To preface, I am by no means an expert, just a curious person who is interested in anthropology. When I read this I first thought of the fact that 98.8% of Chimpanzee and human DNA is same, and yet we are different species with some very large differences from just 1.2% differences. So .5% could lead to a large variation within the species.

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Although humans and chimps have many identical genes, they often use them in different ways. A gene's activity, or expression, can be turned up or down like the volume on a radio. So the same gene can be turned up high in humans, but very low in chimps.

DNA: Comparing Humans and Chimps

I think that to a casual observer, DNA seems absolute, like a math problem 2+2=4, when it is not quite as straight forward as that. It is more like a poem where interpretation can change the meaning. What genes are turned on or off, or which ones are 'stronger' affect the end result.