Parsimony methods (=cladistics)

What are parsimony methods?

The theory and practice of parsimony is called cladistics.

Cladistics or phylogenetic systematics finds its origin with the German entomologist Willi Hennig, who in 1950, published the book Grundzüge einer Theorie der phylogenetischen Systematik. However, it was only after 1966, when his work was translated to English, that his ideas on classification infiltrated systematics and changed it profoundly.

Hennig’s idea was that biological classifications ought to be based exclusively on genealogy, that is, on the branching pattern of phylogeny. Phylogeny is seen as a series of speciation events whereby an ancestral species splits into two sister (daughter) species. The ancestral species dies at the splitting event. Cladistics translates into classification in that sister species are given the same categorical rank and the ancestor together with all of its descendants form monophyletic groups (=clades).

Why use cladistic analysis?

Freeman and Herron (2001: 438) put it as follows: “Two ideas are key to understanding why this approach to phylogenetic inference is valid. The first is that synapomorphies indentify evolutionary branch points. Why? After a species splits into two lineages that begin evolving independently, some of their homologous traits undergo changes due to mutation, selection and drift. These changed traits are synapomorphies that identify populations in the two independent lineages. The second key idea is that synapomorphies are nested. That is, as you move back in time and trace an evolutionary tree backward from its tip to its root, each branching event adds one or more synapomorphies. As a result, the hierarchy described by synapomorphies replicates the hierarchy of branching event”.

The greatest virtue of cladistics is that it allows to test if the groups recognised by taxonomists are monophyletic or not.

How to use cladistic analysis?

Nobody expresses this better than Mayr (1982: 227): ‘The crucial aspect of cladistics is the careful analysis of all characters in the comparison of related taxa and in the partitioning of these chracters into ancestral (plesiomorph) and uniquely derived (apomorph) characters. Branching points in the phylogeny are determined by the backward tracing of uniquely derived characters (synapomorphies) because such apomorph characters are believed to be found only among the descendants of the ancestor in which the character first occurred'.

Cladistics thus starts with the choice of taxa, their characters and an analysis of the characters (=recognition of synapomorphies). There exist several ways to determine if a character is ancestral or derived. The most utilised one is called outgroup comparison whereby the character state in the group of interest (called the ingroup) is compared to the state in a close relative that clearly does not belong to the ingroup (this external relative forms the so-called outgroup). The outgroup is assumed to represent the ancestral state.

Without reversal or convergent evolution all the similarities observed in a dataset can be allocated to a change in the common ancestor. In such a case one says that all sunapomorphies identified are congruent, whereby each branch of the tree corresponds to one or more synapomorphies that distinguish the derived groups.

Course

Cladistic analysis: an introduction

A primer to tree reading

The tree thinking challenge 

References 

• Avise, J.C. & Wollenberg, K. 1997. Phylogenetics and the origin of species. PNAS 94: 7748-7755.
• Becera, J.X. 1997. Insects on Plants: Macroevolutionary Chemical Trends in Host Use. Science 276: 253-256. 
• Berenbrink, M. et al. 2005. Evolution of Oxygen Secretion in Fishes and the Emergence of a Complex Physiological System. Science 307: 1752-1757. 
• Bossuyt, F. & Milinkovitch, M.C. 2001. Amphibians as Indicators of Early Tertiary Out-of-India Dispersal of Vertebrates. Science 292: 93-95.
• Bossuyt, F. et al. 2004. Local Endemism Within the Western Ghats–Sri Lanka Biodiversity Hotspot. Science 306: 479-781.
• Baum, D.A., DeWitt Smith, S. & Donovan, S.S. 2005. The tree thinking challenge. Science 310: 979-980. (supplementary material)
• Darlu, P. & Tassy, P. 1993 (2004, online edition). La Reconstruction phylogénétique. Concepts et Méthodes, 260 pp. 
• Freeman, S. & Herron, J.C. 2001. Evolutionary Analysis. 2nd Edition., Prentice-Hall, New Jersey, 704 pp. 
• Kitching, I.J., Forey, P.L., Humphries, C.J. & Williams, D.M. 1998. Cladistics: The Theory and Practice of Parsimony Analysis. Second Edition. The Systematics Association Publication No. 11. Oxford: Oxford University Press. 
• Mathews, S. & Donoghue, M.J. 1999. The Root of Angiosperm Phylogeny Inferred from Duplicate Phytochrome Genes. Science 286: 947-950. 
• Mayr, E. 1982. The Growth of Biological Thought. Diversity, Evolution and Inheritance. Belknap Press of Harvard University Press, Cambridge, Massachusetts, London, England, 974 pp. 
• Page, R.M. & Charleston, M.A. 1998. Trees within trees: phylogeny and historical associations. TRENDS in Ecology and Evolution 13: 356-359. 
•  Nee, S. 2005. The great chain of being. Nature 435: 429. 
•  Wiley, E.O., Siegel-Causey, D., Brooks, D.R. & Funk, V.A. 1991. The Compleat Cladist. The University of Kansas Museum of Natural History Special Publication No. 19, 12 pp.

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