Actually, no they shouldn't. First, you have repetitive sequence at either end of the ERV's which are the LTR's. Repetitive sequences lend themselves to recombination events. Therefore, there will be more recombination events at LTR's compared to non-repetitive DNA elsewhere in the genome.
I get the logic just not the relevance. This point of clarification is something I found helpful:
multiple integrations (and subsequent fixation) of ERV loci at precisely the same location are highly unlikely (cited and linked below)
The question then becomes how common is it. First you would determine the amount of ERVs in a genome, so what is it for you now, 1%, 4% or 8%. I only ask because when our debate ended you were stuck at 4% and some change.
Second, retroviral insertions may very well be deleterious. This would lead to selection of mutations such as indels.
Selection of mutations whether insertions, deletions, point or rearrangements are most often deleterious when they have an effect strong enough for selection to act. What their connection is to molecular mechanisms that effectively alter the traits of a species is speculative. One thing is clear, to me at least. The DNA repair mechanisms are far more common in genomes then ERVs.
There are only a few hundred PtERV insertions in chims and gorillas, none of which are orthologous. This compares to the over 200,000 ERV's in chimps.
Just the largest and most abundant families of ERVs in the Chimpanzee genome, no big deal right? I have seen some bad homology arguments before but this one gets worse as it goes.
Yes, and all of these insertions are non-orthologous just as the theory of evolution predicts. This prediction was made by looking at the distribution of PtERV insertions amongst primates. If evolution is true then PtERV insertions should be found at non-orthologous positions, and they are.
You left out the null hypothesis, that's just another form of begging the question. Anyway, you are throwing words around without ever bothering to say what they actually mean. It would not be so bad it you did not do it so often.
The term orthologous segment is defined as a set of genomic segments in different organisms descended from a common ancestor without large rearrangements (
Dewey et al., 2006).
That is classic circular reasoning, it is from a common ancestor so if we find it in the sequence it proves common ancestry. The fact of the matter is that they are called orthologous because they are so much alike, it's as simple as that. You would not find them at orthologous locations because if they were significantly different they wouldn't be called orthologous. Your being fallacious.
So we can't test to see if insertions are found at an orthologous base in each genome? Every geneticist I know will completely disagree. The predictions are testable, and they have been tested. They passed.
They were compared dude, just like indels in comparative genomics don't have to be the result of insertions or deletions. Not if the genomes are independently created. They are simply differences and if you want to compare the things that are the same and offer them as proof you have to account for the differences.
The argument is not based on percentages. It is based on orthology and divergence. You might as well claim that finding 8 fingerprints instead of 1 fingerprint at a crime scene somehow negates the evidence. It doesn't.
We are not talking about fingerprints, we are talking about sequences that are prone to mutations. You are talking about fragments in a lot of cases and pretending they are all broken in the same place, that's really shallow. What is worse is that you are so short on particulars.
There are over 200,000 ERV's in the chimp genome. PtERV insertions make up less than 1% of all ERV's.
This one is refreshingly honest:
Several lines of evidence indicate that chimpanzee and gorilla PTERV1 copies arose from an exogenous source. First, there is virtually no overlap (less than 4%) between the location of insertions among chimpanzee, gorilla, macaque, and baboon, making it unlikely that endogenous copies existed in a common ancestor and then became subsequently deleted in the human lineage and orangutan lineage. Second, the PTERV1 phylogenetic tree is inconsistent with the generally accepted species tree for primates, suggesting a horizontal transmission as opposed to a vertical transmission from a common ape ancestor. An alternative explanation may be that the primate phylogeny is grossly incorrect, as has been proposed by a minority of anthropologists.
Yohn et al, 2005
Which they shouldn't if evolution is true. That you don't understand that only highlights your ignorance of how evolution works.
I understand that you are very clumsy with the facts and vague with your terminology. I understand something about evolution you don't, the fact of the matter it is used in at least two different ways at the same time, a fallacy known as equivocation.
Zaius claims just the opposite. You guys need to get together and form a consistent argument.
Zaius raises and interesting point, other then that was are discussion very different things.
So you are saying that all of these scientists are fudging the data to make the ERV's appear to be orthologous? What exactly are you arguing against? You seem to be tilting at windmills.
Not appear, but are orthologous, meaning the sequences are the same.
"I have to be more then a little incredulous about 8% of the human genome being the result of viral invasions."--mark kennedy
Will the real mark kennedy please step forward?
Do you agree that it's 8% at least?.
That will do for now, thanks for the fish in the bowl target practice.
Have a nice day
Mark