Phenetics

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. 

Turner, A. S., Lees, A. K., Rezanoor, H. N., and Nicholson, P. (1998). Refinement of PCR-detection of Fusarium avenaceum and evidence from DNA marker studies for phenetic relatedness to Fusarium tricinctum. Plant Pathol. (Oxford) 47, 278-288. 

Uddin, A.F.M.J. et al.. Seasonal variation in pigmentation and anthocyanidin phenetics in commercial Eustoma flowers, Sci. Hortic. —Amsterdam, 100, 103, 2004. 

Morphological or structural plant features which impair normal feeding or oviposition by insects or contribute to the action of these mortality factors are often grouped as "phenetic resistance" (25). 

Welsh, J., Wolfe, M.S, and Morris, M. 2001. Cereal trials. Organic Farming 69 14-15. Williams, C.E. and St Clair, D.A. 1993. Phenetic relationships and levels of variability detected... 

Phenetidine, AN88 m-Phenet id 1 ne, AN89 -Phenetidine, AN90 Phenkapton, AT74 Phenol, AH04... 

Carlson, D. A. (1988). Hydrocarbons for identification and phenetic comparisons Cockroaches, honey bees and tsetse flies. Florida Entomol., 71, 333-345. 

Table II illustrates how the information in Fig. 1 and Table I can be used to assess the statistical significance of immunological data bearing on phenetic relationships, with attention centered on the position of the giant panda with respect to the bear and lesser panda (see also example 4 in Table III). In essence, we estimate the probability that the bear is molecu-larly as similar to the lesser panda as to the giant panda.

Fig. 2. Schematic representation of phenetic or phylogenetic hypotheses tested immuno-logically. The immunological evidence indicated that the proteins from taxa B and C resemble one another more than they do the protein from taxon A (left-hand side of figure), whereas earlier hypotheses, based on nonmolecular evidence, had suggested the organismal relationships shown on the right-hand side, with C being the outgroup taxon. See Table III and text for examples.

Rodman, J.E. (1991) A taxonomic analysis of glucosinolate producing plants. Part 1. Phenetics Syst. Bot., 16, 598-618. 

To the phenetic school we owe the increase in exactness and explicit treatment of characters for the purpose of dis-... 

Morowitz, H. J. Phenetics, a born-again science. Complexity, 8 (2003), 12-13. 

For evolutionary studies, the classification of species also allows the construction of phytogenies, which may shed light on the relationship between observed pattern of speciation and the nature of evolutionary forces. A distinction should be made between phenetic and cladistic data. The phe-netic relationships are similarities based on the degree of similarity, whereas cladistic relationships contain information about ancestry and can be used to study evolutionary pathways. Both of these relationships are best portrayed as phylogenetic trees or dendrograms, respectively (57). 

Apart from the underlying principles, there are the questions of how the data are obtained and their limitations. With the phenetic method, characters used are those for which it is possible to make the necessary quantitative measurements. With the cladistic method, it is rarely possible to determine each branch point, especially where convergent evolution has occurred. The phenetic method produces a practical classification but lacks the deeper philosophical justification of the cladistic method. However, both methods often give similar results, but differences arise, as in the example in Fig. 1.2. Although the crocodile and lizard show greater morphological similarity to one another than to the bird, birds and crocodiles have more recent common ancestors than crocodiles and lizards. 

Fig. 1.2. An example of phenetic and phylogenetic principles of classification, (a) The probable evolutionary tree for lizard, crocodile and bird. The distances separating the three are a measure of their phenotypic differences, (b) Phenetic relationships, (c) Phylogenetic relationships.

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