My main gripe is with the notion that anything that seems complicated, highly technical and scientific-y must be believed, however thin the evidence and poorly reasoned the arguments. If we ignore enough of the data -- genetic or morphological -- it is easy enough to claim that species A and species B are nearest cousins.
In the back of my mind there are some of these DNA papers that I read years ago, written by people known to me. Checking the details, I learned that the program used by the author(s) calculated 4000 equal probability phylogenetic trees, then printed a few representative examples. What's the point?
Imagine taking a test and answering that you have determined 4000 equally probable answers, and cannot vouch for accuracy of the one or two representative examples you chose to write down.
Some of these papers seem to be based on the assumption that every species evolves in isolation. And if two species are different enough to be distinguished, then differences must also be revealed in all the genetic and morphological details. Random gene mutations, of course, should not be limited to the obvious distinctions.
I think it would be useful to test the methods and assumptions of these researchers with some plants of known origin. I have previously mentioned some 2nd generation seedling of hybrids of Mimulus cardinalis and M. Lewisii that were transplanted to a wild area where neither parent species could be found. After a few years, the hybrid swarm had become resolved by bumblebees and hummingbirds into the original species ... as far as anyone could tell. Would the DNA evidence show that the two species evolved recently from a common ancestor?
Years ago I read 'Introgressive Hybridization' by Edgar Anderson. It has stuck with me. Species can mate, then regain themselves in slightly altered forms. This is not a rare event. But the formation of "hybrid swarms" may be less common, and of shorter duration, than we might have assumed.
Another gripe is the notion that all measurements should be of value. This is not true. Some measurements are merely confusing, even when one tries to compare equivalent parts. Why should we consider the length of a sepal to be a significant measurement when flowers vary so much in size? Raw numbers may suggest overlap, whereas ratios may reveal clear differences. Anderson showed how this works in the superficially similar Iris virginica and I. versicolor, and some other species.
http://bulbnrose.x10.mx/Heredity/Anders ... 928_2.html