Biology and Philosophy

, Volume 21, Issue 3, pp 309–351 | Cite as

The ‘requirement of total evidence’ and its role in phylogenetic systematics

  • Kirk FitzhughEmail author


The question of whether or not to partition data for the purposes of inferring phylogenetic hypotheses remains controversial. Opinions have been especially divided since Kluge's (1989, Systematic Zoology 38, 7–25) claim that data partitioning violates the requirement of total evidence (RTE). Unfortunately, advocacy for or against the RTE has not been based on accurate portrayals of the requirement. The RTE is a basic maxim for non-deductive inference, stipulating that evidence must be considered if it has relevance to an inference. Evidence is relevant if it has a positive or negative effect on a given conclusion. In the case of ℈partitioned’ phylogenetic inferences, the RTE is violated, and the basis for rational belief in any conclusion is compromised, unless it is shown that the partitions are evidentially irrelevant to one another. The goal of phylogenetic systematics is to hypothesize past causal conditions to account for observed shared similarities among two or more species. Such inferences are non-deductive, necessitating consideration of the RTE. Some phylogeneticists claim the parsimony criterion as justification for the RTE. There is no relation between the two – parsimony is a relation between a hypothesis and causal question(s). Parsimony does not dictate the content of premises prior to an inference. ℈Taxonomic congruence,’ ℈supertrees,’ and ℈conditional combination’ methods violate the RTE. Taxonomic congruence and supertree methods also fail to achieve the intended goal of phylogenetic inference, such that ℈consensus trees’ and ℈supertrees’ lack an empirical basis. ℈Conditional combination’ is problematic because hypotheses derived from partitioned data cannot be compared – a causal hypothesis inferred to account for a set of effects only has relevance to those effects, not any comparative relevance to other causal hypotheses. A similar problem arises in the comparisons of hypotheses derived from different causal theories.

Key words

Abductive inference Cladistics Deduction Phylogenetics Total evidence 


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  1. Armstrong, D.M. 1997A World of States of AffairsCambridge University PressCambridgeGoogle Scholar
  2. Avise, J.C. 2000Phylogeography: The History and Formation of SpeciesHarvard University PressCambridgeGoogle Scholar
  3. Ballard, J.W.O., Thayer, M.K., Newton, A.F.,Jr., Grismer, E.R. 1998Data sets, partitions, and characters: philosophies and procedures for analyzing multiple data setsSystemat. Biol.47367396CrossRefGoogle Scholar
  4. Barker, S.F. 1957Induction and HypothesisCornell University PressNew YorkGoogle Scholar
  5. Barrett, M., Donoghue, M.J., Sober, E. 1991Against consensusSystemat. Zool.40486493CrossRefGoogle Scholar
  6. Baum, B.R. 1992Combining trees as a way of combining data sets for phylogenetic inferenceand the desirability of combining gene treesTaxon41310CrossRefGoogle Scholar
  7. Baum, B.R., Ragan, M.A. 1993Reply to A.G. Rodrigo's “A comment on Baum's method for combining phylogenetic trees”Taxon42637640CrossRefGoogle Scholar
  8. Bininda-Emonds, O.R.P. eds. 2004Phylogenetic Supertrees: Combining Information to Reveal the Tree of LifeKluwer Academic PublishersDordrechtGoogle Scholar
  9. Bininda-Emonds, O.R.P., Bryant, H.N. 1998Properties of matrix representation with parsimony analysesSystemat. Biol.47497508Google Scholar
  10. Bininda-Emonds, O.R.P., Sanderson, M.J. 2001Assessment of the accuracy of matrix representation with parsimony analysis supertree constructionSystemat. Biol.50565579CrossRefGoogle Scholar
  11. Bininda-Emonds, O.R.P., Gittleman, J.L., Purvis, A. 1999Building large trees by combining phylogenetic information: a complete phylogeny of the extant carnivora (Mammalia)Biol. Rev.74143175CrossRefGoogle Scholar
  12. Bininda-Emonds, O.R.P., Gittleman, J.L., Steel, M.A. 2002The (super) tree of life: procedures, problems, and prospectsAnnu. Rev. Ecol. Systemat.33265289CrossRefGoogle Scholar
  13. Brady, R.H. 1985On the independence of systematicsCladistics113126Google Scholar
  14. Brower, A.V.Z. 2000Evolution is not a necessary assumption of cladisticsCladistics16143154CrossRefGoogle Scholar
  15. Brower, A.V.Z., Schawaroch, V. 1996Three steps of homology assessmentCladistics12265272Google Scholar
  16. Bryant, H.N. 1989An evaluation of cladistic and character analysis as hypothetico-deductive procedures, and the consequences for character weightingSystemat. Zool.38214227CrossRefGoogle Scholar
  17. Bull, J.J., Huelsenbeck, J.P., Cunningham, C.W., Swofford, D.L., Waddell, P.J. 1993Partitioning and combining data in phylogenetic analysisSystemat. Biol.42384397CrossRefGoogle Scholar
  18. Bunge, M. 1998Philosophy of ScienceVolume 2, From Explanation to JustificationTransaction PublishersNew JerseyGoogle Scholar
  19. Carnap, R. 1950Logical Foundations of ProbabilityUniversity of Chicago PressChicagoGoogle Scholar
  20. Chippindale, P.T., Wiens, J.J. 1994Weighting, partitioning, and combining characters in phylogenetic analysisSystemat. Biol.43278287CrossRefGoogle Scholar
  21. Cleland, C.E. 2001Historical scienceexperimental scienceand the scientific methodGeology29987990CrossRefGoogle Scholar
  22. Cleland, C.E. 2002Methodological and epistemic differences between historical science and experimental sciencePhilos. Sci.69474496CrossRefGoogle Scholar
  23. Copi, I.M., Cohen, C. 1998Introduction to LogicPrentice-HallNew JerseyGoogle Scholar
  24. Crother, B.I. 2002Is Karl Popper's philosophy of science all things to all people?Cladistics18445CrossRefGoogle Scholar
  25. de Pinna, M.C.C. 1991Concepts and tests of homology in the cladistic paradigmCladistics7367394CrossRefGoogle Scholar
  26. Queiroz, A. 1993For consensus (sometimes)Systemat. Biol.42368372CrossRefGoogle Scholar
  27. Queiroz, K. 1996Including the characters of interest during tree construction and the problems of circularity and bias in studies of character evolutionAm. Natural.148700708CrossRefGoogle Scholar
  28. Queiroz, K., Poe, S. 2001Philosophy and phylogenetic inference: a comparison of likelihood and parsimony methods in the context of Karl Popper's writings on corroborationSystemat. Biol.50305321CrossRefGoogle Scholar
  29. Queiroz, A., Donoghue, M.J., Kim, J. 1995Separate versus combined analysis of phylogenetic evidenceAnnu. Rev. Ecol. Systemat.26657681CrossRefGoogle Scholar
  30. Doyle, J.J. 1992Gene trees and species trees: molecular systematics as one-character taxonomySystemat. Bot.17144163CrossRefGoogle Scholar
  31. Eernisse, D., Kluge, A.G. 1993Taxonomic congruence versus total evidenceand amniote phylogeny inferred from fossils, molecules, and morphologyMol. Biol. Evolut.1011701195Google Scholar
  32. Fann, K.T. 1970Peirce's Theory of AbductionMartinus NijhoffThe HagueGoogle Scholar
  33. Farris, J.S. 1983The logical basis of phylogenetic analysisPlatnick, N.I.Funk, V.A. eds. Advances in Cladistics, Volume 2Columbia University PressNew York736Google Scholar
  34. Farris, J.S., Källersjö, M., Kluge, A.G., Bult, C. 1995Testing significance of incongruenceCladistics10315319CrossRefGoogle Scholar
  35. Felsenstein, J. 1973On the use of the parsimony criterion for inferring evolutionary treesSystemat. Zool.22250256CrossRefGoogle Scholar
  36. Felsenstein, J. 1978Cases in which parsimony or compatibility methods will be positively misleadingSystemat. Zool.27401410CrossRefGoogle Scholar
  37. Felsenstein, J. 1988Phylogenies from molecular sequences: inference and reliabilityAnnu. Rev. Genet.22521565CrossRefGoogle Scholar
  38. Felsenstein, J. 2004Inferring PhylogeniesSinauer Associates, Inc.MassachusettsGoogle Scholar
  39. Fetzer, J.H. 1993Philosophy of ScienceParagon HouseNew YorkGoogle Scholar
  40. Fetzer, J.H., Almeder, R.F. 1993Glossary of Epistemology/Philosophy of ScienceParagon HouseNew YorkGoogle Scholar
  41. Fitzhugh, K. 1997The abduction of cladisticsCladistics13170171Google Scholar
  42. Gatesy, J., Matthee, C., DeSalle, R., Hayashi, C. 2002Resolution of a supertree/supermatrix paradoxSystemat. Biol.51652664CrossRefGoogle Scholar
  43. Geiger, D.L., Fitzhugh, K., Thacker, C.E. 2001Matters of the record. Timeless characters: a response to Vermeij 1999Paleobiology27179180CrossRefGoogle Scholar
  44. Godfrey-Smith, P. 2003Theory and Reality: An Introduction to the Philosophy of ScienceUniversity of Chicago PressChicagoGoogle Scholar
  45. Gould, S.J. 2002The Structure of Evolutionary TheoryThe Belknap Press of Harvard University PressCambridgeGoogle Scholar
  46. Grande, L. 1994Repeating patterns in naturepredictability, and ℈impact’ in scienceGrande, L.Rieppel, O. eds. Interpreting the Hierarchy of NatureAcademic PressNew York6184Google Scholar
  47. Hacking, I. 2001An Introduction to Probability and Inductive LogicCambridge University PressNew YorkGoogle Scholar
  48. Hall, B.K. eds. 1994Homology: The Hierarchical Basis of Comparative BiologyAcademic PressSan DiegoGoogle Scholar
  49. Hall, B.K. 2003Descent with modification: the unity underlying homology and homoplasy as seen through an analysis of development and evolutionBiol. Rev.78409433CrossRefGoogle Scholar
  50. Hanson, N.R. 1958Patterns of Discovery: An Inquiry into the Conceptual Foundations of ScienceCambridge University PressNew YorkGoogle Scholar
  51. Hanson, N.R. 1969Perception and Discovery: An Introduction to Scientific InquiryFreeman, Cooper & CompanySan FranciscoGoogle Scholar
  52. Harman, G. 1965The inference to the best explanationPhilos. Rev.748895CrossRefGoogle Scholar
  53. Hempel, C.G. 1962Deductive nomological vs. statistical explanationFeigl, H.Maxwell, G. eds. Minnesota Studies in the Philosophy of Science, Vol. 3University of Minnesota PressMinneapolis98169Google Scholar
  54. Hempel, C.G. 1965Aspects of Scientific Explanation and Other Essays in the Philosophy of ScienceThe Free PressNew YorkGoogle Scholar
  55. Hempel, C.G. 1966Recent Problems of InductionColodny, R.G. eds. Mind and CosmosUniversity of Pittsburgh PressPittsburgh112134Google Scholar
  56. Hempel C.G. 2001. The Philosophy of Carl G. Hempel: Studies in Science, Explanation, and Rationality. In: Fetzer J.H. (eds). Oxford University Press, New York.Google Scholar
  57. Hennig, W. 1966Phylogenetic SystematicsUniversity of Illinois PressUrbanaGoogle Scholar
  58. Hillis, D.M. 1987Molecular versus morphological approaches to systematicsAnnu. Rev. Ecol. Systemat.182342CrossRefGoogle Scholar
  59. Hillis, D.M., Allard, M.W., Miyamoto, M.M. 1993Analysis of DNA sequence data: phylogenetic inferenceMeth. Enzymol.224456487CrossRefGoogle Scholar
  60. Hillis, D.M., Mable, B.K., Moritz, C. 1996Applications of molecular systematics: the state of the field and a look to the futureHillis, D.M.Moritz, C.Mable, B.K. eds. Molecular SystematicsSinauer AssociatesSunderland515543Google Scholar
  61. Huelsenbeck, J.P., Bull, J.J., Cunningham, C.W. 1996Combining data in phylogenetic analysisTrends Ecol. Evolut.11152158CrossRefGoogle Scholar
  62. Huelsenbeck, J.P., Crandall, K.A. 1997Phylogeny estimation and hypothesis testing using maximum likelihoodAnnu. Rev. Ecol. Systemat.28437466CrossRefGoogle Scholar
  63. Jevons, W.S. 1883The Principles of Science: A Treatise on Logic and Scientific MethodMacmillan and CompanyLondonGoogle Scholar
  64. Joseph, H.W.B. 1967An Introduction to LogicOxford University PressNew YorkGoogle Scholar
  65. Josephson, J.R., Josephson, S.G. 1994Abductive Inference: Computation, Philosophy, TechnologyCambridge University PressCambridgeGoogle Scholar
  66. Kitching, I.J., Forey, P.L., Humphries, C.J., Williams, D.M. 1998Cladistics: The Theory and Practice of Parsimony AnalysesOxford University PressNew YorkGoogle Scholar
  67. Kluge, A.G. 1989A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (BoidaeSerpentes)Systemat. Zool.38725CrossRefGoogle Scholar
  68. Kluge, A.G. 1997aSophisticated falsification and research cycles: consequences for differential character weighting in phylogenetic systematicsZool. Scr.26349360CrossRefGoogle Scholar
  69. Kluge, A.G. 1997bTestability and the refutation and corroboration of cladistic hypothesesCladistics138196CrossRefGoogle Scholar
  70. Kluge, A.G. 1998Total evidence or taxonomic congruence: cladistics or consensus classificationCladistics14151158CrossRefGoogle Scholar
  71. Kluge, A.G. 1999The science of phylogenetic systematics: explanation, prediction, and testCladistics15429436CrossRefGoogle Scholar
  72. Kluge, A.G. 2001aParsimony with and without scientific justificationCladistics17199210CrossRefGoogle Scholar
  73. Kluge, A.G. 2001bPhilosophical conjectures and their refutationSystemat. Biol.50322330CrossRefGoogle Scholar
  74. Kluge, A.G. 2003On the deduction of species relationships: a précisCladistics19233239Google Scholar
  75. Kluge, A.G. 2004On total evidence: for the recordCladistics20205207CrossRefGoogle Scholar
  76. Kluge, A.G., Wolf, A.J. 1993Cladistics: what's in a word?Cladistics9183199CrossRefGoogle Scholar
  77. Lankester, E.R. 1870On the use of the term homology in modern zoology, and the distinction between homogenetic and homoplastic agreementsAnn. Mag. Nat. Hist. (Ser. 4)63443Google Scholar
  78. Lecointre, G., Deleporte, P. 2005Total evidence requires exclusion of phylogenetically misleading dataZool. Scr.34101117CrossRefGoogle Scholar
  79. Levasseur, C., Lapointe, F.-J. 2001War and peace in phylogenetics: a rejoinder to total evidence and consensusSystemat. Biol.50881891CrossRefGoogle Scholar
  80. Lipton, P. 1993Inference to the Best ExplanationRoutledgeNew YorkGoogle Scholar
  81. Liu, F.-G.R., Miyamoto, M.M., Freire, N.P., Ong, P.Q., Tennant, M.R., Young, T.S., Gugel, K.F. 2001Molecular and morphological supertrees for eutherian (placental) mammalsScience29117861789CrossRefGoogle Scholar
  82. Mayo, D.G. 1996Error and the Growth of Experimental KnowledgeThe University of Chicago PressChicagoGoogle Scholar
  83. Mill, J.S. 1874A System of Logic, Ratiocinative and Inductive: Being a Connected View of the Principles of Evidence and the Methods of Scientific InvestigationHarper & Bros.New YorkGoogle Scholar
  84. Miyamoto, M.M. 1985Consensus cladograms and general classificationsCladistics1186189CrossRefGoogle Scholar
  85. Miyamoto, M.M., Cracraft, J. 1991Phylogenetic inference, DNA sequence analysis, and the future of molecular systematicsMiyamoto, M.M.Cracraft, J. eds. Phylogenetic Analysis of DNA SequencesOxford University PressNew York317Google Scholar
  86. Miyamoto, M.M., Fitch, W.M. 1995Testing species phylogenies and phylogenetic methods with congruenceSystemat. Biol.446476CrossRefGoogle Scholar
  87. Murphey, M.G. 1994Philosophical Foundations of Historical KnowledgeState University of New York PressAlbanyGoogle Scholar
  88. Naylor, G.J.P., Adams, D.C.,  et al. 2003Total evidence versus relevant evidence: a response to O’Leary (2003)Systemat. Biol.52864865CrossRefGoogle Scholar
  89. Nixon, K.C., Carpenter, J.M. 1996On simultaneous analysisCladistics12221241CrossRefGoogle Scholar
  90. Novacek, M.J. 2001Mammalian phylogeny: genes and supertreesCurr. Biol.11R573575CrossRefGoogle Scholar
  91. Owen, R. 1843Lectures on the Comparative Anatomy and Physiology of the Invertebrate AnimalsLongman, Brown, Green & LongmansLondonGoogle Scholar
  92. Owen R. 1847. On the archetype and homologies of the vertebrate skeleton. In: Report of the Sixteenth Meeting of the British Association for the Advancement of Science: Held at Southampton in September 1846. J. Murray, London, pp. 169–340.Google Scholar
  93. Owen, R. 1849On the Nature of LimbsJ. van VoorstLondonGoogle Scholar
  94. Owen, R. 1866On the Anatomy of Vertebrates, Vol. 1, Fishes and ReptilesLongmans, Green & Co.LondonGoogle Scholar
  95. Page, R.D.M., Holmes, E.C. 1998Molecular Evolution: A Phylogenetic ApproachBlackwell ScienceOxfordGoogle Scholar
  96. Panchen, A.L. 1994Classification, Evolution, and the Nature of BiologyCambridge University PressCambridgeGoogle Scholar
  97. Patterson, C. 1982Morphological characters and homologyJoysey, K.A.Friday, A.E. eds. Problems of Phylogenetic ReconstructionAcademic PressNew York2174Google Scholar
  98. Patterson, C. 1987IntroductionPatterson, C. eds. Molecules and Morphology in Evolution: Conflict or Compromise?Cambridge University PressNew York122Google Scholar
  99. Patterson, C. 1988Homology in classical and molecular biologyMol. Biol. Evolut.5603625Google Scholar
  100. Patterson, C., Williams, D.M., Humphries, C.J. 1993Congruence between molecular and morphological phylogeniesAnnu. Rev. Ecol. Systemat.24153188CrossRefGoogle Scholar
  101. Peirce C.S. 1931–1935. In: Hartshorne C., Weiss P. and Burks A. (eds). Collected Papers of Charles Sanders Peirce, Volumes 1–6. Harvard University Press, Cambridge.Google Scholar
  102. Peirce C.S. 1958. In: Burks A. (eds) Collected Papers of Charles Sanders Peirce, Volumes 7–8. Harvard University Press, Cambridge.Google Scholar
  103. Pisani, D., Wilkinson, M. 2002Matrix representation with parsimony, taxonomic congruenceand total evidenceSystemat. Biol.51151155CrossRefGoogle Scholar
  104. Platnick, N.I. 1979Philosophy and the transformation of cladisticsSystemat. Zool.28537546CrossRefGoogle Scholar
  105. Popper, K.R. 1957The Poverty of HistoricismRoutledgeNew YorkGoogle Scholar
  106. Popper, K.R. 1959The Logic of Scientific DiscoveryBasic Books, Inc.New YorkGoogle Scholar
  107. Popper, K.R. 1992Realism and the Aim of ScienceRoutledgeNew YorkGoogle Scholar
  108. Purvis, A. 1995A modification to Baum and Ragan's method for combining phylogenetic treesSystemat. Biol.44251255CrossRefGoogle Scholar
  109. Reichenbach, H. 1956The Direction of TimeUniversity of California PressBerkeleyGoogle Scholar
  110. Reilly, F.E. 1970Charles Peirce's Theory of Scientific MethodFordham University PressNew YorkGoogle Scholar
  111. Rescher, N. 1970Scientific ExplanationThe Free PressNew YorkGoogle Scholar
  112. Rieppel, O. 2003aSemaphoronts, cladograms and the roots of total evidenceBiol. J. Linn. Soc.80167186CrossRefGoogle Scholar
  113. Rieppel, O. 2003bPopper and systematicsSystemat. Biol.52259271CrossRefGoogle Scholar
  114. Rodrigo, A.G. 1993A comment on Baum's method for combining phylogenetic treesTaxon42631636CrossRefGoogle Scholar
  115. Rupke, N.A. 1993Richard Owen's vertebrate archetypeIsis84231251CrossRefGoogle Scholar
  116. Russell, E.S. 1916Form and Function: A Contribution to the History of Animal MorphologyUniversity of Chicago PressChicagoGoogle Scholar
  117. Salamin, N., Hodkinson, T.R., Savolainen, V. 2002Building supertrees: an empirical assessment using the grass family (Poaceae)Systemat. Biol.51136150CrossRefGoogle Scholar
  118. Salmon, M.H. 1995Introduction to Logic and Critical ThinkingHarcourt Brace College PublishersNew YorkGoogle Scholar
  119. Salmon, W.C. 1967The Foundations of Scientific InferenceUniversity of Pittsburgh PressPittsburghGoogle Scholar
  120. Salmon, W.C. 1984aLogicPrentice-Hall, Inc.Englewood CliffsGoogle Scholar
  121. Salmon, W.C. 1984bScientific Explanation and the Causal Structure of the WorldPrinceton University PressPrincetonGoogle Scholar
  122. Salmon, W.C. 1989Four decades of scientific explanationKitcher, P.Salmon, W.C. eds. Scientific Explanation. Minnesota Studies in the Philosophy of ScienceVolume XIIIUniversity of Minnesota PressMinneapolis3219Google Scholar
  123. Salmon, W.C. 1998Causality and ExplanationOxford University PressNew YorkGoogle Scholar
  124. Sanderson, M.J., Purvis, A., Henze, C. 1998Phylogenetic supertrees: assembling the trees of lifeTrends Ecol. Evolut.13105109CrossRefGoogle Scholar
  125. Schuh, R.T. 2000Biological Systematics: Principles and ApplicationsCornell University PressIthacaGoogle Scholar
  126. Searles, H.L. 1948Logic and Scientific Methods: An Introductory CourseThe Ronald Press CompanyNew YorkGoogle Scholar
  127. Siddall, M.E., Kluge, A.G. 1997Probabilism and phylogenetic inferenceCladistics13313336CrossRefGoogle Scholar
  128. Sober, E. 1975SimplicityOxford University PressNew YorkGoogle Scholar
  129. Sober, E. 1988Reconstructing the Past: Parsimony, Evolution, and InferenceMIT PressCambridgeGoogle Scholar
  130. Sober, E. 2002Reconstructing the character states of ancestors: a likelihood perspective on cladistic parsimonyThe Monist85156176Google Scholar
  131. Strawson, P.F. 1971Individuals: An Essay in Descriptive MetaphysicsRoutledgeNew YorkGoogle Scholar
  132. Swofford, D.L. 1991When are phylogeny estimates from molecular and morphological data incongruent?Miyamoto, M.M.Cracraft, J. eds. Phylogenetic Analysis of DNA SequencesOxford University PressNew York295333Google Scholar
  133. Swofford, D.L., Olsen, G.J., Waddell, P.J., Hillis, D.M. 1996Phylogenetic inferenceHillis, D.M.Moritz, C.Mable, B.K. eds. Molecular SystematicsSinauer AssociatesSunderland407514Google Scholar
  134. Thagard, P. 1988Computational Philosophy of ScienceThe MIT PressCambridgeGoogle Scholar
  135. Fraassen, B.C. 1990The Scientific ImageClarendon PressOxfordGoogle Scholar
  136. Wagner P.J. 2000. Phylogenetic analyses and the fossil record: tests and inferences, hypotheses and models. In: Erwin D.H. and Wing S.L. (eds). Deep Time: Paleobiol. Perspect., Paleobiol. Mem. 26 (Supplement to No. 4): 341–371.Google Scholar
  137. Walton, D.N. 2001Abductivepresumptive and plausible argumentsInformal Logic21141169Google Scholar

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Authors and Affiliations

  1. 1.Research and Collections BranchNatural History Museum of Los Angeles CountyLos AngelesUSA

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