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

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1. Aldous D., Popovic L. A critical branching process model for biodiversity. Adv. Appl. Probab., 2005, 37: 1094–1115. https://doi.org/10.1017/S0001867800000689
2. Aldous D.J., Krikun M.A., Popovic L. Five statistical questions about the tree of life. Syst. Biol., 2011, 60: 318–328. https://doi.org/10.1093/sysbio/syr008 https://www.ncbi.nlm.nih.gov/pubmed/21386112
3. Alroy J. Continuous track analysis: a new phylogenetic and biogeographic method. Syst. Biol., 1995, 44: 152–178. https://doi.org/10.1093/sysbio/44.2.152
4. Ashlock P.D. Monophyly and associated terms. Syst. Biol., 1971, 20(1): 63–69. https://doi.org/10.1093/sysbio/20.1.63
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. https://doi.org/10.1111/j.1469-185X.2011.00178.x https://www.ncbi.nlm.nih.gov/pubmed/21492379
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. https://doi.org/10.1017/pab.2016.34
8. Bremer K. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution, 1988, 42: 795–803. https://doi.org/10.1111/j.1558-5646.1988.tb02497.x https://www.ncbi.nlm.nih.gov/pubmed/28563878
9. Bremer K. Branch support and tree stability. Cladistics, 1994, 10: 295–304. https://doi.org/10.1111/j.1096-0031.1994.tb00179.x
10. Brummitt R.K. How to chop up a tree. Taxon, 2002, 51: 31–41. https://doi.org/10.2307/1554961
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. https://doi.org/10.7751/telopea19963037
13. de Queiroz K., Donoghue M.J. Phylogenetic systematics and the species problem. Cladistics, 1988, 4: 317–338. https://doi.org/10.1111/j.1096-0031.1988.tb00518.x
14. Donoghue M.J. A critique of the biological species concept and recommendations for a phylogenetic alternative. The Bryologist, 1985, 88: 172–181. https://doi.org/10.2307/3243026
15. Farris J.S. The retention index and the rescaled consistency index. Cladistics, 1989, 5: 417–419. https://doi.org/10.1111/j.1096-0031.1989.tb00573.x
16. Farris J.S. A successive approximations approach to character weighting. Syst. Zool., 1969, 18: 374–385. https://doi.org/10.2307/2412182
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. https://doi.org/10.2307/2412495
19. Felsenstein J. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool., 1978, 27: 401–410. https://doi.org/10.2307/2412923
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. https://doi.org/10.1017/S0094837300016146
22. Friday A. Quantitative aspects of the estimation of evolutionary trees. Folia Primatol. (Basel), 1989, 53: 221–234. https://doi.org/10.1159/000156418
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. https://doi.org/10.1146/annurev.ecolsys.34.011802.132421
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. https://doi.org/10.1093/biomet/66.2.393
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. https://doi.org/10.1093/oxfordjournals.jhered.a111190 https://www.ncbi.nlm.nih.gov/pubmed/1624764
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. https://doi.org/10.2307/sysbio/28.4.416
32. Lee M.S.Y. Species concepts and the recognition of ancestors. Hist. Biol., 1995, 10: 329–339. https://doi.org/10.1080/10292389509380528
33. Levin D.A. Local speciation in plants: The rule not the exception. Syst. Bot., 1993, 18: 197–208. https://doi.org/10.2307/2419397
34. Nelson G.J. "Monophyly again?"– A reply to P.D. Ashlock. Syst. Biol., 1973, 22: 310–312. https://doi.org/10.1093/sysbio/22.3.310
35. Paul C.R.C. The recognition of ancestors. Hist. Biol., 1992, 6: 239–250. https://doi.org/10.1080/10292389209380433
36. Podani J. Tree thinking, time and topology: comments on the interpretation of tree diagrams in evolutionary/phylogenetic systematics. Cladistics, 2013, 29: 315–327. https://doi.org/10.1111/j.1096-0031.2012.00423.x
37. Prothero D.R., Lazarus D.B. Planktonic microfossils and the recognition of ancestors. Syst. Zool., 1980, 29: 119–129. https://doi.org/10.2307/2412642
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. https://doi.org/10.1111/brv.12154 https://www.ncbi.nlm.nih.gov/pubmed/25428167
39. Rieseberg L.H., Brouillet L. Are many plant species paraphyletic? Taxon, 1994, 43: 21–32. https://doi.org/10.2307/1223457
40. Ross H.A. The incidence of species-level paraphyly in animals: A re-assessment. Mol. Phylogenet. Evol., 2014, 76: 10–17. https://doi.org/10.1016/j.ympev.2014.02.021 https://www.ncbi.nlm.nih.gov/pubmed/24583289
41. Sankey H. Scientific Realism: An Elaboration and a Defence. Theor. J. Soc. Polit. Theory, 2001, 35–54. http://dx.doi.org/10.3167/004058101782485548
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. https://doi.org/10.1098/rsbl.2014.0875 https://www.ncbi.nlm.nih.gov/pubmed/25589485 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4321153
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. https://doi.org/10.1016/j.ympev.2006.02.013 https://www.ncbi.nlm.nih.gov/pubmed/16581268
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. https://doi.org/10.1162/BIOT_a_00063
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. https://doi.org/10.15407/ukrbotj73.04.319