Absolutely!



I don't even want to get into cryptic species etc. Speciation itself is sometimes a contentious subject, do you subscribe to the biological species concept, the phylogentic species concept, etc. It gets even more complicated when you consider that "reproductive isolation" comes in many forms. And not all forms of reproductive isolation result in outwardly different morphologies (eg differences in gamete morphology). Unfortunately, detailed morphological descriptions are not performed much anymore. Partially because these sorts of things are harder to get funding for, but also because genetics has become MUCH more common and easier to do.



Also, Chris, I'm fairly sure that the genetic studies were performed on wild populations but I don't have the time to dig up the paper to be 100% sure.



I would say that to most scientists, genetic based phylogenies that match morphological based phylogenies are much less interesting than phylogenies that do not match those predicted by morphology. It usually means that they selective regime that had been assumed to be at work to create the extant morphologies is not actually the selective regime that the organisms faced in their evolutionary history. The one that I am most familiar with is hammerhead sharks (as I have done a bit of work with them). Extant species have heads of varying width (~20% - 50% of their lenth). Morphological based phylogenies predicted that the head progressed from relatively narrow toward increasingly wider as a result of some advantage conferred by the wide head. However, molecular based phylogenies actually show that the pattern of head width evolution is exactly the opposite with wider heads arising first and then head width decreasing through evolutionary history. This has very different implications for the selective pressures that these sharks faced.
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Kyle R. Mara



Common sense is genius dressed in its working clothes. - Ralph Waldo Emerson



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