ERV homology argument and comparative genomics

[46AND2]

Exactly. PtERV insertions are not orthologous amongst chimps and gorillas which shoots a huge hole in Mark's argument. In fact, we can use the theory of evolution to predict that they would not be orthologous, and they aren't.



Precisely.



I wasn't aware that they had narrowed down the cause for that yet, so that is good to hear.

One other thing to add: if I am correct in my research, the PtERV virus in the gorilla is not even called PtERV, since the Pt part indicates it's fixation point is unique among pan-troglodytes. It has different names in the gorilla and rhesus genomes, but they are associated with PtERV due to the similarity of their sequences.

But I'm still a little fuzzy on the nomenclature of ERVs.

 

[USincognito]

I noted, and messed up a bit while doing so, Mark's problem with orthologous locations. He's been making that same mistake for years and doesn't seem to get it after all that time.

The problem with Mark's argument is that he considers

Homo
ACGTERV1ACGTERV2ACGTACGTACGT

Pan
ACGTERV1ACGTERV2ACGTACGTACGT

Gorilla
ACGTERV1ACGTACGTACGTACGT

to be the same as

Homo
ACGTERV3ACGTACGTACGTACGT

Pan
ACGTACGTACGTACGTERV4ACGT

edit from original - Gorilla
ACGTACGTERV4ACGTACGTACGT

He can't seem to grasp how important orthologous locations are.

 

[46AND2]

I noted, and messed up a bit while doing so, Mark's problem with orthologous locations. He's been making that same mistake for years and doesn't seem to get it after all that time.

Yeah, I realize that I was basically just re-posting what you had already done. I just wanted to make it clear using his post, and show how he was incorrect about how the PtERV lined up, specifically.

 

[TheBear]

But if you don't mind my asking; what are your qualifications?

Very good question which got bypassed in Mark's reply. So, I'll re post it for you.

 

[Loudmouth]

One other thing to add: if I am correct in my research, the PtERV virus in the gorilla is not even called PtERV, since the Pt part indicates it's fixation point is unique among pan-troglodytes. It has different names in the gorilla and rhesus genomes, but they are associated with PtERV due to the similarity of their sequences.

But I'm still a little fuzzy on the nomenclature of ERVs.

It was first discovered in chimps so the Pt stuck. I think they are also refered to as CERV 1 by other authors.

The following paper is a good resource for the distribution and loci for PtERV1 insertions amongst chimps and gorillas:

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

In it, they discuss how they were unable to find a single unambiguous orthologous PtERV1 insertion out of the hundreds that they screened.

 

[46AND2]

It was first discovered in chimps so the Pt stuck. I think they are also refered to as CERV 1 by other authors.

The following paper is a good resource for the distribution and loci for PtERV1 insertions amongst chimps and gorillas:

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

In it, they discuss how they were unable to find a single unambiguous orthologous PtERV1 insertion out of the hundreds that they screened.

Ah, cool. I hadn't seen that paper. Thanks.