Brief summary of ERV evidence for common descent

[coltcorrea]

Hello everyone - I am trying to put a brief summary of how ERVs in great apes support common descent to a skeptic that has some medical knowledge.

1. Is the summary below a good start?
2. Can anyone else point me to an article, YouTube video or other concise way of presenting this to a skeptic who is trained in medicine?
3. This is the only article I have found but the skeptic is still questions if RV insertion loci are actually random.

Assumptions:

1. It is highly unlikely (approximately 1 in 50,000,000) that an RV insertion will occur at a given loci in the human genome.
2. RV converting into ERV is rare but does occur.
3. Some ERVs will eventually propagate to an entire species over a long period of time.
4. Points 1-3 are observable and repeatable, highly peer reviewed and well established with numerous experiments on bacteria, and other species over decades of time. These items are well established and not controversial for scientists in genetic research
5. We observer not less than 16 of the same ERVs inserted into the genome at the same loci for humans, chimpanzees and other primates.
   Conclusion:
   Given 1-5 → ERVs evidence provides strong support of common descent.

[T_aquaticus]

Here is the analogy I use to explain the evidence. Take two people and lock each person in a separate room with an OED dictionary. Give them instructions to randomly pick 100 entries from the dictionary and write them down. When they are done, compare the lists of words. What are the chances that any of those 100 words will match? Pretty low, right? The same applies to retroviruses when they choose a base in the genome to insert into. Therefore, when you see hundreds of thousands of retroviral insertions that are found at the same place in two different genomes you know that they had to be inherited from a common ancestor because there is no plausible way that many independent retroviral insertions will happen at the same base.

@coltcorrea

• It is highly unlikely (approximately 1 in 50,000,000) that an RV insertion will occur at a given loci in the human genome.
• RV converting into ERV is rare but does occur.
• Some ERVs will eventually propagate to an entire species over a long period of time.

I would describe how retroviral insertions that happen in egg or sperm can be passed on to offspring who also pass the insertion along to all of their descendants. You might also add that the reason you and your siblings/cousins/relatives share the same ERV’s at the same location in each of your genomes is because you share a common ancestor.

@coltcorrea

We observer not less than 16 of the same ERVs inserted into the genome at the same loci for humans, chimpanzees and other primates.

It’s way, way more than 16. Using the human genome paper from 2001 and the chimp genome paper from 2005.

Table 11, 2001 human genome paper
Between ERV class I, II, and III, there are 203,000 ERV’s in the human genome.

Next:

Table 2, 2005 chimp genome paper
They only list the species specific ERV’s which would be the ERV’s not found in the other species. Therefore, of the 203,000 ERV’s found in the human genome there are only 82 that are not found in the chimp genome at the same position. This means chimps also have about 203,000 ERV’s, and of those there are only 279 not found in the human genome. Nearly all 203,000 ERV’s in each species are shared between them. This is smoking gun evidence for common ancestry.

[coltcorrea]

Wow. Thanks for the answer. Learning a lot about ERVs.

[coltcorrea]

Is this simple logic true?

1. Retroviruses insert themselves into DNA in random places. (random is very key!)
2. Sometimes the virus insertion occurs in sperm or eggs.
3. When #2 happens, all descendants get that retrovirus and it becomes “Endogenous” or an ERV.
4. There are roughly 200,000 virus insertions in the human DNA.
5. There are roughly 200,000 virus insertions in chimpanzee DNA.
6. Almost all of the 200,000 virus insertions in chimps are the same virus and the same location in the DNA as humans!
7. ERVs will randomly mutate over time.
8. The ERVs that are shared between chimps and humans at the same location in the DNA also share the same random mutations!

Are there any specific data or studies to support “randomness” that someone can point me to?

[T.j_Runyon]

Good resource:

Endogenous RetroViruses - Frequently Asked Questions

Evidence for the Evolutionary Model

[T_aquaticus]

@coltcorrea

• ERVs will randomly mutate over time.
• The ERVs that are shared between chimps and humans at the same location in the DNA also share the same random mutations!

Those last two points can be a bit confusing. The following paper has a better description of how the sequences within ERVs can be used to evidence common ancestry and evolution:

Endogenous retrovirus loci provide no less than three sources of phylogenetic signal, which can be used in complementary fashion to obtain much more information than simple distance estimates of homologous sequences. First, the distribution of provirus-containing loci among taxa dates the insertion. Given the size of vertebrate genomes (>1 × 109 bp) and the random nature of retroviral integration (22, 23), multiple integrations (and subsequent fixation) of ERV loci at precisely the same location are highly unlikely (24). Therefore, an ERV locus shared by two or more species is descended from a single integration event and is proof that the species share a common ancestor into whose germ line the original integration took place (14). Furthermore, integrated proviruses are extremely stable: there is no mechanism for removing proviruses precisely from the genome, without leaving behind a solo LTR or deleting chromosomal DNA. The distribution of an ERV among related species also reflects the age of the provirus: older loci are found among widely divergent species, whereas younger proviruses are limited to more closely related species. In theory, the species distribution of a set of known integration sites can be used to construct phylogenetic trees in a manner similar to restriction fragment length polymorphism (RFLP) analysis.

Second, as with other sequence-based phylogenetic analyses, mutations in a provirus that have accumulated since the divergence of the species provide an estimate of the genetic distance between the species. Because, for any given provirus, it is highly unlikely that there will be selection for or against any specific sequence, it is safe to assume that the rate of accumulation of mutations approximates the rate of their occurrence, with appropriate corrections for reversion. Analysis of closely related proviruses integrated at different sites should also reveal regional differences in mutation rates.

Third, sequence divergence between the LTRs at the ends of a given provirus provides an important and unique source of phylogenetic information. The LTRs are created during reverse transcription to regenerate cis-acting elements required for integration and transcription. Because of the mechanism of reverse transcription, the two LTRs must be identical at the time of integration, even if they differed in the precursor provirus (Fig. 1A). Over time, they will diverge in sequence because of substitutions, insertions, and deletions acquired during cellular DNA replication. Although it has been noted that the divergence between the two LTRs of an ERV can serve as a molecular clock (8, 15, 18, 25), there are no reported prior attempts to utilize the LTRs of individual ERV loci as a source of phylogenetic signal.
https://www.pnas.org/content/96/18/10254

The differences in the shared ERV sequences can also evidence evolution.

[coltcorrea]

Very much appreciate the information. This is very interesting indeed!