allmendream: "Now where is the data that says that inter-human variability is similarly 99.5%? I have heard more like 99.9%."
That 99.5% is a miscalculation.
The operative number here is "3 million bases", which should calculate to 99.9% identical DNA.
These are the same numbers as amongst modern humans.
Here is my previous post on this subject.
It references this report, from which here is the "money quote":
"Nucleotide diversity is based on single mutations called single nucleotide polymorphisms (SNPs)."The nucleotide diversity between humans is about 0.1%, which is 1 difference per 1,000 base pairs.[4][5][6]
"A difference of 1 in 1,000 nucleotides between two humans chosen at random amounts to approximately 3 million nucleotide differences since the human genome has about 3 billion nucleotides.
"Most of these SNPs are neutral but some are functional and influence phenotypic differences between humans through alleles.
"It is estimated that a total of 10 million SNPs exist in the human population of which at least 1% are functional"
In simple English: any two modern humans can differ by up to one-tenth of one percent of their 3 billion DNA base pairs, or about 3 million SNPs. Amongst the entire human population are about three-tenths of one percent (10 million SNPs) total DNA diversity.
Current estimates of Neanderthal vs. modern Human SNPs are also around 3 million.
These would not, of course, necessarily be the same 3 million differences -- excepting potentially 1% to 4% resulting from alleged interbreeding.
Naturally, you might argue that 3 million Neanderthal SNPs is way too few, the number is underestimated, it has to be higher given the time-spans involved.
Yes, you could argue that, but so far 3 million SNPs is still the number, and it makes Neanderthal DNA 99.9% -- not 99.5% -- identical to modern humans. ;-)
SNP’s are differences in genetic regions, not over the entire genome. As such, one can say based upon the supposed “miscalculation” that our GENETIC DNA is some 99.9% the same. That is not in any way a miscalculation that our GENOME DNA is only 99.5% the same.
Similarly, our GENETIC DNA is 98.5% similar to a chimpanzee, but over our entire GENOME we are some 96% similar to a chimpanzee.
It is common that people outside of science mistake the two numbers, and confuse and/or conflate the two. You are not the first to make this common mistake.
The end result of a genomic comparison puts our similarity with neanderthals at 99.5%, while any two human beings are 99.9% similar.
Exactly what one would expect if we diverged from them some 500,000 years ago, while any two human populations diverged, at most, 100,000 years ago. A 0.1% genomic DNA difference between any two modern humans is about a 0.5% genomic difference between a human and a neanderthal.