Directly Observed Mutation

Do you mean observed in nature or do experiments in the lab count? If lab experiments count then the list of references will grow to include..well my lab notebook for one

Here is a review article of dozens of experiments on this topicElena SF, Lenski RE. Related Articles, Links
Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation.
Nat Rev Genet. 2003 Jun;4(6):457-69. Review.
Microorganisms have been mutating and evolving on Earth for billions of years. Now, a field of research has developed around the idea of using microorganisms to study evolution in action. Controlled and replicated experiments are using viruses, bacteria and yeast to investigate how their genomes and phenotypic properties evolve over hundreds and even thousands of generations. Here, we examine the dynamics of evolutionary adaptation, the genetic bases of adaptation, tradeoffs and the environmental specificity of adaptation, the origin and evolutionary consequences of mutators, and the process of drift decay in very small populations.