Parsimony maximum

Fig. 1.3. (Opposite) COI genes of strongylid and other nematodes. Aligned COI sequences (from Sukhdeo etal., 1997 (where each is designated by the GenBank accession number), except for Ascaris suum ASCOI and C. elegans CECOI which are from Okimoto et al. (1992), O. volvulus COI which is from Keddie etal. (1998) and B. malayiCO sequence which is unpublished data of the author) were analysed using maximum parsimony and neighbour joining.

Fig. 1.5. Delineation of Bursaphelenchus species. (A) Maximum parsimony phylogram of an analysis of the aligned ITS1 and ITS2 regions from Bursaphelenchus isolates. Branch lengths are given above each branch, and bootstrap support below. (B) As for (A) but using NJ analysis (logdet/paralinear distance correction). Adapted from Beckenbach etal. (1999).

The most commonly used techniques for estimating trees for sequences may be grouped into three categories (1) distance methods, (2) maximum parsimony, and (3) maximum likelihood based methods. There are other methods but they are not widely used. Further, each of these categories covers many variations and even distinct methods with different properties and assumptions. These methods have often been divided different ways (different from the three categories here) such as cladistic versus phenetic, character-based versus non-character-based, method-based versus criterion-based, and others. These divisions may merely reflect particular predjudices by the person making them and can be artificial. 

Inferred Minimum. Number of Steps in Maximum Parsimony Trees Generated from 11 Different... 

Fig. 5.2. Phylogeny of monopisthocotylean Monogenea based on SSU rDNA. The tree topology is from a Bayesian analysis with nodal support indicated, from top to bottom, for maximum likelihood (bootstrap%, n = 100), maximum parsimony (bootstrap%, n = 1000) and Bayesian inference (posterior probabilities). Figure from Matejusova etal. (2003).

Figure 18.4 A Phylogenetic relationships of moth ABPXs and DmeIPBPRPs. The primary sequences of the proteins were aligned in Clustal X 1.8 and processed using PAUP 4.0d65 (Swofford, 1999). The tree represents equally most parsimonious trees of 909 steps and consistency index 0.52. The numbers above each branch indicate the percent bootstrap support above 50 percent for the supported node using maximum parsimony (Felsenstein,...

Fig. 1.7 Evolution of alkaloids in the phylogeny of plants. Using nucleotide sequences of the chloroplast gene rbcL a phylogenetic tree was computed with Maximum Parsimony. A bootstrap cladogram is shown with bootstrap values shown at the nodes. Branches leading to taxa that accumulate alkaloids are shown in bold.

Gercideae. (a) The occurrence of alkaloids. Key to branches leading to families that accumulate quinolizidines, pyrrolizidines (No. 1 see arrows) Erythrina (No. 3) indolizidines (No. 4) p-carbolines (No. 5) or simple indoles (No. 2) are marked. The rbcl sequences used (1400 bp) derived from Kass and Wink, 1997a,b Wink and Mohamed (2003). Trees were reconstructed with maximum parsimony. 

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-... 

Fig. 5. Phylogenetic analysis of NRF family amino acid sequences. The amino acid sequences of known or predicted members of the NRF family in zebrafish and pufferfish were obtained from the GenBank or genome databases and aligned with the human NRF family sequences. The tree was inferred using maximum parsimony within PAUP 4b 10. The results illustrate the conservation of NRF proteins in mammals and fish as well as the additional diversity in NRF3 forms present in pufferfish. Danio rerio (Dr), Takifugu (Fugu) rubripes (Fr), Homo sapiens (Hs).

Figure 2 tub2 gene tree of Epichloe spp. form different hosts based on maximum parsimony analysis. The bar represents 5 inferred nucleotide substitutions. Numbers at branches are the percentages of trees containing the corresponding clade based on 500 bootstrap replications. Values greater than 70% are considered supportive of the clade. (Modified from Schardl and Leuchtmann, 1999.)... 

Figure 3 Phylogenetic relationship of the Cordyceps fungi based on the total sequence data. A tandemly concatenated nuclear and mitochondrial rDNA data set (4272 nucleotide sites) was subjected to neighbor-joining (NJ), maximum-likelihood quartet puzzling (ML-PUZZLE) and maximum parsimony (MP) analyses. The strict consensus tree of the three analyses is presented. Numbers at the nodes are bootstrap values (%) obtained by the NJ (left), ML-PUZZLE (center), and MP (right) methods, respectively. Shown on the right side are host organisms, names of the clades, and morphological types of the stromata.

Maximum Parsimony (MP). Maximmn parsimony is an optimization criterion that adheres to the principle that the best explanation of the data is the simplest, which in turn is the one requiring the fewest ad hoc assumptions. In practical terms, the MP tree is the shortest—the one with the fewest changes—which, by definition, is also the one with the fewest parallel changes. There are several variants of MP that differ with regard to the permitted directionality of character state change (Swofford et al., 1996). 

Distance matrix methods simply count the number of differences between two sequences. This number is referred to as the evolutionary distance, and its exact size depends on the evolutionary model used. The actual tree is then computed from the matrix of distance values by running a clustering algorithm that starts with the most similar sequences (i.e., those that have the shortest distance between them) or by trying to minimize the total branch length of the tree. The principle of maximum parsimony searches for a tree that requires the smallest number of changes to explain the differences observed among the taxa under study. 

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... 

Swofford DL, Berlocher SH (1987) Inferring evolutionary trees from gene frequency data under the principle of maximum parsimony. Syst Zool 36 293-325... 

Fig. 3. Minimum phylogenetic tree from tRNA sequences. The tRNA sequences from Fig. 2 were analyzed by a maximum parsimony algorithm. Organisms are abbreviated as in Fig. 2. The branch lengths are proportional to mutational distance and numbers above branches refer to the percentage of bootstrap trees which confirm that branch. is used to represent over 95%. Branches which are not confirmed to more than 50% are collapsed to the next nearest node.

The central tenets of the falsificationist philosophy of Karl R. Popper are reviewed in detail, and the way they do or do not apply to systematics and phylogeny reconstruction is analyzed. Cladistic analysis, cast in either maximum parsimony or in maximum likelihood approaches, is not compatible with Popperian falsificationism. The main reasons are the absence of a deductive link between a hypothesis of phylogenetic relationships and character distribution on a tree, which translates into the absence of the basic asymmetry of falsification versus verification. This sets Popper s philosophy of science apart from inductive systems. In cladistic analysis, falsification (disconfirmation) is symmetrical to verification (confirmation), which reveals an inductive and hence probabilistic background. The basic problem of systematics as an empirical science resides in character conceptualization and its critical evaluation. 

---