What are Long Terminal Repeats (LTRs)?

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" spotters nor creation "scienticians" can account for.