Strange (imaginary) type of scenario in evolution

The following is an imagined scenario which may or may not have a real life analogue:

Suppose three species:

A, B, and C. B came from A. C came from B. A and C possesses trichromatic vision. B possesses bichromatic vision. The switch from bichromatic vision to trichromatic vision occurs via one substitution. Going from trichromatic vision to bichromatic vision occurs via one subsitution (basically the same substitution, but in reverse). A is exitinct and left no traces because, for some reason, it was not fossilized. It is also a herbivore. Only B and C are known by scientists (B has been known for a long time, but C is a recent appearance, and is known to not have an existence preceding B's appearance). One might say that C evolved from B, which is correct. But does this mean that it possesses a completely new gene? Suppose in this scenario that A, B, and C live on an alien planet just beginning its evolution, and we are visitors. Suppose we search the whole planet and undig all the fossils avaliable at this early stage of the planet's history and the only evidence for trichromatic vision among the alien species was found in species C. In this scenario, could we know that trichromatic vision appeared in C first? But if it appeared in A first, then it is not possible for it to have appeared in C first. Of course, A is unobservable, since none of A were fossilized. What if A wasn't the only species that wasn't fossilized. Then there may have been many scenarios like this occuring for species involving characteristics other than vision. But we could never prove this, because extinct species such as A which haven't been fossilized are not observable. On this hypothetical planet, there is at least one occurrence that causes us to misinterpret an evolutionary change as being first when it was actually not the first time it happened. B must have at one point had some kind of advantage over A. Perhaps part of A migrated where it would develop into B via a substitution. The part of A which was left behind was pulverized by an unknown event, and thereby no traces of it were left. Suppose that, later on, after we came to this planet, we observed that some of B migrated to a place. Unknown to us, this place used to be the home of A.

If we jump to the most likely conclusion, then we have been fooled. C was not the first to have trichromatic vision, A was.

Suppose that one of our problems concerns where B came from, and we think we have found the answer, another species called D which was found nearby. Perhaps A evolved from D. Of course, we don't have to know A to explain the existence of B provided that D explains the existence of B. Suppose that D is closely related to B. Suppose that D did evolve from A, also due to some unknown event, but evidence for A does not exist. We can't know A, A was never fossilized. But say we have in the fossil records that D came before B. Our most likely choice for the origin of B would therefore be D. The origin of C would be also be linked to D. Suppose that D was bichromatic and different from both B and C. C obivously came after B since we observed it come from B. However in the second sentence it was noted that "B came from A". This would imply that we were wrong (although we would never know we were wrong since A wasn't preserved).

The End?
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