ISSN 2415-8860 (Online), ISSN 0372-4123 (Print)
logoUkrainian Botanical Journal
  • 1 of 9
Ukr. Bot. J. 2017, 74(2): 103–121
General Issues, Reviews and Discussions

A simple parsimony-based approach to assess ancestor-descendant relationships

Aubert D.

One of the main goals of systematics is to reconstruct the tree of life. Half a century ago, the breakthrough of cladistics was a major step towards this objective because it allowed us to assess relatedness patterns among species, an abstract kind of relationship. Unfortunately, the philosophy of cladism forbade to go further and to seek more realistic relationships, like the ancestor-descendant relationship, which is the expected fundamental kind of relationship of the tree of life according to Darwinian evolution. Here, I describe a simple parsimony-based procedure which can be used to transform a classical cladogram into a genuine phylogenetic tree, i.e. a caulogram. It consists in deleting as many unobserved and unnamed nodes as possible and replacing them with observed and named species. A new Bayesian non-stochastic weighting scheme is used to assess character reliability for both this procedure and classical cladogram construction. I illustrate the whole process by assessing the relationships between the species of the moss genus Didymodon sensu lato (Pottiaceae) and discuss the resulting caulogram by confronting it with the previous methodology from the evolutionary literature. I finally argue that strictly adhering to cladist epistemology is untenable and that we must seek new formal methods to find ancestral species as well as ancestral higher taxa.

Keywords: ancestor, Bayesian analysis, Bremer support, evolutionary systematics, parsimony, weighting

Full text: PDF (Eng) 967K

  1. Aldous D., Popovic L. A critical branching process model for biodiversity. Adv. Appl. Probab., 2005, 37: 1094–1115.
  2. Aldous D.J., Krikun M.A., Popovic L. Five statistical questions about the tree of life. Syst. Biol., 2011, 60: 318–328.
  3. Alroy J. Continuous track analysis: a new phylogenetic and biogeographic method. Syst. Biol., 1995, 44: 152–178.
  4. Ashlock P.D. Monophyly and associated terms. Syst. Biol., 1971, 20(1): 63–69.
  5. Aubert D. A formal analysis of phylogenetic terminology: Towards a reconsideration of the current paradigm in systematics. Phytoneuron, 2015, 2015-66: 1–54.
  6. Aze T., Ezard T.H.G., Purvis A., Coxall H.K., Stewart D.R.M., Wade B.S., Pearson P.N. A phylogeny of Cenozoic macroperforate planktonic foraminifera from fossil data. Biol. Rev. Camb. Philos. Soc., 2011, 86: 900–927.
  7. Bapst D.W., Hopkins M.J. Comparing cal3 and other a posteriori time-scaling approaches in a case study with the pterocephaliid trilobites. Paleobiology, 2017, 43: 49–67.
  8. Bremer K. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution, 1988, 42: 795–803.
  9. Bremer K. Branch support and tree stability. Cladistics, 1994, 10: 295–304.
  10. Brummitt R.K. How to chop up a tree. Taxon, 2002, 51: 31–41.
  11. Crawford D.J. Progenitor-derivative species pairs and plant speciation. Taxon, 2010, 59: 1413–1423.
  12. Crisp M.D., Chandler G.T. Paraphyletic species. Telopea, 1996, 6: 813–844.
  13. de Queiroz K., Donoghue M.J. Phylogenetic systematics and the species problem. Cladistics, 1988, 4: 317–338.
  14. Donoghue M.J. A critique of the biological species concept and recommendations for a phylogenetic alternative. The Bryologist, 1985, 88: 172–181.
  15. Farris J.S. The retention index and the rescaled consistency index. Cladistics, 1989, 5: 417–419.
  16. Farris J.S. A successive approximations approach to character weighting. Syst. Zool., 1969, 18: 374–385.
  17. Farris J.S. The logical basis of phylogenetic analysis. In: Advances in Cladistics, II. Eds Platnick N.I., Funk V.A. New York: Columbia University Press, 1983, pp. 7–36.
  18. Farris J.S. Phylogenetic classification of fossils with recent species. Syst. Biol., 1976, 25: 271–282.
  19. Felsenstein J. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool., 1978, 27: 401–410.
  20. Felsenstein J. The statistical approach to inferring evolutionary trees and what it tells us about parsimony and compatibility. In: Cladistics: Perspectives on the Reconstruction of Evolutionary History. Eds Duncan T., Stuessy T.F. Columbia University Press, New York, 1984, pp. 169–191.
  21. Foote M. On the probability of ancestors in the fossil record. Paleobiology, 1996, 22: 141–151.
  22. Friday A. Quantitative aspects of the estimation of evolutionary trees. Folia Primatol. (Basel), 1989, 53: 221–234.
  23. Funk D.J., Omland K.E. Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annu. Rev. Ecol. Evol. Syst., 2003, 34: 397–423.
  24. Gee H. Deep Time: Cladistics, the Revolution in Evolution. Fourth Estate, London, UK, 2000.
  25. Good I.J. Studies in the History of Probability and Statistics. XXXVII A.M. Turing's statistical work in World War II. Biometrika, 1979, 66: 393–396.
  26. Good I.J. Weight of evidence: A brief survey. Bayesian Stat., 1985, 2: 249–270.
  27. Hennig W. Grundzüge einer Theorie der phylogenetischen Systematik. Deutscher Zentralverlag, Berlin, 1950.
  28. Hennig W. Phylogenetic Systematics. University of Illinois Press, Urbana, 1966.
  29. Hillis D.M., Huelsenbeck J.P. Signal, noise, and reliability in molecular phylogenetic analyses. J. Hered., 1992, 83: 189–195.
  30. Hołyński R.B. Is paraphyly indication of poor taxonomy? – Open letter to Drs. Carvalho and Ebach. Munis Ent. Zool., 2010, 5 (Suppl.): 825–829.
  31. Hull D.L. The limits of cladism. Syst. Biol., 1979, 28: 416–440.
  32. Lee M.S.Y. Species concepts and the recognition of ancestors. Hist. Biol., 1995, 10: 329–339.
  33. Levin D.A. Local speciation in plants: The rule not the exception. Syst. Bot., 1993, 18: 197–208.
  34. Nelson G.J. "Monophyly again?"– A reply to P.D. Ashlock. Syst. Biol., 1973, 22: 310–312.
  35. Paul C.R.C. The recognition of ancestors. Hist. Biol., 1992, 6: 239–250.
  36. Podani J. Tree thinking, time and topology: comments on the interpretation of tree diagrams in evolutionary/phylogenetic systematics. Cladistics, 2013, 29: 315–327.
  37. Prothero D.R., Lazarus D.B. Planktonic microfossils and the recognition of ancestors. Syst. Zool., 1980, 29: 119–129.
  38. Pyron R.A., Costa G.C., Patten M.A., Burbrink F.T. Phylogenetic niche conservatism and the evolutionary basis of ecological speciation. Biol. Rev. Camb. Philos. Soc., 2015, 90: 1248–1262.
  39. Rieseberg L.H., Brouillet L. Are many plant species paraphyletic? Taxon, 1994, 43: 21–32.
  40. Ross H.A. The incidence of species-level paraphyly in animals: A re-assessment. Mol. Phylogenet. Evol., 2014, 76: 10–17.
  41. Sankey H. Scientific Realism: An Elaboration and a Defence. Theor. J. Soc. Polit. Theory, 2001, 35–54.
  42. Sepkoski J.J. Competition in macroevolution: the double wedge revisited. In: Evolutionary Paleobiology. Eds Jablonski D., Erwin D.H., Lipps J.H. University of Chicago Press, Chicago, USA, 1996, pp. 211–255.
  43. Stuessy T.F., König C. Patrocladistic classification. Taxon, 2008, 57: 594–601.
  44. Tsai C.-H., Fordyce R.E. Ancestor-descendant relationships in evolution: origin of the extant pygmy right whale, Caperea marginata. Biol. Lett., 2015, 11: 20140875.
  45. Vanderpoorten A., Long D.G. Budding speciation and neotropical origin of the Azorean endemic liverwort, Leptoscyphus azoricus. Mol. Phylogenet. Evol., 2006, 40: 73–83.
  46. Zander R.H. A phylogrammatic evolutionary analysis of the moss genus Didymodon in North America north of Mexico. Bull. Buffalo Soc. Nat. Sci., 1998, 36: 81–115.
  47. Zander R.H. Structuralism in Phylogenetic Systematics. Biol. Theory, 2011, 5: 383–394.
  48. Zander R.H. A Framework for Post-Phylogenetic Systematics. Zetetic Publications, St. Louis, 2013.
  49. Zander R.H. Classical determination of monophyly, exemplified with Didymodon s. lat. (Bryophyta). Part 1 of 3, synopsis and simplified concepts. Phytoneuron, 2014a, 2014-78: 1–7.
  50. Zander R.H. Classical determination of monophyly, exemplified with Didymodon s. lat. (Bryophyta). Part 2 of 3, concepts. Phytoneuron, 2014b, 2014-79: 1–23.
  51. Zander R.H. Classical determination of monophyly, exemplified with Didymodon s. lat. (Bryophyta). Part 3 of 3, analysis. Phytoneuron, 2014c, 2014-80: 1–19.
  52. Zander R.H. Macrosystematics of Didymodon sensu lato (Pottiaceae, Bryophyta) using an analytic key and information theory. Ukr. Bot. J., 2016, 73: 319–332.