Are there any species where there have been documented evidence (I am talking about an observed, documented account, not a fossil) of a species mutating beyond standard variation?
I am not interested in species that have undergone mutation where the offspring has not survived or has been sterile. I am wondering if there has been any known instances where an actual genetic advancement has taken place, no matter how small, in an extant species beyond simple variation adaptions such as color (i.e. English moths) or texture changes (Mendelian peas).
I know that evolution takes time, and that scientific observation by humans has only been occurring for a blink of an eye, but I am curious about this. It is hard for me to understand how evolution could function properly when seemingly most mutation is not only negative, but usually sterile or recessive and even when something genetically different comes about (such as a liger or a mule) it is again either sterile or shunned by the "true" breeds and will only be mated with if there are absolutely no other options.
Further, how would an aquatic animal develop into a land animal, or even an amphibian? It seemingly would have to develop both lungs and legs simultaneously, and if this was not a complete and instantaneous development (i.e. if it developed one leg and half a lung more or less) how would that adaption be advantageous? It seems like it would not be able to survive on land, and would devastate its ability to compete in the water, or any other half-way scenario...yet if it did spontaneously evolve both adaptations, what would it breed with? How would it still be genetically viable to do so? What are the chances that its adaptations would be not only dominant, but able to be passed on with any lasting success when the rest of the gene-pool (if available in the first place) would be overwhelmingly saturated with non-leg/lung genes?
Again, I am well aware of the timeline we are discussing, but despite the laws of probability supposedly panning out given a long enough time period, it stretches my belief beyond my ability to do so to understand how a species as complex as humanity (not to mention all the other species, extant and extinct) could have achieved its form despite all these factors against even a single positive mutation.
Please try and leave religion out of this. I do not mean to offend. I have my own religious beliefs, and my own scientific beliefs. I am looking for an educated answer, and I would prefer that preaching either science or religion for their own sake be left out of the response.
NOTE: I am aware that most mutation is neutral and occurs in amino acids that cause no noticeable or significant change...when I say most mutation I am referring to mutation that has a observable effect on the species. I tried asking this question in another forum and I kept getting answers that included variations of the existing species (such as antibiotic resistant bacterium) and I am aware of the mudskipper and the lungfish, but this does not answer my question of how even one species would develop to the level of sophistication to transition from water to land, let alone all the creatures who have done so, and even gone back into the water--even in the two billion years that life has been extant on Earth.
Once again, I do not need someone to point out that I am lacking in some way if I cannot understand how this works...I wouldn't ask the question in the first place if I wasn't curious. I guess you could consider curiosity as a lack of knowledge, but why would anyone ask questions here if that was something to put someone down about?
I would like to point out that I made a point about looking for something beyond resident variation within species. To the best of my research, bacterium have always existed that were resistant to antibiotics, but selection pressure due to the saturation of antibiotics has increased their concentration due to their ability to survive and pass on their trait.
One condescending but seemingly informed contributor to this question brought up an example of the black squirrel in Britain. I was curious about this and upon further research, despite the gene being called 'mutant' (it was even put in quotes in the article he provided) there is no real evidence I could find that it was, in fact, a mutation, rather than a recessive variation. This article: http://www.masslive.com/news/index.ssf/2009/02/regions_black_squirrels_offer.html?category=Westfield points out that the black squirrel was, while not common, known since the 1940's and has been classified as a variation of the gray squirrel for as long.
The same contributor also brought up examples of amphibious fish such as the lungfish...their existence does not answer my question either. It seems like splitting hairs to differentiate them from whales or even bats which seemingly have incongruous biological features for their habitat, and ultimately it does not explain my original curiosity (not disbelief...curiosity) of how humans (or any and all of the extant species) could have evolved from muck, through multiple mass extinctions to walking upright, even given 2 billion years.