I understand what you are saying about genome sequencing and mapping. However, there are other factors involved, that alter genes, so what is inferred from the sequencing, is still assumed.
You're not making sense.
The nested hierarchy is produced by reproduction and the way DNA is inherited.
Whatever is altering genes, these alterations are inherited by off spring.
You can of course, sequence the genes within a "species", and find a greater deal of similarities, but to assume that because organisms, or "species" may have a close match, that they must be related, is only based on the presumption that they are.
No. It is based on the knowledge of how DNA and reproduction works.
The patterns we
observe - not "imagine" or "superimpose" or "assume"), but the patterns we
OBSERVE - are the exact patterns that would be produced by the process of evolution.
It's what inevitably happens when you have systems that reproduce with modification and pass on those modifications to off spring.
It accounts for all the known facts and it's explanatory power allows us to accurately predict new facts (like the finding of tiktaalik - and many many many other things).
It's not a "presumption". It is, instead, the
only reasonable and rational account for the data we have and continue to discover, with NOTHING to contradict it. And MANY things could potentially contradict it.
A single creature that rapes the pattern of nested hierarchy would actually suffice. Evolution would be put on its head.
If we take away that supposition, that assumption varnishes, and we have creatures that - in all cases - have DNA, which are affected through mutations, and other factors, which alter their genes.
As explained, not an assumption at all.
Regarding the fruit flies experiment...
Evidence for speciation
Diane Dodd examined the effects of geographic isolation and selection on fruit flies. She took fruit flies from a single population and divided them into separate populations living in different cages to simulate geographic isolation.
Nice. That's quite different from "demonstrating the whole of evolution", now isn't it?
So what were the results and conclusions? Do you know?