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Cladistic Analysis of Restriction Endonuclease Cleavage Maps Within a Maximum-Likelihood Framework

Ronald W. DeBry and Norman A. Slade
Systematic Zoology
Vol. 34, No. 1 (Mar., 1985), pp. 21-34
DOI: 10.2307/2413342
Stable URL: http://www.jstor.org/stable/2413342
Page Count: 14
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Cladistic Analysis of Restriction Endonuclease Cleavage Maps Within a Maximum-Likelihood Framework
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Abstract

Cladistic analysis of restriction endonuclease cleavage map data, particularly from animal mitochondrial DNA, is considered within a maximum-likelihood framework. The required probability model of evolutionary change is developed from current empirical evidence, and is specific to mtDNA. A large asymmetry is shown to exist between the probabilities of gaining a new site and losing an existing site, with the loss of a site being the much more common event. Since Wagner parsimony assumes that the probabilities of forward and reverse changes are equal, it is a very inefficient estimator of relationships for these data. Dollo parsimony, on the other hand, assumes that the probability of a loss is much greater than that of a gain, an assumption of Dollo parsimony which fits restriction map data well. Dollo parsimony is shown to be a consistent and efficient estimator of phylogeny for mtDNA restriction map data.

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