More taxa or more characters revisited: Combining data from nuclear protein-encoding genes for phylogenetic analyses of Noctuoidea (Insecta: Lepidoptera)

Systematic Biology

Volumn 49, Issue 2, 2000, Pages 202-224

  Mitchell, Andrew ^a,b   Mitter, Charles ^a   Regier, Jerome C ^c  

^a UNIVERSITY OF MARYLAND   (United States)

^b UNIVERSITY OF ALBERTA   (Canada)

^c UNIVERSITY OF MARYLAND BIOTECHNOLOGY INSTITUTE   (United States)

Author keywords

Combining data; Independent genes; Noctuidae; Noctuoidea; Taxon sampling

Indexed keywords

HEXAPODA; INSECTA; LEPIDOPTERA; NOCTUIDAE; NOCTUOIDEA;

ELONGATION FACTOR 1; INSECT PROTEIN; NUCLEAR PROTEIN; PRIMER DNA;

ANIMAL; ARTICLE; CLASSIFICATION; COMPARATIVE STUDY; COMPUTER PROGRAM; GENETICS; LEPIDOPTERA; NUCLEOTIDE SEQUENCE; PHYLOGENY; REPRODUCIBILITY;

ANIMALS; BASE SEQUENCE; DNA PRIMERS; INSECT PROTEINS; LEPIDOPTERA; NUCLEAR PROTEINS; PEPTIDE ELONGATION FACTOR 1; PHYLOGENY; REPRODUCIBILITY OF RESULTS; SOFTWARE;

EID: 0034350422     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1093/sysbio/49.2.202     Document Type: Article

References (59)

1. BECK, H. 1960. Die Larvalsystematik der Eulen (Noctuidae). Akademie Verlag, Berlin.
2. BECK, H. 1992. New view of the higher classification of the Noctuidae (Lepidoptera). Nota Lepid. 15:3-28.
3. 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.
4. CHO, S., A. MITCHELL, J. C. REGIER, C. MITTER, R. W. POOLE, T. P. FRIEOLANDER, AND S. ZHAO. 1995. A highly conserved nuclear gene for low-level phylogenetics: Elongation factor-1αrecovers morphology-based tree for heliothine moths. Mol. Biol. Evol. 12:650-656.
5. CUMMINGS, M. P., S. P. OTTO, AND J. WAKELY. 1995. Sampling properties of DNA sequence data in phylogenetic analysis. Mol. Biol. Evol. 12:814-822.
6. CUNNINGHAM, C. W. 1997a. 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.
7. CUNNINGHAM, C. W. 1997b. Can three incongruence tests predict when data should be combined? Mol. Biol. Evol. 14:733-740.
8. FANG, Q. Q., S. CHO, J. C. REGIER, C. MITTER, M. MATTHEWS, R. W. POOLE, T. P. FRIEDLANDER, AND S. ZHAO. 1997. A new nuclear gene for insect phylogenetics: Dopa decarboxylase is informative of relationships within the Heliothinae (Lepidoptera: Noctuidae). Syst. Biol. 46:269-283.
9. FANG, Q. Q., A. MITCHELL, J. C. REGIER, C. MITTER, T. P. FRIEDLANDER, AND R. W. POOLE. 2000. Phylogenetic utility of the nuclear gene dopa decarboxylase (DDC) in noctuoid moths (Insecta: Lepidoptera: Noctuoidea). Mol. Phylogenet. Evol. (in press).
10. FARRIS, J. S., M. KÄLLERSJÖ, A. G. KLUGE, AND C. BULT. 1994. Testing the significance of incongruence. Cladistics 10:315-319.
11. FELSENSTEIN, J. 1978a. The number of evolutionary trees. Syst. Zool. 27:27-33.
12. FELSENSTEIN, J. 1978b. Cases in which parsimony and compatibility methods will be positively misleading. Syst. Zool. 27:401-410.
13. FELSENSTEIN, J. 1995. PHYLIP (phylogeny inference package), version 3.572. Department of Genetics, University of Washington, Seattle.
14. FRATI, F., C. SIMON, J. SULLIVAN, AND D. L. SWOFFORD. 1997. Evolution of the mitochondrial cytochrome oxidase II gene in Collembola. J. Mol. Evol. 44:145-158.
15. FRIEDLANDER, T. P., J. C. REGIER, AND C. MITTER. 1992. Nuclear gene sequences for higher-level phylogenetic analysis: 14 promising candidates. Syst. Biol. 41:483-489.
16. FRIEDLANDER, T. P., J. C. REGIER, C. MITTER, AND D. L. WAGNER. 1996. A nuclear gene for higher-level phylogenetics: Phosophoenolpyruvate carboxykinase tracks Mesozoic-age divergences within Lepidoptera (Insecta). Mol. Biol. Evol. 13:594-604.
17. GALLOWAY, G. L., R. L. MALMBERG, AND R. A. PRICE. 1998. Phylogenetic utility of the nuclear gene arginine decarboxylase: An example from the Brassicaceae. Mol. Biol. Evol. 15:1312-1320.
18. GRAYBEAL, A. 1994. Evaluating the phylogenetic utility of genes: A search for genes informative about deep divergences among vertebrates. Syst. Biol. 43:174-193.
19. GRAYBEAL, A. 1998. Is it better to add taxa or characters to a difficult phylogenetic problem? Syst. Biol. 47:9-17.
20. GUPTA, R. S. 1995. Phylogenetic utility of the 90kD heat shock family of protein sequences and an examination of the relationship among animals, plants and fungi species. Mol. Biol. Evol. 12:1063-1073.
21. HASEGAWA, M., H. KISHINO, AND T. YANO. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 21:160-174.
22. HILLIS, D. M. 1996. Inferring complex phylogenies. Nature 383:130-131.
23. HILLIS, D. M. 1998. Taxonomic sampling, phylogenetic accuracy, and investigator bias. Syst. Biol. 47:3-8.
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. HOLLOWAY, J. D. 1989. The moths of Borneo. Part 12. Noctuidae: Noctuinae, Heliothinae, Hadeninae, Acronictinae, Amphipyrinae, Agaristinae. Southdene, Kuala Lampur.
26. HUELSENBECK, J. P., J. J. BULL., AND C. W. CUNNINGHAM. 1996. Combining data in phylogenetic analysis. Trends Ecol. Evol. 11:152-158.
27. INTERNATIONAL UNION OF BIOCHEMISTRY. 1986. Nomenclature for incompletely specified bases in nucleic acid sequences. Mol. Biol. Evol. 3:99-108.
28. KIM, J. 1996. General inconsistency conditions for maximum parsimony: Effects of branch lengths and increasing numbers of taxa. Syst. Biol. 45:363-374.
29. KISHINO, H., AND M. HASEGAWA. 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J. Mol. Evol. 29:170-179.
30. KITCHING, I. J. 1984. An historical review of the higher classification of the Noctuidae (Lepidoptera). Bull. Br. Mus. Nat. Hist. (Entomol.) 49:153-234.
31. KITCHING, I. J., AND J. E. RAWLINS. 1999. Noctuoidea. Pages 355-401 in Handbook of zoology. Lepidoptera, volume 1: Systematics and evolution (N. P. Kristensen, ed.). W. de Gruyter, Berlin.
32. LAFONTAINE, J. D. 1993. Cutworm systematics: Confusions and solutions. Mem. Entomol. Soc. Can. 165:189-196.
33. LAFONTAINE, J. D., AND R. W. POOLE. 1991. Noctuoidea, Noctuidae (Part), Plusiinae. Moths of America north of Mexico, Fascicle 25.1. The Wedge Entomological Research Foundation, Washington, DC.
34. LANAVE, C., J. PREPARATA, C. SACCONE, AND G. SERIO. 1984. A new method for calculating evolutionary substitution rates. J. Mol. Evol. 20:86-93.
35. LI, W.-H. 1993. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 36:96-99.
36. LOCKART, P. J., M. A. STEEL, M. D. HENDY, AND D. PENNY. 1994. Recovering evolutionary trees under a more realistic model of sequence evolution. Mol. Biol. Evol. 11:605-612.
37. MILLER, J. S. 1991. Cladistics and classification of the Notodontidae (Lepidoptera: Noctuoidea) based on larval and adult morphology. Bull. Am. Mus. Nat. Hist. 204:1-230.
38. MITCHELL, A., S. CHO, J. C. REGIER, C. MITTER, R. W. POOLE, AND M. MATTHEWS. 1997. Phylogenetic utility of elongation factor-1α in Noctuoidea (Insecta: Lepidoptera): The limits of synonymous substitution. Mol. Biol. Evol. 14:381-390.
39. MIYAMOTO, M. M., AND W. M. FITCH. 1995. Testing species phylogenies and phylogenetic methods with congruence. Syst. Biol. 44:64-76.
40. ORTÍ, G., AND A. MEYER. 1996. Molecular evolution of ependymin and the phylogenetic resolution of early divergences among euteleost fishes. Mol. Biol. Evol. 13:556-574.
41. POE, S. 1998. The effect of taxonomic sampling on accuracy of phylogeny estimation: Test case of a known phylogeny. Mol. Biol. Evol. 15:1086-1090.
42. POE, S., AND D. L. SWOFFORD. 1999. Taxon sampling revisited. Nature 398:299-300.
43. POOLE, R. W. 1995. Noctuoidea. Noctuidae (part). Cuculliinae, Stiriinae, Psaphidinae (part). Moths of America north of Mexico, Fascicle 26.1. The Wedge Entomological Research Foundation. Washington, DC.
44. REGIER, J. C., AND J. W. SHULTZ. 1997. Molecular phylogeny of the major arthropod groups indicates polyphyly of crustaceans and a new hypothesis for the origin of hexapods. Mol. Biol. Evol. 14:902-913.
45. RODRIGUEZ, F., J. L. OLIVER, A. MARIN, AND J. R. MEDINA. 1990. The general stochastic model of nucleotide substitution. J. Theor. Biol. 142:485-501.
46. RZHETSKY, A., AND M. NEI. 1992. A simple method for estimating and testing minimum evolution trees. Mol. Biol. Evol. 9:945-967.
47. SCOBLE, M. J. 1992. The Lepidoptera. Form, function and diversity. Oxford Univ. Press, Oxford, U.K.
48. SLADE, R. W., C. MORITZ, AND A. HEIDEMAN. 1994. Multiple nuclear-gene phylogenies: Application to pinnipeds and comparison with a mitochondrial DNA gene phylogeny. Mol. Biol. Evol. 11:341-356.
49. SMITH, S. W., R. OVERBEEK, C. R. WOESE, W. GILBERT, AND P. M. GILLEVET. 1994. The genetic data environ-ment and expandable GUI for multiple sequence analysis. Comput. Appl. Biosci. 10:671-675.
50. SPEIDEL, W., H. FANGER, AND C. M. NAUMANN. 1996. The phylogeny of the Noctuidae (Lepidoptera). Syst. Entomol. 21:219-251.
51. STADEN, R. 1992. STADEN package. MRC Laboratory of Molecular Biology, Cambridge, U.K.
52. SULLIVAN, J. 1996. Combining data with different distributions of among-site variation. Syst. Biol. 45:375-380.
53. 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.
54. SWOFFORD, D. L., G. J. OLSEN, P. J. WADDELL, AND D. M. HILLIS. 1996. Phylogenetic inference. Pages 407-514 in Molecular systematics, 2nd edition (D. M. Hillis, C. Moritz, and B. K. Mable, eds.). Sinauer Associates, Sunderland, Massachusetts.
55. SWOFFORD, D. L. 1999. PAUP*. Phylogenetic analysis using parsimony (* and other methods). Version 4. Sinauer Associates, Sunderland, Massachusetts.
56. WATERS, E. R. 1995. An evaluation of the usefulness of the small heat shock genes for phylogenetic analysis in plants. Ann. Mo. Bot. Gard. 82:278-295.
57. WELLER, S. J., D. P. PASHLEY, J. A. MARTIN, AND J. L. CONSTABLE. 1994. Phylogeny of noctuoid moths and the utility of combining independent nuclear and mitochondrial genes. Syst. Biol. 43:194-211.
58. ZAR, J. H. 1984. Biostatistical analysis, 2nd edition. Prentice Hall, Englewood Cliffs, New Jersey.
59. ZHARKIKH, A., AND W.-H. LI. 1995. Estimation of confidence in phylogeny: The complete-and-partial bootstrap technique. Mol. Phylogenet. Evol. 4:44-63.