Monte Carlo simulation has commonly been used in phylogenetic studies to test different tree-reconstruction methods, and consequently, its application for testing evolutionary models can be considered as a natural extension of this usage. Repetitive simulation of a given evolutionary process, under the restrictions imposed by the model to be tested, along a determinate tree topology allow the estimate of probability distributions for the desired parameters. Next, the phylogenetic tree can be reconstructed again without the constraints of the model, and the parameter of interest, derived from this tree, can be compared to the corresponding probability distribution derived from the restricted, simulated trees. As an example we have used Monte Carlo simulation to test the constancy of evolutionary rates in a set of cytochrome-c protein sequences.
Larval competition experiments involving two wild type and eight mutant strains of Drosophila melanogaster have been carried out following the substitution procedure proposed by Mather and Caligari (1981). Our main goal has been to compare the competitive abilities of two phenotypically indistinguishable strains (wild and Oregon-R) by means of their responses with eight different mutants. Prior to the analyses of viability data, we have studied the normalizing effect of several transformations in order to determine which was best suited for the analyses. The differences found among the five transformations tested and the untransformed data were not very great. The folded power transformation (Mosteller and Tukey, 1977) was finally chosen.No constant pattern in the responses of the two wild type strains to the mutant competitors was detected. This leads us to conclude that the nature of the competition between the two wild type strains cannot be predicted from a knowledge of their competition with other strains.
Larval-to-adult viability was measured for three strains of Drosophila melanogaster: a wild strain and two eye colour mutant strains (cardinal and sepia) starting from seventy different genotypic compositions. Analyses of a sub-set of the data (not considering all genotypic frequencies) demonstrate frequency-dependence in the three strains. These results suggest that in this experiment, frequency-dependent selection may be masked by other selective forces, only being apparent when specific analyses are carried out.
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