John Hawks
Sep 1, 2018 · 1 min read

I appreciate your concern for the measure of genetic similarity, and the relatively larger difference between Neanderthals (for example) and modern people than between living humans today. You are correct that the measure of nucleotide difference between living people is only 0.1%.

However, it is important to put that measure into a temporal context, because without time the value is meaningless. The mutation rate per nucleotide per generation in human genomes is approximately 1.1*10e-8. A difference of 0.001 (that is, 0.1%) between homologous sequences implies that those sequences last shared a common ancestor on average 45,000 generations ago, which is on the order of a million years.

That is to say, the average difference between people’s genes reflects a million years of diversification within ancestral populations of humans. The genes within humanity began diversifying long before the Neandertals existed, much less before they became extinct. This is why a large fraction of Neanderthal alleles found in today’s people have actually resulted from incomplete lineage sorting rather than introgression.

In other words, 99.9 percent similarity sounds very impressive until you see that it must actually reflect very deep divergence within ancestral humans. Some of that divergence today in fact comes from the Neanderthal branch, and other African branches, which merged into the modern human population after some long separation.

Whether a river delta and braided stream make sense as analogies for this situation depends in large part on your attitude about the Atchafalaya River and its contribution to the Mississippi Delta.

    John Hawks

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    Paleoanthropologist. I study human evolution and work to understand the fossil and genetic evidence of our hominin ancestors.