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Cladistics



There are several algorithms available to identify the "best" cladogram.[26] Most algorithms use a metric to measure how consistent a candidate cladogram is with the data. Most cladogram algorithms use the mathematical techniques of optimization and minimization.

In general, cladogram generation algorithms must be implemented as computer programs, although some algorithms can be performed manually when the data sets are trivial (for example, just a few species and a couple of characteristics).

Some algorithms are useful only when the characteristic data is molecular (DNA, RNA) data. Other algorithms are useful only when the characteristic data is morphological data. Other algorithms can be used when the characteristic data includes both molecular and morphological data.

Algorithms for cladograms include least squares, neighbor-joining, parsimony, maximum likelihood, and Bayesian inference.

Biologists sometimes use the term parsimony for a specific kind of cladogram generation algorithm and sometimes as an umbrella term for all cladogram algorithms.[27]

Algorithms that perform optimization tasks (such as building cladograms) can be sensitive to the order in which the input data (the list of species and their characteristics) is presented. Inputting the data in various orders can cause the same algorithm to produce different "best" cladograms. In these situations, the user should input the data in various orders and compare the results.

Using different algorithms on a single data set can sometimes yield different "best" cladograms, because each algorithm may have a unique definition of what is "best".

Because of the astronomical number of possible cladograms, algorithms cannot guarantee that the solution is the overall best solution. A nonoptimal cladogram will be selected if the program settles on a local minimum rather than the desired global minimum.[28] To help solve this problem, many cladogram algorithms use a simulated annealing approach to increase the likelihood that the selected cladogram is the optimal one.[29]

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How complex is the Tree of Life?

One argument in favor of cladistics is that it supports arbitrarily complex, arbitrarily deep trees. Especially when extinct species are considered (both known and unknown), the complexity and depth of the tree can be very large. Every single speciation event, including all the species that are now extinct, represents an additional fork on the hypothetical, complete cladogram representing the full tree of life. Fractals can be used to represent this notion of increasing detail: as a viewpoint zooms into the tree of life, the complexity remains virtually constant[30]. This great complexity of the tree, and the uncertainty associated with the complexity, are among the reasons that cladists cite for the attractiveness of cladistics over traditional taxonomy.

Proponents of noncladistic approaches to taxonomy point to punctuated equilibrium to bolster the case that the tree of life has a finite depth and finite complexity. If the number of species currently alive is finite, and the number of extinct species that we will ever know about is finite, then the depth and complexity of the tree of life is bounded, and there is no need to handle arbitrarily deep trees.

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Phylocode approach to naming species

A formal code of phylogenetic nomenclature, the PhyloCode[31], is currently under development for cladistic taxonomy. It is intended for use by both those who would like to abandon Linnaean taxonomy and those who would like to use taxa and clades side by side. In several instances (see for example Hesperornithes) it has been employed to clarify uncertainties in Linnaean systematics so that in combination they yield a taxonomy that is unambiguously placing the group in the evolutionary tree in a way that is consistent with current knowledge.

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Terminology

The yellow group (sauropsids) is monophyletic, the blue group (reptiles) is paraphyletic, and the red group (warm-blooded animals) is polyphyletic.
The yellow group (sauropsids) is monophyletic, the blue group (reptiles) is paraphyletic, and the red group (warm-blooded animals) is polyphyletic.
Main article: Phylogenetic nomenclature
  • A clade is an ancestor species and all of its descendents
  • A monophyletic group is a clade
  • A paraphyletic group is a monophyletic group that excludes some of the descendants (e.g. reptiles are sauropsids excluding birds). Most cladists discourage the use of paraphyletic groups.
  • A polyphyletic group is a group consisting of members from two non-overlapping monophyletic groups (e.g. flying animals). Most cladists discourage the use of polyphyletic groups.
  • An outgroup is an organism that is considered not to be part of the group in question, but is closely related to the group.
  • A characteristic that is present in both the outgroups and in the ancestors is called a plesiomorphy (meaning "close form", also called an ancestral state).
  • A characteristic that occurs only in later descendants is called an apomorphy (meaning "separate form", also called a "derived" state) for that group. Note: The adjectives plesiomorphic and apomorphic are used instead of "primitive" and "advanced" to avoid placing value-judgments on the evolution of the character states, since both may be advantageous in different circumstances. It is not uncommon to refer informally to a collective set of plesiomorphies as a ground plan for the clade or clades they refer to.
  • A species or clade is basal to another clade if it holds more plesiomorphic characters than that other clade. Usually a basal group is very species-poor as compared to a more derived group. It is not a requirement that a basal group be extant. For example, palaeodicots are basal to flowering plants.
  • A clade or species located within another clade is said to be nested within that clade.

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Origin of the term "cladistics"

Hennig's major book, even the 1979 version, does not contain the term cladistics in the index. He referred to his own approach as phylogenetic systematics, as implied by the book's title. A review paper by Dupuis observes that the term clade was introduced in 1958 by Julian Huxley, cladistic by Cain and Harrison in 1960, and cladist (for an adherent of Hennig's school) by Mayr in 1965.[32]

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Three definitions of clade

There are three ways to define a clade for use in a cladistic taxonomy.[33]

  • Node based: the most recent common ancestor of A and B, and all its descendants. See crown group.
  • Stem based: all descendants of the oldest common ancestor of A and B that is not also an ancestor of Z. See total group.
  • Apomorphy based: the most recent common ancestor of A and B, along with all of its descendants, possessing a certain derived character. This definition is generally discouraged by most cladists.

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Applying cladistics to other disciplines

The processes used to generate cladograms are not limited to the field of biology[34]. The generic nature of cladistics means that cladistics can be used to organize groups of items in many different academic realms. The only requirement is that the items have characteristics that can be identified and measured.

A triple family tree of Linux distributions.
A triple family tree of Linux distributions.

Recent attempts in the use of cladistic methods outside of biology attack problems in anthropology[35], the filiation of manuscripts in textual criticism[citation needed], and the lineage of Linux distros, a class of computer operating system[citation needed].

The attempts to apply cladistic programs on languages overlook that languages are learnt and often subject to sudden loss or acquisition of features, contrasting to biology, where most traits are inherited. The results therefore, are generally unsatisfactory[36].

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Footnotes

  1. ^ Phylogenetic Systematics is the title of Hennig's 1966 book
  2. ^ pp. 45, 78 and 555 of Joel Cracraft and Michael J. Donaghue, eds. (2004). Assembling the Tree of Life. Oxford, England: Oxford University Press.
  3. ^ Singh, Gurcharan (2004). Plant Systematics: An Integrated Approach. Science, 203-4. ISBN 1578083516. 
  4. ^ Albert, Victor (2006). Parsimony, Phylogeny, and Genomics. Oxford University Press, 3-55. ISBN 0199297304. 
  5. ^ Aldous, David (1996), “Probability Distributions on Cladograms”, Random Discrete Structures, Springer, p. 13 
  6. ^ Lowe, Andrew (2004). Ecological Genetics: Design, Analysis, and Application. Blackwell Publishing, 164. ISBN 1405100338. 
  7. ^ Scott-Ram, N. R. (1990). Transformed Cladistics, Taxonomy and Evolution. Cambridge University Press, 83. ISBN 0521340861. 
  8. ^ Freeman, Scott (1998). Evolutionary Analysis. Prentice Hall, 380. ISBN 0135680239. 
  9. ^ Carroll, Robert Lynn (1997). Patterns and Processes of Vertebrate Evolution. Cambridge University Press, 80. ISBN 052147809X. 
  10. ^ Letunic, I (2007). "Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation." (Pubmed). Bioinformatics 23(1): 127–8. doi:10.1093/bioinformatics/btl529. 
  11. ^ Unwin, David M. (2006). The Pterosaurs: From Deep Time. New York: Pi Press, 246. ISBN ISBN 0-13-146308-X. 
  12. ^ Mayr, E. (1985). "Darwin and the Definition of Phylogeny." Systematic Zoology, 34(1): 97-98.
  13. ^ Wheeler, Quentin (2000). Species Concepts and Phylogenetic Theory: A Debate. Columbia University Press. ISBN 0231101430. 
  14. ^ Benton, M. (2000). "Stems, nodes, crown clades, and rank-free lists: is Linnaeus dead?". Biological Reviews 75 (4): 633–648. 
  15. ^ Hull, David (1988). Science as a Process. University of Chicago Press, 232-276. ISBN 0226360512. 
  16. ^ Colin Tudge (2000). The Variety of Life. Oxford University Press. ISBN 0198604262. 
  17. ^ Hennig, Willi (1975). "'Cladistic analysis or cladistic classification': a reply to Ernst Mayr". Systematic Zoology 24: 244–256. doi:10.2307/2412765. 
  18. ^ Mayr, Ernst (1976). Evolution and the diversity of life (Selected essays). Cambridge, MA: Harvard Univ. Press. ISBN 0-674-27105-X. 
  19. ^ Mayr, Ernst (1982). The growth of biological thought: diversity, evolution and inheritance. Cambridge, MA: Harvard Univ. Press, 221. ISBN 0-674-36446-5. 
  20. ^ Hodge T, Cope M (2000). "A myosin family tree". J Cell Sci 113 Pt 19: 3353–4. PMID 10984423. 
  21. ^ a b DeSalle, Rob (2002). Techniques in Molecular Systematics and Evolution. Birkhauser. ISBN 376436257X. 
  22. ^ Hillis, David (1996). Molecular Systematics. Sinaur. ISBN 0878932828. 
  23. ^ West-Eberhard, Mary (2003). Developmental Plasticity and Evolution. Oxford Univ. Press, 353-376. ISBN 0195122356. 
  24. ^ List of Cladistics Software Programs.
  25. ^ Hodkinson, Trevor (2006). Reconstructing the Tree of Life: Taxonomy and Systematics of Species Rich Taxa. CRC Press, 61-128. ISBN 0849395798. 
  26. ^ Kitching, Ian (1998). Cladistics: The Theory and Practice of Parsimony Analysis. Oxford University Press. ISBN 0198501382. 
  27. ^ Stewart, Caro-Beth (1993). "The Powers and Pitfalls of Parsimony". Nature 361: 603–607. doi:10.1038/361603a0. 
  28. ^ Foley, Peter (1993). Cladistics: A Practical Course in Systematics. Oxford Univ. Press, 66. ISBN 0198577664. 
  29. ^ Nixon K. C. (1999). "The Parsimony Ratchet: a new method for rapid parsimony analysis". Cladistics 15: 407–414. doi:10.1111/j.1096-0031.1999.tb00277.x. 
  30. ^ Gordon, Richard (1999). The Hierarchical Genome and Differentiation Waves. World Scientific, 632. ISBN 9810222688. 
  31. ^ Pennisi, E. (2001). "Evolutionary Biology: Preparing the Ground for a Modern 'Tree of Life'". Science 293: 1979–1980. doi:10.1126/science.293.5537.1979. 
  32. ^ Dupuis, Claude (1984). "Willi Hennig's impact on taxonomic thought". Annual Review of Ecology and Systematics 15: 1–24. ISSN 0066-4162. 
  33. ^ de Queiroz, K. and J. Gauthier (1994). "Toward a phylogenetic system of biological nomenclature". Trends in Research in Ecology and Evolution 9 (1): 27–31. doi:10.1016/0169-5347(94)90231-3. 
  34. ^ Mace, Ruth (2005). The Evolution of Cultural Diversity: A Phylogenetic Approach. Routledge Cavendish. ISBN 1844720993. 
  35. ^ Lipo, Carl (2005). Mapping Our Ancestors: Phylogenetic Approaches in Anthropology and Prehistory. Aldine Transaction. ISBN 0202307514. 
  36. ^ Holm, Hans J. (2007). "The new Arboretum of Indo-European 'Trees'. Can New Algorithms Reveal the Phylogeny and Even Prehistory of Indo-European?". Journal of Quantitative Linguistics 14,2 - 3: 167–214. doi:10.1080/09296170701378916. 

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See also

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References

  • Ashlock, Peter D. (1974). "The uses of cladistics". Annual Review of Ecology and Systematics 5: 81–99. doi:10.1146/annurev.es.05.110174.000501. ISSN 0066-4162. 
  • Cuénot, Lucien (1940). "Remarques sur un essai d'arbre généalogique du règne animal". Comptes Rendus de l'Académie des Sciences de Paris 210: 23–27.  Available free online at http://gallica.bnf.fr (No direct URL). This is the paper credited by Hennig (1979) for the first use of the term 'clade'.
  • Cavalli-Sforza, L.L. and A.W.F. Edwards (Sep., 1967). "Phylogenetic analysis: Models and estimation procedures". Evol. 21 (3): 550–570. doi:10.2307/2406616. 
  • de Queiroz, Kevin (1992). "Phylogenetic taxonomy". Annual Review of Ecology and Systematics 23: 449–480. doi:10.1111/j.1096-3642.2006.00293.x. ISSN 0066-4162. 
  • Dupuis, Claude (1984). "Willi Hennig's impact on taxonomic thought". Annual Review of Ecology and Systematics 15: 1–24. ISSN 0066-4162. 
  • Felsenstein, Joseph (2004). Inferring phylogenies. Sunderland, MA: Sinauer Associates. ISBN 0-87893-177-5. 
  • Hamdi, Hamdi; Hitomi Nishio, Rita Zielinski and Achilles Dugaiczyk (1999). "Origin and phylogenetic distribution of Alu DNA repeats: irreversible events in the evolution of primates". Journal of Molecular Biology 289: 861–871. doi:10.1006/jmbi.1999.2797. PMID 10369767. 
  • Hennig, Willi (1950). Grundzüge einer Theorie der Phylogenetischen Systematik. Berlin: Deutscher Zentralverlag. .
  • Hennig, Willi (1982). Phylogenetische Systematik (ed. Wolfgang Hennig). Berlin: Blackwell Wissenschaft. ISBN 3-8263-2841-8. 
  • Hennig, Willi (1975). "'Cladistic analysis or cladistic classification': a reply to Ernst Mayr". Systematic Zoology 24: 244–256. doi:10.2307/2412765.  The paper he was responding to is reprinted in Mayr (1976).
  • Hennig, Willi (1966). Phylogenetic systematics (tr. D. Dwight Davis and Rainer Zangerl). Urbana, IL: Univ. of Illinois Press (reprinted 1979 and 1999). ISBN 0-252-06814-9. 
  • Hennig, Willi (1979). Phylogenetic systematics (3rd edition of 1966 book). ISBN 0-252-06814-9. Translated from manuscript and so never published in German.
  • Hull, David L. (1979). "The limits of cladism". Systematic Zoology 28: 416–440. doi:10.2307/2412558. 
  • Kitching, Ian J.; Peter L. Forey, Christopher J. Humphries and David M. Williams (1998). Cladistics: Theory and practice of parsimony analysis, 2nd ed., Oxford University Press. ISBN 0-19-850138-2. 
  • Luria, Salvador; Stephen Jay Gould and Sam Singer (1981). A view of life. Menlo Park, CA: Benjamin/Cummings. ISBN 0-8053-6648-2. 
  • Mayr, Ernst (1982). The growth of biological thought: diversity, evolution and inheritance. Cambridge, MA: Harvard Univ. Press. ISBN 0-674-36446-5. 
  • Mayr, Ernst (1976). Evolution and the diversity of life (Selected essays). Cambridge, MA: Harvard Univ. Press. ISBN 0-674-27105-X.  Reissued 1997 in paperback. Includes a reprint of Mayr's 1974 anti-cladistics paper at pp. 433-476, "Cladistic analysis or cladistic classification." This is the paper to which Hennig (1975) is a response.
  • Patterson, Colin (1982). "Morphological characters and homology". Joysey, Kenneth A; A. E. Friday (editors) Problems in Phylogenetic Reconstruction, London: Academic Press. 
  • Rosen, Donn; Gareth Nelson and Colin Patterson (1979), Foreword provided for Hennig (1979)
  • Shedlock, Andrew M; Norihiro Okada (2000). "SINE insertions: Powerful tools for molecular systematics". Bioessays 22: 148–160. doi:10.1002/(SICI)1521-1878(200002)22:2. ISSN 0039-7989. PMID 10655034. 
  • Sokal, Robert R. (1975). "Mayr on cladism -- and his critics". Systematic Zoology 24: 257–262. doi:10.2307/2412766. 
  • Swofford, David L.; G. J. Olsen, P. J. Waddell and David M. Hillis (1996). "Phylogenetic inference", in Hillis, David M; C. Moritz and B. K. Mable (editors): Molecular Systematics, 2. ed., Sunderland, MA: Sinauer Associates. ISBN 0-87893-282-8. 
  • Wiley, Edward O. (1981). Phylogenetics: The Theory and Practice of Phylogenetic Systematics. New York: Wiley Interscience. ISBN 0-471-05975-7. 
  • Zwickl DJ, Hillis DM (2002). "Increased taxon sampling greatly reduces phylogenetic error". Systematic Biology 51: 588–598. doi:10.1080/10635150290102339. 

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