Taxonomy and why history of science matters for science

ISIS

Volumn 99, Issue 2, 2008, Pages 331-340

  Hamilton, Andrew ^a   Wheeler, Quentin D ^b  

^a ARIZONA STATE UNIVERSITY   (United States)

^b ARIZONA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ARTICLE; CLASSIFICATION; HISTORY; HUMAN; PHILOSOPHY; RESEARCH; SCIENCE;

CLASSIFICATION; DNA; HISTORIOGRAPHY; HISTORY, 20TH CENTURY; HUMANS; PHILOSOPHY; RESEARCH; SCIENCE;

EID: 47749137344     PISSN: 00211753     EISSN: 15456994     Source Type: Journal    
DOI: 10.1086/588691     Document Type: Article

References (39)

1. Willi Hennig, Phylogenetic Systematics (Urbana: Univ. Illinois Press. 1966). The epigraph is taken from a letter to Henry Fawcett, 18 Sept. 1861, http://www.darwinproject.ac.uk/darwinletters/calendar/entry-3257.html.
2. Julian Huxley, ed., The New Systematics (Oxford: Clarendon, 1940).
3. Robert R. Sokal and Peter H. A. Sneath, Principles of Numerical Taxonomy (San Francisco: Freeman, 1963), pp. 6, 7. Numerical taxonomy has a longer and more complex history than is outlined here; we are looking at just one version over part of its career. Earlier attempts were more ambitious and sought to establish the claim, that, as Hennig put it, "community of similarity = community of descent": Hennig, Phylogenetic Systematics (cit. n. 1), p. 88.
4. Sokal and Sneath, Principles of Numerical Taxonomy, pp. vii, viii, 49, 48, 50.
5. For Hennig's argument see Willi Hennig, Grundzüge einer Theorie der Phylogenetischen Systematik (Berlin: Deutscher Zentralverlag, 1950).
6. George Simpson, "Review: Numerical Taxonomy and Biological Classification," Science, 1964, 144:112-713;
7. and Ernst Mayr, "Numerical Phenetics and Taxonomic Theory," Systematic Zoology, 1965, 74:73-97, on p. 76.
8. Arguments based on similar premises can be found in Simpson's 1964 review piece (cit. n. 5) and in the articles by J. S. Farris discussed below.
9. James S. Farris, "On the Phenetic Approach to Vertebrate Classification," in Major Patterns in Vertebrate Evolution, ed. M. K. Hecht, P. C. Goody, and B. M. Hecht (NATO Advanced Study Institute Series, .14) (New York: Plenum, 1977), pp. 823-850;
10. Farris, "On the Naturalness of Phylogenetic Classification," Systemat. Zool., 1979, 28:200-214;
11. and Farris, "The Information Content of the Phylogenetic System," ibid., pp. 483-519.
12. Peter H. A. Sneath and Robert R. Sokal, Numerical Taxonomy (San Francisco: Freeman, 1973), p. 24. Gilmour's most important papers are J. S. L. Gilmour, "A Taxonomic Problem," Nature, 1937, 759:1040-1042;
13. Gilmour, "Taxonomy and Philosophy," in New Systematics, ed. Huxley (cit. n. 2), pp. 461-474;
14. Gilmour, 'The Development of Taxonomic Theory since 1851," Nature, 1951, 768:400-402;
15. and Gilmour, "Taxonomy," in Contemporary Botanical Thought, ed. A. M. MacLeod and L. S. Cobley (Chicago: Quadrangle, 1961), pp. 27-45.
16. Farris, "On the Phenetic Approach to Vertebrate Classification" (cit. n. 7), p. 831.
17. Eli C. Minkoff, "The Effects of Slight Alterations in Numerical Technique," Systemat. Zool., 1965, 14:196-213. It is worth pointing out as well that repeatability also depended on choice of tools; the methods used gave the same results only if no new characters or taxa were added to the analysis and only if the same algorithm and options therein were employed.
18. Nicholas Jardine and Robin Sibson, "Choice of Methods for Automatic Classification," Computer Journal, 1971, /4:404-406, on p. 404;
19. and Jardine and Sibson, Mathematical Taxonomy (London: Wiley, 1971).
20. Carl Woese and George Fox, "Phylogenetic Structure of the Prokaryotic Domain: The Primary Kingdoms," Proceedings of the National Academy of Sciences, 1977, 74:5088-5090.
21. Paul Hebert, Alina Cywinska, Shelly Ball, and Jeremy deWaard, "Biological Identifications through DNA Barcodes," Proceedings of the Royal Society of London, Series B, 2003, 270:313-321. To avoid confusion, we note that DNA barcoding and DNA taxonomy are not the same enterprise; some who reject the former embrace the latter.
22. See, e.g., two pieces by Diethard Tautz, Peter Arctander, Alessandro Minelli, Richard Thomas, and Alfried Vogler: "DNA Points the Way Ahead in Taxonomy," Nature, 2002, 18:479;
23. and "A Plea for DNA Taxonomy," Trends in Ecology and Evolution, 2003, 18:70-74.
24. It is worth pointing out that some DNA barcoders refer to their groups as "molecular operational taxonomic units" (MOTUs), a reprisal of the operational taxonomic unit (OTU) of the pheneticists (as in Figure .1). See, e.g., Robin Floyd, Eyualem Abebe, Artemis Papert, and Mark Blaxter, "Molecular Barcodes for Soil Nematode Identification," Molecular Ecology, 2002, 11:839-850;
25. Blaxter, "The Promise of DNA Taxonomy," Philosophical Transactions of the Royal Society of London, Series B, 2004, 559:669-679;
26. and Alex Smith, Brian Fisher, and Paul Hebert, "DNA Barcoding for Effective Biodiversity Assessment of a Hyperdiverse Arthropod Group: The Ants of Madagascar," Proc. Nat. Acad. Sci., 2005, 560:1825-1834. As Blaxter points out in "Promise of DNA Taxonomy," some have also referred to MOTUs as "phylotypes" and "genospecies."
27. Hebert et al., "Biological Identifications through. DNA Barcodes" (cit. n. 13), p. 313.
28. In this connection see Quentin D. Wheeler, "Losing the Plot: DNA 'Barcodes' and Taxonomy," Cladistics, 2005, 27:405-407.
29. Craig Moritz and Carla Cicero, "DNA Barcoding: Promise and Pitfalls," PLoS Biology, 2004, 2:1529-1531;
30. Paul Hebert, Mark Stoeckle, Tyler Zemlak, and Charles Francis, "Identification of Birds through DNA Barcodes," ibid., pp. 1657-1663;
31. and Ned K. Johnson and Cicero, "New Mitochondrial DNA Data Affirm the Importance of Pleistocene Speciation in North American Birds," Evolution, 2004, 58:1122-1130.
32. In this connection see also Damon Little and Dennis Stevenson, "A Comparison of Algorithms for the Identification of Specimens Using DNA Barcodes: Examples from Gymnosperms," Cladistics, 2007, 25:1-21. Findings presented there suggest that some current barcoding methods are of limited applicability.
33. For a discussion of the difference between, morphological characters as against phenetic observations see Norman Platnick, "Philosophy and the Transformation of Cladistics," Systemat. Zool., 1979, 28:537-546;
34. for the development of those ideas see Gareth Nelson and Platnick, Systematics and Biogeography: Cladistics and Vicariance (New York: Columbia Univ. Press, 1981).
35. It should be noted that in contemporary morphologically based taxonomy, species are not infrequently described by reference to a single trait when more diagnostic traits are unavailable: genitalia in insects is one familiar example. The structure of the inference in these cases is quite different than in the barcoding case, however, because of the underlying phylogenetic theory. Some taxonomists argue that these classifications issue in empirically testable predictions about constancy of distribution of unique combinations of characters at the species level and about nonconflicting distributions of new apomorphies at the level of monophyletic groups. In this connection see Quentin D. Wheeler and Norman Platnick, "The Phylogenetic Species Concept (Sensu Wheeler and Platnick)," in Species Concepts and Phylogenetic Theory: A Debate, ed. Wheeler and Rudolf Meier (New York: Columbia Univ. Press, 2000), pp. 55-69.
36. Motoo Kimura, "A Simple Method for Estimating Evolutionary Rate of Base Substitutions through Comparative Studies of Nucleotide Sequences," Journal of Molecular Evolution, 1980, 16:111-120;
37. Sudhir Kumar, Koichiro Tamura, Ingrid Jacobsen, and Masatoshi Nei, "MEGA2: Molecular Evolutionary Genetics Analysis Software," Bioinformatics, 2001, 17:1244-1245;
38. and Nei and Kumar, Molecular Evolution and Phylogenetics (Oxford: Oxford Univ. Press, 2001).
39. Mary P. Winsor, "The Practitioner of Science: Everyone Her Own Historian," Journal of the History of Biology, 2001, 54:229-245.