Since posting our recent series on human-chimp genetic differences (see here), we’ve received multiple supportive comments from biologists. One biologist in particular kindly led me to a section of the Supplementary Data from the new Nature paper by Yoo et al. (2025) which I had not previously seen. This section uses a different method of comparing the genomes using a software package called Progressive Cactus, and it turns out that this method indicates a human-chimp percent genetic difference very similar to what we previously reported. 

As we’ve been explaining, this groundbreaking new paper in Nature has reported data showing that there is a 14.0 percent to 14.9 percent difference between the human and chimp genomes — far greater than the 1 percent difference statistic we’re commonly told about. We calculated those numbers by summing the “gap divergence” and “single nucleotide variations,” and noted that the 14.9 percent value was most relevant because it represented how much of the human genome is different from the chimp genome. (A significant portion of those differences represent repetitive DNA, but we have strong reasons to believe that this repetitive DNA performs important functions.)

As I have now realized, the authors also used this Progressive Cactus alignment method to compare haploid (i.e., the set of single, unpaired chromosomes) autosomes (i.e., non-sex chromosomes) between humans and apes, and performed a diploid (i.e., complete set of paired chromosomes) autosomal comparison of the same. The autosomal comparisons of course look at the similarities and differences across the vast majority of the genome — i.e., the entire genome minus the sex chromosomes. But then they also used the Progressive Cactus method to compare just the X and Y sex chromosomes in humans to the X and Y chromosomes in apes. 

Comparison of Non-Sex Chromosomes

To cut to the chase, under the haploid autosomal alignment, only 91.47 percent of the chimp genome could be aligned with human — and more importantly only 84.95 percent of the nucleotides in the chimp genome had an identical 1:1 correspondence with the human genome. So that is basically a haploid genomic difference of 15.05 percent between humans and chimps. 

And when they did the diploid alignment analysis — looking at the full set of autosomal chromosomes in the genomes — the percent difference between humans and chimps grew to 16.11 percent, because only 83.89 percent of nucleotides in the diploid autosomal chimp genome showed an identical 1:1 correspondence to the human genome. 

These results are very similar to the aforementioned ~14.9% genetic difference between humans and chimps calculated by adding the gap divergence and short nucleotide variations. When different methods yield a similar result, this gives you confidence that your numbers are correct.

Let’s Talk about Sex Chromosomes

So far we’ve been talking here about comparisons of autosomes. What about the x and y sex chromosomes? Under this Progressive Cactus alignment (diploid), only 79.88 percent of nucleotides in the chimp X chromosome showed a 1:1 correspondence with the human X chromosome. That amounts to a difference of 20.12 percent! 

But the differences between human and chimp Y chromosomes dwarfed all the other differences. Under this method (again, diploid), their alignment reported that only 4.32 percent of nucleotides in the chimp Y chromosome had a 1:1 correspondence with the human Y chromosome. That’s not a typo — that’s a difference of 95.68 percent!

It’s been long known that the human and chimp Y chromosomes are very different, so this isn’t entirely surprising. But I’ve never seen differences this large reported before. It’s safe to say that the human and chimp Y chromosomes are exceedingly different. 

Again, Buried in the Supplementary Data

Once again, all of these fascinating findings were buried deep in the 174-page-long Supplementary Data. I had to scroll through pages of incomprehensible computer code and opaque technical jargon to find Supplementary Data Tables III.19 and III.20 which reported this data. 

It’s not unusual for Supplementary Data files to be filled with hard-to-read technical material, so it’s not surprising that this was difficult to interpret. But all of this again raises the question: Why couldn’t they state these groundbreaking findings clearly and plainly in the technical paper and/or an explainer article for the public and general scientific community to find?

We should not be the ones breaking this story that is so important on scientific, philosophical, and cultural grounds. But we had to do so because Nature, for some reason, did not. 

More Work Remains to Be Done

The bottom line is that this paper confirms that under multiple methods of genomic analysis, human and chimp genomic differences come out to about 15 percent, and when multiple methods come to the same result, you can reasonably believe you’re on to something correct. But keep in mind that this number is only looking at the non-sex chromosomes. When you look at the sex chromosomes, the differences seem to be even greater.

Additionally, the Progressive Cactus alignment reported in the Supplementary Data always used the human genome as the target and the chimp as the query, meaning that it only asked how much of the chimp genome matched up to the human, and did not report how much of the human genome is similar to the chimp. In the genome comparison numbers we previously reported based upon this paper, human genome differences from ape genomes tended to be a little higher than ape differences from human. It would be fascinating to see what percentage of the human genome is similar to chimp under this technique, and presumably some scientist will want to publish such an analysis. The differences might turn out to be even greater. 

One hopes that, whenever such an analysis is done, the results will be stated clearly for the public, rather than hidden in opaque jargon deep in the Supplemental Data section of a technical paper.