Advertisement

Journal of Biosciences

, Volume 24, Issue 1, pp 121–137 | Cite as

Reconstruction of phylogenetic relationships

  • Chandrika B-Rao
  • Kshitish C. Majumdar
Review

Abstract

In this paper, we provide an introductory overview to the field of phylogenetic analysis, which has wide applications in modern biology.

Keywords

Phylogenetic trees multivariate analysis graphical representation 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Adachi J and Hasegawa M 1995 inMOLPHY: Programs for molecular phylogenetics (Tokyo: Institute of Statistical Mathematics)Google Scholar
  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.PubMedCrossRefGoogle Scholar
  3. Airoldi J-P, Flury B D and Salvioni M 1995 Discrimination between two species ofMicrotus using both classified and unclassified observations;J. Theor. Biol. 177 247–262.CrossRefGoogle Scholar
  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.PubMedGoogle Scholar
  5. Ayala F J 1978 The mechanisms of evolution;Sci. Am. 239 56–69PubMedCrossRefGoogle Scholar
  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.CrossRefGoogle Scholar
  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.PubMedGoogle Scholar
  8. Borg I and Lingoes J 1987Multidimensional similarity structure analysis (New York: Springer-Verlag)Google Scholar
  9. B-Rao C and Majumdar K C 1998 Map-like representation of phylogenetic relationships: Application to tilapiine fish;J. Fish Biol. 52 1199–1217CrossRefGoogle Scholar
  10. B-Rao C and Stewart J 1996 Inverse analysis of empirical matrices of idiotypic network interactions;Bull. Math. Biol. 58 1123–1153.PubMedCrossRefGoogle Scholar
  11. Brown J K M 1994 Bootstrap hypothesis tests for evolutionary trees and other dendrograms;Proc. Natl. Acad. Sci. USA 91 12293–12297PubMedCrossRefGoogle Scholar
  12. Camin J H and Sokal R R 1965 A method for deducing branching sequences in phytogeny;Evolution 19 311–326CrossRefGoogle Scholar
  13. Carroll J D and Pruzansky S 1983 Representing proximities data by discrete, continuous or “hybrid≓ models; inNumerical Taxonomy NATO ASI series (ed.) JFelsenstein (Berlin: Springer) vol. Gl, pp 229–248Google Scholar
  14. Cavalli-Sforza L L and Edwards A W F 1967 Phylogenetic analysis: models and estimation procedures;Am. J. Hum. Genet. 19 233–257PubMedGoogle Scholar
  15. Charleston M A 1998 Spectrum: spectral analysis of phylogenetic data;Bioinformatics 14 98–99PubMedCrossRefGoogle Scholar
  16. DeBry R W and Slade N A 1985 Cladistic analysis of restriction endonuclease cleavage maps within a maximum likelihood framework;Syst. Zool. 34 21–34CrossRefGoogle Scholar
  17. DeQueiroz K and Good D A 1997 Phenetic clustering in biology: A critique;Quart. Rev. Biol. 72 3–72CrossRefGoogle Scholar
  18. Dowling T E, Moritz C, Palmer J D and Rieseberg L H 1996 Nucleic Acids III: Analysis of fragments and restriction sites; inMolecular systematics (eds) D MHillis, CMoritz and B KMable (Sunderland: Sinauer Associates) 2nd edition, pp 249–320Google Scholar
  19. Eck R V and Dayhoff M O (eds) 1966Atlas of protein sequence and structure (Maryland: National Biomedical Research Foundation)Google Scholar
  20. Edwards A W F and Cavalli-Sforza L L 1964 Reconstruction of evolutionary trees; inPhenetic and phylogenetic classification (eds) V HHeywood and JMcNeill (London: Systematics Association) Publ. No. 6, pp 67–76Google Scholar
  21. Efron B, Halloran E and Holmes S 1996 Bootstrap confidence levels for phylogenetic trees;Proc. Natl. Acad. Sci. USA 93 13429–13433PubMedCrossRefGoogle Scholar
  22. Farris J S 1983 The logical basis of phylogenetic analysis; inAdvances in cladistics (eds) N IPlatnick and V AFunk (New York: Columbia Univ. Press) vol. 2, pp 7–36Google Scholar
  23. Felsenstein J 1973a Maximum likelihood and minimum steps methods for estimating evolutionary trees from data on discrete characters;Syst. Zool 22 240–249CrossRefGoogle Scholar
  24. Felsenstein J 1973b Maximum likelihood estimation of evolutionary trees from continuous characters;Am. J. Hum. Genet. 25 471–492PubMedGoogle Scholar
  25. Felsenstein J 1981 Evolutionary trees from DNA sequences: a maximum likelihood approach;J. Mol. Evol. 17 368–376PubMedCrossRefGoogle Scholar
  26. Felsenstein J 1982 Numerical methods for inferring evolutionary trees;Quart Rev. Biol 57 379–404CrossRefGoogle Scholar
  27. Felsenstein J 1984 Distance methods for inferring phytogenies: A justification;Evolution 38 16–24CrossRefGoogle Scholar
  28. Felsenstein J 1985a Phytogenies from gene frequencies: A statistical problem;Syst. Zool. 34 300–311CrossRefGoogle Scholar
  29. Felsenstein J 1985b Confidence limits on phytogenies: an approach using the bootstrap;Evolution 39 783–791CrossRefGoogle Scholar
  30. Felsenstein J 1987 Estimation of hominoid phylogeny from DNA hybridization data set;J. Mol. Evol 26 123–131PubMedCrossRefGoogle Scholar
  31. Felsenstein J 1988 Phytogenies from molecular sequences: Inferences and reliability;Annu. Rev. Genet. 22 521–565PubMedCrossRefGoogle Scholar
  32. Felsenstein J 1991 PHYLIP (Phytogeny Inference Package) v. 3.4, University of Washington, Seattle, USAGoogle Scholar
  33. Felsenstein J 1992 Phytogenies from restriction sites, a maximum likelihood approach;Evolution 46 159–173CrossRefGoogle Scholar
  34. Felsenstein J 1999Inferring phytogenies (Sunderland: Sinauer Assoc.) (in press)Google Scholar
  35. Felsenstein J and Kishino H 1993 Is there something wrong with the bootstrap on phylogenies? A reply to Hillis and Bull;Syst. Biol. 42 193–200CrossRefGoogle Scholar
  36. Fitch W 1971 Toward defining the course of evolution: minimum change for a specific tree topology;Syst. Zool. 20 406–416CrossRefGoogle Scholar
  37. Fitch W M 1975 Toward finding the tree of maximum parsimony; inProc. of Eighth Intl. Conf. on Numerical Taxonomy (ed.) G FEstabrook (San Francisco: W H Freeman) pp 189–230Google Scholar
  38. Fitch W and Margoliash M M 1967 Construction of phylogenetic trees;Science 155 279–284PubMedCrossRefGoogle Scholar
  39. Hasegawa M, Kishino H and Yano T 1985 Dating the human-ape splitting by molecular clock of mitochondrial DNA;J. Mol. Evol. 22 160–174PubMedCrossRefGoogle Scholar
  40. Heiser W 1981Unfolding analysis of proximity data, Ph.D thesis, Rijksuniversiteit, LeidenGoogle Scholar
  41. Hendy M D and Penny D 1992 Spectral analysis of phylogenetic data;J. Classif. 10 5–24CrossRefGoogle Scholar
  42. Hendy M D, Penny D and Steel M A 1994 A discrete Fourier analysis for evolutionary trees;Proc. Natl. Acad. Sci. USA 91 3339–3343PubMedCrossRefGoogle Scholar
  43. Hillis D, Allard M W and Miyamoto M M 1993 Analysis of DNA sequence data: phylogenetic inference;Methods Enzymol. 224 456–487PubMedCrossRefGoogle Scholar
  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. 42 182–192CrossRefGoogle Scholar
  45. Hillis D M, Huelsenbeck J P and Cunningham C W 1994 Application and accuracy of molecular phylogenies;Science 264 671–677PubMedCrossRefGoogle Scholar
  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; inMolecular systematics (eds) D MHillis, CMoritz and B KMable (Sunderland: Sinauer Associates) pp 515–543Google Scholar
  47. Hillis D M, Moritz C and Mable B K (eds) 1996bMolecular systematics (Sunderland: Sinaner Associates)Google Scholar
  48. Holsinger K E and Jansen R K 1993 Phylogenetic analysis of restriction site data;Methods Enzymol. 224 439–455PubMedCrossRefGoogle Scholar
  49. Huson D H 1998 SplitsTree: Analyzing and visualizing evolutionary data;Bioinformatics 14 68–73PubMedCrossRefGoogle Scholar
  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. 57 523–538PubMedGoogle Scholar
  51. Jukes T H and Cantor C R 1969 Evolution of protein molecules; inMammalian protein metabolism (ed.) H NMunro (New York: Academic Press) pp 21–132Google Scholar
  52. Kidd K K and Sgaramella-Zonta L A 1971 Phylogenetic analysis: concepts and methods;Am. J. Hum. Genet 23 235–252PubMedGoogle Scholar
  53. Kimura M 1980 A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences;J. Mol. Evol. 16 111–120PubMedCrossRefGoogle Scholar
  54. Kluge A G and Parris J S 1969 Quantitative phyletics and the evolution of anurans;Syst. Zool. 18 1–32CrossRefGoogle Scholar
  55. Kruskal J 1977 Multidimensional scaling and other methods for discovering structure; inStatistical methods for digital computers (eds) KEnslein, ARalston and H SWilf (New York: Wiley) vol. III, pp 296–339Google Scholar
  56. Kuhner M K and Felsenstein J 1994 A simulation comparison of phytogeny algorithms under equal and unequal evolutionary rates;Mol. Biol. Evol. 11 459–468PubMedGoogle Scholar
  57. Kumar S, Tamura and Nei M 1993 MEGA: Molecular Evolutionary Genetic Analysis v 1.0. Pennsylvania State University, University ParkGoogle Scholar
  58. Lake J A 1994 Reconstructing evolutionary trees from DNA and protein sequences: paralinear distances;Proc. Natl. Acad. Sci USA 91 1455–1459PubMedCrossRefGoogle Scholar
  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 6808–6814PubMedCrossRefGoogle Scholar
  60. Li C C, Weeks D E and Chakravarti A 1993 Similarity of DNA fingerprints due to chance and relatedness;Hum. Hered. 43 45–52PubMedCrossRefGoogle Scholar
  61. Lynch M 1990 The similarity index and DNA fingerprinting;Mol. Biol. Evol. 7 478–484PubMedGoogle Scholar
  62. Mahalanobis P C 1936 On the generalised distance in statistics:Proc. Natl. Inst. Sci. India 12 49–55Google Scholar
  63. Margush T and McMorris F R 1981 Consensus n-trees;Bull. Math. Biol. 43 239–244Google Scholar
  64. Meulman J 1986A distance approach to nonlinear multivariate analysis (Leiden: DSWO Press)Google Scholar
  65. Michener C D and Sokal R R 1957 A quantitative approach to a problem in classification;Evolution 11 130–162CrossRefGoogle Scholar
  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. 38 459–485PubMedCrossRefGoogle Scholar
  67. Mountain J L and Cavalfi-Sforza L L 1994 Inference of human evolution through cladistic analysis of nuclear DNA restriction polymorphisms;Proc. Natl. Acad. Sci. USA 91 6515–6519PubMedCrossRefGoogle Scholar
  68. Nei M 1972 Genetic distance between populations;Am. Nat. 106 283–292CrossRefGoogle Scholar
  69. Nei M 1978 Estimation of heterozygosity and genetic distance from a small number of individuals;Genetics 89 583–590PubMedGoogle Scholar
  70. Nei M 1991 Relative efficiencies of different tree-making methods for molecular data; inPhylogenetic analysis of DNA sequences (eds) M MMiyamoto and JCracroft (New York: Oxford University Press) pp 90–128Google Scholar
  71. Nei M 1996 Phylogenetic analysis in molecular evolutionary genetics;Annu. Rev. Genet. 30 371–403PubMedCrossRefGoogle Scholar
  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 5269–5273PubMedCrossRefGoogle Scholar
  73. Nei M and Tajima F 1983 Maximum likelihood estimation of the number of nucleotide substitutions from restriction sites data;Genetics 105 207–217PubMedGoogle Scholar
  74. Nei M and Tajima F 1985 Evolutionary change of restriction cleavage sites and phylogenetic inference for man and apes;Mol. Biol. Evol. 2 189–205PubMedGoogle Scholar
  75. Nei M, Tajima F and Tateno Y 1983 Accuracy of estimated phylogenetic trees from molecular data;J. Mol. Evol. 19 153–170PubMedCrossRefGoogle Scholar
  76. Nei M and Takezaki N 1994 Estimation of genetic distances and phylogenetic trees from DNA analysis; inProc. 5th World Congress on Genetics Applied to Livestock Production, vol.21, 405–412Google Scholar
  77. Neuhaussen S L 1992 Evaluation of restriction fragment length polymorphism inCucumis Melo:,Theor. Appl. Genet. 83 379–384CrossRefGoogle Scholar
  78. Neyman J 1971 Molecular studies of evolution: a source of novel statistical problems; inStatistical decision theory and related topics (eds) S SGupta and JYackel (New york: Academic Press) pp 1–27Google Scholar
  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. 95 513–527PubMedCrossRefGoogle Scholar
  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 105 767–779PubMedGoogle Scholar
  81. Rohlf W 1970 Adaptive hierarchical clustering schemes;Syst. Zool. 18 58–82CrossRefGoogle Scholar
  82. Russo C A M, Takezaki N and Nei M 1996 Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny;Mol. Biol. Evol. 13 525–536PubMedGoogle Scholar
  83. Rzhetsky A and Nei M 1993 Theoretical foundation for minimum evolution method of phylogenetic inference;Mol. Biol. Evol. 10 1073–1095PubMedGoogle Scholar
  84. Rzhetsky A and Nei M 1995 Tests for applicability of several substitution models for DNA sequence data;Mol. Biol. Evol. 12 131–151PubMedGoogle Scholar
  85. Saitou N 1988 Property and efficiency of the maximum likelihood method for molecular phylogeny;J. Mol. Evol. 27 261–273PubMedCrossRefGoogle Scholar
  86. Saitou N and Nei M 1987 The neighbour joining method: A new method for reconstructing phylogenetic trees;Mol Biol. Evol. 4 406–425PubMedGoogle Scholar
  87. Sanghvi L D 1953 Comparison of genetical and morphological methods for a study of biological differences;Am. J. Phys. Anthropology 11 385–404CrossRefGoogle Scholar
  88. Seber G A F 1984Multivariate observations (New York: John Wiley)Google Scholar
  89. Sherry S T and Batzer M A 1997 Modelling human evolution—To tree or not to tree;Genome Res. 7 947–949PubMedGoogle Scholar
  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. 12 914–920PubMedGoogle Scholar
  91. Sitnikova T, Rzhetsky A and Nei M 1995 Interior-branch and bootstrap tests of phylogenetic trees;Mol. Biol Evol. 12 319–333PubMedGoogle Scholar
  92. Sneath P H A and Sokal R R 1973Numerical taxonomy: The principles and practice of numerical classification (San Francisco: W Freeman)Google Scholar
  93. Springer M S and Britten R J 1993 DNA-DNA hybridization of single-copy DNA sequences;Methods Enzymol. 224 232–243PubMedCrossRefGoogle Scholar
  94. Swofford D L 1990 PAUP: Phylogenetic analysis using parsimony, ver 3.0, Illinois Natural History Survey, Champaign, IllinoisGoogle Scholar
  95. Swofford D L and Olsen G J 1990 Phylogeny reconstruction; inMolecular systematics (eds) D MHillis and CMoritz (Sunderland: Sinaucr Associates) pp 411–501Google Scholar
  96. Swofford D L, Olsen G J, Waddell P J and Hillis D M 1996 Phylogenetic inference; inMolecular systematics (eds) D MHillis, CMoritz and B KMable (Sunderland: Sinauer Associates) 2nd edition, pp 407–514Google Scholar
  97. Takezaki N and Nei M 1996 Genetic distances and reconstruction of phylogenetic trees from microsatellite DNA;Genetics 144 389–399PubMedGoogle Scholar
  98. Tateno Y, Nei M and Tajima F 1982 Accuracy of estimated phylogenetic trees from molecular data I. Distantly related species;J. Mol. Evol. 18 387–404PubMedCrossRefGoogle Scholar
  99. Templeton A R 1983a Congruent evolution and non-parametric inferences from restriction fragment and DNA sequence data; inStatistical analysis of DNA sequence data (ed.) BWeir (New York: Marcel Dekker) pp 151–179Google Scholar
  100. Templeton A R 1983b Phylogenetic inference from restriction endonuclease cleaveage site maps with particular reference to the humans and apes;Evolution 37 221–244CrossRefGoogle Scholar
  101. Templeton A R 1987 Nonparametric inference from restriction cleavage sites;Mol. Biol. Evol. 4 315–319PubMedGoogle Scholar
  102. Waterman M S, Joyce J and Eggert M 1991 Computer alignment of sequences; inPhylogenetic analysis of DNA sequences (eds) M MMiyamoto and JCracrafts (Oxford: OUP) pp 59–72Google Scholar
  103. Waterman M S, Smith T F and Beyer W A 1976 Some biological sequence metrics;Adv. Math. 20 367–387CrossRefGoogle Scholar
  104. Weising K, Nybom H, Wolff K and Meyer W 1995DNA fingerprinting in plants and fungi (Boca Raton: CRC Press)Google Scholar
  105. Wienberg J and Stanyon R 1995 Chromosome painting in mammals as an approach to comparative genetics;Curr. Opin. Genet. Dev. 5 792–797PubMedCrossRefGoogle Scholar
  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 87 836–840CrossRefGoogle Scholar

Copyright information

© Indian Academy of Sciences 1999

Authors and Affiliations

  1. 1.Functional Genomics UnitCentre for Biochemical TechnologyDelhiIndia
  2. 2.Centre for Cellular and Molecular BiologyHyderabadIndia

Personalised recommendations