Are human populations 99.9% identical?

How a correct finding has been incorrectly interpreted.

Written by Peter Frost.

You’ve probably heard that humans and chimpanzees are genetically 98 to 99% the same. You’ve probably also heard that human populations are 99.9% the same. The second finding has often been cited, for example by Hillary Clinton. In a speech to high school graduates, the former First Lady mentioned “genetic research that shows humans are 99.9 percent the same”.

The differences in how we look — in our skin color, our eye color, our height — stem from just one-tenth of 1 percent of our genes. And the differences among us — our cultures, our religious beliefs, the music we like — it is all so small a distinction in our sea of common humanity.

Of course, one tenth of one percent is still a lot. In a post criticizing Clinton’s speech, anthropologist John Hawks observed that “one-tenth of 1 percent of 3 billion is a heck of a large number — 3 million nucleotide differences between two random genomes” (Hawks, 2007). He added, “We differ by one-tenth of 1 percent of nucleotides, this is enough to make coding differences in a large fraction of our genes.”

In other words, the 0.1% figure is not the percentage of genes that are different. It’s the percentage of individual nucleotides that are different. A single gene is a long chain of nucleotides, often a very long one, and a single nucleotide mutation can significantly alter how the entire gene works. In theory, then, each and every human gene could work differently from one population to another.

Moreover, as Hawks himself showed in a study published the same year, at least 7% of the human genome has changed over the last 40,000 years — mostly the last 10,000 (Hawks et al., 2007). This was when our ancestors were spreading over the globe and differentiating into today’s geographic populations. Those populations cannot all share the same 7% change.

Clearly, 0.1% isn’t the fraction of genes that differ among human populations. The true figure is certainly larger. Again, each and every gene could differ among human populations by 0.1%, and such a difference could affect how each and every one functions. Also, genes do not differ solely in nucleotide sequences. They also differ in the way those sequences are arranged on the chromosomes. The same sequence may be repeated consecutively or it may be copied and inserted somewhere else. Such rearrangements can likewise affect how a gene functions. “Structural variations, such as copy-number variation and deletions, inversions, insertions and duplications, account for much more human genetic variation than single nucleotide diversity” (Wikipedia, 2025).

This structural variation became apparent during the first complete sequencing of a human genome:

Of the 4.1 million variations between chromosome sets, 3.2 million were SNPs, while nearly one million were other kinds of variants, such as insertion/deletions (“indels”), copy number variants, block substitutions, and segmental duplications. While the SNPs outnumbered the non-SNP types of variants, the non-SNP variants involved a larger portion of the genome. This suggests that human-to-human variation is much greater than previously thought. (Phys.org, 2007; see also Levy et al., 2007)

If we return to comparing humans and chimpanzees, we can measure the total genetic difference between them by looking at what the genes make, i.e., proteins. The two species differ in about 80% of their proteins — a figure far higher than the 1 to 2% difference in their nucleotide sequences (Glazko et al., 2005).

Even this 80% figure is not the whole story. Some genes regulate how other genes are expressed, often thousands of others, and thus play a key role in growth and development. These “regulator” genes are much fewer in number than other genes but far greater in their effects. Plus, they differ much more between humans and chimpanzees than other genes do. Whereas the two species are almost identical in the nucleotide sequences of their genes and the amino acid sequences of their proteins, and relatively similar in the proteins that make up their tissues, they differ radically in the way their tissues grow and develop, notably the neural tissues of the brain.

This was already clear to two researchers, Mary-Claire King and A.C. Wilson, when, half a century ago, they discovered the startling similarity of nucleotide sequences and amino acid sequences between humans and chimpanzees:

The molecular similarity between chimpanzees and humans is extraordinary because they differ far more than sibling species in anatomy and way of life. Although humans and chimpanzees are rather similar in the structure of the thorax and arms, they differ substantially not only in brain size but also in the anatomy of the pelvis, foot, and jaws, as well as in relative lengths of limbs and digits. Humans and chimpanzees also differ significantly in many other anatomical respects, to the extent that nearly every bone in the body of a chimpanzee is readily distinguishable in shape or size from its human counterpart. Associated with these anatomical differences there are, of course, major differences in posture, mode of locomotion, methods of procuring food, and means of communication. Because of these major differences in anatomy and way of life, biologists place the two species not just in separate genera but in separate families …

The contrasts between organismal and molecular evolution indicate that the two processes are to a large extent independent of one another. Is it possible, therefore, that species diversity results from molecular changes other than sequence differences in proteins? … According to this hypothesis, small differences in the time of activation or in the level of activity of a single gene could in principle influence considerably the systems controlling embryonic development. The organismal differences between chimpanzees and humans would then result chiefly from genetic changes in a few regulatory systems, while amino acid substitutions in general would rarely be a key factor in major adaptive shifts. (King & Wilson, 1975, pp. 113–114)

Genetic distance between humans and chimpanzees, compared to genetic distances in other taxa. (King & Wilson, 1975, p. 113)

In this context, the two researchers were thinking not only about the human-chimpanzee difference but also about the differences within our species:

[The human-chimpanzee] distance is 25 to 60 times greater than the genetic distance between human races. In fact, the genetic distance between Caucasian, Black African, and Japanese populations is less than or equal to that between morphologically and behaviorally identical populations of other species. (King & Wilson, 1975, p. 113)

The above paragraph appears in the middle of a discussion about the human-chimpanzee genetic distance, and its paradoxical smallness. In fact, the two researchers highlight this paradox right after:

However, with respect to genetic distances between species, the human-chimpanzee D value is extraordinarily small, corresponding to the genetic distance between sibling species of Drosophila or mammals. Nonsibling species within a genus … generally differ more from each other, by electrophoretic criteria, than humans and chimpanzees. The genetic distances among species from different genera are considerably larger than the human-chimpanzee genetic distance. (King & Wilson, 1975, p. 113)

How should we measure the genetic distance between two human populations? There is no easy answer because few species resemble our own. Our species is unusual in that it evolved rapidly at the very time it was splitting up into populations across different environments — not only natural environments from the equator to the arctic but also an ever-wider range of cultural environments. In fact, this entry into so many environments largely explains the concurrent rapidity of human genetic evolution. Natural selection has thus shaped human populations in highly divergent ways (Akbari et al., 2024; Cochran & Harpending, 2009; Frost, 2023a; Hawks et al., 2007; Kuijpers, et al., 2022; Libedinsky et al., 2025; Piffer & Kirkegaard, 2024; Rinaldi, 2017).

In such a situation, differences in selection contribute much more to genetic diversity between populations than to genetic diversity within populations. Keep in mind that natural selection causes a population to diversify only in certain limited cases (e.g., frequency-dependent selection). In most cases, a population is diversified by stochastic processes of little adaptive consequence, since everybody is adapting to the same environment and the same selection pressures.

We thus return to the same paradox: Fst is relatively low in our species even though human populations differ much more anatomically than do most sibling species in the animal kingdom. As Charles Darwin noted, a naturalist would consider some human groups to be “as good species as many to which he had been in the habit of affixing specific names.” The paradox exists because humans split rapidly to colonize highly divergent environments, with the result that genetic diversity between populations is much more consequential than genetic diversity within populations. We are therefore comparing apples to oranges when we calculate human Fst (Darwin, 1936 [1888], pp. 530-531; King & Wilson, 1975; Frost, 2023b).

What’s more, relatively little of our evolution has been at the level of nucleotide sequences or amino acid sequences. It has been largely at a higher level — the duplication, rearrangement and regulation of existing DNA in new ways (Yoo et al., 2025). This point came up in a recent discussion on X:

The widely cited Chimpanzee-Human 98-99% DNA similarity figures refer exclusively to nucleotide sequence similarity within alignable genomic regions, which become misleading when portrayed as the total amount of DNA shared. While this metric is important, as it highlights the strength of the evolutionary constraints within the protein-coding and non-coding sequences found in alignable regions, it ignores the structural and regulatory differences that are key for shaping the phenotypic differences between Chimpanzees and Humans. When combining these metrics, total Chimpanzee-Human DNA similarity figures drop to ~84.7% (Origins Unveiled, 2025)

Admittedly, I have no idea how the author combined these metrics.

I don’t blame Hillary Clinton for drawing the wrong conclusion from the 99.9% estimate, but I’m less forgiving toward those who have silently gone along with this fallacy while knowing better. Two decades ago, John Hawks pointed out its flaws in a post criticizing Hillary’s speech. The post remained on his website until he deleted it in 2021 — when many American academics got the memo that Hillary had been right all along… on this issue and on any other.

“Nice research lab you have there. Pity if anything happened to it.”

When academics choose the path of silence, and withhold their objections, they help create a fake consensus that ultimately brings academia into disrepute.

Peter Frost has a PhD in anthropology from Université Laval. His main research interest is the role of sexual selection in shaping highly visible human traits. Find his newsletter here.

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References

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