Bacterial populations have served as model systems for studying evolutionary processes ever since the classic experiments of Luria and Delbrück, which demonstrated the occurrence of mutations prior to selection for the traits they conferred. However, several authors have recently presented experiments suggesting that bacteria may have mechanisms for directing which mutations occur, such that the rate of adaptive mutations is enhanced. Before the hypothesis of directed mutation is accepted, it is imperative to consider alternative hypotheses that might account for the same observations. To this end, we expand upon existing mathematical theory of the dynamics of mutation and selection in clonal populations for two cases of particular interest. The first case concerns selection against mutants before plating; this selection occurs as the result of differences in growth rate between mutants and nonmutants. We demonstrate that this selection model gives rise to distributions of mutants, obtained by plating from sister cultures, that are very similar to those expected when some mutations are induced by the selective environment. The second case concerns the sequential incorporation of two mutations as the result of selection for an intermediate genotype after plating. We demonstrate that this two-step mutation model also yields distributions that are similar to those expected when some mutations are induced by the selective environment. These two cases therefore provide alternatives to the hypothesis of directed mutation. We suggest experiments that might be used to examine our alternative hypotheses. We also contrast the hypothesis of directed mutation with the notion of inheritance of acquired characteristics.

The pigmentation patterns of shells in the genus Conus can be generated by a neural-network model of the mantle. We fit model parameters to the shell pigmentation patterns of 19 living Conus species for which a well resolved phylogeny is available. We infer the evolutionary history of these parameters and use these results to infer the pigmentation patterns of ancestral species. The methods we use allow us to characterize the evolutionary history of a neural network, an organ that cannot be preserved in the fossil record. These results are also notable because the inferred patterns of ancestral species sometimes lie outside the range of patterns of their living descendants, and illustrate how development imposes constraints on the evolution of complex phenotypes.