70% Chimp?

I recently wrote here on the genetic difference between humans and chimpanzees. This proved to be more controversial than I expected. Several people have emailed me to ask questions, or tell me I am wrong. Today I will revisit this topic to clarify a few things.

My major point was that we now know that the genetic difference between humans and chimps is much bigger than we once thought. Our genomes are not 99% the same as chimpanzee genomes. Just a few months ago, a top science journal said this in a news report entitled "Relative differences: The myth of 1%" (Science 316:1836).

This report highlighted a recent study showing that that 6.4% of all genes in the human genome do not have closely similar counterparts in the chimpanzee genome (Demuth et al, PLoS ONE 1: e85). It also cited the chimpanzee draft genome paper that I mentioned in my previous article (Nature 437:69-87), and stated how the authors of this study had aligned 2.4 billion bases of the human genome with the chimpanzee genome, and found a 1.23% difference in single nucleotide polymorphisms (SNPs) and a 3% difference in insertion/deletions (indels).

Given these statistics, it is factually incorrect to say that humans are 99% the same as chimpanzees. Yet, just last month, the Natural History Museum in London and the University of Chicago Press in the USA published a book entitled "99% Ape: How evolution adds up". This misleading title was doubtless chosen by a marketing guru rather than the editor, who is a reputable and distinguished scientist in plant evolutionary ecology (the field in which I did my doctoral research). Such promotion of the "myth of 1%" to the public as evidence for evolution is probably why some non-scientists have suggested on the internet that my earlier article, dispelling this myth, is somehow a death-blow to evolution - it is not. My article on chimpanzees went one simple step further than the Science report. I took the amount of the chimp genome which has been aligned with the human genome (2.4 billion bases) and divided this by the size of the human genome (3.16 billion bases), to work out that only 76% of the human genome shows the 1.23% SNP and 3% indel differences (see above). Using these figures, and citing 2.7% copy number variation between the two species (Nature 437:88-93), I argued for a total similarity of around 70%.

This is a conservative estimate of what we can be quite sure is similar. Like all estimates, it makes assumptions. The key one here is that the parts of the chimpanzee genome that did not align to the human genome are different to the human genome. In general this is obviously true - only similar sequences can be lined up - but it is possible that the complex procedure by which the scientists aligned the two genomes may have caused some similar sequences not to be included. In addition, the 4% of the chimpanzee genome that has not yet been sequenced, or portions that have not been sequenced accurately, may also prove to have some similarity to the human genome. These could raise the overall similarity by a few percent, but I predict that when we have a reliable, complete chimpanzee genome, the overall similarity of the human genome will prove to be close to 70% (and very far from 99%).

The author is a research geneticist at the University of Florida

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