[Interesting Times]

As they test more markers on the Y chromosome, they should be able to establish a DNA profile (haplotype) that can show with a stated level of confidence how many generations back to the most recent common ancestor.

That may be how they calculated this:

They estimate that modern humans and Neanderthals split from a common ancestor at least 370,000 years ago, and possibly 500,000 years ago, although we share 99.95 percent of our DNA.

[zot]

I'm not sure they have sequenced enough Y-DNA to support the statement that we share 99.95 percent of our DNA. To prove that percent would take 100 percent sequencing of both human and Neanderthal DNA.