quote:
Similarity, either in the phenotype or the genotype, does not prove relationship unfortunately.
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Though it's one of the many strands of evidence that do, collectively, prove exactly that.
Some of the genotypic similarities are in themselves strong evidence of relationship - particularly elements that are non-functional such as ERVs, LINES, and pseudogenes.
Likewise similarities in genotype between creatures with strongly different phenotypes is very good evidence of relationship - when supported by fossils that show intermediates between them.
In the theropod / bird case, we don't have access to genetic data about theropods, but we do for birds, and they show the existence of pseudogenes, for example, for teeth. Here's info on some research on a mutant chicken with teeth.
Surprise: Chickens Can Grow Teeth | Live Science
We also have a wide variety of intermediates between the birds of today and their ancestors, most discovered quite recently. It's clear that feathers evolved first, in flightless dinosaurs, and were then co-opted for flight. There are intermediate feather types in the fossil record which have a simpler structure then feathers now.
Here's a nice link on feather evolution.
Feather evolution
This link makes clear that feathers are unlikely to have evolved from scales - so I think you're right about that (although this article is not primary literature).
Edited by Peepul, : mis-spelling of theropod