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| Constructing primate phylogenies from ancient retrovirus sequences https://www.pnas.org/content/96/18/10254.full https://barryhisblog.blogspot.com/p/long-terminal-repeats-ltrs.html |
A quick overview follows in the next paragraph. More can be found out if you click on 'ERV FAQ' at the top of this page.
Retroviruses replicate by converting their RNA genomes into DNA by reverse transcription and by inserting or 'integrating' the DNA version (the provirus) with the nuclear DNA of host cells. The host cells then dutifully produce more copies of the retrovirus by transcribing the proviral DNA back into RNA using RNA polymerase II under the influence of proviral promoter sequences. The promoters are necessary to promote transcription.
But RNA polymerase II does not normally transcribe promoters. Retroviruses have to make it do so, otherwise the newly replicated viruses would not be able to continue the replication cycle.
Retroviruses overcome this problem by polymerising copies of their promoters during reverse transcription, forming what are called long terminal repeats (LTRs) which can be transcribed back into RNA. LTRs appear at either end of the provirus and are always identical to one another when they are formed.
Upon examining LTRs from endogenous retroviruses, however, we find that many pairs of LTRs from ERVs have diverged. We call these divergences discontinuities. Discontinuities can be explained by mutation. The longer an ERV has been part of the species' genomes, the larger the discontinuity is likely to be.
When discontinuities are inherited by cousin species from common ancestors, this data, together with the degree of discontinuity should reflect already established taxonomy and phylogeny.
It does.
This is a prediction from evolutionary science, borne out by direct observation, that neither "intelligent design" nor creation "science" can account for.
You seem to be saying the it is the genetic divergence in the LTRs that occurs AFTER the ERV inserts itself that provide the evidence for common ancestry, whereas other sources suggest it is the location of the original insertion point itself the provides the evidence for common ancestry.
ReplyDeleteCan you clarify?
Yes. Unlike reverse transcriptase that makes many errors, the LTRs are duplicated faithfully and without errors. As time goes by they mutate and one can compare them between species and form a nested hierarchy that confirms great ape shared ancestry.
DeleteThe random insertion of retroviruses and that fact that they are shared between ape species (includes humans) is a separate line of evidence. When one finds the same ERVs in the same homologous locations often with the same mutations the only rational explanation is that the retrovirus inserted before the species split.
"Layer 2
As previously explained, although the LTRs of a provirus must be identical upon insertion, once endogenized, they begin accumulating mutations. Any mutations to one LTR become quite apparent, as they are not accompanied by the same mutations in the other. Thus each mutation causes the ratio of discontinuity between the two LTRs of a full-length ERV to increase. Since ERVs in identical loci among greater numbers species of wider taxonomic separation correlate to older insertions, if the evolutionary model is correct, they should also have higher ratios of discontinuity between their LTRs. And what do we find? We find just that; a pattern, where the degree of a shared ERVs’ LTR-LTR discontinuity is proportional to the degree of taxonomic separation between the species that share it (Johnson and Coffin, 1999). There is deviation from the pattern—likely caused by viral transfer and interelement recombination/conversion (Hughes & Coffin, 2005) and viral transfer (Belshaw et al., 2004)—but the pattern is holds for many full-length ERVs and is explainable only by decent with modification from a specific series of common ancestral species. Once again, we see strong evidence for ERV orthology."
https://evolutionarymodel.com/ervs.htm
Thank you!
DeleteThough you seem to be limiting yourself to "rational" explanations. Creationists don't suffer under such constraints!