Parsimony methods

Three different parsimony methods have been used for the analysis of restriction site data Wagner parsimony,25 Dollo parsimony,26 and weighted parsimony or generalized parsimony.27 As the names suggest, they all invoke a parsimony principle to select the best tree (or trees) from the set of all possible trees. Specifically, the trees selected are those that require the minimum amount of evolutionary change. The methods differ from one another in how the amount of evolutionary change is calculated. 

In a bifurcating tree, the ancestral node (or root) could theoretically fall along any of the lineages (see Fig. 2). Parsimony methods for constructing molecular phylogenies do not produce a rooted tree automatically this is a... 

In view of such developments, it is not surprising that there have been several attempts in 1985-1989 to reconsider the evolutionary relationships. The approach in many studies has been to construct parsimony trees using methods and computer programs based essentially on the maximum parsimony methods of Farris (1970, 1972) or Fitch and Mar-... 

Character-state weight matrices have usually been estimated more or less by eye, but they can also be derived from a rate matrix. For example, if it is presumed that each of the two transitions occurs at double the frequency of each transversion, a weight matrix can simply specify, for example, that the cost of A-G is 1 and the cost of A-T is 2 (Fig. 14.5). (The parsimony method dictates that the diagonal elements of the matrix, or the cost of having the same base in different sequences, be zero. This proves to be a shortcoming of parsimony this will be discussed further below.) In the subsequent tree-building step, this set of assumptions will minimize the overall number of transversions and tend to cluster sequences differing mainly by transitions. 

The third (default) method uses a table of empirically observed transitions between amino acids (the Dayhoff PAM 001 matrix). The character-based analysis of sequence data can be initiated via the appropriate executable file (e.g. DnaPars, DnaML or ProtPars). PHYLIP comprises DnaPars and DnaML to estimate phylogenetic relationships by the parsimony method and the maximum likelihood methods from nucleotide sequences respectively. ProtPars is the parsimony program for protein sequences. 

Several phylogenetic analysis programs use a generalized parsimony method in which the user (Swofford 1990, Maddison and Maddison 1990) or the program (Williams and Fitch 1989) defines a matrix which describes the cost associated with a transition from state i to state j.. Modification of the cost matrix allows experimentation with different kinds of weighting. 

Character-based parsimony methods search for the shortest length tree for the data as a best estimate of tree topology i.e. patterns of... 

Goodman M, Moore GW, Barnabas J, Matsuda G (1974) The phylogeny of human globin genes investigated by the maximum parsimony method. J Mol Evol 3 1-48... 

DeQueiroz, K. and Poe, S., Philosophy and phylogenetic inference a comparison of likelihood and parsimony methods in the context of Karl Popper s writings on corroboration, Syst. Biol, 50, 305-321, 2001. 

The introduction and use of parsimony methods in phylogenetic estimation is described and discussed against the background of Ockham s razor and extremum principles in science generally. It is argued that the method of maximum likelihood applied to realistic models of evolutionary divergence is the optimum procedure, to which parsimony methods are often an acceptable approximation. 

The number of nucleotide substitutions or the consistency index at each site of the different sequence data sets were calculated using the CHART STATE CHANGES AND STASIS option in MacClade (Maddison and Maddison 1992). Parameters were estimated from the traditional morphology-based tree (Eignre 9.1) using nonoverlapping 20-bp windows, and the maximum parsimony method with 1000 random... 

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