Quite a bit of the DNA code is "junk", not required for the creature to survive. Mutations in the required parts of DNA tend to be weeded out of the genome because the critter may not survive with those errors, but changes in the junk DNA happen at a relatively steady rate, and are passed down and can be measured.
The "bursts of evolution" you talk about, often associated with environment changes, exploit mutations in the non-junk DNA and result in separate species.
I think this is how it works. I don't claim to be a genetic scientist.
The "junk" DNA is not junk at all. Much of it is regulatory genes and likely stuff we do not yet comprehend.