>>Forgive me if this is a stupid question but I only have a high school education. Assuming we could even correctly calibrate this molecular clock all we can determine from it is rate of divergence of the non nuetral genes, correct? Then what does this really tell us? Does it only tell us how long there has been no gene flow? What good does that do? Isn't it the nonneutral genes that will ultimately allow the animal to adapt, change and become something else? Couldn't these changes occur anywhere along that timeline on the molecular clock?

Answer:

As I said before, only non-adaptive genes can be used for calibrating a molecular clock, because changes of adaptive genes (non-neutral genes) are constrained by natural selection. An adaptive gene can change if 1) the change is adaptive to a new environment, or 2) if the change has no effect on its function. An example of the second type of change would be a substitution of the 3rd nucleotide in a codon, which does not change the amino acid that this codon represents.

It is true that the molecular clock only tells us how long two populations have become isolated from one another. In fact, it does not tell us whether these two populations represent different species. In the simple case when two populations co-exist in the same area, the fact that they are isolated from one another is the strongest evidence yet that they represent two different species. Difficulties arise when two populations are geographically isolated from one another so that there is no chance for them to meet under natural conditions. In these cases, biologists must determine whether the two populations represent the same or different species. And indeed it is these cases of geographic isolation of morphologically similar species which is the source of a great deal of taxonomic controversy in the current literature.

Many biologists subscribe to the view that if two geographically isolated populations differ by a single morphological character (no matter how trivial), then this is evidence that these two populations are on "different evolutionary trajectories," which means they will in time diverge into two different species. Many other biologists do not subscribe to this view, because they do not accept the claim that a single, possibly adaptively neutral mutation or morphological variation as evidence that these populations are on different "trajectories." There is of course no middle ground between these two schools of taxonomic thought and therefore no possibility of compromise.

For this reason and others, taxonomy is currently in a chaotic state, and it is unlikely to be resolved soon.

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