U3rU5-gag-pol-env-U3rU5

My MolecularBioVids account was suspended, and every comment I left on every video I left them on was removed by YouTube.

This was either the result of a false harassment claim by NephilimFree, or a mistake on YouTube's behalf, when attempting to delete an account with a genuine harassment complaint leveled against its owner. NephilimFree denies involvement, but he engaged in far too much dishonesty in our latest discussion for me to take his word at face value. There is simply no way to know which scenario is accurate, given that YouTube saw fit to take action without sending me any e-mail message explaining their motivation.

I have re-uploaded my series on the endogenous retroviral evidence for common ancestry.



The following is a summary of the three layers of ERV evidence:

Layer 1: the presence of ERVs in orthologous loci among species of various degrees of taxonomic separation, and of the nested hierarchies they fall into.

Since they're passed on through sexual reproduction, ERVs fixed in orthologous loci in different species necessitates the past presence of a species ancestral to both, that has since diverged into the two modern ones. And the patterns of their distribution indicate a specific sequence of divergence.

Layer 2: the comparative degrees of LTR-LTR discontinuity among orthologous full-length ERVs.

Since LTRs are identical upon reverse transcription and subsequent insertion, greater divergence correlates to an older insertion. Thus the patterns of discontinuity indicate sequences of divergences consistent with those indicated by distribution.

Layer 3: shared mutations among orthologous ERV and the nested hierarchies they fall into.

Since mutations accumulate and fix in populations of organisms, the distribution of shared mutation indicate a sequence of speciation events consistent with that which is indicted by both distribution and LTR-LTR discontinuity.

Even just ERV evidence alone is definitive; the most parsimonious model is one in which all primates—including humans—share common ancestry



~Recommended online, open-access reading~

Download this reading list:

Folder with PDFs: http://tinyurl.com/dgenx3

Layout of ERV evidence (simple to complex):

Coffin, J.M. 2004. Evolution of retroviruses: Fossils in our DNA. Proc. Am. Phil. Soc. 148: 264-280.

http://tinyurl.com/dxd4hm


Johnson, W. E., Coffin, J. M. (1999). Constructing primate phylogenies from ancient retrovirus sequences. Proc. Natl. Acad. Sci. USA 96: 10254-10260.

http://tinyurl.com/cylf4g


---not open access---
Lebedev, Y. B., Belonovitch, O. S., Zybrova, N. V, Khil, P. P., Kurdyukov, S. G., Vinogradova, T. V., Hunsmann, G., and Sverdlov, E. D. (2000) "Differences in HERV-K LTR insertions in orthologous loci of humans and great apes." Gene 247: 265-277.

http://tinyurl.com/daafrq
---not open access---


John M. Coffin, Stephen H. Hughes and Harold E. Varmus, eds., Retroviruses, Cold Spring Harbor Laboratory Press, 1997. p 336.

http://tinyurl.com/canhlz


Belshaw, R., V. Pereira, A. Katzourakis, G. Talbot, J. Paces, A. Burt, and M. Tristem. 2004. Long-term reinfection of the human genome by endogenous retroviruses. Proc. Natl. Acad. Sci. USA 101:4894-4899.

http://tinyurl.com/c8h9xn


Hughes JF, Coffin JM: Human endogenous retroviral elements as indicators of ectopic recombination events in the primate genome. Genetics 2005, 171:1183-1194.

http://tinyurl.com/3tyau



Use of ERVs as molecular clocks:

---not open access---
Dangel, A. W., B. J. Baker, A. R. Mendoza and C. Y. Yu, 1995 Complement component C4 gene intron 9 as a phylogenetic marker for primates: long terminal repeats of the endogenous retrovirus ERV-K(C4) are a molecular clock of evolution. Immunogenetics 42: 4152.

http://tinyurl.com/d4y8te
---not open access---


ERV classification:

Jern, P; Sperber, GO; Blomberg, J. Use of endogenous retroviral sequences (ERVs) and structural markers for retroviral phylogenetic inference and taxonomy. Retrovirology. 2005;2:50.

http://tinyurl.com/dlk645



Function of integrase:

Skinner, L. M., Sudol, M., Harper, A. L., Katzman, M. (2001). Nucleophile Selection for the Endonuclease Activities of Human, Ovine, and Avian Retroviral Integrases. J. Biol. Chem. 276: 114-124

http://tinyurl.com/d5y34b



ERV reconstruction:

---requires free registration---
Kaiser, S. M., Malik, H. S., Emerman, M. (2007). Restriction of an Extinct Retrovirus by the Human TRIM5{alpha} Antiviral Protein. Science 316: 1756-1758

http://tinyurl.com/dh4fz2
---requires free registration---


Lavie, L; Medstrand, P; Schempp, W; Meese, E; Mayer, J. Human endogenous retrovirus family HERV-K(HML-5): status, evolution, and reconstruction of an ancient betaretrovirus in the human genome. J Virol. 2004;78:87888798. doi: 10.1128/JVI.78.16.8788-8798.20 04.

http://tinyurl.com/d8vzuy


Lee, YN; Bieniasz, PD. Reconstitution of an infectious human endogenous retrovirus. PLoS Pathog. 2007;3:e10.

http://tinyurl.com/cg6py

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