Reasons to Believe

DNA Comparisons between Humans and Chimps: A Response to the Venema Critique of the RTB Human Origins Model, Part 2

What is the best evidence for human evolution? For many biologists it’s the high degree of genetic similarity between humans and chimpanzees. The similarity in DNA sequences between humans and chimps is often regarded as evidence that we evolved from a common ancestor, making chimps our closest living “relative” in the animal kingdom.

As I discussed last week and elsewhere, it’s possible to understand the DNA similarity between humans and other animals (including chimps) as reflecting the work of a Creator. The biological similarities can be understood as a Creator’s use of the same materials and the same design templates to make humans and chimps. Likewise, some of the genetic difference could be understood as intentionally introduced by the Creator to make each creature unique. (A detailed presentation of the RTB human origins model can be found in our book Who Was Adam?)

As part of our critique of human evolution, we question whether there is as strong a genetic connection between humans and chimps as is commonly communicated to the general public. Most people are familiar with the claim that there is a 99 percent DNA similarity between humans and chimpanzees. Our assertion, however, is that the genetic commonality between these two primates is closer to 90 percent.1

This claim has prompted one biologist, Dennis Venema of Trinity Western University, to critique our human origins model2 in an article published on The Biologos Foundation website. Venema complains that we 1) intentionally ignored key scientific papers about genetic comparisons between humans and chimpanzees that went against our model; and 2) that we erroneously claim that the genetic similarity between humans and chimpanzees is around 90 percent, not 95 percent (or about 99 percent) as the most recent scientific papers report.3

How Similar Is Human and Chimp DNA?
As discussed in Who Was Adam?, researchers have performed a number of studies that indicate a 98 to 99 percent genetic similarity between humans and chimps. But as Hugh Ross and I point out, these comparisons were based on relatively limited genetic regions and focused on a single type of genetic difference (called substitutions or single nucleotide polymorphisms, SNPs). Comparisons that encompass larger regions of the genomes and include other types of genetic differences (like indels) show that the DNA similarity between humans and chimpanzees is much less than 98 to 99 percent.

Consider several studies discussed in Who Was Adam?. One study, conducted by Roy J. Britten and mentioned in Venema’s critique, compared five regions of the chimpanzee genome collectively (encompassing about 780,000 nucleotide base pairs) with corresponding regions of the human genome. Britten found a 1.4 percent difference when substitutions were considered, but a 3.4 percent difference when these five regions were examined for indels. Both types of differences combined show a 95 percent genetic similarity—not 99 percent.4

Another study we referred to used this same approach. These researchers uncovered a more limited genetic similarity when comparing a 1,870,955 base-pair segment of the chimp genome with the corresponding human genome region. When substitutions only were considered, the sequence similarity proved about 98.6 percent. Including indels in the comparison dropped the similarity down to 86.7 percent.5 Venema notes this study in his critique as well, but dismisses it because it focused on genes that are part of the immune system, making them variable inherently. According to Venema, this property in immune system genes means that the genetic comparison in this study shouldn’t reflect comparisons made with the whole genomes. He makes a good point. However, he also overlooks the larger point we are trying to make: namely, that including indels reduces the genetic similarity between humans and chimps.

We also cite other studies in Who Was Adam? of which Venema makes no mention. These studies affirm our main point: indels appear to account for significant differences between human and chimpanzee genomes. For example, we cite a comparative analysis of 27,000,000 base pairs of human chromosome 21 with the corresponding chimpanzee chromosome (number 22). This anaylsis identified 57 indels ranging in size from 200 to 800 base pairs, 21 of which were found in regions containing genes.6 In spring of 2004, The International Chimpanzee Chromosome 22 Consortium confirmed this initial observation when they generated a detailed sequence of chimp chromosome 22 and compared it to human chromosome 21.7 They discovered a 1.44 percent sequence difference when they lined up the two chromosomes and made a base-by-base comparison. But, they also discovered 68,000 indels in the two sequences with some indels up to 54,000 nucleotides in length.

Who Was Adam? also discusses work that compared a 1,800,000 base-pair region of human chromosome 7 with the corresponding region in the genomes of several vertebrates. Only a third of the differences between humans and chimpanzees involved substitutions. Indels accounted for roughly two-thirds of the sequence differences between these two primates and about one-half of these were greater than 100 base-pairs long.8

In fall of 2005, The Chimpanzee Sequencing and Analysis Consortium published a rough draft sequence of the chimp genome and performed an extensive comparison with the human genome. Though a rough draft, about 98 percent of the chimp genome was considered of extremely high quality. This work’s results remained consistent with those of the earlier studies. Considering substitutions only produced a 1.23 percent difference between the genomes, which amounted to about 35 million base pairs (genetic letters). But including indels in the comparison uncovered another 1.5 percent difference, corresponding to another 5 million changes. So instead of being 99 percent, the actual genetic similarity is around 97 percent.

This figure, however, overestimates genetic similarity. When performing the comparison, the researchers examined only about 2.4 billion base pairs, which represent around 75 to 80 percent of the genomes. As the authors note:

Best reciprocal nucleotide-level alignments of the chimpanzee and human genomes cover ~2.4 gigabases (Gb) of high-quality sequence, including 89 Mb from chromosome X and 7.5 Mb from chromosome Y.9

The reason for this limited comparison stems from the fact that they struggled to get a significant fraction of the genomes to align, in part, because of differences. The authors of the study described the nature of the difficulties:

On the basis of comparisons with the primary donor, some small supercontigs (most <5 kb) have not been positioned within large supercontigs (~1 event per 100 kb); these are not strictly errors but nonetheless affect the utility of the assembly. There are also small, undetected overlaps (all <1 kb) between consecutive contigs (~1.2 events per 100 kb) and occasional local misordering of small contigs (~0.2 events per 100 kb). No misoriented contigs were found. Comparison with the finished chromosome 21 sequence yielded similar discrepancy rates (see Supplementary Information “Genome sequencing and assembly”). The most problematic regions are those containing recent segmental duplications. Analysis of BAC clones from duplicated (n = 75) and unique (n = 28) regions showed that the former tend to be fragmented into more contigs (1.6-fold) and more supercontigs (3.2-fold). Discrepancies in contig order are also more frequent in duplicated than unique regions (~0.4 versus ~0.1 events per 100 kb). The rate is twofold higher in duplicated regions with the highest sequence identity (> 98%). If we restrict the analysis to older duplications (≤98% identity) we find fewer assembly problems: 72% of those that can be mapped to the human genome are shared as duplications in both species. These results are consistent with the described limitations of current WGS assembly for regions of segmental duplication.10

Given that the reason for the investigation’s failure to align 0.6 to 0.8 billion base pairs in the two genomes stems from the extensive genetic differences, it is unlikely that these regions display only a 3 percent difference, as is the case for the rest of the genomes. Instead the genetic difference in these regions must be greater. When this greater genetic difference is considered, it is reasonable to conclude that the overall difference between humans and chimpanzees is less than 97 percent and may well be as low as about 90 percent. In direct response to Venema’s criticisms, this is why we state the genetic similarity between humans and chimpanzees may be as low as 90 percent, not 95.

Earlier work presaged the Chimpanzee Sequencing and Analysis Consortium’s struggle in their attempts to align large regions of the human and chimp genomes. In early 2002, The International Consortium for the Sequencing of Chimpanzee Chromosome 22 reported one of the first studies to make a large scale genome-to-genome comparison.11 To make this comparison, the Chimpanzee Genome Project team cut the chimp genome into fragments, sequenced them, then compared them to corresponding sequences found in the Human Genome Database. The team found that those chimp DNA fragments able to align with human sequences displayed a 98.77 percent agreement. However, the researchers also found that about 15,000 of the 65,000 chimp DNA fragments did not align with any sequence in the Human Genome Database. These fragments appeared to represent unique genetic regions. Furthermore, during a detailed comparison of the chimp DNA fragments with human chromosome 21, the team discovered that this human chromosome possesses two regions apparently unique to humans.

A few months later, a team from the Max Planck Institute achieved a similar result when they compared over 10,000 regions (encompassing nearly 3,000,000 nucleotide base pairs). Only two-thirds of the sequences from the chimp genome aligned with the sequences in the human genome. As expected in those that did align, a 98.76 percent genetic similarity was measured—yet one-third found no matches.12

It is interesting that when evolutionary biologists discuss genetic comparisons between human and chimpanzee genomes, the fact that, again, as much as 25 percent of the two genomes won’t align receives no mention. Instead, the focus is only on the portions of the genome that display a high-degree of similarity. This distorted emphasis makes the case for the evolutionary connection between humans and chimps seem more compelling than it may actually be.

In many respects this discussion is moot, unless there is a clear understanding as to how the genetic differences between humans and chimpanzee translate into the biological and profound behavioral differences between these two species. In Who Was Adam? and elsewhere we have made the point that these types of genetic comparisons are meaningless. Next week, I will address why and, in doing so, respond to another charge leveled against Hugh Ross and me by Dennis Venema: namely, that this assertion doesn’t reflect, but rather misrepresents, the scientific community’s viewpoint.


Part 1 | Part 2 | Part 3 | Part 4 | Part 5

Subjects: Humans vs. Chimps

Dr. Fazale Rana

In 1999, I left my position in R&D at a Fortune 500 company to join Reasons to Believe because I felt the most important thing I could do as a scientist is to communicate to skeptics and believers alike the powerful scientific evidence—evidence that is being uncovered day after day—for God’s existence and the reliability of Scripture. Read more about Dr. Fazale Rana

  1. “Chimp Genome Project,” Creation Update, Reasons To Believe, aired September 20, 2005, webcast, http://www.reasons.org/cu-outline-2005.
  2. Dennis Venema, “An Evangelical Geneticist’s Critique of Reasons To Believe’s Testable Creation Model, Pt. 1,” The Biologos Forum, posted November 6, 2010, http://biologos.org/blog/an-evangelical-geneticists-critique-of-reasons-to-believe-pt-1/.
  3. The key paper in question is: The Chimpanzee Sequencing and Analysis Consortium, “Initial Sequence of the Chimpanzee Genome and Comparison with the Human Genome,” Nature 437 (September 1, 2005): 69–87.
  4. Roy J. Britten, “Divergence between Samples of Chimpanzee and Human DNA Sequences is 5%, Counting Indels,” The Proceedings of the National Academy of Sciences, USA 99, no. 21 (October 15, 2002): 13633–35.
  5. Tatsuya Anzai et al., “Comparative Sequencing of Human and Chimpanzee MHC Class 1 Regions Unveils Insertions/Deletions as the Major Path to Genome Divergence,” The Proceedings of the National Academy of Sciences, USA 100, no. 13 (June 24, 2003): 7708–13.
  6. Kelly A. Frazer et al., “Genomic DNA Insertions and Deletions Occur Frequently Between Humans and Nonhuman Primates,” Genome Research 13, no. 3 (March 2003): 341–46; Elizabeth Pennisi, “Jumbled DNA Separates Chimps and Humans,” Science 298, no. 5594 (October 25, 2002): 719–21.
  7. The International Chimpanzee Chromosome 22 Consortium, “DNA Sequence and Comparative Analysis of Chimpanzee Chromosome 22,” Nature 429 (May 27, 2004): 382–88; Jean Weissenbach, “Genome Sequencing: Differences with the Relatives,” Nature 429 (May 27, 2004): 353–55.
  8. J. W. Thomas et al., “Comparative Analyses of Multi-Species Sequences from Targeted Genomic Regions,” Nature 424 (August 14, 2003): 788–93.
  9. The Chimpanzee Sequencing and Analysis Consortium, “Initial Sequence of the Chimpanzee Genome and Comparison with the Human Genome,” Nature 437 (September 1, 2005): 71.
  10. Ibid., 70.
  11. Asao Fujiyama et al., “Constructions and Analysis of a Human-Chimpanzee Comparative Clone Map,” Science 295, no. 5552 (January 4, 2002): 131–34.
  12. Ingo Ebersberger et al., “Genomewide Comparison of DNA Sequences between Humans and Chimpanzees,” American Journal of Human Genetics, 70, no. 6 (June 1, 2002): 1490–97.