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Geneticist: On Human-Chimp Genome Similarity, There Are “Predictions” Not “Established Fact”

David Klinghoffer | @d_klinghoffer

Claims floating around the Internet about the similarity of human and chimp genomes are curiously exact yet inconsistent.

  • “What Does it Really Mean to Be 99 Percent Chimp?” (Smithsonian.com)
  • “We share more than 98% of our DNA and almost all of our genes with our closest living relative, the chimpanzee.” (Nature)
  • “[A]bout 99 percent of our DNA is identical to that of chimpanzees.” (Kevin Williamson, National Review)
  • “Most studies indicate that when genomic regions are compared between chimpanzees and humans, they share about 98.5 percent sequence identity.” (Scientific American)
  • “Humans and chimps share a surprising 98.8 percent of their DNA.” (American Museum of Natural History)
  • “[H]umans share about 99% of our DNA with chimpanzees, making them our closest living relatives.” (Science)
  • “Chimps, Humans 96 Percent the Same, Gene Study Finds.” (National Geographic News)

Geneticist Richard Buggs at Queen Mary University of London, whom we’ve met before, conducted an extensive conversation about the question over at the BioLogos message board. When last seen, in the same arena, Buggs had driven theistic evolutionist Dennis Venema to back down from a claim in his book Adam and the Genome against an originating human pair.

A “Bit Pedantic”?

At one point, Buggs turned the focus on Venema’s own statement in his book that “our entire genomes are either around 95 per cent or 98 per cent identical depending on how one counts the effects of deletions of small blocks of DNA.” He asked Venema to “substantiate his claim,” leading to a complaint from Dennis that Buggs was being a “bit pedantic” and a comical disquisition by Venema on the meaning of the word “entire.”

The discussion extends to 133 posts and it gets quite complicated and technical. And that, I think, is the point. Buggs has reproduced his final post and summary at his website. He writes:

I recently participated in a discussion on the BioLogos forum on the degree of similarity between the human and chimpanzee genomes. I was asked for my current view on this issue by Dennis Venema, who had found an old quote online from a newspaper article that I had written in 2008 on this issue. In 2008, in a couple of newspaper articles, I did some simple calculations based on the 2005 Chimpanzee genome paper. On the basis of these, I had come to the surprising conclusion that these data suggested that the human and chimpanzee genomes in their entirety could be only 70% identical. Dennis Venema asked me if this was still my view. You can read the whole discussion here. It is rather long, with lots of tangential contributions. 

I encourage you to read the entire post. 

Inside the Sausage Factory

Buggs gives us a look inside the sausage factory where figures on the subject are calculated. Seeking the “most accurate current assessment,” here is how Buggs himself would do some of the math:

To come up with the most accurate current assessment that I could of the similarity of the human and chimpanzee genome, I downloaded from the UCSC genomics website the latest alignments (made using the LASTZ software) between the human and chimpanzee genome assemblies, hg38 and pantro6. See discussion post #35 for details. This gave the following for the human genome:

4.06% had no alignment to the chimp assembly
5.18% was in CNVs relative to chimp
1.12% differed due to SNPs in the one-to-one best aligned regions
0.28% differed due to indels within the one-to-one best aligned regions

The percentage of nucleotides in the human genome that had one-to-one exact matches in the chimpanzee genome was 84.38%

In order to assess how improvements in genome assemblies can change these figures, I did the same analyses on the alignment of the older PanTro4 assembly against Hg38 (see discussion post #40). The Pantro4 assembly was based on a much smaller amount of sequencing than the Pantro6 assembly (see discussion post #39). In this Pantro4 alignment:

6.29% had no alignment to the chimp assembly
5.01% was in CNVs relative to chimp
1.11% differed due to SNPs in the one-to-one best aligned regions
0.28% differed due to indels within the one-to-one best aligned regions

The percentage of nucleotides in the human genome that had one-to-one exact matches in the chimpanzee genome was 82.34%.

While rejecting the prediction he himself made in 2008, based on the 2005 paper, he now gives his bottom line:

As 5% of the human genome is still unassembled, and 5% seems to be CNVs relative to chimp, and 4% is unaligned to the chimp genome, I cannot agree with Dennis Venema [here] and Steve Schaffner [here] that “95% is the best estimate we have for the genome-wide identity of chimps and humans”. I would accept 95% as a prediction, but not as a statement of established fact.

I predict that the 95% figure will prove to be wrong, because (on the basis of my comparison of the PanTro4 and PanTro6 alignments to Hg38) I think that the CNV differences are here to stay, and I doubt that all of the currently unaligned or unsequenced regions of the human genome will prove to all be 95% the same as the chimpanzee genome. Some of the “unaligned” human sequences are medium-sized indels, and it is hard to see why they would not have been assembled in the chimp if they were present. I also expect at least some of these unaligned or unsequenced sequences to be rapidly evolving.

In short, despite the impression you’d get from a Google search on the topic, there is not as yet an “established fact” quantifying human-chimp genomic similarity.

How High?

Based on undoubted physiological similarities alone, whether due to common descent or common design, anyone wandering in off the street would naturally expect the percentage to be high. But how high? There are predictions, but with the data still incomplete, no known “fact.” 

Glib statements in the media, including the science media, including by scientists themselves, should be regarded with skepticism, not least the patently absurd claim that we are “99 percent chimp.” (Yes, you can get a t-shirt with that emblazoned on it.) But why do you think the media and many scientists insist on leading the public to think the question is simpler than it really is? That’s an interesting question, not one that genetics can answer.

Photo credit: Republica, via Pixabay.