Hi everyone, Gutsick Gibbon (Erika) here. I know I don’t post as much as I used to, but life is busy! I will always find time to talk about this particular topic though (And I’ll cross post this to Peaceful Science).
I recently did a video about the gross misrepresentation of a recent paper by the Discovery Institute’s Casey Luskin over on Evolution News (Link to his works: Author: Casey Luskin | Evolution News and Science Today) called “Every Creationist got this Wrong Because Casey Luskin Lied (Human/Chimp Similarity)” which you can find here: https://www.youtube.com/watch?v=8A9R5e3YR34&t=12304s
It’s over 3.5 hours long though, so I think a summary writeup is in order for ease of access.
The paper is by Yoo and colleagues and is titled “Complete Sequencing of Ape Genomes”: Complete sequencing of ape genomes | Nature and Luskin + every other creationist siphoning from him are screaming from the rooftops that it proves at long last that humans are way less similar to chimps than previously thought. That is not true.
This paper is a stunning and collaborative work that reports the “complete” genomes (T-T or Telomere to Telomere) of a chimp, bonobo, gorilla, bornean orangutan, sumatran orangutan, and siamang. Since the human genome (T-T) was completed in 2022, we could now compare all these species “in full”.
What the Paper discovered:
The paper presents “complete” (although some still have minor gaps) genomes for the previously listed species and compares them to the complete human genome (CHM13, Hg002, and GRCh38) as well as one another, while also analyzing them independently. It’s a beast of a paper! One major discovery was just how different the non-human apes were even in closely related dyads (chimps/bonobos and bornean /sumatran orangs). The abstract summarizes: “Such regions include newly minted gene families in lineage-specific segmental duplications, centromeric DNA, acrocentric chromosomes and subterminal heterochromatin.” I’ll also note that while the phylogeny did not change, the divergence times for the apes from one another increased in nearly every case (See Fig. 2 phylogeny) with one major exception being the human/panin (chimp +bonobo) divergence (reported as 6.2 MYA but traditionally in the 6-7 MYA range). This is important because Luskin loves gap divergence so much.
I spoke with three authors involved in the comparative analysis to confirm my understanding of the study and was told point blank: this paper does not change our understanding of the humans/chimp relationship, or even the ape relationships generally. The same phylogeny forms every time regardless of method.
The Creationist (Luskin) Spin
Obviously the human/chimp similarity is problematic for creationists, even ID ones like the geologist Casey Luskin. So Luskin homes in on the number that is the sexiest: the alignment numbers. He quotes the main text of the study and the supplement for this: “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.”
He also references Supplementary Figure III.12. ( https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-025-08816-3/MediaObjects/41586_2025_8816_MOESM1_ESM.pf ) which can be read by taking the small color coded numbers and subtracting them from 100 to get a “percent similarity”. For example, PanTro3 to Hg002 has the purple autosome number as 0.124732. We can calculate the like this: 100-12.4= 87.6. Luskin then takes the SNV (single nucleotide variant) number from the preceding figure and subtracts it from the gap divergence number to get an “absolute alignment”: 100-(12.4 +1.4) = ~86.2%
Wow that sure does seem different compared to the normal range we see of 96-99% isn’t it!
Too bad it’s nothing new.
Different Methods, Different Numbers, Decades Old.
Alignment and sequence identity are different things in genetics. The former measures how much of one genome can line up to the other, and the latter is the % similarity of those aligned portions. I typically see four numbers floating around:
Protein coding percent similarity: What is the similarity in the protein coding regions of the genome? H/C = >99%.
Whole Genome, SNPs/SNVs only: What is the similarity of the aligned regions, just looking at single nucleotide polymorphisms (single base pair changes or substitutions)? H/C = ~98-99%
Whole Genome, SNPs + INDELS: What is the similarity of the aligned regions, with SNPs and large Insertions/Deletions accounted for? H/C = ~96%
Alignment (1:1 identical: How much of genome one aligns identically to genome two? H/C = 85-90% depending on method and year.
I asked a researcher working closely with the chimpanzee genome project if we have always known these differences in numbers/methods and he said yes. This was corroborated by my undergraduate genetics course on the subject.
In fact, we can find these numbers (including alignment) reported in one way or another (as data or as a plain number, sequence identity in question is clarified by study) in the following papers:
(Original chimp genome sequence) Initial sequence of the chimpanzee genome and comparison with the human genome | Nature , Richard Buggs calculated an alignment estimate using reported data
(Prufer et al., 2013) The bonobo genome compared with the chimpanzee and human genomes - PubMed , Sequence identity reported in main text, alignment can be calculated using Table 1 (H/C), phylogeny is standard
(Prado-Martinez et al., 2013) Great ape genetic diversity and population history | Nature, Sequence identity reported in main text, alignment not reported (that I could find), phylogeny is standard
(Rogers & Gibbs 2014) Comparative primate genomics: emerging patterns of genome content and dynamics - PubMed ,Sequence identity reported in main text (cited), alignment not reported but CNV influence stated outright, phylogeny is standard
Marcais et al., 2018) MUMmer4: A fast and versatile genome alignment system - PubMed, Sequence identity reported in main text, alignment reported in main text, no phylogeny performed
(Kronenberg et al., 2018) https://www.science.org/doi/10.1126/science.aar6343 , Sequence identity reported in main text, alignment reported in table S45, phylogeny is standard
(Seaman & Buggs, 2020) Frontiers | FluentDNA: Nucleotide Visualization of Whole Genomes, Annotations, and Alignments, Sequence identity reported in main text, alignment reported in main text, no phylogeny performed
(Yoo et al., 2025) Complete sequencing of ape genomes | Nature , Sequence identity reported in main text and supplement, Alignment reported i main text and supplement, phylogeny is standard.
The point here is simple: the alignment numbers in Yoo et al. are not new estimates. So why is Luskin reporting them as if they are?
What do the Newest Estimates Say about Ape Relationships, and about Creationism?
The paper says point blank that 99.0-99.6% of “human” protein coding genes are found in part or entirely in other apes. We can look to the previously mentioned supplementary figures, or we can consult tables Supplementary Table III.17 to Supplementary Table III.20 to get our whole genome (SNPs) estimates and alignment numbers (although these will differ slightly due to the pairwise/progressive cactus methodology differences). We can also use the supplementary github (ape_pangenome/divergence/basic-div/README.md at main · T2T-apes/ape_pangenome · GitHub) to get similar numbers for a few other pairs of apes. Here is what we get for the autosomes (all non-sex chromosomes) for Hg002 to several hominids.
Whole Genome (SNPs only) ranges:
Human/Chimp: 98.4-98.5%
Human/Bonobo: 98.4-98.5%
Human/Gorilla: 98.0-98.1%
Human/Orangutan (B and S): 96.3-96.4%
Chimp/Bonobo: 99.1-99.2%
B. Orang/S. Orang: 99.5%
Full Raw Alignment (Gap. Div - SNPs)
Human/Chimp: 85.9-87.4%
Human/Bonobo: 85.5-86.7%
Human/Gorilla: 72.6-81.3%
Human/Orangutan (B and S): 83.0-83.7%
Chimp/Bonobo: 88.2-89.9%
B. Orang/S. Orang: 90.9-91.2%
It should be immediately obvious that Yoo et al. report similar numbers to previous papers, and confirm again that alignment will always be lower than sequence identity…but what should also stick out is that human/chimp is not significantly less similar than chimp/bonobo: 85.9 to 88.2 at closest. This tells us immediately that whatever is causing the drop in similarity from sequence identity to alignment it is impacting all species proportionally. This is not good if alignment is meant to separate humans from chimps…
It Gets Worse
Alignments are reported in the supplementary material not just for humans vs other apes, but for within each species. These are below all the human/other ape comparisons in the Supplementary Figure III.11 and 12.
Gap divergence (add the SNV data for the alignment if you’d like)
Within Humans: 96.6%
Within Chimps: 92%
Within Bonobos: 91.2%
Within Gorillas: 86.2%
Within Orangs: 93.4%
That’s right, within gorillas as a species we see a greater gap divergence than that seen between humans and chimps: 13.8 vs 13.3.
Additionally, specific comparisons of human haplotypes (CHM13 to Hg002 and GRCh38) are also included in the previously mentioned supplementary tables. What do these full alignments report?
Supplementary Table III.17.
CHM13/GRCh38: 92.04%
CHM13/Hg002: 93.07%
Supplementary Table III.19
CHM13/GRCh38: 86.96%
Supplementary Table III.20
CHM13/GRCh38: 87.87%
CHM13/Hg002: 88.8%
That’s right, humans vs humans by Casey’s preferred method can be ~8-13% different from one another.
This confirms additional papers supplied to me by Richard Buggs and Joel Duff:
Why can bonobos/chimps, two orang species, or even two humans differ so much in alignment when all of these pairs are >99% (>99.9% in humans) similar in sequence identity? Because the alignment disparities are a result of mutations that can impact thousands of base pairs at once: large scale deletions/duplications/inversions/insertions. These accumulate in the non-coding DNA and are thus not weeded out by selection, allowing them to run rampant. But this is why we do not use the alignment numbers when asking the question: How similar are to organisms genetically?
For the record, rats and mice have a >70% alignment. I don’t suppose creationists like Luskin would propose them to be different kinds, would you?
And Also, Casey Luskin Originally Lied
Luskin omitted talking about the human/human comparisons in his original series of articles, despite pulling data directly adjacent to it in Supplementary Table III.19. But he also dishonestly edited Supplementary Table III.12, hiding the within-species gap divergences and stitching the label back on: https://web.archive.org/web/20250521143923/https://evolutionnews.org/2025/05/fact-check-new-complete-chimp-genome-shows-14-9-percent-difference-from-human-genome/
This is probably because the human/chimp gap divergence of 13.3% is a lot less impressive when gorillas to other gorillas are 13.8%. He has since edited the article to show the whole figure, denying the allegations of originally lying: Chimp Genome, 14.9% Difference | Evolution News and Science Today
Dan of Creation Myths (And here as well) outlined it briefly here: https://www.youtube.com/watch?v=VNs_lgWM6R8&t=1s
The Take Home
The newest paper doesn’t change our understanding of humans/chimps+bonobos as one another’s closest relatives, nor does it greatly impact previous estimates of any method of comparison.
Still, we will likely see a new wave of creationist insisting humans and chimps are “now only 85% similar”. When you encounter this in the wild, simply respond by saying “We’ve known about that method for years and using it means humans can be only 87% similar to each other.”
Take care, Gentle and (of course) very Modern Apes
GG
