Combining data in phylogenetic analysis

Trends in Ecology and Evolution

Volumn 11, Issue 4, 1996, Pages 152-158

  Huelsenbeck, John P ^a   Bull, J J ^b   Cunningham, Clifford W ^c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^c DUKE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHARACTER INFORMATION; EVOLUTION; PHYLOGENY;

EID: 0029751363     PISSN: 01695347     EISSN: None     Source Type: Journal    
DOI: 10.1016/0169-5347(96)10006-9     Document Type: Review

References (45)

1. Harvey, P.H. and Pagel, M.D. (1991) The Comparative Method in Evolutionary Biology, Oxford University Press
2. Wolfe, K.H. et al. (1988) Mutation rates differ among regions of the mammalian genome, Nature 337, 283-285
3. Luo, C-C. et al. (1989) Structure and expression of dog apolipoprotein A-I, E, and C-I mRNAs: Implications for the evolution and functional constraints of apolipoprotein structure, J. Lipid Res. 30, 1735-1746
4. Stewart, C-B. and Wilson, A.C. (1987) Sequence convergence and functional adaptation of stomach lysozymes from foregut fermenters, Cold Spring Harbor Symp. Quant. Biol. 52, 891-899
5. Kluge, A.G. (1989) A concern for evidence and a phylogenetic hypothesis of relationships among Epic rates (Boidae, Serpentes), Syst. Zool. 38, 7-25
6. Hillis, D.M. (1987) Molecular versus morphological approaches to systematics, Annu. Rev. Ecol. Syst. 18, 23-42
7. Miyamoto, M.M. and Fitch, W.M. (1995) Testing species phylogenies and phylogenetic methods with congruence, Syst. Biol. 44, 64-76
8. de Queiroz, A. (1993) For consensus (sometimes), Syst. Biol. 42, 368-372
9. Penny, D. and Hendy, M.D. (1986) Estimating the reliability of evolutionary trees, Mol. Biol. Evol. 3, 403-417
10. Swofford, D.L. (1991) When are phylogeny estimates from molecular and morphological data incongruent? in Phylogenetic Analysis of DNA Sequences (Miyamoto, M.M. and Cracraft, J., eds), pp. 295-333, Oxford University Press
11. Bull, J.J. et al. (1993) Partitioning and combining data in phylogenetic analysis, Syst. Biol. 42, 384-397
12. Rodrigo, A.G. et al. (1993) A randomization test of the null hypothesis that two cladograms are sample estimates of a parametric phylogenetic tree, N. Z. J. Bot. 31, 257-268
13. Chippindale, P.T. and Wiens, J.J. (1994) Weighting, partitioning, and combining characters in phylogenetic analysis, Syst. Biol. 43, 278-287
14. Eernisse, D.J. and Kluge, A.G. (1993) Taxonomic congruence versus total evidence, and the phylogeny of amniotes inferred from fossils, molecules and morphology, Mol. Biol. Evol. 10, 1170-1195
15. Jones, T.R. et al. (1993) When theories and methodologies clash: a phylogenetic reanalysis of the North American ambystomatid salamanders (Caudata: Ambystomatidae), Syst. Biol. 42, 92-102
16. Kluge, A.G. and Wolf, A.J. (1993) Cladistics: what's in a word? Cladistics 9, 183-199
17. Lanyon, S.M. (1993) Phylogenetic frameworks: towards a firmer foundation for the comparative approach, Biol. J. Linn. Soc. 49, 45-61
18. Barrett, M. et al. (1991) Against consensus, Syst. Biol. 40, 486-493
19. Miyamoto, M.M. et al. (1994) A congruence test of reliability using linked mitochondrial DNA sequences, Syst. Biol. 43, 236-249
20. Michevich, M.F. and Farris, J.S. (1981) The implications of congruence in Menidia, Syst. Zool. 30, 351-370
21. Farris, J.S. et al. (1995) Testing significance of incongruencies, Cladistics 10, 315-319
22. Huelsenbeck, J.P. and Bull, J.J. (1996) A likelihood ratio test for detection of conflicting phylogenetic signal, Syst. Biol. 45, 92-98
23. Graybeal, A. (1994) Evaluating the phylogenetic utility of genes: a search for genes informative about deep divergences among vertebrates, Syst. Biol. 43, 174-193
24. Gardiner, B.G. (1982) Tetrapod classification, Zool. J. Linn. Soc. 74, 207-232
25. Gauthier, J. et al. (1988) Amniote phylogeny and the importance of fossils, Cladistics 4, 105-209
26. Hedges, S.B. et al. (1990) Tetrapod phylogeny inferred from 18S and 28S ribosomal RNA sequences and a review of the evidence for amniote relationships, Mol. Biol. Evol. 7, 607-633
27. Løvtrup, S. (1985) On the classification of the taxon Tetrapoda, Syst. Zool. 34, 463-470
28. Hedges, S.B. and Maxson, L.R. (1991) Pancreatic polypeptide and the sister group of birds, Mol. Biol. Evol. 8, 888-891
29. Hedges, S.B. (1994) Molecular evidence for the origin of birds, Proc. Natl Acad. Sci. USA 91, 2621-2624
30. Jukes, T.H. and Cantor, C.R. (1969) Evolution of protein molecules, in Mammalian Protein Metabolism (Munro, H., ed.), pp. 21-132, Academic Press
31. Hasegawa, M. et al. (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA, J. Mol. Evol. 22, 160-174
32. Yang, Z. (1993) Maximum likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites, Mol. Biol. Evol. 10, 1396-1401
33. Felsenstein, J. (1978) Cases in which parsimony or compatibility methods will be positively misleading, Syst. Zool. 27, 401-410
34. Dykhuizen, D.E. and Green, L. (1991) Recombination in Escherichia coli and the definition of biological species, J. Bacteriol. 173, 7257-7268
35. Maynard Smith, J. et al. (1991) Localized sex in bacteria, Nature 349, 29-31
36. Médigue, C. et al. (1991) Evidence for horizontal gene transfer in Escherichia coli speciation, J. Mol. Biol. 222, 851-856
37. Souza, V.T. et al. (1992) Hierarchical analysis of linkage disequilibrium in Rhizobium populations: Evidence for sex? Proc. Natl Acad. Sci. USA 89, 8389-8393
38. Valdez, A.M. and Piñero, D. (1992) Phylogenetic estimation of plasmid exchange in bacteria, Evolution 46, 641-656
39. Wilson, A.C. et al. (1977) Biochemical evolution, Annu. Rev. Biochem. 46, 473-639
40. Pesole, G. et al. (1991) The branching order of mammals: Phylogenetic trees inferred from nuclear and mitochondrial molecular data, J. Mol. Evol. 33, 537-542
41. Doyle, J.J. (1992) Gene trees and species trees: Molecular systematics as one-character taxonomy, Syst. Bot. 17, 144-163
42. Hillis, D.M. et al. (1991) Evidence for biased gene conversion in concerted evolution of ribosomal DNA, Science 251, 308-310
43. Lockhart, P.J. et al. (1994) Recovering evolutionary trees under a more realistic model of sequence evolution, Mol. Biol. Evol. 11, 605-612
44. Huelsenbeck, J.P. and Hillis, D.M. (1993) Success of phylogenetic methods in the four-taxon case, Syst. Biol. 42, 247-264
45. Hendy, M. and Penny, D. (1989) A framework for the quantitative study of evolutionary trees, Syst. Zool. 38, 297-309