The Live Science website has just published an article on Do humans and chimps really share nearly 99% of their DNA? subtitled: “The frequently cited 99% similarity between human and chimp DNA overlooks key differences in the genomes.“
This includes an email interview with a leading figure in the field, Tomas Marques-Bonet. Tomas was the final author of the 2013 Nature paper Great ape genetic diversity and population history. Since then he has published numerous papers on both ape and human genomes.
The Live Science article reports:
But the 99% figure is misleading because it focuses on stretches of DNA where the human and chimp genomes can be directly aligned and ignores sections of the genomes that are difficult to compare, Tomas Marques-Bonet, head of the Comparative Genomics group at the Institute of Evolutionary Biology (CSIC/UPF) in Barcelona, Spain, told Live Science in an email.
Sections of human DNA without a clear counterpart in chimp DNA make up approximately 15% to 20% of the genome, Marques-Bonet said. For example, some bits of DNA are present in one species but missing in the other; these are known as “insertions and deletions.” In the course of evolution from a common ancestor, some pieces of DNA in one species broke off and reattached elsewhere along the chromosome.
So, while earlier studies suggested a 98% to 99% similarity, comparisons that include harder-to-align regions push that difference closer to 5% to 10%, Marques-Bonet said. “And if we account for the regions still too complex to align properly with current technology, the true overall difference is likely to exceed 10%,” he said.
In fact, a 2025 study found that human and chimpanzee genomes are approximately 15% different when compared directly and completely. But if this direct method is used, then there is even a lot of variability within species themselves — up to 9% among chimpanzees, the 2025 study found.”
Another article reporting Tomas Marques-Bonet’s comments can be found on primatology.net.
For more on the 2025 study, see my earlier blog post here.