Process partitions, congruence, and the independence of characters: inferring relationships among closely related Hawaiian Drosophila from multiple gene regions

Systematic Biology

Volumn 46, Issue 4, 1997, Pages 751-764

  Desalle, Rob ^a   Brower, Andrew V Z ^a,b  

^a DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

^b OREGON STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HAWAIIA;

DNA; MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; CLASSIFICATION; COMPARATIVE STUDY; DROSOPHILA; GENE; GENETICS; ISOLATION AND PURIFICATION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; STATISTICAL ANALYSIS; UNITED STATES;

ANIMALS; BASE SEQUENCE; DATA INTERPRETATION, STATISTICAL; DNA; DNA, MITOCHONDRIAL; DROSOPHILA; GENES, INSECT; HAWAII; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE HOMOLOGY, NUCLEIC ACID; SPECIES SPECIFICITY;

EID: 0031350120     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1093/sysbio/46.4.751     Document Type: Article

References (90)

1. ALLARD, M. W., AND J. M. CARPENTER. 1996. On weighting and congruence. Cladistics 12:183-198.
2. AVISE, J. C. 1994. Molecular markers, natural history and evolution. Chapman and Hall, New York.
3. BAKER, R., AND R. DESALLE. 1997. Multiple sources of character information and the phylogeny of Hawaiian drosophilids. Syst. Biol. 46:654-673.
4. BARRETT, M., M. J. DONOGHUE, AND E. SOBER. 1991. Against consensus. Syst. Zool. 40:486-493.
5. BECKENBACH, A. T., Y. W. WEI, AND H. LIU. 1993. Relationships in the Drosophila obscura species group, inferred from mitochondrial cytochrome oxidase II sequences. Mol. Biol. Evol. 10:619-634.
6. BOOKSTEIN, F. L. 1994. Can biometrical shape be a homologous character? Pages 197-227 in Homology: The hierarchical basis of comparative biology (B. K. Hall, ed.). Academic Press, San Diego, California.
7. BRADY, R. H. 1983. Parsimony, hierarchy, and biological implications. Pages 49-60 in Advances in cladistics, Volume 2 (N. I. Platnick and V. A. Funk, eds.). Columbia Univ. Press, New York.
8. BRADY, R. H. 1985. On the independence of systematics. Cladistics 1:113-126.
9. BRADY, R. H. 1994. Pattern description, process explanation, and the history of morphological sciences. Pages 7-31 in Interpreting the hierarchy of nature (L. Grande and O. Rieppel, eds.). Academic Press, San Diego, California.
10. BREMER, K. 1988. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42:795-803.
11. BREMER, K. 1990. Combinable component consensus. Cladistics 6:369-372.
12. BREMER, K. 1994. Branch support and tree stability. Cladistics 10:295-304.
13. BROWER, A. V. Z. 1994a. Phylogeny of Heliconius butterflies inferred from mitochondrial DNA sequences (Lepidoptera: Nymphalidae). Mol. Phylogenet. Evol. 3:159-174.
14. BROWER, A. V. Z. 1994b. Rapid morphological radiation and convergence among races of the butterfly Heliconius erato inferred from patterns of mitochondrial DNA evolution. Proc. Natl. Acad. Sci. USA 91: 6491-6495.
15. BROWER, A. V. Z. 1996. Combining data in phylogenetic analysis (a response to Huelsenbeck et al. 1996). Trends Ecol. Evol. 11:334-335.
16. 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.
17. BROWER, A. V. Z., R. DESALLE, AND A. P. VOGLER. 1996. Gene trees, species trees and systematics: A cladistic perspective. Annu. Rev. Ecol. Syst. 27:423-450.
18. 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.
19. CARSON, H. L. 1982. The evolution of Drosophila on the newer Hawaiian volcanoes. Heredity 48:3-25.
20. CARSON, H. L. 1987. Tracing ancestry with chromosomal sequences. Trends Ecol. Evol. 2:203-207.
21. CHIPPINDALE, P. T., AND J. J. WIENS. 1994. Weighting, partitioning, and combining characters in phylogenetic analysis. Syst. Biol. 43:278-287.
22. CRACRAFT, J. 1987. DNA hybridization in avian systematics. Pages 47-96 in Evolutionary biology, Volume 21 (M. K. Hecht, B. Wallace, and G. T. Prance, eds.). Plenum, New York.
23. CRACRAFT, J., AND K. HELM-BYCHOWSKI. 1991. Parsimony and phylogenetic inference using DNA sequences: Some methodological strategies. Pages 184-220 in Phylogenetic analysis of DNA sequences (M. M. Miyamoto and J. Cracraft, eds.). Oxford Univ. Press, New York.
24. CRADDOCK, E. M., AND W. E. JOHNSON. 1979. Genetic variation in Hawaiian Drosophila. V. Chromosomal and allozymic diversity in Drosophila silvestris and its homosequential species. Evolution 33:137-155.
25. DE PINNA, M. C. C. 1991. Concepts and tests of homology in the cladistic paradigm. Cladistics 7:367-394.
26. DE QUEIROZ, A. 1993. For consensus (sometimes). Syst. Biol. 42:368-372.
27. DE QUEIROZ, A., M. J. DONOGHUE, AND J. KIM. 1995. Separate versus combined analysis of phylogenetic evidence. Annu. Rev. Ecol. Syst. 26:657-681.
28. DESALLE, R., T. FREEDMAN, E. M. PRAGER, AND A. C. WILSON. 1987. Tempo and mode of sequence evolution in mitochondrial DNA of Hawaiian Drosophila. J. Mol. Evol. 26:157-164.
29. DESALLE, R., AND L. V. GIDDINGS. 1986. Discordance of nuclear and mitochondrial DNA phylogenies in Hawaiian Drosophila. Proc. Natl. Acad. Sci. USA 83: 6902-6906.
30. DESALLE, R., AND J. A. HUNT. 1987. Molecular evolution in Hawaiian drosophilids. Trends Ecol. Evol. 2:212-216.
31. DESALLE, R., AND A. P. VOGLER. 1994. Phylogenetic analysis on the edge: The application of cladistic techniques at the population level. Pages 154-174 in Non-neutral evolution - Theories and molecular data (B. Golding, ed.). Chapman and Hall, New York.
32. DESALLE, R., A. K. WILLIAMS, AND M. GEORGE. 1993. Isolation and characterization of animal mitochondrial DNA. Methods Enzymol. 224:176-204.
33. DOYLE, J. J. 1992. Gene trees and species trees: Molecular systematics as one-character taxonomy. Syst. Bot. 17:144-163.
34. EERNISSE, 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.
35. FARRIS, J. S. 1971. The hypothesis of nonspecificity and taxonomic congruence. Annu. Rev. Ecol. Syst. 2: 277-302.
36. FARRIS, J. S. 1981. Distance data in phylogenetic analysis. Pages 3-23 in Advances in cladistics, Volume 1 (V. A. Funk and D. R. Brooks, eds.). New York Botanical Garden, New York.
37. 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.
38. FARRIS, J. S. 1985. Distance data revisited. Cladistics 1:67-8-5.
39. FARRIS, J. S., M. KÄLLERSJÖ, A. G. KLUGE, AND C. BULT. 1994. Testing significance of congruence. Cladistics 10:315-320.
40. FARRIS, J. S., M. KÄLLERSJÖ, A. G. KLUGE, AND C. BULT. 1995. Constructing a significance test for incongruence. Syst. Biol. 44:570-572.
41. FARRIS, J. S., AND A. G. KLUGE. 1979. A botanical clique. Syst. Zool. 28:400-411.
42. FARRIS, J. S., AND A. G. KLUGE. 1985. Parsimony, synapomorphy, and explanatory power: A reply to Duncan. Taxon 34:130-135.
43. FELSENSTEIN, J. 1983. Parsimony in systematics: Biological and statistical issues. Annu. Rev. Ecol. Syst. 14:313-333.
44. FOURNIER, D., J. M. BRIDE, AND M. NAVAJAS. 1994. Mitochondrial DNA from a spider mite: Isolation, restriction map and partial sequence of the cytochrome oxidase subunit I gene. Genetica 94:73-75.
45. GRIMALDI, D. A., AND G. FENSTER. 1989. Evolution of extreme sexual dimorphisms: Structural and behavioral convergence among broad-headed male Drosophilidae (Diptera). Am. Mus. Novit. 2939:1-25.
46. HEDGES, S. B., AND L. R. MAXSON. 1996. Re: Molecules and morphology in amniote phylogeny. Mol. Phylogenet. Evol. 6:312-314.
47. HILLIS, D. M. 1987. Molecules versus morphological approaches to systematics. Annu. Rev. Ecol. Syst. 18: 23-42.
48. HO, K.-F. 1994. Phylogeny of Hawaiian Drosophiln inferred from yolk protein gene evolution. Ph.D. Thesis, New York Univ., New York.
49. HUELSENBECK, J. P., AND J. J. BULL. 1996. A likelihood ratio test to detect conflicting phylogenetic signal. Syst. Biol. 45:92-98.
50. HUELSENBECK, J. P., J. J. BULL, AND C. W. CUNNINGHAM. 1996. Combining data in phylogenetic analysis. Trends Ecol. Evol. 11:152-158.
51. HUNT, J. A., AND H. L. CARSON. 1983. Evolutionary relationships of four species of Hawaiian Drosophila as measured by DNA reassociation. Genetics 104: 353-364.
52. KAMBYSELLIS, M. P., K.-F. HO, E. M. CRADDOCK, F. PIANO, M. PARISI, AND J. COHEN. 1995. Pattern of ecological shifts in the diversification of Hawaiian Drosophila inferred from a molecular phylogeny. Curr. Biol. 5:1129-1139.
53. KANESHIRO, K. Y. 1983. Sexual selection and the direction of evolution in the biosystematics of Hawaiian Drosophilid ae. Annu. Rev. Entomol. 28:161-178.
54. KANESHIRO, K. Y., AND C. R. B. BOAKE. 1987. Sexual selection and speciation: Issues raised by Hawaiian Drosophila. Trends Ecol. Evol. 2:207-212.
55. KLUGE, A. G. 1989. A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Syst. Zool. 38:7-25.
56. KLUGE, A. G., AND A. J. WOLF. 1993. Cladistics: What's in a word? Cladistics 9:183-199.
57. KRAFT, R., AND JÄCKLE, H. 1994. Drosophila mode of metamerization in the embryogenesis of the lepidopteran insect Manduca sexta. Proc. Natl. Acad. Sci. USA 91:6634-6638.
58. LANYON, S. M. 1993. Phylogenetic frameworks: Towards a firmer foundation for the comparative approach. Biol. J. Linn. Soc. 49:45-61.
59. LARSON, A. 1994. The comparison of morphological and molecular 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.
60. MADDISON, W. P., AND D. R. MADDISON. 1992. MacClade, version 3.0. Sinauer, Sunderland, Massachusetts.
61. MAYNARD SMITH, J., AND N. H. SMITH. 1996. Site-specific codon bias in bacteria. Genetics 142:1037-1043.
62. MICKEVICH, M. F. 1978. Taxonomic congruence. Syst. Zool. 27:143-158.
63. MICKEVICH, M. F., AND J. S. FARRIS. 1981. The implications of congruence in Menidia. Syst. Zool. 30:351-370.
64. MILLER, J. S., A. V. Z. BROWER, AND R. DESALLE. 1997. Phylogeny of the neotropical moth tribe Josiini (Notodontidae: Dioptinae): Comparing and combining evidence from DNA sequences and morphology. Biol. J. Linn. Soc. 60:297-316.
65. MINDELL, D. P. 1992. DNA-DNA hybridization and avian phylogeny. Syst. Biol. 41:126-134.
66. MIYAMOTO, M. M. 1985. Consensus cladograms and general classifications. Cladistics 1:186-189.
67. MIYAMOTO, M. M., M. W. ALLARD, R. M. ADKINS, L. L. JANECEK, AND R. L. HONEYCUTT. 1994. A congruence test of reliability using linked mitochondrial DNA sequences. Syst. Biol. 43:236-249.
68. MIYAMOTO, M. M., AND J. CRACRAFT. 1991. Phylogenetic inference, DNA sequence analysis, and the future of molecular systematics. Pages 3-17 in Phylogenetic analysis of DNA sequences (M. M. Miyamoto and J. Cracraft, eds.). Oxford Univ. Press, New York.
69. MIYAMOTO, M. M., AND W. M. FITCH. 1995. Testing species phylogenies and phylogenetic methods with congruence. Syst. Biol. 44:64-76.
70. NIXON, K. C., AND J. M. CARPENTER. 1996. On simultaneous analysis. Cladistics 12:305-321.
71. PAGE, R. D. M. 1996. On consensus, confidence, and "total evidence." Cladistics 12:83-92.
72. PANCHEN, A. L. 1992. Classification, evolution and the nature of biology. Cambridge Univ. Press, Cambridge, England.
73. PHILIPPE, H., G. LECOINTRE, H. L. V. LÊ, AND H. LE GUYADER. 1996. A critical study of homoplasy in molecular data with the use of a morphologically based cladogram, and its consequences for character weighting. Mol. Biol. Evol. 13:1174-1186.
74. POPPER, K. R. 1959 (1965). The logic of scientific discovery. Harper Torchbooks, New York.
75. RIJSEWIJK, F., M. SCHUERMANN, E. WAGENAAR, P. PARREN, D. WEIGEL, AND R. NUSSE. 1987. The Drosaphila homologue of the mouse mammary oncogene int-1 is identical to the segment polarity gene wingless. Cell 50:649-657.
76. ROWAN, R. G., AND J. A. HUNT. 1991. Rates of DNA change and phylogeny from the DNA sequences of the alcohol dehydrogenase gene for five closely related species of Hawaiian Drosophila. Mol. Biol. Evol. 8:49-70.
77. SANDERSON, M. J. 1995. Objections to bootstrapping phylogenies: A critique. Syst. Biol. 44:299-320.
78. SIMON, C., F. FRATI, A. BECKENBACH, B. CRESPI, H. LIU, AND P. FLOOK. 1994. Evolution, weighting and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers. Ann. Entomol. Soc. Am. 87:651-701.
79. SULLIVAN, J. 1996. Combining data with different distributions of among-site rate variation. Syst. Biol. 45: 375-380.
80. 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.
81. SWOFFORD, D. L. 1993. PAUP: Phylogenetic analysis using parsimony, version 3.1. Illinois Natural History Survey, Champaign.
82. TAUTZ, D., R. LEHMANN, H. SCHNÜRCH, R. SCHUH, E. SEIFERT, A. KIENLIN, K. JONES, AND H. JACKLE. 1987. Finger protein of novel structure encoded by hunchback, a second member of the gap class of Drosophila segmentation genes. Nature 327:383-389.
83. THOMAS, R. H., AND J. A. HUNT. 1993. Phylogenetic relationships in Drosophila: A conflict between molecular and morphological data. Mol. Biol. Evol. 10: 362-374.
84. WÄGELE, J. W. 1995. On the information content of characters in comparative morphology and molecular systematics. J. Zool. Syst. Evol. Res. 33:42-47.
85. WENZEL, J. W., AND J. M. CARPENTER. 1994. Comparing methods: Adaptive traits and tests of adaptation. Pages 79-101 in Phylogenetics and ecology (P. Eggleton and R. I. Vane-Wright, eds.). Academic Press, London.
86. WHEELER, W. C. 1991. Congruence among data sets: A Bayesian approach. Pages 334-346 in Phylogenetic analysis of DNA sequences (M. M. Miyamoto and J. Cracraft, eds.). Oxford Univ. Press, New York.
87. WHEELER, W. C., AND D. S. GLADSTEIN. 1994. Malign: A multiple sequence alignment program. J. Hered. 85:417-418.
88. WILLIAMS, J. A., S. W PADDOCK, K. VORWERK, AND S. B. CARROLL. 1994. Organization of wing formation and induction of a wing-patterning gene at the dorsal/ventral compartment boundary. Nature 368: 299-305.
89. YANG, Z. 1996. Phylogenetic analysis using parsimony and likelihood methods. J. Mol. Evol. 42:294-307.
90. YANG, Z. 1997. How often do wrong models produce better phylogenies? Mol. Biol. Evol. 14:105-108.