'Total evidence' in phylogenetic systematics

Biology and Philosophy

Volumn 24, Issue 5, 2009, Pages 607-622

  Rieppel, Olivier ^a  

^a FIELD MUSEUM OF NATURAL HISTORY   (United States)

Author keywords

Direct optimization; K. R. Popper; Systematics; Total evidence

Indexed keywords

CLADISTICS; OPTIMIZATION; PHYLOGENETICS; TAXONOMY;

EID: 76349110782     PISSN: 01693867     EISSN: 15728404     Source Type: Journal    
DOI: 10.1007/s10539-008-9122-1     Document Type: Review

References (105)

1. Apesteguía S, Zaher H (2006) A Cretaceous terrestrial snake with robust hindlimbs and a sacrum. Nature 440: 1027-1040. doi: 10. 1038/nature04413.
2. Ball IR (1982) Implication, conditionality and taxonomic statements. Bijdr Dierkd 52: 186-190.
3. Barnes B, Bloor D, Henry J (1996) Scientific knowledge a sociological analysis. The University of Chicago Press, Chicago.
4. Beatty J (1982) Classes and cladists. Syst Zool 31: 25-34. doi: 10. 2307/2413411.
5. Brady RH (1982) Theoretical issues and 'pattern cladistics'. Syst Zool 31: 286-291. doi: 10. 2307/2413235.
6. Bullet P (1942) Beiträge zur Kenntnis des Gebisses von Varanus salvator Laur. Viertejahresschr. Natf Ges Zürich 87: 139-192.
7. Caldwell MW, Lee MSY (1997) A snake with legs from the marine Cretaceous of the Middle East. Nature 386: 705-709. doi: 10. 1038/386705a0.
8. Carnap R (1950) Logical foundations of probability. The University of Chicago Press, Chicago.
9. Carroll RL (1988) Vertebrate paleontology and evolution. W. H. Freeman & Co, New York.
10. Cleland CE (2002) Methodological and epistemic differences between historical science and experimental science. Philos Sci 69: 474-496. doi: 10. 1086/342455.
11. Conrad JL (2008) Phylogeny and systematics of Squamata (Reptilia) based on morphology. Bull Am Mus Nat Hist 310: 1-182. doi: 10. 1206/310. 1.
12. Cope ED (1869) On the reptilian order Pythonomorpha and Streptosauria. Proc Boston Soc Nat Hist 12: 250-261.
13. Cope ED (1872) On the geology and paleontology of the Cretaceous strata of Kansas. In: Hayden FV (ed) Preliminary report on the United States geological survey of Montana and portions of adjacent territories; being a fifth annual report of progress, part 3, paleontology. Washington, pp 318-349.
14. Cope ED (1878) Professor Owen on the Pythonomorpha. Bull US Geol Geogr Surv Territ 4: 299-311 Hayden Survey.
15. DePinna MCC (1991) Concepts and tests of homology in the cladistic paradigm. Cladistics 7: 367-394. doi: 10. 1111/j. 1096-0031. 1991. tb00045. x.
16. Estes R, de Queiroz K, Gauthier J (1988) Phylogenetic relationships within Squamata. In: Estes R, Pregill G (eds) Phylogenetic relationships of the lizard families. Stanford University Press, Stanford, pp 119-281.
17. Faith DP, Trueman WH (2001) Towards an inclusive philosophy for phylogenetic inference. Syst Biol 50: 331-350. doi: 10. 1080/106351501300317969.
18. Farris SJ (1983) The logical basis of phylogenetic analysis. In: Platnick NI, Funk VA (eds) Advances in cladistics, vol 2. Columbia University Press, New York, pp 7-36.
19. Farris JS, Platnick NI (1989) Lord of the flies: the systematist as study animal. Cladistics 5: 295-310.
20. Felsenstein J (1978) The number of evolutionary trees. Syst Zool 27: 27-33. doi: 10. 2307/2412810.
21. Frost DR, Grant T, Faivovich J, Bain RH, Haas A, Haddad CFB et al (2007) Is the Amphibian Tree of Life really fatally flawed? Cladistics 24: 385-395. doi: 10. 1111/j. 1096-0031. 2007. 00181. x.
22. Gaffney ES (1979) An introduction to the logic of phylogeny reconstruction. In: Cracraft J, Eldredge N (eds) Phylogenetic analysis and paleontology. Columbia University Press, New York, pp 79-111.
23. Grant T, Kluge AG (2004) Transformation series as an ideographic character concept. Cladistics 20: 29-31. doi: 10. 1111/j. 1096-0031. 2004. 00003. x.
24. Greene HW, Cundall D (2000) Limbless tetrapods and snakes with legs. Science 287: 1939-1941. doi: 10. 1126/science. 287. 5460. 1939.
25. Haas G (1979) On a new snakelike reptile from the Lower Cenomanian of Ein Jabrud, near Jerusalem. Bull Mus Natn Hist Nat 1(4): 51-64.
26. Haas G (1980a) Pachyrhachis problematicus Haas, snakelike reptile from the Lower Cenomanian: ventral view of the skull. Bull Mus natn Hist Nat 2(4): 87-104.
27. Haas G (1980b) Remarks on a new ophiomorph reptile from the lower Cenomanian of Ein Jabrud, Israel. In: Jacobs LL (ed) Aspects of vertebate history. Museum of Northern Arizona Press, Flagstaff, pp 177-192.
28. Härlin M (1999) The logical priority of the tree over characters and some of its consequences for taxonomy. Biol J Linn Soc 68: 497-503.
29. Hempel G (1965) Aspects of scientific explanation and other essays in the philosophy of science. Free Press, New York.
30. Hempel C (1966) The philosophy of natural science. Prentice-Hall, Englewood Cliffs.
31. Hempel G, Oppenheim P 1948 [1965] Studies in the logic of explanation. In: Hempel G (ed) Aspects of scientific explanation and other essays in the philosophy of science. Free Press, New York, pp 245-296.
32. Hull DL (1988) Science as a process. An evolutionary account of the social and conceptual development of science. The University of Chicago Press, Chicago.
33. Jenner RA (2004) The scientific status of metazoan cladistics: why current research practice must change. Zool Scr 33: 293-310. doi: 10. 1111/j. 0300-3256. 2004. 00153. x.
34. Kase T, Shigeta Y, Futakami M (1994) Limpet home depressions in Cretaceous ammonites. Lethaia 27: 49-58. doi: 10. 1111/j. 1502-3931. 1994. tb01555. x.
35. Kase T, Shigeta Y, Futakami M (1995) Limpet pits on ammonoids living in surface waters. Lethaia 28: 315-316. doi: 10. 1111/j. 1502-3931. 1995. tb01821. x.
36. Kase T, Johnston PA, Seilacher A, Boyce JB (1998) Alledged mosasaur bite marks on Late Cretaceous ammonites are limpet (patellogastropod) home scars. Geology 26: 947-950. doi: 10. 1130/0091-7613(1998)026<0947: AMBMOL> 2. 3. CO; 2.
37. Kauffman EG, Kesling RV (1960) An upper Cretaceous ammonite bitten by a mosasaur. Contr Mus Paleont Univ Mich 15: 193-248.
38. Kearney M, Rieppel O (2006a) Rejecting "the given" in systematics. Cladistics 22: 369-377. doi: 10. 1111/j. 1096-0031. 2006. 00110. x.
39. Kearney M, Rieppel O (2006b) An investigation into the occurrence of plicidentine in the teeth of squamate reptiles. Copeia (3): 337-350. doi: 10. 1643/0045-8511(2006)2006[337: AIITOO]2. 0. CO; 2.
40. Kluge AG (1989) A concern for evidence, and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Syst Zool 38: 7-25. doi: 10. 2307/2992432.
41. Kluge AG (1997a) Sophisticated falsification and research cycles: consequences for differential character weighting in phylogenetic systematics. Zool Scr 26: 349-360. doi: 10. 1111/j. 1463-6409. 1997. tb00424. x.
42. Kluge AG (1997b) Testability and the refutation and corroboration of cladistic hypotheses. Cladistics 13: 81-96. doi: 10. 1111/j. 1096-0031. 1997. tb00242. x.
43. Kluge AG (2001) Parsimony with and without scientific justification. Cladistics 17: 199-210. doi: 10. 1111/j. 1096-0031. 2001. tb00117. x.
44. Kluge AG (2003a) On the deduction of species relationships: a précis. Cladistics 19: 233-239.
45. Kluge AG (2003b) The repugnant and the mature in phylogenetic inference: atemporal similarity and historical identity. Cladistics 19: 356-368. doi: 10. 1111/j. 1096-0031. 2003. tb00379. x.
46. Kluge AG (2004) On total evidence: for the record. Cladistics 20: 205-207. doi: 10. 1111/j. 1096-0031. 2004. 00020. x.
47. Lee MSY (1997) The phylogeny of varanoid lizards and the affinities of snakes. Philos Trans R Soc Lond B Biol Sci 352: 53-91. doi: 10. 1098/rstb. 1997. 0005.
48. Lee MSY (1998) Convergent evolution and character correlation in burrowing reptiles: towards a resolution of squamate relationships. Zool J Linn Soc 65: 369-453.
49. Lee MSY, Caldwell MW (1998) Anatomy and relationships of Pachyrhachis problematicus, a primitive snake with hind limbs. Philos Trans R Soc Lond B Biol Sci 352: 1521-1552. doi: 10. 1098/rstb. 1998. 0308.
50. Lee MYS, Scanlon JD (2002) Snake phylogeny based on osteology, soft anatomy, and ecology. Biol Rev Camb Philos Soc 77: 333-401. doi: 10. 1017/S1464793102005924.
51. Lee MSY, Bell GL Jr, Caldwell MW (1999) The origin of snake feeding. Nature 400: 655-657. doi: 10. 1038/23236.
52. Lipton P (2004) Inference to the best explanation, 2nd edn. Routledge, London.
53. Mainx F 1955 [1971] Foundations of biology. In: Neurath O, Carnap R, Morris C (eds) Foundations of the unity of science, vol 1. The University of Chicago Press, Chicago, pp 568-654.
54. Miyamoto MM, Fitch WM (1995) Testing species phylogenies and phylogenetic methods with congruence. Syst Biol 44: 64-76. doi: 10. 2307/2413483.
55. Nixon KC, Carpenter JM (1996) On simultaneous analysis. Cladistics 12: 221-241. doi: 10. 1111/j. 1096-0031. 1996. tb00010. x.
56. Newton-Smith WH 1981 [1994] The rationality of science. Routledge, London.
57. Odermatt C (1940) Beiträge zur Kenntnis des Gebisses von Heloderma Vierteljahresschr. Natf Ges Zürich 85: 98-141.
58. Ogden TH, Rosenberg MS (2007) Alignment and topological accuracy of the Direct Optimization approach via POY and taditional phylogenetics via ClustalW + PAUP*. Syst Biol 56: 182-193. doi: 10. 1080/10635150701281102.
59. O'Leary MA, Gatesy J, Novacek MJ (2003) Are the dental data really at odds with the molecular data? Morphological evidence for whale phylogeny (re)reexamined. Syst Biol 52: 853-564. doi: 10. 1080/10635150390252279.
60. Patterson C (1982a) Morphological characters and homology. In: Joysey KA, Friday AE (eds) Problems of phylogenetic reconstruction. Academic Press, London, pp 21-74.
61. Patterson C (1982b) Classes and cladists or individuals and evolution. Syst Zool 31: 284-286. doi: 10. 2307/2413234.
62. Philippe H, Delsuc F, Brinkman H, Lartillot N (2005) Phylogenomics. Annu Rev Ecol Evol Syst 36: 541-562. doi: 10. 1146/annurev. ecolsys. 35. 112202. 130205.
63. Platnick NI (1982) Defining characters and evolutionary groups. Syst Zool 31: 282-284. doi: 10. 2307/2413233.
64. Platnick NI (1985) Philosophy and the transformation of cladistics revisited. Cladistics 1: 87-96.
65. Platnick NI, Gaffney ES (1977) Systematics: a Popperian perspective. Syst Zool 26: 360-365.
66. Platnick NI, Gaffney ES (1978a) Evolutionary biology: a Popperian perspective. Syst Zool 27: 137-141. doi: 10. 2307/2412831.
67. Platnick NI, Gaffney ES (1978b) Systematics and the Popperian paradigm. Syst Zool 27: 381-388. doi: 10. 2307/2412895.
68. Popper KR (1935) Logik der Forschung. Julius Springer, Vienna.
69. Popper KR 1963 [1997] The demarcation between science and metaphysics. In: Schilpp PA (ed) The philosophy of Rudolph Carnap. Open Court, La Salle, IL, pp 183-226.
70. Popper KR (1974) Replies to my critics. In: Schilpp PA (ed) The philosophy of Karl Popper, vol 2. Open Court, La Salle, IL, pp 961-1197.
71. Ramirez MJ (2007) Homology as a parsimony problem: a dynamic homology approach for morphological data. Cladistics (OnlineEraly Articles). doi: 10. 1111/j. 1096-0031. 2007. 00162.
72. Reichenbach H (1938) Experience and prediction. The University of Chicago Press, Chicago.
73. Rieppel O (1978) Tooth replacement in anguinomorph lizards. Zoomorph 91: 77-90. doi: 10. 1007/BF00994155.
74. Rieppel O (1979) A functional interpretation of the varanid dentition (Reptilia, Lacertilia, Varanidae). Gegenbaurs Morphol Jahrb 125: 797-817.
75. Rieppel O (1988) Fundamentals of comparative biology. Birkhäuser Verlag, Basel.
76. Rieppel O (2004a) The language of systematics, and the philosophy of 'total evidence'. Syst Biodivers 2: 9-19. doi: 10. 1017/S147720000400132X.
77. Rieppel O (2004b) What happens when the language of science threatens to break down in systematics-A Popperian perspective. In: Williams DM, Forey PL (eds) Milestones in systematics. CRC Press, Boca Raton, FL, pp 57-100.
78. Rieppel O (2007) Parsimony, likelihood, and instrumentalism in systematics. Biol Philos 22: 141-144. doi: 10. 1007/s10539-006-9026-x.
79. Rieppel O, Kearney M (2001) The origin of snakes: limits of a scientific debate. Biologist 48: 110-114.
80. Rieppel O, Kearney M (2007) The poverty of taxonomic characters. Biol Philos 22: 95-113. doi: 10. 1007/s10539-006-9024-z.
81. Rieppel O, Rieppel M, Rieppel L (2006) Logic in systematics. J Zool Syst Evol Res 44: 186-192. doi: 10. 1111/j. 1439-0469. 2006. 00370. x.
82. Rosenberg A (2005) Philosophy of science. A contemporary introduction, 2nd edn. Routledge, London.
83. Salmon WC (1998) Causality and explanation. Oxford University Press, Oxford.
84. Scheffler I (1982) Science and subjectivity, 2nd edn. Hackett Publ. Co, Indianapolis, IA.
85. Scotland RW, Olmstead RG, Bennet JR (2003) Phylogeny reconstruction: the role of morphology. Syst Biol 52: 539-548.
86. Seilacher A (1998) Mosasaurs, limpets or diagenesis: how Placenticeras shells got punctured. Mitt Mus Natkd Berl, Geowiss Reihe 1: 93-102.
87. Sereno P (2007) Logical basis for morphological characters in phylogenetics. Cladistics 23: 565-587.
88. Simmons MP (2004) Independence of alignment and tree search. Mol Phylogenet Evol 31: 874-879. doi: 10. 1016/j. ympev. 2003. 10. 008.
89. Simmons MP, Ochoterena H (2000) Gaps as characters in sequence-based phylogenetic analyses. Syst Biol 49: 369-381. doi: 10. 1080/10635159950173889.
90. Sober E (1983) Parsimony methods in systematics. In: Platnick NI, Funk VA (eds) Advances in cladistics, vol 2. Columbia University Press, New York, pp 37-47.
91. Sober E (1988) Reconstructing the past. Parsimony, evolution, and inference. The MIT Press, Cambridge, MA.
92. Sober E (2006) Simplicity. In: Newton-Smith WH (ed) A companion to the philosophy of science. Blackwell, Malden, MA, pp 433-441.
93. Tchernov E, Rieppel O, Zaher H, Polcyn MJ, Jacobs LJ (2000) A new fossil snake with limbs. Science 287: 2010-2012. doi: 10. 1126/science. 287. 5460. 2010.
94. Vaeth RH, Rossman DA, Shoop W (1985) Observations on tooth surface morphology in snakes. J Herpetol 19: 20-26. doi: 10. 2307/1564416.
95. Vogt L (2008) The unfalsifiability of cladograms and its consequences. Cladistics 24: 62-73. doi: 10. 1111/j. 1096-0031. 2007. 00169. x.
96. Westermann GEG, Hewitt RA (1995) Do limpet pits indicate that desmoceratacean ammonites lived mainly in surface waters? Lethaia 28: 24. doi: 10. 1111/j. 1502-3931. 1995. tb01590. x.
97. Wheeler WC (1998) Alignment characters, dynamic programming and heuristic solutions. In: De Salle R, Schierwater B (eds) Molecular approaches to ecology and evolution. Birkhäuser, Basel, pp 243-251.
98. Wheeler WC (2001a) Homology and DNA sequence data. In: Wagner GP (ed) The character concept in evolutionary biology. Academic Press, San Diego, CA, pp 303-317.
99. Wheeler WC (2001b) Homology and the optimization of DNA sequence data. Cladistics 17: S1-S11. doi: 10. 1111/j. 1096-0031. 2001. tb00099. x.
100. Wheeler WC (2003a) Implied alignment: a synapomorphy-based multiple-sequence alignment method and its use in cladogram search. Cladistics 19: 261-268. doi: 10. 1111/j. 1096-0031. 2003. tb00369. x.
101. Wheeler WC (2003b) Search-based optimization. Cladistics 19: 348-355. doi: 10. 1111/j. 1096-0031. 2003. tb00378. x.
102. Wheeler WC (2005) Alignment, dynamic homology, and optimization. In: Albert VA (ed) Parsimony, phylogeny, and genomics. Oxford University Press, Oxford, UK, pp 71-80.
103. Wheeler WC, Aagesen L, Arango CP, Faivovich J, Grant T, D'Haese C et al (2006) Dynamic homology and phylogenetic systematics: a unified approach using POY. American Museum of Natural History, New York.
104. Wiley EO (1981) Phylogenetics. The theory and practice of phylogenetic systematics. Wiley, New York.
105. Williams PA (1992) Confusion in cladism. Synthese 91: 135-152. doi: 10. 1007/BF00484973.