Stephen W. Schaeffer (Professor Emeritus of Biology) claims that the theory of common descent has proven useful in identifying so-called conserved sequences in human DNA (if "conserved", such sequences are understood to serve a functional purpose ... as opposed to so-called junk DNA, which is generally understood to serve no functional purpose).
My understanding is that process involves comparing human and chimps DNA, then finding similar DNA sequences, which are alleged (according to the theory of common descent) to have been "conserved" by natural selection from a common ancestor.
But it seems debatable to me if identifying conserved sequences has actually proven fruitful in curing or improving the treatment of any disease.
Conserved sequences aren't just compared with chimpanzees and other primates, we see them in comparisons throughout the rest of life. Here's a paper comparing the genomes of humans and pufferfish, which found "nearly 1,400 highly conserved non-coding sequences".
Highly Conserved Non-Coding Sequences Are Associated with Vertebrate Development - PMC
In addition to protein coding sequence, the human genome contains a significant amount of regulatory DNA, the identification of which is proving somewhat recalcitrant to both in silico and functional methods. An approach that has been used with some ...

What's really cool is that despite last sharing a common ancestor about 450 million years ago, the comparison found that: "Without exception, all reported examples of non-coding conservation between these two species have been associated with genes that play critical roles in development." Which suggests that purifying negative selection is at play here (and has been for a very, very long time).
Here's another paper that shows humans have around 500 'ultraconserved' elements in common with the rat and mouse genomes. Ultraconserved meaning regions of at least 200 contiguous nucleotides that are perfectly conserved between the genomes.
Perfect and imperfect views of ultraconserved sequences - PMC
Across the human genome, there are nearly 500 ‘ultraconserved’ elements: regions of at least 200 contiguous nucleotides that are perfectly conserved in both the mouse and rat genomes. Remarkably, the majority of these sequences are non-coding, and ...

What's fascinating is that there are still lots of unanswered questions about these 'ultraconserved' regions. We know that a majority of these regions play critical roles in regulating gene expression that is responsible for the development/growth of an organism - yet, when deleted half of them don't actually seem to have no impact on an organism's "viability, fertility, or fecundity". Why?
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