Adams E (1972) Consensus techniques and the comparison of taxonomic trees. Syst Zool 21: 390-397

Andrews P (1992) Evolution and environment in the Hominoidea. Nature 360: 641-646 Ayres RU (1994) Information, entropy and progress: A new evolutionary paradigm. American Institute of Physics Press, New York

Barnard GA, Bayes T (1958) Studies in the history of probability and statistics: IX. Thomas Bayes's essay towards solving a problem in the doctrine of chances. Biometrica 45: 293-315 Begun DR (2001) African and Eurasian Miocene hominoids and the origins of the Homi-nidae. In: de Bonis L, Koufos G, Andrews P (eds) Phylogeny of the neogene homi-noid primates of Eurasia, Cambridge University Press, Cambridge, pp 231-253 Begun DR, Ward CV, Rose MD (1997) Events in hominoid evolution. In: Begun DR, Ward CV, Rose MD (eds) Function, phylogeny and fossils: Miocene hominoid evolution and adaptations. Plenum Press, New York, pp 389-415

Bremer K (1988) The limits of amino-acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42: 795-803 Brillouin L (1951) Physical entropy and information. J Appl Phys 22: 338-343 Brillouin L (1953) Negentropy principle of information. J Appl Phys 24: 1152-1163 Brillouin L (1962) Science and information theory, 2nd edn. Academic Press, New York Brooks DR (1981) Classifications as languages of empirical comparative biology. In: Funk VA, Brooks DR (eds) Advances in Cladistics: Proceedings of the First Meeting of the Willi Hennig Society, New York Botanical Garden, New York, pp 61-70. Brooks DR, McLennan DA (2002) The nature of diversity. Chicago University Press, Chicago

Brooks DR, O'Grady RT, Wiley EO (1986) A measure of the information content of phylogenetic trees, and its use as an optimality criterion. Syst Zool 35: 571-581 Camin JH, Sokal RR (1965) A method for deducing branching sequences in phylogeny. Evolution 19: 311-326 Cavalli-Sforza LL, Edwards AWF (1967) Phylogenetic analysis: Models and estimation procedures. Evolution 21: 550-570 Charlesworth MJ (1956) Aristotle's razor.

Philos Stud 6: 105-112 Churchill SP, Wiley EO, Hauser LA (1984) A critique of Wagner Groundplan-divergence studies and a comparison with other methods of phylogenetic analysis. Taxon 33: 212-232 Collard M, Wood B (2001) How reliable are current estimates of fossil catarrhine phyloge-ny? An assessment using extant great apes and old world monkeys. In: de Bonis L, Koufos G, Andrews P (eds) Phylogeny of the neogene hominoid primates of Eurasia. Cambridge University Press, Cambridge, pp 118-150 Colless DH (1966) A note on Wilson's consistency test for phylogenetic hypotheses. Syst Zool 15: 358-359 Colless DH (1985) On "Character" and related terms. Syst Zool 34: 229-233 Danser BH (1950) A theory of systematics. Bib-

lioth Biotheor 4: 113-180 Darwin C (1859) On the origin of species. John

Murray, London Darwin C (1872) On the origin of species, 6th edn. John Murray, London de Queiroz K, Poe S (2001) Philosophy and phylogenetic inference: A comparison of likelihood and parsimony methods in the context of Karl R. Popper's writings on corroboration. Syst Biol 50: 305-321 de Queiroz K, Poe S (2003) Failed refutations: Further comments on parsimony and likelihood methods and their relationship to Popper's degree of corroboration. Syst Biol 52: 352-367

Disotell T (1996) The phylogeny of old world monkeys. Evol Anthropol 5: 18-24 Doolittle WF (2000) Uprooting the tree of life.

Sci Am 282(2): 90-95 Edwards AWF (1972) Likelihood. Cambridge

University Press, Cambridge Edwards AWF (1996) The origin and early development of the method of minimum evolution for the reconstruction of phyloge-netic trees. Syst Biol 45: 79-91 Edwards AWF, Cavalli-Sforza LL (1963) The reconstruction of evolution. Ann Hum Genet 27: 105-106 Edwards AWF, Cavalli-Sforza LL (1964) Reconstruction of evolutionary trees. In: Heywood VH, McNeill J (eds) Phenetic and phylogenetic classification. Systematics Association Publication No. 6, London, pp 67-76 Efron B (1979) Bootstrap methods: Another look at the jackknife. Ann Stat 7: 1-26. Eldredge N, Cracraft J (1980) Phylogenetic patterns and the evolutionary process. Columbia University Press, New York Engelmann GF, Wiley EO (1977) The place of ancestor-descendant relationships in phylogeny reconstruction. Syst Zool 26: 1-11 Faith DP, Trueman JWH (2001) Towards an inclusive philosophy for phylogenetic inference. Syst Biol 50: 331-350 Farris JS (1970) Methods of computing Wagner trees. Syst Zool 19: 83-92 Farris JS (1972) Estimating phylogenetic trees from distance matrices. Am Nat 106: 645-668

Farris JS (1973) A probability model for inferring evolutionary trees. Syst Zool 22: 250-25 Farris JS (1977) Phylogenetic analysis under

Dollo's Law. Syst Zool 26: 77-88 Farris JS (1979) The information content of the phylogenetic system. Syst Zool 28: 483-519 Farris JS (1983) The logical basis of phylogenetic analysis. In: Platnick NI, Funk VA (eds) Advances in cladistics, vol 2. Columbia University Press, New York Farris JS (1989) The retention index and rescaled consistency index. Cladistics 5: 417-419 Farris JS, Kluge AG, Eckardt MJ (1970) A numerical approach to phylogenetic systemat-ics. Syst Zool 19: 172-191 Farris JS, Albert VA, Kallersjo M, Lipscomb D, Kluge AG (1996) Parsimony jackknifing outperforms neighbour-joining. Cladistics 12: 99-124

Felsenstein J (1968) Statistical inference and the estimation of phylogenies. PhD Thesis, University of Chicago Felsenstein J (1973) Maximum likelihood and minimum steps methods for estimating evolutionary trees from data on discrete characters. Syst Zool 22: 240-249 Felsenstein J (1978) Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool 27: 401-410 Felsenstein J (1981a) A likelihood approach to character weighting and what it tells us about parsimony and compatibility. Biol J Linn Soc 16: 183-196

Felsenstein J (1981b) Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol 17: 368-376 Felsenstein J (1983) Parsimony in systematics: Biological and statistical issues. Ann Rev Ecol Syst 14: 313-333 Felsenstein J (1985a) Confidence limits on phy-logenies: An approach using the bootstrap. Evolution 39: 783-791 Felsenstein J (1985b) Statistical inference and the estimation of phylogenies. Ph.D. dissertation, University of Chicago, Chicago Felsenstein J (2004) Inferring phylogenies.

Sinauer Associates, Inc., Sunderland Felsenstein J, Sober E (1986) Parsimony and likelihood: An exchange. Syst Zool 35: 617-626

Fisher RA (1922) On the mathematical foundations of theoretical statistics. Phil Trans Roy Soc Lon Ser A 222: 309-368 Fitch WM (1971) Toward defining the course of evolution: Minimum change for a specified tree topology. Syst Zool 20: 406-416 Gaffney ES (1979) An introduction to the logic of phylogeny reconstruction. In: Cracraft J, Eldredge N (eds) Phylogenetic analysis and paleontology. Columbia University Press, New York, pp 79-111 Gatlin L (1975) Information theory and the living system. Columbia University Press, New York

Geyer CJ (1991) Constrained maximum-likelihood exemplified by isotonic convex logistic-regression. J Am Stat Assoc 86: 717-724 Gissi C, Reyes A, Pesole G, Saccone C (2000) Lineage-specific evolutionary rate in mammalian mtDNA. Mol Biol Evol 17: 1022-1031

Goldman N (1990) Maximum likelihood inference of phylogenetic trees, with special reference to a poisson process model of

DNA substitution and to parsimony analysis. Syst Zool 39: 345-361 Goloboff PA (2003) Parsimony, likelihood and simplicity. Cladistics 19: 91-103 Green PJ (1995) Reversible jump Markov chain Monte Carlo computation and Bayesian model determination. Biometrika 82: 711 1995 Groves C (1978) Phylogenetic and population systematics of the mangabeys (Primates: Cer-copithecoidea). Primates 19: 1-34 Harper CW Jr (1979) A Bayesian probability view of phylogenetic systematics. Syst Zool 28: 547-533 Harris E (2000) Molecular systematics of the old world monkey tribe Papionini: Analysis of the total available genetic sequences. J Hum Evol 38: 235-256 Hastings WK (1970) Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57: 97-109 Hawks J (2004) How much can cladistics tell us about early hominid relationships? Am J Phys Anthropol 125: 207-219 Hendy MD, Penny D (1982) Branch and bound algorithms to determine minimal evolutionary trees. Math Biosci 59: 277-290 Hennig W (1950) Grundzüge einer theorie der phylogenetischen systematik. Deutscher Zentralverlag, Berlin Hennig W (1966) Phylogenetic systematics. Illinois University Press, Urbana Hillis DM, Huelsenbeck JP, Swofford DL (1994) Hobgloblin of phylogenetics? Science 369: 363-364

Hillis DM, Bull JJ, White ME, Badgett MR, Molineaux IJ (1992) Experimental phylogenetics: Generation of a known phylogen. Science 255: 589-592 Hillis DM, Bull JJ, White ME, Badgett MR, Molineaux IJ (1993) Experimental approaches to phylogenetic analysis. Syst Biol 42: 90-92 Honderich T (1995) The Oxford companion to philosophy. Oxford University Press, Oxford

Huelsenbeck JP (1997) Is the Felsenstein zone a fly trap? Syst Biol 46: 69-74 Huelsenbeck JP, Crandall KA (1997) Phylogeny estimation and hypothesis testing using maximum likelihood. Ann Rev Ecol Syst 28: 437-466

Huelsenbeck JP, Hillis DM (1993) Success of phylogenetic methods in the four-taxon case. Syst Biol 42: 247-264 Huelsenbeck JP, Nielsen R (1999) Effect of non-independent substitution on phylogenetic accuracy. Syst Biol 48: 317-328 Huelsenbeck JP, Rannala B (1997a) Phylogenetic methods come of age: Testing hypotheses in an evolutionary context. Science 276: 227-232

Huelsenbeck JP, Rannala B (1997b) Maximum likelihood of phylogenies using stratigraphic data. Paleobiology 23: 174-180 Huelsenbeck JP, Larget B, Miller RE, Ronquist F (2002) Potential applications and pitfalls of Bayesian inference in phylogeny. Syst Biol 51: 673-688

Huelsenbeck JP, Ronquist B, Nielsen R, Bollback JP (2001) Bayesian inference of phylog-eny and its impact on evolutionary biology. Science 294: 2310-2314 Jaynes ET (1957a) Information theory and statistical mechanics I. Phys Rev 106: 620 Jaynes ET (1957b) Information theory and statistical mechanics II. Phys Rev 108: 171 Johnson JB, Omland KS (2004) Model selection in ecology and evolution. Trends Ecol Evol 19: 101-108 Kluge AG (1989) Metacladistics. Cladistics 5: 291-294

Kluge AG (1990) Species as historical individuals. Biol Philos 5: 417-431 Kluge AG (1991) Boine snake phylogeny and research cycles. Misc Publ Museum Zool UnivMich 178: 1-58. Kluge AG (1997) Sophisticated falsification and research cycles: Consequences for differential character weighting in phylogenetic system-atics. Zool Scripta 26: 349-360 Kluge AG (1997) Testability and the refutation and corroboration of cladistic hypotheses. Cladistics 13: 81-96 Kluge AG (1999) The science of phylogenetic systematics: Explanation, prediction, and test. Cladistics 15: 429-436 Kluge AG (2001) Philosophy and phylogenetic inference: A comparison of likelihood and parsimony methods in the context of Karl Popper's writings on corroboration. Cladistics 17: 395-399

Kluge AG (2003) On the deduction of species relationships: A précis. Cladistics 19:233-239 Kluge AG, Farris JS (1969) Quantitative phy-letics and the evolution of anurans. Syst Zool 18: 1-32

Kluge AG, Wolf AJ (1993) Cladistics: What's in a word? Cladistics 9: 183-199 Kullbach S (1951) Information theory and statistics. John Wiley & Sons, New York Larget B, Simon DL (1999) Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol Biol Evol 16: 750-759

Lewis GN (1930) The Principle of Identity and the Exclusion of Quantum States. Phys Rev 36: 1144-1153 Lewis PO (2001) A likelihood approach to estimating phylogeny from discrete morphological character data. Syst Biol 50: 913-925

Li S (1996) Phylogenetic tree construction using Markov Chain Monte Carlo. Ph.D. dis-seration, Ohio State University, Columbus Lieberman D (1999) Homology and hominid phylogeny: Problems and potential solutions. Evol Anthropol 7: 142-151 Lockhart PJ, Steel MA, Hendy MD, Penny D (1994) Recovering evolutionary trees under a more realistic model of sequence evolution. Mol Biol Evol 11: 605-612 Lundberg JG (1972) Wagner networks and ancestors. Syst Zool 18: 1-32 Maddison WP, Donoghue MJ, Maddison DR (1984) Outgroup analysis and parsimony. Syst Zool 33: 83-103 Margush T, McMorris FR (1981) Consensus n-trees. Bull Math Biol 43: 239-244 Mau B (1996) Bayesian phylogenetic inference via Markov chain Monte Carlo Methods. Ph.D. dissertation, University of Wisconsin, Madison (abstract) Mau B, Newton MA (1997) Phylogenetic inference for binary data on dendrograms using Markov chain Monte Carlo. J Comp Graph Stat 6: 122-131 Mau B, Newton MA, Larget B (1999) Bayesian phylogenetic inference via Markov chain Monte Carlo methods. Biometrics 55: 1-12 Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E (1953) Equation of state calculations by fast computing machines. J Chem Phys 21: 1087-1092 Mitchell A, Mitter C, Regier JC (2000) More taxa or more characters revisited: Combining data from nuclear protein coding genes for phylogenetic analyses of Noctuoi-dea (Insecta: Lepidoptera). Syst Biol 49: 202-224

Mitchell PC (1901) On the intestinal tract of birds. Trans Linn Soc Lond, Zool 8: 173-275 Mitchell PC (1905) On the intestinal tract of mammals. Trans Zool Soc Lond 17: 437-536

Nelson CH, Van Horne GS (1975) A new simplified method for constructing Wagner networks and the cladistics of pentachaeta (Compositae, Asteraeae). Brittonia 27: 362-372

Newman TK, Jolly C, Rogers J (2004) Mitochon-drial phylogeny and systematics of baboons (Papio). Am J Phys Anthropol 124: 17-27 Newton MA, Zhang YL (1999) A recursive algorithm for nonparametric analysis with missing data. Biometrika 86: 15-26 Neyman J (1974) Molecular studies: A source of novel statistical problems. In: Gupta SS, Yackel J (eds) Statistical decision theory and related topics. Academic Press, New York, pp 1-27

Nylander JA, Ronquist F, Huelsenbeck JP, Nieves-Aldrey JL (2004) Bayesian phyloge-netic analysis of combined data. Syst Biol 53: 47-67

Pagel M, Meade A, Barker D (2004) Bayesian estimation of ancestral character states on phylogenies. Syst Biol 53: 673-684 Pagel MD (1992) A method for the analysis of comparative data. J Theor Biol 156: 431-442 Penny D, Hendy MD, Steel MA (1992) Progress with methods for constructing evolutionary trees. Trends Ecol Evol 7: 73-79 Platnick NI, Funk VA (eds) (1983) Advances in cladistics, vol 2. Columbia University Press, New York

Popper KR (1968) The logic of scientific discovery. Harper and Row, New York Popper KR (1997) The demarcation between science and metaphysics. In: Schilpp PA (ed) The philosophy of Rudolph Carnap. Open Court, La Salle, pp 183-226

Posada D, Crandall KA (1998) ModelTest: Testing the model of DNA substitution. Bioin-formatics 14: 817-818 Prim RC (1957) Shortest connection networks and some generalizations. Bell Syst Tech J 36: 1389-1401

Rae T (1997) The early evolution of the homi-noid face. In: Begun DR, Ward CV, Rose MD (eds) Function, phylogeny and fossils: Miocene hominoid evolution and adaptations. Plenum Press, New York, pp 59-77 Rannala B, Yang Z (1996) Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference. J Mol Evol 43: 304-311 Rieppel O (2003) Popper and systematics. Syst

Biol 52: 259-271 Rodriguez F, Oliver JL, Marin A, Medina JR (1990) The general stochastic model of nu-cleotide substitution. J Theor Biol 142: 485-501

Rokas A, Williams BL, King N, Carroll SB (2003) Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425: 796-804 Ronquist F (2004) Bayesian inference of charc-ter evolution. Trends Ecol Evol 19: 475-481 Ross C, Williams B, Kay RF (1998) Phylogenetic analysis of anthropoid relationships. J Hum Evol 35: 221-306 Shannon C (1948) A mathematical theory of communication. Bell Syst Tech J 27: 379-423 Siddall ME, Kluge AG (1997) Probabilism and phylogenetic inference. Cladistics 13: 313-336

Sneath PHA, Sokal RR (1973) Numerical taxonomy: The principles and practice of numerical classification. W.H. Freeman, San Francisco

Sober E (1983) Parsimony in systematics: Philosophical issues. Ann Rev Ecol Syst 14: 335-357

Sober E (1988) Reconstructing the past. Parsimony, evolution, and inference. MIT Press, Cambridge

Sokal RR, Sneath PHA (1963) Numerical taxonomy. W.H. Freeman, San Francisco Sokal RR, Rohlf FJ (1981) Taxonomic congruence in the Leptopodomorpha re-examined. Syst Zool 30: 309-325

Soltis PS, Soltis DE (2003) Applying the bootstrap in phylogeny reconstruction. Stat Sci 18: 256-267 Sorenson MD (1999) TreeRot. Boston University, Boston

Sporne KR (1949) A new approach to the problem of the primitive flower. New Phytol 48: 259-276

Sporne KR (1953) Statistics and the evolution of dicotyledons. Evol 8: 55-64 Steel M, Penny D (2000) Parsimony, likelihood, and the role of models in molecular phylo-genetics. Mol Biol Evol 17: 839-850 Steel MA, Hendy MD, Penny D (1993) Parsimony can be consistent! Syst Biol 42: 581-587

Strait DS, Grine FE, Moniz MA (1997) A reappraisal of early hominid phylogeny. J Hum Evol 23: 17-82 Strasser E, Delson E (1987) Cladistic analysis of cercopithecoid relationships. J Hum Evol 16: 81-99

Swofford DL (1998) Phylogenetic analysis using parsimony (*and other methods). Sinaur Associates, Sunderland Massachusetts Swofford DL, Maddison WP (1987) Reconstructing ancestral character states under Wagner parsimony. Math Biosci 87: 199-229

Swofford DL, Olsen GJ, Waddell PJ, Hillis DM (1996) Phylogenetic inference. In: Hillis DM, Moritz C, Mable BK (eds) Molecular systematics, 2nd edn. Sinauer Associates, Sunderland Massachusetts, pp 407-514 Tateno Y, Takezaki N, Nei M (1994) Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum parsimony methods when substitution rate varies with site. Mol Biol Evol 11: 261-277 Tierney L (1994) Markov chains for exploring posterior distributions. Ann Stat 22: 1701-1728

Tillyard RJ (1921) A new classification of the order Perlaria. Can Entomol 53: 35-43 Tribus M, McIrvine MC (1971) Energy and information. Sci Am 225: 179-188 Tuffley C, Steel M (1997) Links between maximum likelihood and maximum parsimony under a simple model of site substitution. Bull Math Biol 59: 581-607

Wagner PJ (1998) A likelihood approach for evaluating estimates of phylogenetic relationships among fossil taxa. Paleobiology 24: 430-449 Wagner WH Jr (1952) The fern genus Diellia: Structure, affinities, and taxonomy. Univ Calif Publ Botany 26: 1-212 Wagner WH Jr (1961) Problems in the classification of ferns. In: Recent advances in botany. From lectures and symposia presented to the IX International Botanical Congress, Montreal, 1959. University of Toronto Press, Toronto, pp 841-844 Wagner WH Jr (1969) The construction of a classification. In: Systematic biology. National Academy of Science USA, Publication 1692, pp 67-90 Wagner WH Jr (1980) Origin and philosophy of the groundplan-divergence method of cla-distics. Syst Bot 5: 173-193 Watrous LE, Wheeler QD (1981) The outgroup comparison method of character analysis. Syst Zool 30: 1-11 Wenzel JW, Carpenter JM (1994) Comparing methods: Adaptive traits and tests of adaptation. In: Eggleton P, Vane-Wright RI (eds) Phylogenetics and ecology. Academic Press, London, pp 79-101 Wenzel JW, Siddall ME (1999) Noise. Cladistics 15: 51-64

Whiffin T, Bierner MW (1972) A quick method for computing Wagner trees. Taxon 21: 83-90 Wiens J (1995) Polymorphic characters in phylogenetic systematics. Syst Biol 44: 482-500

Wiley EO (1975) Karl R. Popper, systematics, and classification: A reply to Walter Bock and other evolutionary taxonomists. Syst Zool 24: 233-243 Wiley EO (1981) Phylogenetics: The theory and practice of phylogenetic systematics. John Wiley and Sons, New York Wiley EO, Siegel-Causey DJ, Brooks DR, Funk VA (1991) The compleat cladist: A primer of phylogenetic procedures. Mus Nat Hist Univ Kansas, Spec Publ 19: 1-158 Wilkinson, M (1994) Common cladistic information and its consensus representation: Reduced Adams and reduced cladistic consensus trees and profiles. Syst Biol 43: 343-368

Wilson EO (1965) A consistency test for phylo-genies based on contemporaneous species. Syst Zool 14: 214-200 Wilson EO (1967) The validity of the "consistency test'' for phylogenetic hypotheses. Syst Zool 16: 104 Wu CFJ (1986) Jackknife, bootstrap and other resampling methods in regression analysis. Ann Stat 14: 1261-1295 Yang Z (1994) Statistical properties of the maximum likelihood method of phylogenetic estimation and comparison with distance matrix methods. Syst Biol 43: 329-342

Yang Z (1996) Phylogenetic analysis using parsimony and likelihood methods. J Mol Evol 42: 294-307 Yang ZH, Rannala B (1997) Bayesian phylogenetic inference using DNA sequences: A Markov Chain Monte Carlo method Mol Biol Evol 14: 717-724 Yang Z, Bielawski JP (2000) Statistical methods for detecting molecular adaptation. Trends Ecol Evol 15: 496-503

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