(Last updated 24/5/96)

CLADISTIC LITERATURE by topics

I. BOOKS, REVIEWS AND OTHER MAJOR WORKS

Cavalli-Sforza, L. L. and A. W. F. Edwards. 1967. Phylogenetic analysis: modelsand estimation procedures. Evolution 32: 550-570.

Christoffersen, M. L. 1995. Cladistic taxonomy, phylogenetic systematics,and evolutionary ranking. Systematic Biology 44: 440-454.

Colless, D. H. 1982. Review of phylogenetics: the theory and practice ofphylogenetic systematics. Systematic Zoology 31: 100-104.

Crandall, K. and A. R. Templeton. 1993. Empirical tests of some predictionsfrom coalescent theory with applications to intraspecific phylogeny reconstruction.Genetics 134:989-99.

Day, W. H. E. and D. Sankoff. 1986. Computational complexity of inferring phylogenies by compatibility. Systematic Zoology 35: 224-229.

Duncan, T. and T. Steussey [eds.]. 1984. Cladistics: perspectives on the reconstruction of evolutionary history, 24-38. Columbia University Press, New York.

Estabrook, G. F. 1972. Cladistic methodology: a discussion ofthe theoretical basis for the induction of evolutionary history. Annual Review of Ecology and Systematics 3: 427-456.

Felsenstein, J. 1982. Numerical methods for inferring evolutionary trees. Quarterly Review of Biology 57: 379-404.

Felsenstein, J. 1983. Parsimony in systematics: biological and statistical issues. Annual Review of Ecology and Systematics 14: 313-333.

Felsenstein, J. 1988. Phylogenies from molecular sequences: inference and reliability. Annual Review of Genetics 2: 521-565.

Forey, P. L., C. J. Humphries, I. L. Kitching, R .W. Scotland, D. J. Siebert, and D. M. Williams. 1992. Cladistics: a practical course in systematics. The Systematics Association Publication No. 10, Oxford Science Publications, Clarendon Press,Oxford.

Garey, M. and D. S. Johnson. 1979. Computers and intractability: a guide to the theory of NP-Completeness. W. H. Freeman and Co., New York.

Harvey P. H. and M. D. Pagel. 1991. The comparative method in evolutionary biology. Oxford University Press, New York.

Hennig, W. 1966. Phylogenetic systematics. University of Illinois Press, Urbana.

Hillis, D. M. 1995. Approaches for assessing phylogenetic accuracy. Systematic Biology 44: 3-16.

Noreen, E. W. 1989. Computer intensive methods for resting hypotheses: and introduction. John Wiley & Sons, NY.

Penny, D. L.R. Foulds, and M.D. Hendy. 1982. Testing the theory of evolution by comparing phylogenetic trees constructed from five different protein sequences. Nature 297: 197-200.

Penny, D. , M. D. Hendy, and M.A. Steel. 1992. Progress with methods for constructing evolutionary trees. Trends in Ecology and Evolution 7:73-79.

Patterson, C. [ed.]. 1987. Molecules and morphology in evolution: conflict or compromise. Cambridge University Press, Cambridge.

Ridley, M. 1986. Evolution and classification: the reformation of cladism. Longman Press, London.

Salthe, S. M. 1985. Evolving hierarchial systems: their structure and representation. Columbia University Press, NewYork.

Sneath, P. H. A. and R. R. Sokal. 1973. Numerical taxonomy. The principles and practice of numerical classification. W. H. Freeman, San Francisco.

Steel, M., P. J. Lockhart, and D. Penny. 1993. Confidence in evolutionarytrees from biological sequence data. Nature 364: 440-442.

Stevens, P. F. 1980. Evolutionary polarity of character states. Annual Review of Ecology and Systematics 11: 333-358.

Warnow, T. J. 1993. Constructing phylogenetic trees using compatibility criteria. New Zealand Journal of Botany 31: 239-248.

Wheeler, W. C. 1992. Extinction, sampling, and molecular phylogenetics. Columbia University Press, New York.

Wiley, E. O. 1981. Phylogenetic systematics: the theory and practice of phylogeneticsystematics. John WIley & Sons, NY.

II. MEASUREMENT OF INFORMATION

A. GENERAL DISCUSSION

Bottjer, P. D. 1980. Farris' "Information Content" and phylogenetic versus evolutionary classification: the philosophical differences remain. Systematic Zoology 29: 382-386.

Brooks, D. R., R. T. O'Grady, and E. O. Wiley. 1986. A measure of the information content of phylogenetic trees, and its use as an optimality criterion. Systematic Zoology 35: 571-581.

Farris, J. S. 1979. The information content of the phylogenetic system. Systematic Zoology 28: 483-519.

Mickevich, M. F. and N. I. Platnick. 1989. On the information content of classifications. Cladistics 5: 33-47.

Page, R. D. M. 1992. On the information content of classifications. Cladistics 8: 87-95.

Sanderson, M. J. and G. Bharathan. 1993. Does cladistic information affect inferences about branching rates? Systematic Biology 42: 1-17.

Wicken, J. S. 1983. Entropy, information, and nonequilibrium evolution. Systematic Zoology 32: 438-443.

Wicken, J. S. 1986. Entropy and evolution: Ground rules for discourse. Systematic Zoology 35: 22-36.

B. HOMOLOGY

Barriel, V. and P. Tassy. 1993. Characters, observations and steps: comment on Lipscomb's "Parsimony, homology and the analysis of multistate characters." Cladistics 9: 223-232.

Hillis, D. M. 1993. Homology in molecular biology. In: B. Hall [ed.], Homology. Academic Press, San Diego.

Patterson, C. 1988. Homology in classical and molecular biology. Molecular Biology and Evolution 5: 603-625.

Roth, V. L.1984. On homology. Biological Journal of the Linnean Society 22: 13-29.

Roth, V. L. 1988. The biological basis of homology. In: C. J. Humpries [ed.], Ontogeny and Systematics. Columbia University Press, New York.

Roth, V. L. 1991. Homology and hierarchies: problems solved and unresolved. Journal of Evolution Biology 4: 167-194.

Valen, L. M. V. 1982. Homology and causes. Journal of Morphology 173: 305-312.

Wagner, G. P. 1989. The origin of morphological characters and the biological basis of homology. Evolution 43: 1157-1171.

Williams, D. M. 1993. A note of molecular homology: Multiple patterns from single data sets. Cladistics 9: 233-245.

Zelditch, M. L., W. L. Fink, and D. L. Swiderski. 1995. Morphometrics, homology, and phylogenetics: quantified characters as synapomorphies. Systematic Biology 44: 179-189.

C. POST-HOC (TOPOLOGY-BASED) MEASURES OF HOMOPLASY

Albrecht, G. H. 1978. Some comments on the use of ratios. Systematic Zoology 27: 67-71.

Archie, J. W. 1989. Homoplasy excess ratios: New indices for measuring levels of homoplasy in phylogenetic systematics and a critique of the consistency index. Systematic Zoology 38: 253-269.

Archie, J. W. 1990. Homoplasy excess statistics and retention indices: a reply to Farris. Systematic Zoology 39: 169-174.

Atchley W. R. 1978. Ratios, regression intercepts, and the scaling of data. Systematic Zoology 27: 78-83.

Atchley, W. R. and D. Anderson. 1978. Ratios and the statistical analysis of biological data. Systematic Zoology 27: 71-78.

Dodson, P. 1978. On the use of ratios in growth studies. Systematic Zoology 27: 62-67.

Donoghue M. J. and M. J. Sanderson. 1989. Patterns in variation in levels ofhomoplasy. Evolution 43: 1781-1795.  Faith, D. P. 1989. Homoplasy as pattern: multivariate analysis of morphological convergence in Anseriformes. Cladistics 5: 235-258.

Farris, J. S. 1989. The retention index and homoplasy excess. Systematic Zoology 38: 406-407.

Farris, J. S. 1989. The retention index and the rescaled consistency index. Cladistics 5: 47-419.

Farris, J. S. 1991. Excess homoplasy ratios. Cladistics 7: 81-91.

Goloboff, P. A. 1991. Homoplasy and the choice among cladograms. Cladistics 7: 215-232.

Hillis, D. M. 1978. On ratios- a response to Atchly, Gaskins, and Anderson. Systematic Zoology 27: 61-62.

Klassen, G. J., R. D. Mooi, and A. Locke. 1991. Consistency indices and random data. Systematic Zoology 40: 446-457.

Meier, R., P. Kores, and S. Darwin. 1991. Homoplasy slope ratio: a better measurement of observed homoplasy in cladistic analyses. Systematic Zoology 40: 74-88.

Sanderson, M. J. 1990. Estimating rates of speciation and evolution: a bias due to homoplasy. Cladistics 6: 387-391.

Sanderson, M. J. 1991. In search of homoplastic tendencies: statistical inference of typological patterns in homoplasy. Evolution 45: 351-358.

Sharkey M. J. 1993. Exact indices, criteria to select from minimum length trees. Cladistics 9: 211-222.

Wilkinson, M. 1991. Homoplasy and parsimony analysis. Systematic Zoology 40: 105-109.

D. PERMUTATIONS

Alroy, J. 1994. Four permutation tests for the presence of phylogenetic structure. Systematic Biology 43: 430-437.

Archie, J. W. 1989. A randomization test for phylogenetic information in systematic data. Systematic Zoology 38: 239-252.

Bryant, H. N. 1992. The role of permutation tail probability tests in phylogenetic systematics. Systematic Biology 41: 258-263.

Carpenter, J. M. 1992. Random cladistics. Cladistics 8: 147-153.

Faith, D. P. 1991. Cladistic permutation tests for monophyly and nonmonophyly. Systematic Zoology 40: 366-375.

Faith, D. P. 1992. On corroboration: a reply to Carpenter. Cladistics 8: 265-273.

Faith, D. P. and J. W. O. Ballard. 1994. Length differences and topology-dependent tests: a response to Källersjö: et al. Cladistics 10: 57-64.

Faith, D. P. and P. S. Cranston. 1991. Could a cladogram this short have arisen by chance alone?: on permutationtests for cladistic structure. Cladistics 7: 1-28.

Faith, D. P. and P. S. Cranston. 1992. Probability, parsimony, and Popper. Systematic Biology 41: 252-257.

Farris, J. S., M. Källersjö, A. G. Kluge, and C. Bult. 1994. Permutations. Cladistics 10: 65-76.

Fishman, G. S. and L. R. Moore. 1982. A statistical evaluation of multiplicative congruential random number generators with modulus 231-1. Journal of American Statistical Association 77: 129-136.

Goloboff, P. A. 1991. Random data, homoplasy and infomation. Cladistics 7: 395-406.

Källersjö, M., J. S. Farris, A.G. Kluge, and C. Bult.1992. Skewness and permutation. Cladistics 8: 275-287.  Page 1991. Random dendrograms and null hypotheses in cladistic biogeography. Systematic Zoology 40: 54-62.

Trueman, J. W. H. 1993. Randomization confounded: a response to Carpenter. Cladistics 9: 101-109.

Trueman, J. W. H. 1995. Sponges, plants and T-PTP. Systematic Biology 44: 429-434

Wilkinson, M. 1994. The permutation method and character compatibility. Systematic Biology 43: 274-277.

E. TREE-LENGTH DISTRIBUTION CENTRAL MOMENTS

Hillis, D. M. 1991. Discriminating between phylogenetic signal and random noise in DNA sequences. In: M. M. Miyamoto and J. Cracraft [eds.], Phylogenetic Analysis of DNA Sequences, 278-294. Oxford University Press, New York, N.Y.

Hillis, D. M., and J. P. Huelsenbeck. 1992. Signal, noise, and reliability in molecular phylogenetic analyses. Journal of Heredity 83: 189-195.

Huelsenbeck, J. P. 1991. Tree-length distribution skewness: an indicator of phylogenetic information. Systematic Zoology 40: 257-270.

Källersjö, M., J. S. Farris, A.G. Kluge, and C. Bult.1992. Skewness and permutation. Cladistics 8: 275-287.

Le Quesne, W. J 1989. Frequency distributions of lengths of possible networks from a data matrix. Cladistics 5: 395-407.

Novacek, M. J. 1991. "All tree histograms" and the evaluation of cladistic evidence: some ambiguities. Cladistics 7: 345-349.

F. RASA Theory

Forster, M. R. 1986. Statistic covariance as measure of phylogenetic relationship. Cladistics 2: 297-317.

Lyons-Weiler, J., G.A. Hoelzer, and R.J. Tausch. 1996. Relative apparent synapomorphy analysis (RASA) I: the statistical measurement of phylogenetic signal. Molecular Biology and Evolution (in press).

Lyons-Weiler, J., G.A. Hoelzer, and R.J. Tausch. in prep. Relative apparent synapomorphy analysis (RASA) I: optimal outgroup analysis.

G. RESAMPLING

Efron, B. 1982. The jacknife, the bootstrap, and other resampling plans. CBMS-NSF Regional Conference Series in Applied Mathematics, Philadelphia, PA.

Efron, B. and G. Gong. 1983. A lesiurely look at the boostrap, thejacknife, and cross-validation. American Stat. 37: 36-48.

Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791.

Felsenstein, J. and H. Kishino. 1993. Is there something wrong with the bootstrap on phylogenies? A reply to Hillis and Bull. Systematic Biology 42: 193-200.

Hillis, D. M. and J. J. Bull. 1993. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Systematic Biology 42: 182-192.

Krejewski, C. and A. W. Dickerman. 1990. Bootstrap analysis of phylogenetic trees derived from DNA hybridization distances. Systematic Zoology 39: 383-390.

Li, W.-H. and A. Zharkikh. 1994. What is the bootstrap technique? Systematic Biology 43: 424-430.

Sanderson, M. J. 1989. Confidence limits on phylogenies: the bootstrap revisited. Cladistics 5: 113-129.

Sanderson, M.J. 1995. Objection to bootstrapping phylogenies: a critique.Systematic Zoology 44:299-320.

Zharkikh, A. and W-H Li. Estimation and confidence in phylogeny:the complete-and-partial bootstrap. Molecular Phylogenetics Evolution. (in press)

H. TREENESS INDICES AND TREE COMPARISONS

Astolfi, P. and L. Zonta-Sparamella. 1984. Phylogenetic trees: an analysis of the treeness test. Systematic Zoology 33: 159-166.

Brown, J. K. M. 1994. Probabilities of evolutinary trees. Systematic Biology 43: 78-91.

Felsenstein, J. 1978. The number of evolutionary trees. Systematic Zoology 27: 27-33.

Guyer, C. and J. B. Slowinski. 1991. Comparison of observed phylogenetic topologies with null expectations among three monophyletic lineages. Evolution 45: 340-350.

Harding, E. F. 1971. The probabilities of rooted tree-shapes generated by random bifurcation. Advances in Applied Probability 3: 44-77.

Hendy, M. D., M. A. Steel, D. Penny, and I. M. Henderson. 1988. Families of trees and consensus. 355-362. In: H. H. Bock [ed.], Classification and Related Methods of Data Analysis, 355-362. Elsevier, Amsterdam.

Heard, S.B. 1992. Patterns in tree balance among cladistic, phenetic andrandomly generated phylogenetic trees. Evolution 46: 1818-1826.

Losos, J. B. and F. Alder. 1995. Stumped by trees? a generalized null model for patterns of organismal diversity. American Naturalist 15: 329-342.

Mooers, A. O. 1995. Tree balance and tree completeness. Evolution 49: 379-384.

Page, R. D. M. 1993. Tree comparison software for Microsoft Windows, version 2.0. Natural History Museum, London.

Penny, D. and M. D. Hendy. 1985. The use of tree comparison metrics. Systematic Zoology 34: 75-82.

Robinson, D. F. and L. R. Foulds. 1981. Comparison of phylogenetic trees. Mathematical Biosciences 53: 131-147.

Rogers, J. S. 1993. Response of Colless's tree imbalance to number of terminal taxa. Systematic Biology 42: 102-105.

Rogers, J. S. 1994. Central moments and probability distribution of Colless's coefficient of tree imbalance. Evolution 48:2026-2036.

Shao, K.-T. and R. R. Sokal. 1990. Tree balance. Systematic Zoology 39: 66-276.

Slowinski, J. B. and C. Guyer. 1989. Testing the stochasticity of patterns of organismal diversity: an improved null model. American Naturalist 134: 907-921.

Simberloff, D. 1987. Calculating probabilites that cladograms match: a method of biogeographical inference. Systematic Zoology 36: 175-195.

Steel, M. A. and D. Penny. 1993. Distributions of tree comparison metrics- some new results. Systematic Biology 42: 126-141.

Williams, W. T. and H. T. Clifford. 1971. On the comparison of two classifications of the same setof elements. Taxon 20: 519-522.

III. GENERAL REFERENCES

Astolfi, P., A. Piazzi, and K. K. Kidd. 1978. Testing evolutionary independence in simulated phylogenetic trees. Systematic Zoology 27: 391-400.

Baum, B. R. and G. F. Estabrook. 1978. Application of compatability analysis in numerical cladistics at the infraspecific level. Canadian Journal of Botany 56: 1130-1135.

Beyer, W. A., M. L. Stein, T. F. Smith,and S. M. Ulman. 1974. A molecular sequence metric and evolutionary trees. Mathematical Biosciences 19: 9-25.

Brooks, D. R. 1981. Raw similarity measures of shared parasites: an empirical tool for determining host phylogenetic relationships? Systematic Zoology 30: 203-207.

Bryant, H. N. 1994. Comments on the phylogenetic definition of taxon names and conventions regarding the naming of crown clades. Systematic Biology 43: 124-130.

Buckup, P. A. 1991. Cladogram characters: predictions, not observations. Cladistics 7: 191-195.

Bull, J. J., J.P. Huelsenbeck,C. W. Cunningham, D. L.Swofford, and P. J. Waddell. 1993. Partioning and combining data in phylogenetic analysis. Systematic Biology 42: 384-397.

Cavalli-Sforza, L. L. and A. W. F. Edwards. 1967. Phylogenetic analysis: models and estimation procedures. Evolution 32:550-570.

Cavender, J.A. 1978. Taxonomy with confidence. Mathematical Biosciences 40: 271-280. (erratum 1979 44:309) 40: 271-280.

Crandall, K. A. 1994. Intraspecific cladograms estimation: accuracy at higher levels of divergence. Systematic Biology 43: 222-235.

Day, W. H. E. and D. Sankoff. 1986. Computational complexity of inferring phylogenies by compatibility. Systematic Zoology 35: 224-229.

DeBry, R. 1995. The relationship between parsimony and maximum-likelihoodanalyses: tree scores and confidence estimates for three real data sets. Molecular Biology and Evolution 12:291-297.

Dobson, A. J. 1974. Unrooted trees innumerical taxonomy. Journal of Applied Probability 11: 32-42.

Eades, D. C. 1970. Theoretical and procedural aspectsof numerical phyletics. Systematic Zoology 19: 142-171.

Estabrook, G. F. 1972. Cladistic methodology: a discussion of the theoretical basis for the induction of evolutionary history. Annual Review of Ecology and Systematics 3: 427-456.

Estabrook, G. F., C. S. Johnson, Jr., and F. R. McMorris. 1976. An algebraic analysis of cladistic characters. Mathematical Biosciences 29: 181-187.

Estabrook, G. F., C. S.Johnson, Jr., and F. R. McMorris. 1976. A mathematical foundation for the analysis of cladistic character compatibility. Discrete Mathematics 16: 141-147.

Estabrook, G. F., C. S.Johnson, Jr., and F. R.McMorris. 1977. When are two quantitative characters compatible? Joural of Mathematical Biology 4: 195-200.

Estabrook, G. F. and C. A. Meaam. 1979. How to determine the compatability of undirected character state trees. Mathematical Biosciences 46: 251-256.

Farris, J. S. 1973. A probability model for inferring evolutionary trees. Systematic Zoology 22: 250-256.

Farris, J. S. 1986. Distances and statistics. Cladistics 2: 144-157.

Farris, J. S. 1988. Hennig86, version 1.5 manual/software and MSDOS program. Distributed by the author. Port Jefferson Stion, New York.

Farris, J. S. and A. G. Kluge. 1979. A botanical clique. Systematic Zoology 28: 400-411.

Farris, J. S., A. G. Kluge, and M. J. Eckhart. 1970. A numerical approach to phylogenetic systematics. Systematic Zoology 19: 172-189.

Felsenstein, J. 1973. Maximum likelihood estimation of evolutionary trees from continuous characters. Amerian Journal of Genetics 25: 471-492.

Felsenstein, J. 1973. Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters. Systematic Zoology 22: 240-249.

Felsenstein, J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Systematic Zoology 27: 401-410.

Felsenstein, J. 1979. Alternative methods of phylogenetic inference and their interrelationship. Systematic Zoology 28: 49-6.

Felsenstein, J. 1981. A likelihood approach to character weighting and what it tells us about parsimony and compatibility. Biological Journal of Linnean Society 16: 183-196.

Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution 17: 368-376.

Felsenstein, J. 1981. Evolutionary trees from gene frequencies and quantitative characters: Finding maximum likelihood estimates and testing hypotheses. Evolution 35: 1229-1246.

Felsenstein, J. 1982. Numerical methods for inferring evolutionary trees. Quarterly Review of Biology 57: 379-404.

Felsenstein, J. 1983. Parsimony in systematics: biological and statistical issues. Annual Review of Ecology and Systematics 14: 313-333.

Felsenstein, J. 1983. Statistical inference of phylogenies. Journal of the Royal Statistical Society A146: 246-272.

Felsenstein, J. 1984. Distance methods for inferring phylogenies: a justification. Evolution 38: 16-24.

Felsenstein, J. 1984. The statistical approach to inferring phylogeny and what it tells us about parsimony and compatibility. In:T. Duncan and T. F. Stuessy [eds.], Cladistics: perspectives on the reconstruction of evolutionary history, 169-191. Columbia University Press, New York.

Felsenstein, J. 1985. Phylogenies and the comparative method. American Naturalist 125: 1-15.

Felsenstein, J. 1985. Confidence limits on phylogenies with a molecular clock. Systematic Zoology 34: 152-161.

Felsenstein, J. 1985. Phylogenies from gene frequencies: a statistical problem. Systematic Zoology 34: 300-311.

Felsensein, J. 1986. Distance methods: a reply to Farris. Cladistics 2: 130-143.

Felsenstein, J. 1988. Phylogenies and quantitative characters. Annual Review of Ecology and Systematics 19: 445-471.

Felsenstein, J. 1988. Phylogenies from molecular sequences: inference and reliability. Annual Review of Genetics 2: 521-565.

Felsenstein, J. 1988. Perils of molecular introspection. Nature 335: 118.

Felsenstein, J. 1989. PHYLIP manual, version 3.2. University of California Herbarium, Berkeley, California.

Felsenstein, J. 1990. PHYLIP manual, version 3.3. University of California Herbarium, Berkeley, California.

Felsenstein, J. 1991. PHYLIP (Phylogeny Inference Package), Version 3.4. Distributed by the author, University of Washington, Seattle, Washington.

Felsenstein, J.and E. Sober. 1986. Parsimony and likelihood: an exchange. Systematic Zoology 35: 617-626.

Forster, M. R. 1986. Statistic covariance as measure of phylogenetic relationship. Cladistics 2: 297-317.

Garland, T., Jr., A. W. Dickerman, C. M. Janis, and J. A. Jones. 1993. Phylogenetic analysis of covariance by computer simulation. Systematic Biology 42: 265-292.

Garland T., Jr., P. H. Harvey, and A. R. Ives. 1992. Procedures for the analysis of comparative data using phylogenetically independent contrasts. Systematic Biology 41: 8-32.

Gould, I. and G. Underwood. 1986. Some applications of the Le Quesne compatibility test. Biological Journal of Linnean Society 29: 191-222.

Gittleman, J. L. and M. Kot. 1990. Adaptation: statisics and a null model for estimating phylogenetic effects. Systematic Zoology 39: 227-241.

Glen, D. R. and D. R. Brooks. 1985. Phylogenetic relationships of some Nematodes of Primates. Proceedings of the Helminthological Society of Washington 52: 227-236.

Goldman, N. 1988. Methods of discrete coding of morphological characters for numerical analysis. Cladistics 4: 59-71.

Goldman, N. 1989. Fewest variables coding method for multistate characters. Systematic Zoology 38: 79-85.

Goldman, N. 1990. Maximum liklihood inference of phylogenetic trees, with special reference to a Poisson process model of DNA substitution and to parsimony analyses. Systematic Zoology 39: 345-361.

Goloboff, P. A. 1993. Estimating character weights duing tree search. Cladistcs 9: 83-91.

Goloboff, P. A. 1993. Character optimization and calculation of tree lengths. Cladistics 9: 433-436.

Gould, R. 1988. Graph Theory. Benjamin/Cummings, Menlo Park, California.

Grafen, A. 1989. The phylogenetic regression. Philosophical Transactions of the Royal Society of London B 326: 119-157.

Graham, R. L. and L. R.Foulds. 1982. Unlikelihood that minimal phylogenies for a realistic biological study can be constructed in reasonable computational time. Mathematical Biosciences 60: 133-142.

Griffiths, G. C. D. 1973. Some fundamental problems in biological classification. Systematic Zoology 22: 338-343.

Griffiths, G. C. D. 1974. On the foundations of biological systematics. Acta Biotheoretica 23: 85-131.

Harper, C. W., Jr. 1979. A Bayesian probability view of phylogenetic systematics. Systematic Zoology 28: 547-553.

Harper, C. W., Jr., and N. I. Platnick. 1978. Phylogenetic and cladistic hypotheses: a debate. Systematic Zoology 27: 354-362.

Harvey, P. H. and M. D. Pagel. 1991. The comparative method in evolutionary biology. Oxford University Press, Oxford.

Hazel, J. E. 1972. On the use of cluster analysis in biogeography. Systematic Zoology 21: 240-242.

Hendy, M. D. and D. Penny. 1989. A framework for the quantitative study of evolutionary trees. Systematic Zoology 38: 297-309.

Hill, L. R. 1975. Problems arising from some tests of LeQuesne's concept of uniquely derived characters. In: G. F. Estabrook [ed.], Proceedingsof the Eighth International Conferenceon Numerical Taxonomy, 375-398.W. H. Freeman, San Francisco, California.

Hillis, D. M. 1984. Misuse and modification of Nei's genetic distance. Systematic Zoology 33: 238-240.

Hillis, D. M. 1995. Approaches for assessing phylogenetic accuracy. Systematic Biology 44: 3- .

Hillis, D. M., J. J. Bull, M. E. White, M. R. Badgett, and I. J. Molineux. 1992. Experimental phylogenetics: generation of known phylogeny. Science 255: 589-592.

Hillis, D. M., J. J. Bull, M. E. White, M. R. Badgett, and I. J. Molineux. 1993. Experimental approaches to phylogenetic analysis. Systematic Biology 42: 90-92.

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Huelsenbeck, J.P. 1995. Performance of phylogenetic methods in simulation. Systematic Biology 44: 17-48.

Huelsenbeck, J. P. and D. M. Hillis. 1993. Success of phylogeetic methods in the four-taxon case. Systematic Biology 42: 247-264.

Hull, D. L. 1967. Certainty and circulariry in evolutionary taxonomy. Evolution 21: 174-189.

Hull, D. L. 1981. The principles of biological classification: the use and abuse of philosophy. Proceedings of the National Academy of Sciences USA 78: 130-153.

Hull, D L. 1988. Science as a process. An evolutionary account of the social and conceptual development of science. University of Chicago Press, Chicago.

Hull, D. L. 1990. Farris on Haeckel, history, and Hull. Systematic Zoology 39: 397-399.

Kellogg, E. A. and L. Watson. 1993. Phylogenetic studies of a large data set. I. Bambusoideae, Andropogonoideae, and Pooideae (Gramineae). Botanical Review 59: 273-343.

Kim, J. 1993. Improving the accuracy of phylogenetic estimation by combining different methods. Systematic Biology 42: 331-340.

Kim, J., F. J. Rohlf, and R. R. Sokal. 1993. The accuracy of phylogenetic estimation using the neighbor-joining method. Evolution 47: 471-486.

Klotz, L. C. and R. L. Blanken. 1981. A practical method for calculating evolutionary trees from sequence data. Journal of Theoretical Biology 91: 261-272.

Klotz, L. C., N. Komar, R. L. Blanken, and R. M. Mitchell. 1979. Calculating of evolutionary trees from sequence data. Proceedings of the National Academy of Science USA 76: 4516-1520.

Kluge, A. G. 1984. The relevance of parsimony to phylogenetic inference, In: T. Duncan and T. Steussey [eds.], Cladistics: perspectives on the reconstruction of evolutionary history, 24-38. Columbia University Press, New York.

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Kluge, A. G. 1989. A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Systematic Zoology 38: 7-25.

Kluge, A. G. and A. J. Wolf. 1993. Cladistics: what's in a word? Cladistics 9: 183-199.

Knight, A., D. Styer, S. Pelikan, J. A. Campbell, L. D. Densmore III, and D. P. Mindell. 1993. Choosing among hypotheses of rattlesnake phylogeny: A best-fit rate test for DNA sequence data. Systematic Biology 42: 356-367.

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