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  • Writer's pictureJon Peters

DNA Repair and Evolution

Updated: Oct 5, 2023


"DNA breaks are random and potentially catastrophic. The molecular details... are yielding to stringent molecular analysis, which have revealed that the telltale messiness of the repair patch is inherent to the repair system. Random breaks are fixed by the desperate co-option of any available DNA... Such patches are sufficient evidence of great ape monophylicity." ~ Graeme Finlay.



Introduction


As many people know, DNA is the molecule of life that holds instructions for maintaining, growing and starting new life. Some forms like occasional viruses use RNA instead of DNA, so perhaps it is more accurate to say strings of nucleic acids are responsible for life. Most organisms we are interested in use DNA however. DNA is not actually like a blueprint because it is constantly changed and modified through recombination, deletions, insertions, and mutations. Many of these modifications can cause damage and they need to be repaired as quickly as possible to keep the instructions and directions for life intact. DNA is actually fragile. Fortunately, cells have various mechanisms for detecting and repairing double stranded breaks in DNA.


As Finlay discusses in his book (see full citation and acknowledgment at the end of this article), broken DNA ends are often stitched back together using whatever pieces of DNA that are close at hand, more like a Band-Aid patch. This “repair-or-die” as he calls it sets up an emergency repair that is unique because not only is the break random but so is the repair patch, producing a unique signature or DNA scar. It leaves a unique mark on that section of DNA where it was repaired with a section of DNA that will vary by unique ATCG letter sequences.


These patch fixes represent types of repaired errors or scars. Scientists studying genomes have found many of these previous scars and we can compare them between species. If these DNA repair scars are found between species in the same chromosomal locations with the same piece of DNA that was grabbed and inserted to glue the broken DNA ends together, we can be certain that the only rational explanation is the two species at one time shared a common ancestor. It is as if an authentic artist's signature is found on two paintings, we can be sure they had the same person painting them. These repair scars then are powerful evidence for common ancestry. This results in a test of evolution because the pattern of inheritance of the same random damaged and randomly repaired DNA sections across species should reveal shared ancestry and common descent. Phylogenetic trees result showing evolution and conclusive common ancestry. And the tree from DNA repairs can be compared to phylogenetic trees from other independent fields of science.



NHEJ Repairs


The acronym NHEJ stands for non-homologous end-joining . If the break and repair occurs in a sex cell it will be passed down through the generations. Scientists can find these repairs by noting sections of matching DNA copied from one site to another with losses and gains of DNA bases at the recipient site. According to the cell biologist and cancer researcher Finlay, hundreds of such emergency repair jobs have been found in genomes of various apes, including humans. See Figure 1 below of an actual DNA repair patch. "Non-templated" refers to bases added but not copied from a DNA strand.

Figure 1. DNA repair. From: Finlay, Graeme. 2013. Human Evolution: Genes, Genealogies and Phylogenies. p 140. Figure 3.3. Cambridge University Press. Social sharing and Fair dealing applied per publisher's web instructions.


Finlay's explanation: “The original, undisturbed sequence in the macaque genome is shown. However, in humans and chimps this sequence is disrupted, and an extensive length of foreign DNA (starting ATCTT…) has been imported to join the ends. Six randomly inserted filler bases (GCTTCC) are present on the left-hand side of the break, and two bases (GC) have been deleted from the right-hand side. This example provides compelling evidence that humans and chimps share a common ancestor. Moreover, 36 other examples of shared repair patches linking humans to chimps to a common ancestor have also been found.” [p. 140]. See above diagram of the DNA findings.


As Finlay points out, hundreds of DNA repair scars have been found. Some are shared between only some species. For example, 142 are shared by orangutans, humans and chimps only. Others are shared by all great apes, old world monkeys, and new world monkeys (389). Some even are shared across large groups (22). Thus, just by tabulating which repairs are shared and which are not, evolution is demonstrated.


“These represent a relatively well-preserved selection of sites that have survived vast tracts of time since the Euarchontoglires and Boreoeutheria ancestors lived… The distribution of shared repair patches generates a phylogenetic tree that is congruent with that generated from ERV and retrotransposon insertions. NEHEJ and retrotransposition are wholly independent processes…” .(Finlay)


See Figure 2 below of shared DNA findings producing an evolutionary phylogenic tree.

Figure 2. Identical DNA repairs compared between species. They nest in a hierarchal pattern demonstrating shared ancestry. OWM = Old World Monkeys. NWM = New World Monkeys. From: Finlay, Graeme. 2013. Human Evolution: genes, genealogies and phylogenies. p 140. Figure 3.3. Cambridge University Press. Social sharing and Fair dealing applied per publisher's web instructions.


Numts Repairs


As has been discussed, these DNA breaks are random and the repairs involve grabbing random DNA copies or pieces nearby for the repair. Sometimes that is a section of native DNA that is copied. Other times random nucleotides are inserted (what are called “non-templated” DNA in Figure 1 above). Still other times the cell will even grab old parasitic fossilized viral DNA from transposons such as LINE-1s. An additional surprising source even has been found to be mitochondrial DNA. As you may remember mitochondria were originally free living bacteria that evolved into our ATP power generating organelles through endosymbiotic capture and they have their own bacterial DNA. (see Moms and Mitochondria, this site)


It turns out that sections of mitochondrial DNA are found in nuclear genomes of nearly all organisms from fungi to animals according to Finlay. How did mitochondrial DNA get into host cell nuclear DNA? Because when some cellular DNA was repaired the repair involved grabbing DNA as a patch and the DNA close by was from mitochondrial DNA. These repair patches have their own designation, nuclear sequences of mitochondrial origin or numts, (pronounced "new-mites") also called mitochondrial pseudogenes because they are non-coding mitochondrial genes that have been inserted into host nuclear DNA. (Finlay, 2021)


The number of human numts found averages about 600, depending on the criteria used. About 50 are found in only humans. Others have been shown to date from early ape-monkey history (Finlay) and about 550 are shared by chimps and humans.


Some in humans are polymorphic which means that some modern humans have them and some don't - they are repairs more recently and show that these repairs are not under selection and have no biological function. "All of it is junk because mitochondrial DNA is not supposed to be in the nuclear genome, and once inserted, it rapidly acquires mutations." (Moran, 2023)


Moran further writes, "This is all very interesting , but it doesn't make much of a difference in our genome. It's just a little bit more of junk DNA that comes and goes. Remember that we're talking about small, random pieces of mitochondrial DNA - most of them are only a few hundred base pairs in length, and they don't include any full-length mitochondrial genes."


If grouped by shared occurrence this produces a phylogenetic tree that matches those phylogenic trees independently produced by shared ERVs, LTRs, and fossils (see Shared ERVs and evolution, this site, shared pseudogenes, and of course the NHEJ repair scars discussed in Figure 2. See Table from Finlay:


Table 1. Listing of some numts shared by various groups and also across species. Numts refers to random DNA patches/repairs using nearby pieces of mitochondrial DNA. From: Finlay, Graeme. 2013. Human Evolution: genes, genealogies and phylogenies. p 141. Table 3.1. Cambridge University Press. Social sharing and Fair dealing applied per publisher's web instructions.


As Finlay writes, “Whole-genome surveys have indicated that most of the numts in our genome, ... (that is over 80%) are present also in the chimp genome… But analysis of the presence and absence of individual numts in multiple primate genomes…. have shown that humans, chimps and gorillas are monophyletic [we and they share a common ancestor]. So are the great apes (incorporating the orangutans) and further back in time, the apes (incorporating the lesser apes and gibbons). It appears the majority of numts in our genome are shared with old world monkeys”.


“Are numts functional today? Quite possibly - but functionality is irrelevant to the issue whether numts constitute markers of descent. It is the complex molecular pathway by which numts arose that makes them such compelling signatures of our shared ancestry with other primates.”



Conclusion


The DNA molecule is fragile and easily broken. Because of its importance to heredity and the function of the cell, breaks must be repaired quickly. This repair produces a DNA patch or scar that can be identified and studied across species. The breaks are random and also is the DNA patch material. Thus, when we find the same breaks in some species with the same patch material we can be certain the only rational explanation is common descent or evolution from common ancestors. To further solidify this conclusion different repaired patches can be grouped across species into a phylogenetic tree that not only confirms evolution but replicates the same evolutionary conclusion using other independent lines of scientific inquiry and phylogenic trees. Newer DNA evidence such as the same DNA repair scars across species points to the same conclusion - evolution is true. This is another example, as is shared ERVs , pseudogenes , and segmental duplications discussed on this site, that specific DNA findings support evolution in a spectacular way. The approach with DNA scars is similar to how we can use random retroviral inserts and random duplications to show common ancestry that rises to the level of proof of common ancestry.



Acknowledgement

I am grateful for the effort and time Dr. Finlay took to write an excellent review of newer DNA findings that dramatically confirm human evolution. His writing style is clear to the non-scientist and his conclusions supported by copious examples. As a theist, he should also be regarded as above reproach in terms of motivations. Highly recommended. The subject of DNA scars and the writing in this article are based solely on his book and not original to this author.

Finlay, Graeme. 2021. Human Evolution: Genes, Genealogies and Phylogenies. Cambridge University Press. 359 pp. 283 pp. not including References and Index.

Paperback edition. 2021 - ISBN 978-1-009-00525-8. Original 2013.

Social sharing and Fair dealing applied per publisher's web instructions.


Moran, Laurence A. 2023. What's in Your Genome?: 90% of your genome is junk. University of Toronto Press. Aevo UTP. 372 pp. Hardback edition.



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