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April1_Phenetics - IB 200A Principals of Phylogenetic...

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IB 200A Principals of Phylogenetic Systematics Spring 2008 Phenetics The fundamental positions of numerical taxonomy: 1. The greater the content of information in the taxa of a classification and the more characters on which it is based, the better a given classification will be. 2. A priori , every character is of equal weight in creating natural taxa. 3. Overall similarity between any two entities is a function of their individual similarities in each of the many characters in which they are being compared. 4. Distinct taxa can be recognized because correlations of characters differ in the groups of 5. Phylogenetic inferences can be made from the taxonomic structures of a group and from character correlations, given certain assumptions about evolutionary pathways and mechanisms. 6. Taxonomy is viewed and practiced as an empirical science. 7. Classifications are based on phenetic similarity. Phenetic methodology 1. Phenetic classification starts with the collection of raw measurement data on the chosen set of morphs, called Operational Taxonomic Units , or OTU 's. 2. The data may then be transformed in some manner to remove redundancy, and to normalize the values to a common scale. Commonly used transformations include simple normalization, principle component analysis, and factor analysis. 3. A measure of similarity or dissimilarity is computed for each pair of OTU's. This is usually a generalized distance measure, based on a generalization of Euclidean distance, or some form of correlation coefficient. 4. A clustering method is used to group OTU's that are most similar. The agglomerative clustering algorithms are popular for this purpose. These method involve joining the two most similar OTU's into a new, compound, OTU, and recomputing the similarity measure for the resulting cluster. This is repeated until all OTU's have been merged into
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one. The different agglomerative clustering methods differ mainly in the way that the
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April1_Phenetics - IB 200A Principals of Phylogenetic...

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