@Sdaji For a trained geneticist you are rather cynical of your chosen profession. Tell me, Is the lack of integrity that you indicate in the misuse of results an opinion shared by the majority of your work colleagues?
Just as an aside, you stated “...and also we have extremely long generation intervals and small litter sizes/average reproductive output.” Can you please explain how a lengthy generation time and low fecundity helps facilitate adaptive radiation resulting in increased phenotypic variation. It is generally touted to have the opposite effect.
The importance and reliance on phenotypic characteristics in classification is undeniable. That, in conjunction with a measure of observations in nature, are all that taxonomists had to work with for centuries. However, you make the error of oversimplifying the manner in which morphology is and has been used in taxonomy. Morphological differences are only as useful as the degree to which they reflect underlying genetic differences. So the reality is that not all morphological characteristics are of equal importance in classifying.
Taxonomists have been aware of this for centuries. While they knew nothing of the mechanisms of inheritance before Mendel’s work came to light, they still had a good understanding of heredity. They had natural populations to observe and the varieties and breeds of domestic animals that were produced by artificial selection. For example, just because an albino popped up in a population, it was not considered a new species, subspecies or race. This because it was observed to breed freely and produce viable, fertile offspring with other members of its population. It was clearly just another member of that species.
Speaking of artificial selection, one only has look at the results of what has be done with domesticated animals to recognise that a great many population have an inherent capacity for substantial phenotypic variation. To take one average example, the wild population of the Red Jungle Fowl remains similar to what it was many centuries ago. Yet there are over 100 breeds of chicken been produced from that one species. Other examples abound. Just look at all the varieties of agricultural and pet animals - from cats and dogs to rabbits and guinea pigs or pigeons, sheep, goats, pigs and many more. Just because it did not happen in nature, does not mean that any given species necessarily lacks the same potential for phenotypic variation as the human species.
Humans are certainly not the only species where the importance of phenotypic variation has been downplayed as a result of newly acquired genetic evidence. Take the domestic dog and its many breeds for example. Domestic dogs show way much greater phenotypic variation that mankind. Yet on the basis of their underlying genetic makeup, they have been down-graded taxonomically from a separate species to a subspecies of the Grey Wolf.
...but then again, I suppose the geneticists cannot be trusted here either???