There is no "standard genome" -- no "reference sequence" in humans, but rather a collection of common consensus sets (haplotypes) that varies from individual to individual. While it is observed that single beneficial mutations can rapidly sweep through a population, it is also important to note that fitness is also likely to be governed by the combination of mutations rather than a single mutation. Evolutionary theory supposes beneficial point mutations to be unusual events that sweep through a population. Benefit and selection are not simply dependent on these single unusual events, because an individual's sum total of variation (mutation) through their genome -- numbering in the millions across the human species -- is likely to be more the source of fitness than a single point change. One must ask what is the context of this beneficial mutation, how does it give an advantage over the previous form of the gene in the context of the creature's environment.

There are several studied examples of these rare mutations occurring which can increase fitness, including those done on bacteria and other organisms. However, let me cite such a one that has been observed in humans. This example is particularly interesting, because evolutionary theory suggests that human diets have rapidly changed over the past several thousand years from their original form. Our diets are now rich in fat and refined carbohydrate, clearly not the previous diet of our nomadic or foraging ancestors. In addition, Westernized society has made its members more sedentary. These changes may have out-paced selection, so that as an extreme example, it can be suggested that many humans in a Westernized context are not fit -- not fully adapted -- for a sedentary, food-rich environment. Heart disease, higher serum ratios of LDL to HDL, high blood pressure, and other cardiovascular symptoms are indicative of chronic cardiovascular disease, which results from the inability of human physiology to cope with this change in diet. Individuals unable to cope with such a diet will suffer as a result, so that the human population can experience selective pressure, and beneficial mutations allowing individuals the ability to survive with this changed diet should be expected to appear.

One such mutation has already been found, though this is not to say that others will not be found as well. This particular mutation renders the lipoprotein gene as a shorter form and confers a survival advantage on the humans with this mutation. This mutation shortens the lipoprotein lipase (LPL) protein by inserting a "stop" signal upstream of the original stop signal, while the majority of other humans share the non-mutated, "full length" version of this gene.

There have been several papers on this example, as it is important to medical research to understand the basis of cardiovascular disease. One set of authors studying this mutation write, "LPL S447X single nucleotide polymorphism has been associated with decreased triglycrides, incrased high density lipoprotein cholesterol, and a decreased risk of coronary artery disease, which may occur independently of its beneficial lipid changes." Researchers found that carriers of this mutation had decreased incidence of hypertension across men/women, youth/adults, and was independent of triglyceride levels as well, suggesting that this variant has protective affects to humans carrying this mutation, not only in the healthier change in plasma lipid levels, but also in healthier regulation of blood pressure and a decreased trend in vascular disease. The researchers conclude, "These studies on the S447X variant provide a novel potential mechanism whereby carriers have a reduced risk of CAD and stroke, namely through decreasing blood pressure. In addition to its association with an improved lipoprotein profile, these data illustrate another mechanism whereby the S447X variant has beneficial activities compared to wildtype LPL. Furthermore, these findings suggest a novel function of the LPL protein, namely influencing endothelial cell biology." [1]

This is one example of a beneficial mutation. Note it has a context: the mutation benefits humans in a modern context. It has a cause: a mutation that causes a shorter version of the LPL gene while the "orignal" form of the gene is still obviously present. The mutation has a clinically observed outcome in several studies: increased survival rates, increased vascular health, higher HDL levels, and lower incidence of hypertension. This mutation ranges from a few percent in some populations in up to to 30 percent in others, indicating that the variation has spread into a population. There have also been several studies supporting these findings (a few given in references 2-4 for example) making this likely one of the best studied and established beneficial mutations that we are aware of.

My response to Lillith's challenge: You are asking for me to provide evidence that there have been no observed helpful mutations (which by the way did not appear in your post). The problem is that anyone who thinks about it can see that you cant provide evidence for a claim that something does not exist. You can only prove me wrong by showing that that thing does exist. So your challenge is oxymoronic.