Monday, 24 November 2014

The Genomic Evidence for Common Descent: 6. Scars of DNA repair and out of place DNA elements

The consonance of molecular and morphological phylogenetic trees, coupled with the pattern of distribution of pseudogenes, retrotransposons, and endogenous retroviral elements makes the case for common descent just from comparative genomics alone unassailable. Yet, there is even more genomic evidence from scars of DNA repair, elements of mitochondrial DNA in nuclear DNA, and ectopic telomeric DNA. Arguing that God has created humans and apes with:
  • identical scars of DNA repair
  • identical mitochondrial DNA elements in nuclear DNA
  • identical telomeric DNA elements
all at the same places in their genomes simply to deceive human beings poses insuperable theological problems. Common descent however readily and easily explains these patterns.

NHEJ (Non-Homologous End Joining)

NHEJ is one of the main mechanisms [7] used to repair double stranded DNA breaks. It can be used to repair DNA breaks which normally occur such as in immunoglobulin and T cell receptor recombination, as well as damage to DNA caused by environmental damage.

There are four steps involved in NHEJ: detecting the DNA break, bridging both DNA ends, preparing the ends to make them suitable for joining, and the final repair. As a direct consequence of the repair method, NHEJ leaves a 'scar.'

Outline of NHEJ. Source

NUMTs (Nuclear Copies of Mitochondrial DNA)

NUMTs occur when an element of mtDNA becomes incorporated into nuclear DNA. They range in size from 31 bases to almost the entire length of the mitochondrial genome. Sometimes, mtDNA elements have been used to effect repairs in nuclear DNA. Needless to say, shared identical sections of repaired DNA using mtDNA would be hard to ascribe to design.
One way in which NUMTS are formed. Source

Shared NUMTS

Similarly, the presence of identical mtDNA elements at the same place in the genomes of humans and apes (either as repair elements or as insertions) would be powerful evidence of common ancestry of humans and apes, with such a mtDNA insertion taking place in a common ancestor, and being subsequently inherited by both descendant lines. Shared NUMTS have been found in:

  • Human and neanderthal DNA
  • Humans and apes
  • Humans and Old World Monkeys
  • Humans, Old World Monkeys and (likely) New World Monkeys [1-5]

Finlay notes that we share most of our NUMTS with chimpanzees, with 502 of the 616 NUMTS in our genome also found in the chimpanzee genome. In fact most of the NUMTS jn our genome are also shared with old world monkeys:
The presence of individual numts in both human and chimp genomes has abundantly demonstrated he monophylicity of humans and chimps. We and the chimps are indeed sister species, derived from common ancestors. But analysis of the presence and absence of individual numts in multiple primate genomes has also been initiated. Several partial studies have shown that humans, chimps and gorillas are monophyletyic. So are the great apes (incorporating the orang-utans) and, further back in time, the apes (incorporating the lesser apes or gibbons. It appears that the majority of numts in our genome are shared with OWMs. [6]
When faced with this overwhelming evidence, science denialists have resorted to claiming that because some of these elements have been secondarily co-opted by the genome for another purpose, they are not evidence for common descent. This is a feeble explanation which ignores the fact that functionality is not the issue, but rather the presence of shared identical genomic elements which are either alien to the original site, or are performing a completely unrelated function. Finlay skewers this argument perfectly:
Are numts functional today? Quite possibly - but functionality is irrelevant to the issue of 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. Each numt is a potent demonstration that the individuals and species possessing it are clonally related products of the reproductive cell in which the initiating repair event occurred. [7]
A linguistic analogy makes this example clear. The presence of the same semitic loanword in all Romance languages would be best explained by the ingress of this loanword into the common ancestor of all Romance languages (Vulgar Latin), which was then subsequently inherited by the descendant languages.  The fact that the loanword is still used is irrelevant to the argument of common descent.

Shared Telomeric DNA

Telomeric DNA is found at the end of chromosomes, and exist to prevent the ends of chromosomes being mistaken for DNA breaks and being joined together.  They have a distinctive structure consisting of multiple repeats of the sequence TTAGG. When we find the characteristic signature of telomeric DNA within chromosomes, we have evidence either of chromosomal fusion, or insertion via the action of telomerase.

Telomere location. Source

The best-known example is the telomeric DNA in human chromosome 2 which confirms that it was the product of an ancestral fusion of two chromosomes homologous to ape chromosomes. Our understanding of the origin of chromosome 2 in a fusion event is not new. We've known about the close similarity between human and ape chromosomes as long as thirty years ago, with the researchers behind the seminal paper in Science in which this data was published noting:
"The telomeric fusion of chromosomes 2p and 2q accounts for the reduction of the 24 pairs of chromosomes of the great apes to 23 in modern man. [8]"
As one can see below, the similarities are striking:
Over the following 30 years, further work has pinpointed the exact location in human chromosome 2 where the fusion event occurred. Twenty years ago, careful examination of human chromosome 2 showed that it was the result of an ancient telomere to telomere fusion:
“The inverted arrangement of the 1TAGGG array and the adjacent sequences, which are similar to sequences found at present-day human telomeres, is precisely that predicted for a head-to-head telomeric fusion of two chromosomes...These data provide strong evidence that the inverted repeats in c8.1 arose from the head-to-head fusion of ancestral telomeres.” [9]
One year later, further research showed evidence [10] of an ancient centromere in human chromosome 2, giving us evidence of both centromeric and telomeric remnant DNA which is what one would expect if human chromosome 2 was the product of a fusion event. This is no longer controversial in molecular biology. For example, a decade ago, researchers investigating the structure and evolution of human chromosome two noted in passing:
"Humans have 46 chromosomes, whereas chimpanzee, gorilla, and orangutan have 48. This major karyotypic difference was caused by the fusion of two ancestral chromosomes to form human chromosome 2 and subsequent inactivation of one of the two original centromeres (Yunis and Prakash 1982). As a result of this fusion, sequences that once resided near the ends of the ancestral chromosomes are now located in the middle of chromosome 2, near the borders of bands 2q13 and 2q14.1. For brevity, we refer henceforth to the region surrounding the fusion as 2qFus. Two head-to-head arrays of degenerate telomere repeats are found at this site; their head-to-head orientation indicates that chromosome 2 resulted from a telomere to telomere fusion. (Emphasis mine). [44]
That chromosome 2 owes its origin to a fusion event is no longer in doubt. Recently, DNA from a hominid bone found in the Denisova cave in Siberia was sequenced, showing that it came from a species closely related to the Neanderhals. It turns out that the Denisovan hominids also had the fused second chromosome. Palaeoanthropologist John Hawks quotes the researchers, noting that:
Sometime in our evolution, two separate chromosomes fused into one, giving us a karyotype of 46 chromosomes where chimpanzees, bonobos and gorillas have 48 chromosomes. The high-coverage genome was sufficient to show that Denisova shared the human fusion: 
"Of more relevance may be examination of aspects of the Denisovan karyotype. The great apes have 24 pairs of chromosomes while humans have 23. This difference is caused by a fusion of two acrocentric chromosomes that formed the metacentric human chromosome 2 , and resulted in the unique head-to-head joining of the telomeric hexameric repeat GGGGTT. A difference in karyotype would likely have reduced the fertility of any offspring of Denisovans and modern humans. We searched all DNA fragments sequenced from the Denisovan individual and identified twelve fragments containing joined repeats. By contrast, reads from several chimpanzees and bonobos failed to yield any such fragments. We conclude that Denisovans and modern humans (and presumably Neandertals) shared a karyotype consisting of 46 chromosomes." 
We still have no idea whether this fusion made any difference to any phenotype in ancient humans. 
Many, many people have written me over the years to ask whether this fusion of two ancestral chromosomes might have been important to our evolution. Perhaps, many suggested, if Neandertals had a chromosomal incompatibility with us, that would explain why they became extinct. I have always doubted this, but without information it was impossible to be certain. 
It's nice to now have the information in hand: This fusion happened earlier in our evolution. [12]
This poses a huge problem for special creationists. Why would God not only create humans with chromosome 2 looking like the product of a fusion of two ape chromosomes, but do the same thing to an extinct species of humans who lived thouisands of years before Adam (assuming we place Adam around the time animals and plants were domesticated in the ANE)? Common descent solves this problem neatly - the Denisovans and Homo sapiens share a common ancestor in which he chromosomal fusion took place. 

More evidence for human-ape common ancestry comes from shared telomeric DNA insertion (remember, telomeric DNA belongs at the end of chromosomes. Its presence elsewhere is proof either of an insertion event or a chromosomal fusion). Finlay once again notes:
Some 50 short, well-conserved interstitial telomeric repeats…are present in the human genome. Sequencing studies indicated that they arose as distinct insertion events, probably generated by the action of the enzyme telomerase, which has the function of adding TTAGG units at the authentic telomeres. These inserts have the characteristics of emergency DNA repair patches that were recruited to hold double-stranded breaks together.

The presence of absence of ten of these telomeric repeats was ascertained in humans and other primate species. ,Each repeated was shown to have arisen at a particular state of primate evolution. In some cases they precisely interrupt the pre-insertion sequence. The inserts shown…is not associated with any gains or losses of base sequence. It is a clean insertion, shared by humans, chimps and gorillas The Asian great ape (orang-utan) and OWMs retain the uninterrupted pre-insertion site. This repeat unambiguously demonstrates African great ape monophylicity. [13]

Interstitial telomeric repeats shared by the african great apes (upper diagram) and the apes (lower diagram).
 Source: Finlay (2013)


As with shared identical pseudogenes, retrotransposons, and ERV elements, the presence of shared identical telomeric DNA, NUMTs, and NHEJs provide powerful evidence for common descent for reasons previously stated. In the case of NHEJs, which are clearly scars of DNA repair, the chance of exactly the same scar of repair occurring at exactly the same place in human and ape DNE is once again so remote as to be negligible. Conversely, any attempt to argue that God deliberated created humans and apes with identical scars of DNA repair that never happened, simply to deceive people is theologically repellent. This is not creation with an 'appearance of age', itself a theologically dubious concept that was rightly rejected in the 19th century shortly after it was proposed, but creation with an intent to deceive.

The most parsimonious explanation is common descent: these genetic 'glitches' occurred in the common ancestor of humans and apes, and were inherited by their descendants. The genomic evidence has spoken, and the only logical explanation is that we share common ancestry with the apes.


1. Finlay G Human Evolution: Genes, Genealogies and Phylogenies (2013: Cambridge University Press) p 140-141

2. Zischler H, Geisert H, Castresana J "A hominoid-specific nuclear insertion of the mitochondrial D-loop: implications for reconstructing ancestral mitochondrial sequences" Molecular Biology and Evolution (1998) 15:463-469

3. Zischler H "Nuclear integrations of mitochondrial DNA in primates; inferences of associated mutational events" Electrophoresis (2000) 21:531-536

5. Ovchinnikov IV, Kholina OI "Genome digging: insight into the mitochondrial genome of Homo.PLoS ONE (2010) 5,e14278

6. Finlay, op cit p 144-145

7. ibid, p 145

8. Yunis J.J. Prakash O, "The origin of man: a chromosomal pictorial legacy". Science (1982)215:1525–1530.

9. IJdo JW, Baldini A, Ward DC, Reeders ST, Wells RA, Origin of human chromosome 2: an ancestral telomere-telomere fusion. Proc Natl Acad Sci USA (1991) 88:9051-5

10. Avarello R et al "Evidence for an ancestral alphoid domain on the long arm of human chromosome 2" Hum Genet (1992) 89:247-9

11. Fan Y, Linardopoulou E, Friedman C, et al "Genomic Structure and Evolution of the Ancestral Chromosome Fusion Site in 2q13–2q14.1 and Paralogous Regions on Other Human Chromosomes" Genome Res. (2002) 12:1651-1662

12.  Hawks, J "The fused chromosome 2 was in Denisova" John Hawks Weblog 1st Sep 2012

13. Finlay, op cit p 146-147