{II} Endogenous Retroviruses: The Three Layers of ERV Evidence for Common Ancestry

Second Video: http://www.youtube.com/watch?v=_kfLo4Wd6cc

First Video: http://www.youtube.com/watch?v=xIAd8Zx_JKY

The script for this video is an article I wrote for my website:
ERVs: http://www.evolutionarymodel.com/ervs.htm
Homepage: http://evolutionarymodel.com/

Series References:

Download zipped folder of PDFs: http://www.mediafire.com/file/eutzygv5okt/erv_refs.zip

Anderssen, S., E. Sjøttem, G. Svineng, and T. Johansen. "Comparative Analyses of LTRs of the ERV-H Family of Primate-Specific Retrovirus-like Elements Isolated from Marmoset, African Green Monkey, and Man." Virology 234.1 (1997): 14-30.
http://www.ncbi.nlm.nih.gov/pubmed/9234943

Belshaw, R., V. Pereira, A. Katzourakis, G. Talbot, J. Paces, A. Burt, and M. Tristem. "Long-term reinfection of the human genome by endogenous retroviruses." Proceedings of the National Academy of Sciences USA 101.14 (2004): 4894-899.
http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=...

Boeke, J. D., and J. P. Stoye. "Retrotransposons, endogenous retroviruses and the evolution of retroelements." (1997). In. Coffin, J. M., S. H. Hughes, and H. E. Varmus. Retroviruses. New York: Cold Spring Harbor Laboratory Press, 1997.
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=rv.chapter.3430

Cann, Alan. "Retroviruses." MicrobiologyBytes. Web. 26 Oct. 2009.
http://www.microbiologybytes.com/virology/Retroviruses.html

Cohen, C. J., W. M. Lock, and D. L. Mager. "Endogenous retroviral LTRs as promoters for human genes: a critical assessment." Gene 448.2 (2009): 105-14.
http://www.ncbi.nlm.nih.gov/pubmed/19577618

Dangel, A. W., B. J. Baker, A. R. Mendoza, and C. Y. Yu. "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 42.1 (1995): 41-52.
http://www.ncbi.nlm.nih.gov/pubmed/7797267

Dunlap, K. A., M. Palmarini, M. Varela, R. C. Burghardt, K. Hayashi, J. L. Farmer, and T. E. Spencer. "Endogenous retroviruses regulate periimplantation placental growth and differentiation." Proc Natl Acad Sci U S A. 103.39 (2006): 14390-5.
http://www.pnas.org/content/103/39/14390.full

Hughes, J. F., and J. M. Coffin. "Human endogenous retroviral elements as indicators of ectopic recombination events in the primate genome." Genetics 171 (2005): 1183-194.
http://www.genetics.org/cgi/content/abstract/genetics.105.043976v1

International Human Genome Sequencing Consortium. "Initial sequencing and analysis of the human genome." Nature 409.6822 (2001): 860-921.
http://www.nature.com/nature/journal/v409/n6822/full/409860a0.html

Johnson, W. E., and J. M. Coffin. "Constructing primate phylogenies from ancient retrovirus sequences USA." Proceedings of the National Academy of Sciences 96.18 (1999): 10254-0260.
http://www.pnas.org/content/96/18/10254.full

Lebedev, Y. B., O. S. Belonovitch, N. V. Zybrova, P. P. Khil, S. G. Kurdyukov, T. V. Vinogradova, G. Hunsmann, and E. D. Sverdlov. "Differences in HERV-K LTR insertions in orthologous loci of humans and great apes." Gene 247.1-2 (2000): 265-77.
http://www.ncbi.nlm.nih.gov/pubmed/10773466?dopt=Abstract

Mitchell, R. S., B. F. Beitzel, A. R. Schroder, P. Shinn, H. Chen, C. C. Berry, J. R. Ecker, and F. D. Bushman. "Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site preferences." PLoS Biology 2.E234 (2004).
http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=...

Polavarapu, N., N. J. Bowen, and J. F. McDonald. "Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses." Genome Biology 7.R51 (2006).
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1779541

Skinner, L. M., M. Sudol, A. L. Harper, and M. Katzman. "Nucleophile Selection for the Endonuclease Activities of Human, Ovine, and Avian Retroviral Integrases." Journal of Biological Chemistry 276.1 (2001): 114-24.
http://www.jbc.org/cgi/content/full/276/1/114

Murcia, P. R., F. Arnaud, and M. Palmarini. "The transdominant endogenous retrovirus enJS56A1 associates with and blocks intracellular trafficking of Jaagsiekte sheep retrovirus Gag." J Virol. 81.4 (2007): 1762-72.
http://jvi.asm.org/cgi/content/full/81/4/1762

Steinhuber, S., M. Brack, G. Hunsmann, H. Schwelberger, M. P. Dierich, and W. Vogetseder. "Distribution of human endogenous retrovirus HERV-K genomes in humans and different primates." Human Genetics 96.2 (1995): 188-92.
http://www.ncbi.nlm.nih.gov/pubmed/7635468

Targeting HIV replication. Boehringer Ingelheim. Web. 3 Nov. 2009.
http://hiv.boehringer-ingelheim.com/com/HIV/Information_material/popup_video1...

Category:

Science & Technology

Tags:

• DNA
• endogenous
• retroviruses
• ERVs
• evidence
• common
• ancestry
• evolution
• evolutionary
• model
• theory
• Darwin

[hamzah938]

ATTENTION (TheRationalizer): Well as a self-proclaimed Atheist I owned you pretty good! Your use of the 'F' word and blocking me from comment on your channel was childlike. Your accusation of 'threat by proxy' was a flimsy EXCUSE to avoid my logic, and your hasty retreat avoided defeat.............NOT ! --------------> TOUCHDOWN CELEBRATION ! In your Face ! <----------------

[Kuartus]

Sure, but we see that duplicated genes can affect the phenotype enough to cause an organism to be at a serious disadvantage. Down syndrome is one example. It is believe that the extra copy of a gene in the extra 21 chromosome causes abnormal levels of purines which in turn cause retardation. Surely if at the mercy of natural selection, such individuals would perish. Thankfully that is not the case. Besides, there is so much so called "junk DNA" that it would be considerable energy to maintain.

[Uhlbelk]

@Kuartus Evolution does not have the option of thought. It is like a train on railroad tracks, it simply goes forward. If you dump an extra extra car onto it, it continues to go forward unless that car is a sufficient hindrance to make it stop. People have something like 22,000 genes and fast turn over cells can replicate daily. One gene getting duplicated, means nothing to that cell unless it disrupts the metabolic balance of the cell, and energy expenditure will not do that.

[Kuartus]

@FiverBeyond

This time dont paste them into the address bar. I tried it and they weren't being pasted correctly.

[Kuartus]

@Uhlbelk

That is not entirely true. An organism which reproduces non essential dna is expending energy in copying it and passing it on. The fact that so much non coding dna exists implies that is serves essential functions. An organism would be at a disadvantage copying useless dna since it is wasting energy and would then be influenced by natural selection into getting rid of it. If a gene is useless then it would be weeded out of the phenotype.

[FiverBeyond]

@Kuartus

I've tried them again and am still getting errors.

[Uhlbelk]

@Kuartus As for the mutation comment, it is misleading because while mutation in the DNA is generally a constant rate, which makes genetic dating possible, it is misleading because a redundant gene can be non-functional, or changing it will not change the phenotype. This means that the mutation cannot be selected for. His statement is also true of non-coding DNA, but we know that mutates fast enough to distinguish one human from another, or give paternity tests ect...

[Uhlbelk]

@Kuartus SOME phenotypes can be influenced by a single gene and others can't, that is why they have whole libraries of genetic knockouts and there is always a list of genes that cannot be knocked out because it would be a lethal mutation. It is also completely false because a gene only has a selectable advantage based on specific conditions/environments that selected for that gene. Once the selective pressure is gone, it is no longer an advantage, this is how vestigial structures come about. 

[Uhlbelk]

@Kuartus I don't need a paper to say "because according to the Darwinian paradigm, all genes should have a selectable advantage" is false. Darwin talked about species as entire entities, i.e. natural selection works on phenotype, but phenotype is not based on a single gene and nowhere in any literature do scientists make that claim.

[Kuartus]

@Uhlbelk

Hmm, care to cite some credible papers in favor of your claims?