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In popular science books and articles, I often see it stated that humans are >99 % similar to each other (wikipedia has it a 99.5 %, referencing Craig Venter and this PLOS Biology article) and ~96-99 % similar to chimpanzees or bonobos (Smithsonian Institute, National geographic). I have previously thought that this referred to the entire genome, but the wording on the Smithsonian Institute page I linked, makes it appear that it might refer to genes only, which also seems to be the case according to the answers to this post Do apes and humans share 99% of DNA or 99% of genes? What is the difference?.

How big are these percentages when comparing only the coding regions (exons) instead of entire genes, both within our species and compared to other species, such as primates? And, not as importantly, what are these numbers when including the entire genome with all non-coding DNA?

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One of the references to the chimpanzee genome paper linked by Maximillian is Inferring Nonneutral Evolution from Human-Chimp-Mouse Orthologous Gene Trios, where the authors seems to have focused on exons only:

Here we apply evolutionary tests to identify genes and pathways from a new collection of more than 200,000 chimpanzee exonic sequences that show patterns of divergence consistent with natural selection along the human and chimpanzee lineages.

They conclude that:

Perhaps the best way to understand the relation between DNA sequence divergence and the differences between human and chimpanzee physiology and morphology is to compare these differences to the variability among humans. Human-chimp DNA sequence divergence is roughly 10 times the divergence between random pairs of humans.

Unfortunately, they didn't compare this to the fold-difference of non-exonic DNA, so the comparative quantification between coding vs non-coding regions remains to be determined.

However, this does directly answer the question of how big the genomic differences are between individuals of the same species vs those of other species, when comparing only coding regions. I also found it useful to quantify the differences in these relative terms in addition to the previously stated percentages.

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This paper seems to have relevant estimates for human-ape divergences. Note again that it isn't using the entire genome, but selected regions of exons, introns, pseudogenes, etc. The chimpanzee genome paper has a nice bullet-point list towards the beginning of relevant statistics for you for that species specifically, that is on the order of 1% overall. The section on "gene evolution" has some specific numbers for coding sequences.

For among-human variation, there is a bionumbers page on that subject based on 1000 genomes project numbers, that comes out at 0.1% divergence among humans.

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  • $\begingroup$ Correct me if I missed something (didn't read the entire paper), but doesn't the first paper you linked specifically not use coding regions? From the abstract: "...we selected 53 autosomal intergenic nonrepetitive DNA segments..." $\endgroup$
    – joelostblom
    Commented Mar 28, 2017 at 0:46
  • $\begingroup$ The chimpanzee genome paper states: "When CpG and non-CpG sites are considered separately, we find that both CpG sites and non-CpG sites show markedly lower divergence in exonic synonymous sites than in introns (~50% and ~30% lower, respectively)." To me this indicates that the interspecies differences within exonic regions would be smaller than within intronic regions... $\endgroup$
    – joelostblom
    Commented Mar 28, 2017 at 0:52
  • $\begingroup$ ...My understanding is that this is due to the survival constraints put on exonic regions, i.e. some exonic mutations kills the organism and will not be passed on to the offspring, while mutations in non-exonic regions don't impact survival to the same extent. This is not my area of expertise though, so I am happy to hear if I have misinterpreted something. $\endgroup$
    – joelostblom
    Commented Mar 28, 2017 at 0:53
  • $\begingroup$ First comment: note that Table 5 of the first paper compares coding region distances. Again, probably not the best example because it's only selected regions; but in my experience these estimates tend not to change that dramatically with sample size. $\endgroup$
    – Maximilian Press
    Commented Mar 29, 2017 at 1:19
  • $\begingroup$ Comments 2+3: You are correct that the mechanism for the lower rate of divergence in exons is due to selection. Indeed, the inference of functionally important chunks of sequence by comparative analysis depends on this; see for instance compgen.cshl.edu/~acs/phylohmm.pdf. But that didn't seem to be part of the original question. There is a very large literature on this subject, but for a concise review by a well-known author you could look at sciencedirect.com/science/article/pii/S0959437X02003489. Note that among-site variation in divergence is also important in proteins. $\endgroup$
    – Maximilian Press
    Commented Mar 29, 2017 at 1:28

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