Acta Biotheoretica

, Volume 57, Issue 1–2, pp 295–305 | Cite as

Reflections on Systematics and Phylogenetic Reconstruction

Regular Article


I attempt to raise questions regarding elements of systematics—primarily in the realm of phylogenetic reconstruction—in order to provoke discussion on the current state of affairs in this discipline, and also evolutionary biology in general: e.g., conceptions of homology and homoplasy, hypothesis testing, the nature of and objections to Hennigian “phylogenetic systematics”, and the schism between (neo)Darwinian descendants of the “modern evolutionary synthesis” and their supposed antagonists, cladists and punctuationalists.


Systematics Phylogenetic reconstruction Classification Developmental biology Modern evolutionary synthesis 


  1. Ast G (2005) The alternative genome. Sci Am 292(April):59–65Google Scholar
  2. Bateson W (1894) Materials for the study of variation, treated with especial regard to discontinuity in the origin of species. Macmillan, New YorkGoogle Scholar
  3. Cain AJ, Harisson GA (1960) Phyletic weighting. Proc Zool Soc Lond 131:1–31Google Scholar
  4. Charlesworth B, Lande R, Slatkin M (1982) A neo-Darwinian commentary on macroevolution. Evol Int J Org Evol 36:474–498. doi:10.2307/2408095 Google Scholar
  5. Duboule D, Dollé P (1989) The structural and functional organization of the murine HOX gene family resembles that of Drosophila homeotic genes. EMBO 8:1497–1505Google Scholar
  6. Eldredge N, Gould SJ (1972) Punctuated equilibria: an alternative to phyletic gradualism. In: Schopf TJM (ed) Models in paleobiology. Freeman, Cooper & Co., San FranciscoGoogle Scholar
  7. Fisher RA (1930) The genetical theory of natural selection. Oxford University Press, OxfordGoogle Scholar
  8. Gerhart J, Kirschner M (1997) Cells, embryos, and evolution: toward a cellular and developmental understanding of phenotypic variation and evolutionary adaptability. Blackwell, MaldenGoogle Scholar
  9. Gould SJ, Eldredge N (1977) Punctuated equilibria: the tempo and mode of evolution reconsidered. Paleobiology 3:115–151Google Scholar
  10. Gould SJ, Vrba ES (1982) Exaptation—a missing term in science of form. Paleobiology 8:581–598Google Scholar
  11. Haldane JBS (1932) The causes of evolution. Harper & Brothers, New YorkGoogle Scholar
  12. Hennig W (1950) Grundzüge einer Theorie der Phylogenetischen Systematik. Deutscher Zentralverlag, BerlinGoogle Scholar
  13. Hennig W (1966) Phylogenetic systematics. University of Chicago Press, ChicagoGoogle Scholar
  14. Huxley TH (1863) Evidence as to man’s place in nature. D. Appleton, New YorkGoogle Scholar
  15. Krings M, Stone A, Schmitz RW, Krainitzki H, Stoneking M, Pääbo S (1997) Neandertal DNA sequences and the origin of modern humans. Cell 90:19–30. doi:10.1016/S0092-8674(00)80310-4 CrossRefGoogle Scholar
  16. Kuhn TS (1996) Structure of scientific revolutions, 3rd edn. University of Chicago Press, ChicagoGoogle Scholar
  17. Maresca B, Schwartz JH (2006) Sudden origins: a general mechanism of evolution based on stress protein concentration and rapid environmental change. Anat Rec B New Anat 2898:38–46. doi:10.1002/ar.b.20089 Google Scholar
  18. Mayr E (1942) Systematics and the origin of species. Columbia University Press, New YorkGoogle Scholar
  19. Mayr E (1965a) From molecules to organic diversity. Fed Proc 23:1231–1235Google Scholar
  20. Mayr E (1965b) Numerical phenetics and taxonomic theory. Syst Zool 14:73–97. doi:10.2307/2411730 CrossRefGoogle Scholar
  21. Mayr E (1968) The role of systematics in biology. Science 159:595–599. doi:10.1126/science.159.3815.595 CrossRefGoogle Scholar
  22. Mayr E (1969) Principles of systematic zoology. McGraw-Hill, New YorkGoogle Scholar
  23. Mivart SG (1871) On the genesis of species. John Murray, LondonGoogle Scholar
  24. Noonan JP, Coop G, Kudaravalli S, Smith D, Krause J, Alessi J, Chen F, Platt D, Pääbo S, Pritchard JK, Rubin EM (2006) Sequencing and analysis of Neanderthal genomic DNA. Science 314:1113–1118. doi:10.1126/science.1131412 CrossRefGoogle Scholar
  25. Patterson C, Rosen DE (1977) Review of icthyodectiform and other mesozoic teleost fishes and the theory and practice of classifying fossils. Bull Am Mus Nat Hist 158:81–172Google Scholar
  26. Popper KR (1968) The logic of scientific discovery. Harper Torchbooks, New YorkGoogle Scholar
  27. Raff RA (1996) The shape of life: genes, development, and the evolution of animal form. The University of Chicago Press, ChicagoGoogle Scholar
  28. Rensch B (1947) Neuere Probleme der Abstammungslehre. Die transspezifische Evolution. Ferdinand Enke Verlag, StuttgartGoogle Scholar
  29. Schedlock AM, Okada N (2000) SINE insertions: powerful tools for molecular systematics. Bioessays 22:148–160. doi:10.1002/(SICI)1521-1878(200002)22:2<148::AID-BIES6>3.0.CO;2-Z CrossRefGoogle Scholar
  30. Schmitz J, Roos C, Zischler H (2005) Primate phylogeny: molecular evidence from retroposons. Comp Genomics Mol Evol 108:26–37Google Scholar
  31. Schwartz JH (1999) Sudden origins: fossils, genes, and the emergence of species. Wiley, New YorkGoogle Scholar
  32. Schwartz JH (2008) Cladistics. In: Regal B (ed) Icons of evolution. Greenwood Press, Westport CT, pp 517–544Google Scholar
  33. Schwartz JH (2009a) Organismal biology, molecular systematics, and phylogenetic reconstruction. In: Masters J, Gamba M, Génin F (eds) Leaping ahead: advances in prosimian biology. Springer, New York (in press)Google Scholar
  34. Schwartz JH (2009b) Organismal innovation. In: O’Brien MJ, Shennan SJ (eds) In: Innovations in cultural systems: contributions from evolutionary anthropology MIT Press, Cambridge (in press)Google Scholar
  35. Schwartz JH, Maresca B (2006) Do molecular clocks run at all? a critique of molecular systematics. Biol Theory 1:1–15. doi:10.1162/biot.2006.1.4.357 CrossRefGoogle Scholar
  36. Shubin N, Tabin C, Carroll S (1997) Fossils, genes and the evolution of animal limbs. Nature 388:639–648. doi:10.1038/41710 CrossRefGoogle Scholar
  37. Shubin N, Tabin C, Carroll SB (2009) Deep homology and the origins of evolutionary novelty. Nature 457:818–823. doi:10.1038/nature07891 CrossRefGoogle Scholar
  38. Simpson GG (1944) Tempo and mode in evolution. Columbia University Press, New YorkGoogle Scholar
  39. Simpson GG (1945) The principles of classification and a classification of the mammals. Bull Am Mus Nat Hist 85:1–350Google Scholar
  40. Simpson GG (1949) Essay-review of recent works on evolutionary theory by Rensch, Zimmermann, and Schindewolf. Evolution 3:178–184. doi:10.2307/2405553 CrossRefGoogle Scholar
  41. Simpson GG (1952) Review of O. Schindewolf, Grundfragen der Paleontologie and Der Zeitfaktor in Geologie und Palaontologie. Q Rev Biol 27:388–389. doi:10.1086/399136 CrossRefGoogle Scholar
  42. Simpson GG (1961) Principles of animal taxonomy. Columbia University Press, New YorkGoogle Scholar
  43. Sordino P, van der Hoeven F, Duboule D (1995) Hox gene expression in teleost fins and the origin of vertebrate digits. Nature 375:678–681. doi:10.1038/375678a0 CrossRefGoogle Scholar
  44. Stern CD, Charité J, Deschamps J, Duboule D, Durston AJ, Kmita M, Nicolas J-F, Palmeirem I, Smith JC, Wolpert L (2006) Head-tail patterning of the vertebrate embryo: one, two or many unresolved problems? Int J Dev Biol 50:3–15. doi:10.1387/ijdb.052095cs CrossRefGoogle Scholar
  45. Thompson DAW (1917) On growth and form. Cambridge University Press, CambridgeGoogle Scholar
  46. Waddington CH (1940) Organisers and genes. Cambridge University Press, CambridgeGoogle Scholar
  47. Wright S (1931) Evolution in Mendelian populations. Genetics 16:97–159Google Scholar

Copyright information

© Springer Science+Business Media B.V. 2009

Authors and Affiliations

  1. 1.Departments of Anthropology and History and Philosophy of ScienceUniversity of PittsburghPittsburghUSA

Personalised recommendations