the human-ape split by a molecular clock of mitochondrial DNA. J. Mol. Evol. 4:144-158.
23. HILLIS, D. M. 1987. Molecular versus morphological approaches to systematics. Annu. Rev. Ecol. Syst. 18:23-42.
24. HILLIS, D. M., and J. J. BULL. 1993. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst. Biol. 42:182-192.
25. HUELSENBECK, J. P. 1995. Performance of phylogenetic methods in simulation. Syst. Biol. 44:17-48.
26. HUELSENBECK, J. P., J. J. BULL, and C. W. CUNNINGHAM. 1996. Combining data in phylogenetic analysis. Trends Ecol. Evol. 11:152-158.
27. 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.
28. KUHNER, M. K., and J. FELSENSTEIN. 1994. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol. Biol. Evol. 11:459-468.
29. LI, W.-H. 1997. Molecular evolution. Sinauer, Sunderland, Mass.
30. LUTZONI, F. M. 1997. Phylogeny of lichen- and non-lichen-forming omphalinoid mushrooms and the utility of testing for combinability between multiple data sets. Syst. Biol. 46: 373-406.
31. MADDISON, D. R., D. L. SWOFFORD, and W. P. MADDISON. 1997. NEXUS: an extensible file format for systematic information. Syst. Biol. 46:590-621.
32. MADDISON, W. P. 1997. Gene trees in species trees. Syst. Biol. 46:523-536.
33. MADDISON, W. P., and D. R. MADDISON. 1996. MacClade: analysis of phylogeny and character evolution. Version 3.06. Sinauer, Sunderland, Mass.
34. 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.
35. MILLER, J. S. 1987. Phylogenetic studies in the Papilioninae (Lepidoptera: Papilionidae). Bull. Am. Mus. Nat. Hist. 186: 365-512.
36. MITCHELL, A., S. CHO, J. C. REGIER, C. MITTER, R. W. POOLE, and M. MATTHEWS. 1997. Phylogenetic utility of elongation factor-1 α in Noctuoidea (Insecta: Lepidoptera): the limits of synonymous substitutions. Mol. Biol. Evol. 14:381-390.
37. MIYAMOTO, M. M., and W. M. FITCH. 1995. Testing species phylogenies and phylogenetic methods with congruence. Syst. Biol. 44:64-76.
38. MUNROE, E. 1961. The classification of the Papilionidae (Lepidoptera). Can. Entomol. Suppl. 17:1-51.
39. PENNINGTON, R. T. 1996. Molecular and morphological data provide phylogenetic resolution at different hierarchical levels in Andira. Syst. Biol. 45:496-515.
40. SANDERSON, M. J. 1989. Confidence limits on phylogenies: the bootstrap revisited. Cladistics 5:113-129.
41. SPERLING, F. A. H. 1993. Mitochondrial DNA variation and Haldane's rule in the Papilio glaucus and Papilio troilus species groups. Heredity 71:227-233.
42. SPERLING, F. A. H., and R. G. HARRISON. 1994. Mitochondrial DNA variation within and between species of the Papilio machaon group of swallowtail butterflies. Evolution 48: 408-422.
43. SWOFFORD, D. L. 1991. Manual for PAUP: phylogenetic analysis using parsimony. Version 3.1. Formerly distributed by Illinois Natural History Survey, Champaign, Illinois.
44. SWOFFORD, D. L., G. J. OLSEN, P. J. WADDELL, and D. M. HILLIS. 1996. Phylogenetic inference. Pp. 407-514 in D. M. HILLIS, C. MORITZ, and B. K. MABLE, eds. Molecular systematics. 2nd edition. Sinauer, Sunderland, Mass.
45. TAMURA, K., and M. NEI. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10:512-526.
46. VANE-WRIGHT, R. I., and C. R. SMITH. 1991. Phylogenetic relationships of three African swallowtail butterflies, Papilio dardanus, P. phorcas and P. constantinus: a cladistic analysis (Lepidoptera: Papilionidae). Syst. Entomol. 16: 275-291.
47. _. 1992. Occurrence and significance of natural hybrids between Papilio dardanus and P. phorcas (Lepidoptera: Papilionidae). Syst. Entomol. 17:269-272.
48. VILLABLANCA, F. X. 1993. Population genetics and phylogenetics in kangaroo rats (Rodentia: Heteromyidae). Ph.D. dissertation, University of California, Berkeley.
49. WAKELEY, J. 1993. Substitution rate variation among sites in hypervariable region 1 of human mitochondrial DNA. J. Mol. Evol. 37:613-623.
50. WHITING, M. F., J. C. CARPENTER, Q. D. WHEELER, and W. C. WHEELER. 1997. The Strepsiptera problem: phylogeny of the holometabolous insect orders inferred from 18S and 28S ribosomal DNA sequences and morphology. Syst. Biol. 46: 1-68.
51. YANG, Z. 1993. Maximum likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol. Biol. Evol. 10:1396-1401.
52. _. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39:306-314.
53. _. 1996. Maximum-likelihood models for combined analyses of multiple sequence data. J. Mol. Evol. 42:587-596.
54. _. 1997. Phylogenetic analysis by maximum likelihood (PAML). Version 1.3. Department of Integrative Biology, University of California, Berkeley.
55. ZAMUDIO, K. R., K. B. JONES, and R. H. WARD. 1997. Molecular systematics of short-horned lizards: biogeography and taxonomy of a widespread species complex. Syst. Biol. 46: 284-305.