Acta Biotheoretica

, Volume 55, Issue 3, pp 269–281 | Cite as

Congruence of Morphological and Molecular Phylogenies

  • Davide Pisani
  • Michael J. Benton
  • Mark Wilkinson
Regular Article


When phylogenetic trees constructed from morphological and molecular evidence disagree (i.e. are incongruent) it has been suggested that the differences are spurious or that the molecular results should be preferred a priori. Comparing trees can increase confidence (congruence), or demonstrate that at least one tree is incorrect (incongruence). Statistical analyses of 181 molecular and 49 morphological trees shows that incongruence is greater between than within the morphological and molecular partitions, and this difference is significant for the molecular partition. Because the level of incongruence between a pair of trees gives a minimum bound on how much error is present in the two trees, our results indicate that the level of error may be underestimated by congruence within partitions. Thus comparisons between morphological and molecular trees are particularly useful for detecting this incongruence (spurious or otherwise). Molecular trees have higher average congruence than morphological trees, but the difference is not significant, and both within- and between-partition incongruence is much lower than expected by chance alone. Our results suggest that both molecular and morphological trees are, in general, useful approximations of a common underlying phylogeny and thus, when molecules and morphology clash, molecular phylogenies should not be considered more reliable a priori.


Congruence Morphology Molecules Phylogenetic accuracy Tree distance metrics 



This work was partially funded by a Leverhulme Trust grant to MJB, and by a BBSRC grant 40/G18385, and an NHM-MRF award to MW. DP was supported by a Marie Curie Intra European Individual Fellowship (MEIF-CT-2005-010022). We would like to thank Anthony Bledsoe, Andy Purvis and Clive Moncrieff for the useful advice on statistical data analyses, and Richard Olmstead and two anonymous reviewers for their helpful and insightful comments.


  1. Benton MJ (1999) Early origins of modern birds and mammals: molecules vs. morphology. BioEssays 21:1043–1051CrossRefGoogle Scholar
  2. Bledsoe AH, Raikow RJ (1990) A quantitative assessment of congruence between molecular and nonmolecular estimates of phylogeny. J Mol Evol 30:247–259CrossRefGoogle Scholar
  3. Critchlow DE, Pearl DK, Quian C (1996) The triplet distance for rooted bifurcating phylogenetic trees. Syst Biol 45:323–334CrossRefGoogle Scholar
  4. Day WHE (1983) Distribution of distances between pairs of classifications. In: Felsenstein J (ed) Numerical taxonomy. NATO ASI Series, vol G1. Springer-Verlag, Berlin, pp 127–131Google Scholar
  5. Driskell AC, Ane C, Burleigh JG, McMahon MM, O’Meara BC, Sanderson MJ (2004) Prospects for building the tree of life from large sequence databases. Science 306:1172–1174CrossRefGoogle Scholar
  6. Easteal S (1999) Molecular evidence far the early divergence of placental mammals. BioEssays 21:1052–1058CrossRefGoogle Scholar
  7. Estabrook GF, McMorris FR, Meacham CA (1985) A Comparison of undirected phylogenetic trees based on subtrees of four evolutionary units. Syst Zool 34:193–200CrossRefGoogle Scholar
  8. Fleischmann RD, Adams MD, White O et al (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496–512CrossRefGoogle Scholar
  9. Gura T (2000) Bones, molecules...or both? Nature 406:230–233CrossRefGoogle Scholar
  10. Harris SR, Pisani D, Gower DJ, Wilkinson M (2007) Investigating stagnation in morphological phylogenetics using consensus data. Syst Biol 56:125–129CrossRefGoogle Scholar
  11. Hedges SB, Maxson LR (1996) Molecules and morphology in amniote phylogeny. Mol Phylogenet Evol 6:312–319CrossRefGoogle Scholar
  12. Hedges SB, Maxson LR (1997) Complementary uses of molecules and morphology: a reply to Lee. Mol Phylogenet Evol 8:445CrossRefGoogle Scholar
  13. Hillis DM, Wiens JJ (2000) Molecules versus morphology in systematics: conflicts, artefacts, and misconceptions. In: Wiens JJ (ed) Phylogenetic analysis of morphological data. Smithsonian Institution Press, Washington, pp 1–19Google Scholar
  14. Huelsenbeck JP, Hillis DM (1994) Success of phylogenetic methods in the four-taxon case. Syst Biol 42:247–264CrossRefGoogle Scholar
  15. Jenner RA (2004) Accepting partnership by submission? Morphological phylogenetics in a molecular millennium. Syst Biol 53:333–342CrossRefGoogle Scholar
  16. Lee MSY (1995) Historical burden in systematics and the interrelationships of ‘parareptiles’. Biol Rev 70:459–547Google Scholar
  17. Lee MSY (1997) Molecules, morphology, and phylogeny: a response to Hedges and Maxson. Mol Phylogenet Evol 7:394–395CrossRefGoogle Scholar
  18. Miyamoto MM, Fitch WM (1995) Testing species phylogenies and phylogenetic methods with congruence. Syst Biol 44:64–76CrossRefGoogle Scholar
  19. Nei M, Kumar S, Takahashi K (1998) The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids used is small. Proc Natl Acad Sci USA 95:12390–12397CrossRefGoogle Scholar
  20. Page RDM (1997) Component lite v.0.1. Department of Zoology, University of GlasgowGoogle Scholar
  21. Pagel M (1999) Inferring the historical pattern of biological evolution. Nature 401:877–884CrossRefGoogle Scholar
  22. Penny D, Hendy MD, Steel MA (1991) Testing the theory of descent. In: Miyamoto MM, Cracraft J (eds) Phylogenetic analysis of DNA sequences. Oxford University Press, New York, pp 155–183Google Scholar
  23. Pisani D (2002) Comparing and combining data and trees in phylogenetic analysis. Ph.D. Thesis. Department of Earth Sciences, University of BristolGoogle Scholar
  24. Pisani D (2004) Identifying and removing fast-evolving sites using compatibility analysis: an example from the Arthropoda. Syst Biol 53:978–989CrossRefGoogle Scholar
  25. Pisani D, Wilkinson M (2002) Matrix representation with parsimony, taxonomic congruence and total evidence. Syst Biol 51:151–155CrossRefGoogle Scholar
  26. Rieppel O, Kearney M (2002) Similarity. Biol J Linn Soc Lond 75:59–82CrossRefGoogle Scholar
  27. Robinson DF, Foulds LR (1981) Comparison of phylogenetic trees. Math Biosci 53:131–147CrossRefGoogle Scholar
  28. Scotland RW, Olmstead RG, Bennett JR (2003) Phylogeny reconstruction: the role of morphology. Syst Biol 52:539–548Google Scholar
  29. Siegel S, Castellan NJ Jr (1989) Nonparametric statistics for the behavioral sciences. McGraw-Hill, New YorkGoogle Scholar
  30. Sokal RR, Rohlf FJ (1995) Biometry: the principles and practice of statistics in biological research, 3rd edn. W.H. Freeman and Company, New YorkGoogle Scholar
  31. Swofford DL, Olsen GJ, Waddell PJ, Hillis DM (1996) Phylogenetic inference. In: Hillis DM, Moritz C, Mable BK (eds) Molecular systematics. Sinauer, Sunderland, pp 407–514Google Scholar
  32. Thorley JL, Page RDM (2000) RadCon: phylogenetic tree comparison and consensus. Bioinformatics 16:486–487CrossRefGoogle Scholar
  33. Thorley JL, Wilkinson M, Charleston M (1998) The information content of consensus trees. In: Rizzi A, Vichi M, Bock HH (eds) Advances in data science and classification. Springer-Verlag, Berlin, pp 91–98Google Scholar
  34. Wiens JJ (2004) The role of morphological data in phylogeny reconstruction. Syst Biol 53:653–661CrossRefGoogle Scholar
  35. Wilkinson M (1994) Common cladistic information and its consensus representation: reduced Adams and reduced cladistic consensus trees and profiles. Syst Biol 43:343–368CrossRefGoogle Scholar
  36. Yang H, Golenberg EM, Shoshani J (1996) Phylogenetic resolution within the Elephantidae using fossil DNA sequence from the American mastodon (Mammut americanum) as an outgroup. Proc Natl Acad Sci USA 93:1190–1194CrossRefGoogle Scholar
  37. Zuckerkandl E, Pauling L (1965) Molecules as documents of evolutionary history. J Theoret Biol 8:357–366CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2007

Authors and Affiliations

  • Davide Pisani
    • 1
    • 2
    • 3
  • Michael J. Benton
    • 3
  • Mark Wilkinson
    • 2
  1. 1.Laboratory of Evolutionary Biology, Department of BiologyThe National University of IrelandMaynoothIreland
  2. 2.Department of ZoologyThe Natural History MuseumLondonUK
  3. 3.Department of Earth SciencesUniversity of BristolBristolUK

Personalised recommendations