Reconstruction of phylogenetic relationships

Journal of Biosciences

Volumn 24, Issue 1, 1999, Pages 121-137

  B Rao, Chandrika ^a   Majumdar, Kshitish C ^b  

^a CSIR INSTITUTE OF GENOMICS AND INTEGRATIVE BIOLOGY   (India)

^b CENTRE FOR CELLULAR AND MOLECULAR BIOLOGY   (India)

Author keywords

Graphical representation; Multivariate analysis; Phylogenetic trees

Indexed keywords

ALGORITHM; BIOLOGY; DATA ANALYSIS; EVOLUTION; PHYLOGENY; REVIEW;

EID: 0032911560     PISSN: 02505991     EISSN: None     Source Type: Journal    
DOI: 10.1007/BF02941116     Document Type: Review

References (106)

1. Adachi J and Hasegawa M 1995 in MOLPHY: Programs for molecular phylogenetics (Tokyo: Institute of Statistical Mathematics)
2. Aggarwal R, Majumdar K C, Lang J W and Singh L 1994 Generic affinities among crocodilians as revealed by DNA fingerprinting with Bkm-derived probe; Proc. Natl. Acad. Sci. USA 91 10601-10605.
3. Airoldi J-P, Flury B D and Salvioni M 1995 Discrimination between two species of Microtus using both classified and unclassified observations: J. Theor. Biol. 177 247-262.
4. Allard M W and Miyamoto M M 1992 Testing phylogenetic approaches with empirical data, as illustrated with the parsimony method; Mol. Biol. Evol. 9 778-786.
5. Ayala F J 1978 The mechanisms of evolution; Sci. Am. 239 56-69
6. Bandelt H-J and Dress A W M 1992 Split decomposition: a new and useful approach to phylogenetic analysis of distance data; Mol. Phylog. Evol. 1 242-252.
7. Bandelt H-J, Forster P, Sykes B C and Richards M B 1995 Mitochondrial portraits of human populations using median networks; Genetics 141 743-753.
8. Borg I and Lingoes J 1987 Multidimensional similarity structure analysis (New York: Springer-Verlag)
9. B-Rao C and Majumdar K C 1998 Map-like representation of phylogenetic relationships: Application to tilapiine fish; J. Fish Biol. 52 1199-1217
10. B-Rao C and Stewart J 1996 Inverse analysis of empirical matrices of idiotypic network interactions; Bull. Math. Biol. 58 1123-1153.
11. Brown J K M 1994 Bootstrap hypothesis tests for evolutionary trees and other dendrograms; Proc. Natl. Acad. Sci. USA 91 12293-12297
12. Camin J H and Sokal R R 1965 A method for deducing branching sequences in phylogeny; Evolution 19 311-326
13. Carroll J D and Pruzansky S 1983 Representing proximities data by discrete, continuous or "hybrid" models; in Numerical Taxonomy NATO ASI series (cd.) J Felsenstein (Berlin: Springer) vol. G1, pp 229-248
14. Cavalli-Sforza L L and Edwards A W F 1967 Phylogenetic analysis: models and estimation procedures; Am. J. Hum. Genet. 19 233-257
15. Charleston M A 1998 Spectrum: spectral analysis of phylogenetic data; Bioinformatics 14 98-99
16. DeBry R W and Slade N A 1985 Cladistic analysis of restriction endonuclease cleavage maps within a maximum likelihood framework; Syst. Zool. 34 21-34
17. DeQueiroz K and Good D A 1997 Phenetic clustering in biology: A critique; Quart. Rev. Biol. 72 3-72
18. Dowling T E, Moritz C, Palmer J D and Rieseberg L H 1996 Nucleic Acids III: Analysis of fragments and restriction sites; in Molecular systematics (eds) D M Hillis, C Moritz and B K Mable (Sunderland: Sinauer Associates) 2nd edition, pp 249-320
19. Eck R V and Dayhoff M O (eds) 1966 Atlas of protein sequence and structure (Maryland: National Biomedical Research Foundation)
20. Edwards A W F and Cavalli-Sforza L L 1964 Reconstruction of evolutionary trees; in Phenetic and phylogenetic classification (eds) V H Heywood and J McNeill (London: Systematics Association) Publ. No. 6, pp 67-76
21. Efron B, Halloran E and Holmes S 1996 Bootstrap confidence levels for phylogenetic trees; Proc. Natl. Acad. Sci. USA 93 13429-13433
22. Farris J S 1983 The logical basis of phylogenetic analysis; in Advances in cladistics (eds) N I Platnick and V A Funk (New York: Columbia Univ. Press) vol. 2, pp 7-36
23. Felsenstein J 1973a Maximum likelihood and minimum steps methods for estimating evolutionary trees from data on discrete characters; Syst. Zool. 22 240-249
24. Felsenstein J 1973b Maximum likelihood estimation of evolutionary trees from continuous characters; Am. J. Hum. Genet. 25 471-492
25. Felsenstein J 1981 Evolutionary trees from DNA sequences: a maximum likelihood approach; J. Mol. Evol. 17 368-376
26. Felsenstein J 1982 Numerical methods for inferring evolutionary trees; Quart. Rev. Biol. 57 379-404
27. Felsenstein J 1984 Distance methods for inferring phylogenies: A justification; Evolution 38 16-24
28. Felsenstein J 1985a Phylogenies from gene frequencies: A statistical problem; Syst. Zool. 34 300-311
29. Felsenstein J 1985b Confidence limits on phylogenies: an approach using the bootstrap; Evolution 39 783-791
30. Felsenstein J 1987 Estimation of hominoid phylogeny from DNA hybridization data set; J. Mol. Evol. 26 123-131
31. Felsenstein J 1988 Phylogenies from molecular sequences: Inferences and reliability; Annu. Rev. Genet. 22 521-565
32. Felsenstein J 1991 PHYLIP (Phylogeny Inference Package) v. 3.4, University of Washington, Seattle, USA
33. Felsenstein J 1992 Phylogenies from restriction sites, a maximum likelihood approach; Evolution 46 159-173
34. Felsenstein J 1999 Inferring phylogenies (Sunderland: Sinauer Assoc.) (in press)
35. Felsenstein J and Kishino H 1993 Is there something wrong with the bootstrap on phylogenies? A reply to Hillis and Bull; Syst. Biol. 42 193-200
36. Fitch W 1971 Toward defining the course of evolution: minimum change for a specific tree topology; Syst. Zool. 20 406-416
37. Fitch W M 1975 Toward finding the tree of maximum parsimony; in Proc. of Eighth Intl. Conf. on Numerical Taxonomy (ed.) G F Estabrook (San Francisco: W H Freeman) pp 189-230
38. Fitch W and Margoliash M M 1967 Construction of phylogenetic trees; Science 155 279-284
39. Hasegawa M, Kishino H and Yario T 1985 Dating the human-ape splitting by molecular clock of mitochondrial DNA; J. Mol. Evol. 22 160-174
40. Heiser W 1981 Unfolding analysis of proximity data, Ph.D thesis, Rijksuniversiteit, Leiden
41. Hendy M D and Penny D 1992 Spectral analysis of phylogenetic data; J. Classif. 10 5-24
42. Hendy M D, Penny D and Steel M A 1994 A discrete Fourier analysis for evolutionary trees; Proc. Natl. Acad. Sci. USA 91 3339-3343
43. Hillis D, Allard M W and Miyamoto M M 1993 Analysis of DNA sequence data: phylogenetic inference; Methods Enzymol. 224 456-487
44. Hillis D M and Bull J J 1993 An empirical test for bootstrapping as a method for assessing confidence in phylogenetic analysis; Syst. Biol. 42 182-192
45. Hillis D M, Huelsenbeck J P and Cunningham C W 1994 Application and accuracy of molecular phylogenies; Science 264 671-677
46. Hillis D M, Mable B K and Moritz C 1996a Applications of molecular systematics: The state of the field and a look to the future; in Molecular systematics (eds) D M Hillis, C Moritz and B K Mable (Sunderland: Sinauer Associates) pp 515-543
47. Hillis D M, Moritz C and Mable B K (eds) 1996b Molecular systematics (Sunderland: Sinaner Associates)
48. Holsinger K E and Jansen R K 1993 Phylogenetic analysis of restriction site data; Methods Enzymol. 224 439-455
49. Huson D H 1998 SplitsTree: Analyzing and visualizing evolutionary data; Bioinformatics 14 68-73
50. Jorde L B, Bamshad M J, Watkins W S, Zenger R, Fraley A E, Krakowiak P A, Carpenter K D, Soodyall H, Jenkins T and Rogers A R 1995 Origins and affinities of modern humans: A comparison of mitochondrial and nuclear genetic data; Am. J. Hum. Genet. 57 523-538
51. Jukes T H and Cantor C R 1969 Evolution of protein molecules; in Mammalian protein metabolism (ed.) H N Munro (New York: Academic Press) pp 21-132
52. Kidd K K and Sgaramella-Zonta L A 1971 Phylogenetic analysis: concepts and methods; Am. J. Hum. Genet. 23 235-252
53. 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
54. Kluge A G and Farris J S 1969 Quantitative phyletics and the evolution of anurans; Syst. Zool. 18 1-32
55. Kruskal J 1977 Multidimensional scaling and other methods for discovering structure; in Statistical methods for digital computers (eds) K Enslein, A Ralston and H S Wilf (New York: Wiley) vol. III, pp 296-339
56. Kuhner M K and Felsenstein J 1994 A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates; Mol. Biol. Evol. 11 459-468
57. Kumar S, Tamura and Nei M 1993 MEGA: Molecular Evolutionary Genetic Analysis v 1.0. Pennsylvania State University, University Park
58. Lake J A 1994 Reconstructing evolutionary trees from DNA and protein sequences: paralinear distances; Proc. Natl. Acad. Sci. USA 91 1455-1459
59. Lenski R E and Travisano M 1994 Dynamics of adaptation and diversification: A 10,000 generation experiment with bacterial populations; Proc. Natl. Acad. Sci. USA 91 6808-6814
60. Li C C, Weeks D E and Chakravarti A 1993 Similarity of DNA fingerprints due to chance and relatedness; Hum. Hered. 43 45-52
61. Lynch M 1990 The similarity index and DNA fingerprinting; Mol. Biol. Evol. 7 478-484
62. Mahalanobis P C 1936 On the generalised distance in statistics: Proc. Natl. Inst. Sci. India 12 49-55
63. Margush T and McMorris F R 1981 Consensus n-trees; Bull. Math. Biol. 43 239-244
64. Meulman J 1986 A distance approach to nonlinear multivariate analysis (Leiden: DSWO Press)
65. Michener C D and Sokal R R 1957 A quantitative approach to a problem in classification; Evolution 11 130-162
66. Moore G W, Barnabas J and Goodman M 1973 A method for constructing maximum parsimony ancestral amino acid sequences on a given network; J. Theor. Biol. 38 459-485
67. Mountain J L and Cavalli-Sforza L L 1994 Inference of human evolution through cladistic analysis of nuclear DNA restriction polymorphisms; Proc. Natl. Acad. Sci. USA 91 6515-6519
68. Nei M 1972 Genetic distance between populations; Am. Nat. 106 283-292
69. Nei M 1978 Estimation of heterozygosity and genetic distance from a small number of individuals; Genetics 89 583-590
70. Nei M 1991 Relative efficiencies of different tree-making methods for molecular data; in Phylogenetic analysis of DNA sequences (eds) M M Miyamoto and J Cracroft (New York: Oxford University Press) pp 90-128
71. Nei M 1996 Phylogenetic analysis in molecular evolutionary genetics; Annu. Rev. Genet. 30 371-403
72. Nei M and Li W-H 1979 Mathematical model for studying genetic variation in terms of restriction endonucleases; Proc. Natl. Acad. Sci. USA 76 5269-5273
73. Nei M and Tajima F 1983 Maximum likelihood estimation of the number of nucleotide substitutions from restriction sites data; Genetics 105 207-217
74. Nei M and Tajima F 1985 Evolutionary change of restriction cleavage sites and phylogenetic inference for man and apes; Mol. Biol. Evol. 2 189-205
75. Nei M, Tajima F and Tateno Y 1983 Accuracy of estimated phylogenetic trees from molecular data; J. Mol. Evol. 19 153-170
76. Nei M and Takezaki N 1994 Estimation of genetic distances and phylogenetic trees from DNA analysis; in Proc. 5th World Congress on Genetics Applied to Livestock Production, vol. 21, pp 405-412
77. Neuhaussen S L 1992 Evaluation of restriction fragment length polymorphism in Cucumis Melo.; Theor. Appl. Genet. 83 379-384
78. Neyman J 1971 Molecular studies of evolution: a source of novel statistical problems; in Statistical decision theory and related topics (eds) S S Gupta and J Yackel (New york: Academic Press) pp 1-27
79. Peacock D and Boulter D 1975 Use of amino acid sequence data in phylogeny and evaluation of methods using computer simulation; J. Mol. Biol. 95 513-527
80. Reynolds J B, Weir B S and Cockerham C C 1983 Estimation of the coancestry coefficient: basis for a short-term genetic distance; Genetics 105 767-779
81. Rohlf W 1970 Adaptive hierarchical clustering schemes; Syst. Zool. 18 58-82
82. Russo C A M, Takezaki N and Nei M 1996 Efficiencie of different genes and different tree-building methods in recovering a known vertebrate phylogeny; Mol. Biol. Evol. 13 525-536
83. Rzhetsky A and Nei M 1993 Theoretical foundation for minimum evolution method of phylogenetic inference; Mol. Biol. Evol. 10 1073-1095
84. Rzhetsky A and Nei M 1995 Tests for applicability of several substitution models for DNA sequence data; Mol. Biol. Evol. 12 131-151
85. Saitou N 1988 Property and efficiency of the maximum likelihood method for molecular phylogeny; J. Mol. Evol. 27 261-273
86. Saitou N and Nei M 1987 The neighbour joining method: A new method for reconstructing phylogenetic trees; Mol. Biol. Evol. 4 406-425
87. Sanghvi L D 1953 Comparison of genetical and morphological methods for a study of biological differences; Am. J. Phys. Anthropology 11 385-404
88. Seber G A F 1984 Multivariate observations (New York: John Wiley)
89. Sherry S T and Batzer M A 1997 Modelling human evolution - To tree or not to tree; Genome Res. 7 947-949
90. Shriver M D, Jin L, Boerwinkle E, Deka R, Ferrell R E and Chakraborty R 1995 A novel measure of genetic distance for highly polymorphic tandem repeat loci; Mol. Biol. Evol. 12 914-920
91. Sitnikova T, Rzhetsky A and Nei M 1995 Interior-branch and bootstrap tests of phylogenetic trees; Mol. Biol. Evol. 12 319-333
92. Sneath P H A and Sokal R R 1973 Numerical taxonomy: The principles and practice of numerical classification (San Francisco: W Freeman)
93. Springer M S and Britten R J 1993 DNA-DNA hybridization of single-copy DNA sequences; Methods Enzymol. 224 232-2 43
94. Swofford D L 1990 PAUP: Phylogenetic analysis using parsimony, ver 3.0, Illinois Natural History Survey, Champaign, Illino
95. Swofford D L and Olsen G J 1990 Phylogeny reconstruction; in Molecular systemalics (eds) D M Hillis and C Moritz (Sunderland: Sinauer Associates) pp 411-501
96. Swofford D L, Olsen G J, Waddell P J and Hillis D M 1996 Phylogenetic inference; in Molecular systematics (eds) D M Hillis, C Moritz and B K Mable (Sunderland: Sinauer Associates) 2nd edition, pp 407-514
97. Takezaki N and Nei M 1996 Genetic distances and reconstruction of phylogenetic trees from microsatellite DNA; Genetics 144 389-399
98. Tateno Y, Nei M and Tajima F 1982 Accuracy of estimated phylogenetic trees from molecular data 1. Distantly related species; J. Mol. Evol. 18 387-404
99. Templeton A R 1983a Congruent evolution and non-parametric inferences from restriction fragment and DNA sequence data; in Statistical analysis of DNA sequence data (ed.) B Weir (New York: Marcel Dekker) pp 151-179
100. Templeton A R 1983b Phylogenetic inference from restriction endonuclease cleaveage site maps with particular reference to the humans and apes; Evolution 37 221-244
101. Templeton A R 1987 Nonparametric inference from restriction cleavage sites; Mol. Biol. Evol. 4 315-319
102. Waterman M S, Joyce J and Eggert M 1991 Computer alignment of sequences; in Phylogenetic analysis of DNA sequences (eds) M M Miyamoto and J Cracrafts (Oxford: OUP) pp 59-72
103. Waterman M S, Smith T F and Beyer W A 1976 Some biological sequence metrics; Adv. Math. 20 367-387
104. Weising K, Nybom H, Wolff K and Meyer W 1995 DNA fingerprinting in plants and fungi (Boca Raton: CRC Press)
105. Wienberg J and Stanyon R 1995 Chromosome painting in mammals as an approach to comparative genetics; Curr. Opin. Genet. Dev. 5 792-797
106. Yukhi N and O'Brien S J 1990 DNA variation of the mammalian major histocompatibility complex reflects genomic diversity and population history; Proc. Natl. Acad. Sci. USA 87 836-840