Abstract This project focuses on elucidating the mechanisms of evolution at the molecular and population-genetic levels by integrating theoretical and experimental work in a wide phylogenetic framework. The molecular focus is on cellular rates of error production in prokaryotic and eukaryotic species, in particular erroneous protein production resulting from messenger RNA mistranslation. This work will test the drift-barrier hypothesis, which postulates that the level of refinement that natural selection can achieve with any trait is limited by the power of random drift but enhanced by the effective genome size and/or number of molecular transactions. Newly developed methods in proteomics will yield rigorous estimates of the apparently high rates at which erroneous amino acids are incorporated into proteins, complementing prior work at DNA and RNA levels. The genetic mechanisms of evolution will be clarified by integrating population-genomic surveys of 1000s of genotypic isolates of the model microcrustacean Daphnia pulex and related species with functional analyses of key genes known to be involved phenotypic divergence. This work will reveal the relative magnitudes of drift, mutation, and recombination in a collection of ~30 populations, far beyond that for any other species. Combined with a long-term temporal survey, the results will enable a test of the hypothesis that variation at the level of gene structure and genomic architecture is directly driven by the local population-genetic environment. The D. pulex system has unique features for gaining insights into major unsolved mysteries in evolutionary genetics, including the causes and consequences of the loss of meiotic recombination, the genetic mechanisms of sex determination, and the coevolutionary constraints within and among mitochondrial and nuclear-encoded genes as determinants of ribosome structure and bioenergetic capacity. A third project develops evolutionary theory, which combined with the empirical observations, is designed to clarify how phenotypic divergence emerges among isolated lineages. Special attention will be given to the joint roles played by genetic drift and fluctuating selection in driving adaptive and nonadaptive patterns of evolution, as well as to matters of molecular coevolution that form the basis of most intracellular features. Because cellular integrity depends on the production of proper proteins, our work on translation fidelity has broad significance for diverse human-health issues, including matters related to cellular toxicity and protein aggregation. By integrating direct observations on the relative power of drift, mutation, recombination, and fluctuating selection, the population-genomics work will yield insight into the factors driving the efficiencies and mechanisms by which all species respond to natural selection. Elucidation of the molecular/cellular mechanisms converting sexual reproduction to asexual propagation via unfertilized eggs and the...