Fact Check: New “Complete” Chimp Genome Shows 14.9 Percent Difference from Human Genome
May 21,
2025, 6:20 AM
https://evolutionnews.org/2025/05/fact-check-new-complete-chimp-genome-shows-14-9-percent-difference-from-human-genome/
A
groundbreaking paper in Nature reports the “Complete sequencing
of ape genomes,” including the genomes for chimpanzees, bonobos, gorillas,
Bornean orangutans, Sumatran orangutans, and siamangs. I noted this in an article
here yesterday, reporting that an evolutionary icon — the famous “1 percent
difference” between the human and chimp genomes, touted across the breadth of
popular and other scientific writing and teaching — has fallen. The
researchers, for whatever reason — I’m not a mind reader — chose to bury that
remarkable finding in technical jargon in their Supplementary Data section. Now
for more on the scientific details.
You might
be thinking, “Hey, weren’t these genomes sequenced long ago?” The answer is yes
but also no. Yes, we had sequenced genomes from these species in the past, but,
as the paper explains, “owing to the repetitive nature of ape genomes, complete
assemblies have not been achieved. Current references lack sequence resolution
of some of the most dynamic genomic regions, including regions corresponding to
lineage-specific gene families.”
Or, as an
accompanying explainer
article puts it:
In the
past, scientists had deciphered segments of non-human apes’ genomes, but they
had never managed to assemble a complete sequence for any species. In the
current study, however, [Kateryna] Makova and her collaborators used advanced
sequencing techniques and algorithms that allowed them to read long segments of
DNA and assemble them into a sequence that stretched from one end of each
chromosome to the other, without any gaps. “This has never been done before,”
says Makova.
In other
words, the complete ape genomes were never fully sequenced. And they used the
human genome as a reference sequence, which made the ape genomes look more
human-like than they actually were.
You Don’t
Believe Me?
From the
technical paper:
Most
previous genome-wide comparative studies of apes have been limited by the
mapping of inferior assemblies to a higher quality human genome. Consequently,
human reference biases were introduced.
This is
consistent with what the National Center for Biotechnology Information said
in 2007 about an early draft of the chimp genome:
Contigs
were assembled using the human genome as a guide, and are therefore “humanized”
in their construction. This is an important distinction, as some sequences,
such as insertions, deletions, and gene duplications, may not be accurately
represented by the current chimpanzee assembly.
Thus, up
until now, most versions of the chimp and other ape genomes were effectively
“humanized” because they were “assembled using the human genome as a guide.”
This effectively makes them appear more similar to the human genome than they
truly are. Can these new drafts of ape genomes help fix the problem?
Problem
Solved?
Another explainer article
in Nature seems to suggest that these “complete” drafts of
the ape genomes will prove that they are less similar to the human genome than
has been claimed:
Shortly
after the first human genome sequence was finalized in 2003, a chimpanzee
assembly was released. This was followed by assemblies for other great apes,
such as the gorilla, Sumatran orangutan and bonobo, and small apes that are
less closely related to humans than are great apes. These genomes offered a
valuable opportunity to catalogue the genetic differences that have accumulated
during the evolution of apes, including changes that are unique to humans. But,
because these initial releases were incomplete drafts, comparisons could be
made only between properly resolved portions of the genome. These studies
therefore focused only on relatively small differences, and excluded extremely
repetitive sequences and large-scale structural differences, such as inversions
and duplications of genomic sequences. [Emphasis added.]
That last
sentence seems to hint that previous comparisons between human and ape genomes
“only focused on relatively small differences” and “excluded” the sections that
entail “large-scale structural differences.” The explainer article notes that
this study has “fully sequenced the genomes of six living ape species, enabling
long-awaited comparisons of hard-to-assemble genomic regions.” Thus, one could
expect that these newly “complete” ape genomes would reveal much greater
differences compared to the human genome.
The New
Ape Genomes and the Human Genome
What’s
odd is that as one reads the technical paper, a direct comparison between the
ape and the human genomes is hard to find. This passage seems to be as close as
it gets:
Overall,
sequence comparisons among the complete ape genomes revealed greater divergence
than previously estimated (Supplementary Notes III–IV). Indeed, 12.5–27.3% of
an ape genome failed to align or was inconsistent with a simple one-to-one
alignment, thereby introducing gaps.
What
exactly does this mean? Well, first they admit that “sequence comparisons among
the complete ape genomes revealed greater divergence than previously
estimated.” But the technical Nature paper considers human
beings to be an “ape,” so implicit in this statement is their belief that
comparing “ape genomes” includes comparisons between human and ape (i.e.,
non-human hominoid)
genomes. So for the rest of this article, I’ll call humans “humans” and I’ll
refer to non-human hominoids as “apes,” just like most normal people
do.
Interestingly,
two preprints of the paper (v1 and v2)
published last year on BioRxiv (which are presumably the
versions of the manuscript submitted to Nature initially and
after one round of revisions) preface this result with these two sentences:
The
oft-quoted statistic of ∼99% sequence identity between
chimpanzee and human holds for most of the genome when considering
single-nucleotide variants (SNVs). However, comparisons of T2T genomes suggest
a much more nuanced estimate.
T2T means
examining “telomere to telomere” — i.e., examining the entire chromosomes
throughout the genome. These sentences were evidently removed during revisions
for the published version in Nature — an interesting editorial
decision. So what is the paper saying about the difference between humans and
chimpanzees?
As we’ll
see, the statement above — that “sequence comparisons among the complete ape
genomes revealed greater divergence than previously estimated” — is true. But
it doesn’t reveal the extent of the differences between human and ape genomes
that this study uncovered. So let me cut to the chase:
Look back
at those numbers, “12.5–27.3%.” The same numbers show up again buried deep in
the Supplemental
Data where they compare various ape to human genomes. They’re findable
if you know where to look, but should I say “buried” — or “hidden”? From what I
can tell, the Supplemental Data reports that the ape genome that is most
similar to the human genome is the chimpanzee genome. And it shows a 12.5
percent “gap-divergence” — i.e., difference — from the human genome! And when
you look at the “gap divergence” where the human genome is the target and the
chimp is the query, the difference is 13.3 percent. Let me be clear: According
to this study, the human and chimp genomes aren’t 98.8 percent the same (or 1.2
percent different) — as, for instance, the Smithsonian Institution’s National
Museum of Natural History claims (see my “Visitor’s
Guide” for more). In fact, they are no more than 87.5 percent similar —
i.e., the human and chimp genomes are at least 12.5 percent different if not
13.3 percent different! In fact, the 13.3 percent difference is more relevant
since this reflects how similar the whole human assembly is to the chimp
genome.
What
Exactly is the “Gap Divergence”
Before we
go further, I want to explore exactly what the authors mean by “gap divergence”
or “gap difference.” The paper defines the “gap divergence” as follows:
Gap
divergence is defined as the fraction of positions in the target haplotype that
are not aligned to the other haplotype, which could be due to biological
processes (e.g., gene loss/gain and insertions/deletions), missing data, or
technical problems (e.g., alignment failure due to SVs, repetitive elements,
etc.).
So how do
they determine the gap divergence? From what I can tell, it’s based upon
dividing the target genome within the genome alignment into 1 million base pair
(1 Mbp) segments and seeing how many of the bases within each 1 Mbp segment
have no aligning base within the query genome that has been aligned to it. If
the entire 1 Mbp segment has no alignment by the target genome, it has gap
divergence of 100 percent. If 10,000 bp have no alignment, it has gap
divergence of 1 percent; if 1,000 bp have no alignment, it has gap divergence
of 0.1 percent, etc. According to the study’s results, the mean gap divergence
in each 1 Mbp segment of the human genome (as target) aligned to the chimp
genome (as query) is 12.5 percent. Thus, 12.5 percent of bases in the human
genome have no aligning base in the chimpanzee genome within the whole
genome-alignment.
The
figure below — created for illustrative purposes and not from the study — helps
show the differences between “SNVs” and “Gaps” between the two genomes:
As you
can see, the Gaps represent nucleotides or segments of nucleotides that simply
don’t exist in one genome or the other, while the SNVs represent nucleotides
that do exist but are different. The two types of differences can be added up
to calculate the total difference between the genomes.
An Upper
Estimate
And why
is there a range of 12.5 percent to 27.3 percent in the main text? That’s
because the upper estimate of the non-alignability between the gorilla genome
and human genome is a whopping 27.3 percent. In fact, if we look at the
Supplementary Figure III.12, we find the following percentages of
“gap-divergence” between various ape genomes when compared to the human genome
(non-sex chromosomes):
- Sumatran orangutan (Pongo
abelii) vs human: 15.4 percent and 16.5 percent “gap-divergence”
(i.e., minimum difference)
- Gorilla (Gorilla gorilla)
vs human: 17.9 percent and 27.3 percent “gap-divergence” (i.e., minimum
difference)
- Bonobo (Pan paniscus) vs
human: 12.5 percent and 14.4 percent “gap-divergence” (i.e., minimum
difference)
- Chimpanzee (Pan troglodytes)
vs human: 12.5 percent and 13.3 percent “gap-divergence” (i.e., minimum
difference)
Do you
see how easy it is to summarize that data? These are huge findings for both
science and the wider culture, yet the technical Nature paper,
and the two Nature explainer articles, failed to clearly bring
out these points. They buried them in technical jargon and a lack of clarity
deep in the Supplemental Data, and the sentence about “The oft-quoted statistic
of ~99% sequence identity” was removed in the revisions of the paper. Nature,
I feel confident in assuring you, is not a haphazardly edited journal. These
were deliberate choices by someone during the editing process. The lack of
clarity is simply incredible.
The
Technical Details
Deep in
the Supplementary Data we find Figure III.12 which explains the gap divergence
between different species:
The
caption reads: “Plots show 1 Mbp segments binned by gap divergence for each
pairwise alignment,” where a pairwise alignment is an attempt to align two
sequences to determine their degree of similarity or difference. Thus, we’re
looking at a direct measure of the minimum degree of difference between
the two genomes.
Adding in
the Single Nucleotide Variation (SNV)
But
there’s another type of variation between genomes also identified in the paper
— single nucleotide differences (called “single nucleotide variations” or
sometimes “short nucleotide variations” or SNVs). Again, buried in the
Supplemental Data we find Figure III.11 which shows the percentage of SNVs
between human and various ape genomes reported in this study. Here’s what they
found:
- Sumatran Orangutan (Pongo
abelii) vs Human: ~3.6 percent different
- Gorilla (Gorilla gorilla)
vs Human: 1.9 percent – 2.0 percent different
- Bonobo (Pan paniscus) vs
Human: 1.5 percent – 1.6 percent different
- Chimpanzee (Pan troglodytes)
vs Human: 1.5 percent – 1.6 percent different
If we add
the gap divergence to the SNV differences, we end up with these total degrees
of difference between human and ape genomes:
- Sumatran Orangutan (Pongo
abelii) vs Human: ~19 percent – 20.1 percent different
- Gorilla (Gorilla gorilla)
vs Human: ~19.8 percent – 29.3 percent different
- Bonobo (Pan paniscus) vs
Human: ~14.0 percent – 16.0 percent different
- Chimpanzee (Pan troglodytes)
(target) vs. Human: ~14.0 percent different
- Human (target) vs. Chimpanzee (Pan
troglodytes): ~14.9 percent different
So now
what we’re seeing is that there is about a 14.9 percent total difference
between the human genome and the chimp genome. That represents a much greater
degree of difference than the often-claimed statistic that we are only 1
percent genetically different from chimpanzees!
Is This
the Final Word?
Undoubtedly
more analysis is needed to determine the extent to which nucleotides exhibit
“one-to-one exact matches” between the human and chimp genomes, even in the
regions that could be more easily aligned. So I suspect that the degree of
difference between human and chimp genomes may go up in the future.
For now,
we can safely say that this latest study shows that the human and chimp genomes
are at least 14.9 percent different. This means that the human and chimp
genomes are at least a full order of magnitude more dissimilar
than the public is typically told.
Of course
we’re talking here about the 44 non-sex chromosomes in the human genome. It’s
also worth noting that compared to chimps, the human Y chromosome has a
whopping 56.6 percent gap divergence (and 3.9 percent SNV divergence), and the
human X chromosome has 4.4 percent gap divergence (and 1.1 percent SNV
divergence). But that too is all buried in the Supplemental Data.
These are
all groundbreaking findings — and it’s a shame that Nature would
not report the data clearly and would make all of this so hard to find — using
jargon that most non-experts won’t understand. Why did they do this? It’s
important to realize that publishing scientific papers can be a bit like
sausage-making: it’s often messy, and the final form that you read usually
represents compromise language that all of the authors, reviewers, and editors
were willing to publish — and may not represent precisely how every author of a
paper feels. So perhaps some authors of this study would have preferred to
state the implications more plainly. But we can still ask, Why
didn’t Nature state the results clearly and let the chips fall
where they may?
I suspect
that this radical finding has implications — not just for science, but also for
human exceptionalism, for the reliability of heavily marketed talking points,
and more — that people will be discussing for a long time. And perhaps for some
in the worlds of science and science reporting, especially those who touted the
now discredited figure about a mere 1 percent difference from chimps, those
conversations may not be welcome.
Photo by
Nathan Jacobson, © Discovery Institute (CC BY-SA 4.0)
Associate
Director and Senior Fellow, Center for Science and Culture
Casey
Luskin is a geologist and an attorney with graduate degrees in science and law,
giving him expertise in both the scientific and legal dimensions of the debate
over evolution. He earned his PhD in Geology from the University of
Johannesburg, and BS and MS degrees in Earth Sciences from the University of
California, San Diego, where he studied evolution extensively at both the
graduate and undergraduate levels. His law degree is from the University of San
Diego, where he focused his studies on First Amendment law, education law, and
environmental law.