In situations where we see contradictions, the answer is often that there are two dimensions that are involved but we are only acknowledging one of them.
That is what is going on with the subject we are looking at - the origin and development of species.
There are actually two dimensions. You could call one the horizontal and one the vertical.
Cladistics for example, does not acknowledge the vertical dimension and tries to collapse everything into the horizontal line of time. This can never be successful of course.
The Linnaean conception acknowledges the vertical dimension but not the horizontal dimension.
Both dimensions must be acknowledged because REALITY is in two dimensions.
It is only when we acknowledge both dimensions that we will understand the underlying reality.
For what it is worth, the closest we come now, is the conception of serial anagenesis with parallel evolution. That is the model I use in the pterosaur to bird theory.
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