When you are stuck across the table from the local evolution bore:
The old statistic that we are about 99 percent or 98 percent similar to chimps pertains only to alignable protein-coding sequences. In fact the statistic first originated based upon similarity between humans and chimps in just one single gene! But many non-coding sequences are highly dissimilar, and there are sequences of the human and chimp genomes that are so different that they can’t be aligned for comparison. For example, there are some parts of our genome, such as the human y chromosome, that are radically different from the chimp genome.
Geneticist Richard Buggs has tried to refine the methods for comparing human and chimp genomes. In a 2018 post, he observes that “The percentage of nucleotides in the human genome that had one-to-one exact matches in the chimpanzee genome was 84.38%.” In 2020 he co-published an article in the journal Frontiers in Genetics providing a different method of estimating of human-chimp genetic differences, finding that human-chimp genetic similarity is about 96 percent. This paper’s estimate of ~4 percent genetic difference includes both coding and non-coding DNA, but it does not include centromeric DNA. If that DNA were included, the percent of genetic similarity between humans and chimps could drop to as low as ~93 percent, but probably not lower. Computational biologist Steve Schaffner has roughly estimated human-chimp genetic similarity to be ~95 percent. However, one criticism I’ve heard of all current estimates is that they are based upon versions of the chimp genome that used the human genome as a “scaffolding,” potentially making certain sections of the chimp genome more humanlike than they ought to be. This could also artificially inflate the degree of human-chimp similarity.
What this means is that until more accurate and complete versions of the chimp genome are produced, any estimate of human-chimp genetic similarity will undoubtedly be refined in the future, and current numbers may very well be overestimates. Nonetheless, any of the above estimates of human-chimp genetic similarity — 96 percent, 95 percent, 93 percent, 84 percent — carries meaning in different contexts. But what exactly do they mean?Casey Luskin, “Human-Chimp Similarity: What Is It and What Does It Mean?” at Evolution News and Science Today (October 20, 2021)
You may also wish to read: But, in the end, did the chimpanzee really talk? A recent article in the Smithsonian Magazine sheds light on the motivations behind the need to see bonobos as something like an oppressed people, rather than apes in need of protection.