ERVs: Evidence for the Origin of Humans

[Thermos aquaticus]

In this thread I will be presenting evidence that supports the origin of humans. That origin is descent through modification (i.e. evolution) from ape-like ancestors. The specific evidence I will be presenting is focused on endogenous retroviruses, or ERVs.

Retroviruses are usually RNA based viruses that reverse transcribe their genomes into DNA and then insert that DNA into the host genome. The long terminal repeats at the ends of the inserted viral genome act as strong gene promoters causing the host genetic systems to transcribe and translate the genes found in the viral genome. This results in the construction of new virus that buds off from the host cell and moves to new cells where the process is repeated. Retroviruses that invade and insert into the genome of a sperm or egg have the chance of being passed on to the next generation. When this happens it is called an endogenous retrovirus, or ERV.

We can watch this process in action in both the wild and in the lab. We have also constructed viral genomes from the consensus sequence of several human ERVs, and the result is a viable retrovirus. Again, we can observe new retroviral insertions occurring in real time, and ERVs already in the human genome can be reconstructed into retroviruses. There is absolutely no reason to doubt that ERVs are from retroviral insertions.

We also know that retroviral insertion can occur almost anywhere in the genome. When scientists infect cells with retroviruses and determine where in the genome the insertion occurred these are the results they get:

click here:
http://journals.plos.org/plosbiology/article/figure?id=10.1371/journal.pbio.0020234.g001

Those are the 22 human chromosomes, and each colored circle marks a retroviral insertion that occurred in the lab. As you can see, insertions happened all over the place in each of the chromosomes.

What this means is that two insertions that happen independently of one another should occur at different spots in the genome in the vast majority of cases. Therefore, when we find the same insertion at the same spot in the genomes of two individuals this means that the insertion happened only once in a common ancestor. Again, if two individuals do not share common ancestry then their ERVs should be found at different places in their genome. If they share a relatively recent ancestor then they should share nearly all of their ERVs at the same location in their genomes which are called orthologous ERVs. This is the scientific test for common ancestry.

So how does this apply to human ancestry? The human genome has over 200,000 ERVs. There are about the same number in the chimp genome. Of the ERVs in the human genome, nearly all of them are found at the same position in the chimp genome. Less than 100 human ERVs do not have an ortholog (i.e. same ERV at the same position) in the chimp genome. This is smoking gun evidence for common ancestry between chimps and humans.

References:

https://www.nature.com/articles/35057062

https://www.nature.com/articles/nature04072

 

[metis]

And one byproduct of all the genome testing when taken as a whole is the confirmation of what we have long seen and deduced with the fossil record.

 

[sealchan]

In this thread I will be presenting evidence that supports the origin of humans. That origin is descent through modification (i.e. evolution) from ape-like ancestors. The specific evidence I will be presenting is focused on endogenous retroviruses, or ERVs.

Retroviruses are usually RNA based viruses that reverse transcribe their genomes into DNA and then insert that DNA into the host genome. The long terminal repeats at the ends of the inserted viral genome act as strong gene promoters causing the host genetic systems to transcribe and translate the genes found in the viral genome. This results in the construction of new virus that buds off from the host cell and moves to new cells where the process is repeated. Retroviruses that invade and insert into the genome of a sperm or egg have the chance of being passed on to the next generation. When this happens it is called an endogenous retrovirus, or ERV.

We can watch this process in action in both the wild and in the lab. We have also constructed viral genomes from the consensus sequence of several human ERVs, and the result is a viable retrovirus. Again, we can observe new retroviral insertions occurring in real time, and ERVs already in the human genome can be reconstructed into retroviruses. There is absolutely no reason to doubt that ERVs are from retroviral insertions.

We also know that retroviral insertion can occur almost anywhere in the genome. When scientists infect cells with retroviruses and determine where in the genome the insertion occurred these are the results they get:

click here:
http://journals.plos.org/plosbiology/article/figure?id=10.1371/journal.pbio.0020234.g001

Those are the 22 human chromosomes, and each colored circle marks a retroviral insertion that occurred in the lab. As you can see, insertions happened all over the place in each of the chromosomes.

What this means is that two insertions that happen independently of one another should occur at different spots in the genome in the vast majority of cases. Therefore, when we find the same insertion at the same spot in the genomes of two individuals this means that the insertion happened only once in a common ancestor. Again, if two individuals do not share common ancestry then their ERVs should be found at different places in their genome. If they share a relatively recent ancestor then they should share nearly all of their ERVs at the same location in their genomes which are called orthologous ERVs. This is the scientific test for common ancestry.

So how does this apply to human ancestry? The human genome has over 200,000 ERVs. There are about the same number in the chimp genome. Of the ERVs in the human genome, nearly all of them are found at the same position in the chimp genome. Less than 100 human ERVs do not have an ortholog (i.e. same ERV at the same position) in the chimp genome. This is smoking gun evidence for common ancestry between chimps and humans.

References:

https://www.nature.com/articles/35057062

https://www.nature.com/articles/nature04072

A wonderful example of providing evidence/proof of the accuracy of one idea by later investigations that had a chance of qualifying or even disproving that original idea.

Thanks for sharing.

 

[A Vestigial Mote]

In this thread I will be presenting evidence that supports the origin of humans. That origin is descent through modification (i.e. evolution) from ape-like ancestors. The specific evidence I will be presenting is focused on endogenous retroviruses, or ERVs.

Retroviruses are usually RNA based viruses that reverse transcribe their genomes into DNA and then insert that DNA into the host genome. The long terminal repeats at the ends of the inserted viral genome act as strong gene promoters causing the host genetic systems to transcribe and translate the genes found in the viral genome. This results in the construction of new virus that buds off from the host cell and moves to new cells where the process is repeated. Retroviruses that invade and insert into the genome of a sperm or egg have the chance of being passed on to the next generation. When this happens it is called an endogenous retrovirus, or ERV.

We can watch this process in action in both the wild and in the lab. We have also constructed viral genomes from the consensus sequence of several human ERVs, and the result is a viable retrovirus. Again, we can observe new retroviral insertions occurring in real time, and ERVs already in the human genome can be reconstructed into retroviruses. There is absolutely no reason to doubt that ERVs are from retroviral insertions.

We also know that retroviral insertion can occur almost anywhere in the genome. When scientists infect cells with retroviruses and determine where in the genome the insertion occurred these are the results they get:

click here:
http://journals.plos.org/plosbiology/article/figure?id=10.1371/journal.pbio.0020234.g001

Those are the 22 human chromosomes, and each colored circle marks a retroviral insertion that occurred in the lab. As you can see, insertions happened all over the place in each of the chromosomes.

What this means is that two insertions that happen independently of one another should occur at different spots in the genome in the vast majority of cases. Therefore, when we find the same insertion at the same spot in the genomes of two individuals this means that the insertion happened only once in a common ancestor. Again, if two individuals do not share common ancestry then their ERVs should be found at different places in their genome. If they share a relatively recent ancestor then they should share nearly all of their ERVs at the same location in their genomes which are called orthologous ERVs. This is the scientific test for common ancestry.

So how does this apply to human ancestry? The human genome has over 200,000 ERVs. There are about the same number in the chimp genome. Of the ERVs in the human genome, nearly all of them are found at the same position in the chimp genome. Less than 100 human ERVs do not have an ortholog (i.e. same ERV at the same position) in the chimp genome. This is smoking gun evidence for common ancestry between chimps and humans.

References:

https://www.nature.com/articles/35057062

https://www.nature.com/articles/nature04072

This is great stuff. Smoking gun is right. Argue with this and you are arguing against nature basically having SIGNED DOCUMENTATION (that signature being in the form of virus-induced DNA transcriptions) that conclusively states that chimps were our ancestors.

 

[Subduction Zone]

And let's not forget for the deniers that claim they are not viruses in the first place that a human retrovirus was revived:

https://www.nature.com/news/2006/061030/full/news061030-4.html

"Heidmann's team focused on a particular type of retrovirus that infected human cells less than 5 million years ago and left a legacy of some 30 copies of itself in the modern human genome. These duplicates have all become slightly different over time as they acquired various mutations. By comparing them, the researchers worked out the most likely sequence of the original virus from which they were copied."

The retrovirus as found in the genome of any one human would not work, but by comparing at least thirty different variations they were able to deduce the most likely original virus and it did "come to life" when rebuilt.

 

[Thermos aquaticus]

And let's not forget for the deniers that claim they are not viruses in the first place that a human retrovirus was revived:

It also shines a light on the other arguments that creationists make. We will often see them claiming that we don't observe new species being formed, or that we haven't seen life emerge from non-living chemicals in the lab. Well, we can directly observe retroviruses creating ERVs in the lab, but is that good enough? Nope.

https://www.nature.com/news/2006/061030/full/news061030-4.html

"Heidmann's team focused on a particular type of retrovirus that infected human cells less than 5 million years ago and left a legacy of some 30 copies of itself in the modern human genome. These duplicates have all become slightly different over time as they acquired various mutations. By comparing them, the researchers worked out the most likely sequence of the original virus from which they were copied."

The retrovirus as found in the genome of any one human would not work, but by comparing at least thirty different variations they were able to deduce the most likely original virus and it did "come to life" when rebuilt.

This process can also test an important hypothesis. Scientists are proposing that these ERVs were produced by a functional retrovirus inserting itself into the host genome at some point in the past. There will be cases where mutations were introduced during insertion which resulted in a non-functional pro-viral insertion which is why the sperm or egg was able to survive and pass on that insertion. The ERVs will also accumulate mutations over time as it is passed down through the generations. Therefore, removing the mutations that have accumulated in those ERVs over time should result in a functional virus.

This is where a consensus sequence comes into play. This is where you align the ERVs and use the most common base at each position in the viral genome. This will remove a lot of the mutations that have accumulated in these ERVs as they were passed down through the generations. However, it isn't perfect because it will also remove any beneficial mutations that occurred over time in the viral population. Nonetheless, a consensus sequence will be much closer to a functional sequence than the ERVs, and that is what we see in this example.

 

[Thermos aquaticus]

This is great stuff. Smoking gun is right. Argue with this and you are arguing against nature basically having SIGNED DOCUMENTATION (that signature being in the form of virus-induced DNA transcriptions) that conclusively states that chimps were our ancestors.

Every genome is a direct record of ancestry which makes it a much more powerful piece of evidence than the fossil record. With fossils we can't determine who is directly related to who, but we can do that with DNA. If all we had was DNA and not a single fossil we would still have overwhelming evidence for common ancestry and evolution.

"Arguments against macroevolution, based on so-called gaps in the fossil records, are also profoundly weakened by the much more detailed and digital information revealed from the study of genomes. Outside of a time machine, Darwin could hardly have imagined a more powerful data set than comparative genomics to confirm his theory."--Dr. Francis Collins, "Faith and the Human Genome"

 

[Thermos aquaticus]

For creationists who continue to argue that the same retrovirus will insert into the same position in multiple species even in the face of evidence otherwise there is another piece of evidence that they have to contend with. That evidence is the PtERV-1 insertions found in the chimp and gorilla genomes.

Here is the proposed phylogeny for humans and other apes:

We see that chimps and humans share a recent common ancestor, humans/chimps/gorillas share a more distant common ancestor, and humans/chimps/gorillas/orangutans share a more distant ancestor than the other groups. This can be used to make predictions about which ERV insertions should be found at the same position and which should not.

As it turns out, chimps and gorillas have insertions from a retrovirus called PtERV-1. These insertions are not found in the orangutan or human genomes. If those insertions had occurred in the common ancestor of all those species then we would expect to find them in all of those genomes, but we don't. Therefore, the theory of evolution would predict that PtERV-1 insertions occurred after chimps split from the human lineage and occurred independently in the chimp and gorilla genomes.

In addition, the theory of evolution would predict that these insertions should be found at different places in the chimp and gorilla genomes since these insertions occurred independently in each lineage and did not descend from a common ancestor. Creationists, on the other hand, would predict that these insertions would be at the same places in each genome because they contend that the same retrovirus will insert into the same place in similar genomes. In this case we have the theory of evolution and creationism making very different predictions and easily testable predictions.

So do we find PtERV-1 insertions in the same place in the chimp and gorilla genomes? Of the nearly 200 PtERV-1 insertions that they looked at they were unable to find a single unambiguous example of a PtERV-1 insertion occurring at the same base in the chimp and gorilla genome just as the theory of evolution predicts and contrary to the predictions made by creationists.

In the end, it is the pattern of both orthologous ERVs (i.e. ERVs at the same genomic location) AND non-orthologous ERVs that evidences evolution, and this pattern can't be explained by creationism.

Reference:
Lineage-Specific Expansions of Retroviral Insertions within the Genomes of African Great Apes but Not Humans and Orangutans