27 differences between Homo Sapiens and Neanderthal — what does this mean for DNA ID?

Factual Questions
1

I watched a television documentary, “Humans: Who Are We?”.

Discussing the comparison between the DNA of homo sapiens and homo neanderthalis and whether one could have descended from the other, Dr. Lynn Jorde (he’s male despite the name), a geneticist at the University of Utah, said: “For human versus Neanderthal, there were 27 differences, many more than what we usually find when we compare modern humans to one another. This argues that Neanderthals and anatomically modern humans are really quite distinct.”

My question has to do with identification by DNA analysis. If there are indeed far fewer DNA differences than 27 among all living humans, how can there be enough combinations to establish to a statistical certainty that Mr. Smith was the one who had to rape Ms. Jones? Or are permutations all that are needed, i.e., the set {A, B, C} would not match the set {A, C, B}?

2

These differences were all inside a single, tiny (387 base pair) piece of mitochondrial DNA. If the researchers had had a bigger piece of DNA to work with, they’d certainly have found more than 27 differences.

3

Thanks, Squink. That would explain it. It is possible that Dr. Jorde had mentioned that but editors cut it.

4

But it’s not at all clear if the ratio of the differences would be higher or lower. That’s what matters in determining the relative relatedness of Sapiens and Neanderthals. Althought that’s not what the OP is asking, it’s possible that someone could misread your explanation to mean that the data presented underestimates the relatedness of the two populations.

5

Yes, I tried to avoid giving that impression. Of course the only way to find the actual percentage difference would be to compare much larger pieces of the genomes. Those aren’t available, so we’re stuck with what we have.