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Author Topic:   ERV's: Evidence of Common Ancestory
Mammuthus
Member (Idle past 6475 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 3 of 166 (151302)
10-20-2004 4:32 AM
Reply to: Message 1 by Loudmouth
10-19-2004 12:51 PM


First, I don't understand that this is not in the Contributor's forum. It certainly merits that status.
quote:
As to the falsification of evolution, if you were able to find a sequence shared by gorillas and humans that was not found in chimps then the theory of evolution would be in serious doubt. Additionally, find an ERV only shared by orangutans and humans and not chimps or gorillas, you would again cast serious doubt on the theory of evolution. However, these potential falsifications have never been observed. Only recently has the human genome been decoded, and even more recently the chimp genome. Soon, the gorilla genome will be complete, so even more ERV’s may show up. As more genomes are completed this test can be continually applied as new ERV’s are discovered in other primate and ape species, not to mention other non-primate species. Therefore, ERV’s are a fine example of a repeatable and falsifiable data set that can be used to test the theory of evolution.
There is a problem with this for example,
Curr Biol. 2001 May 15;11(10):779-83. Related Articles, Links
A HERV-K provirus in chimpanzees, bonobos and gorillas, but not humans.
Barbulescu M, Turner G, Su M, Kim R, Jensen-Seaman MI, Deinard AS, Kidd KK, Lenz J.
Department of Molecular Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA.
Evidence from DNA sequencing studies strongly indicated that humans and chimpanzees are more closely related to each other than either is to gorillas [1-4]. However, precise details of the nature of the evolutionary separation of the lineage leading to humans from those leading to the African great apes have remained uncertain. The unique insertion sites of endogenous retroviruses, like those of other transposable genetic elements, should be useful for resolving phylogenetic relationships among closely related species. We identified a human endogenous retrovirus K (HERV-K) provirus that is present at the orthologous position in the gorilla and chimpanzee genomes, but not in the human genome. Humans contain an intact preintegration site at this locus. These observations provide very strong evidence that, for some fraction of the genome, chimpanzees, bonobos, and gorillas are more closely related to each other than they are to humans. They also show that HERV-K replicated as a virus and reinfected the germline of the common ancestor of the four modern species during the period of time when the lineages were separating and demonstrate the utility of using HERV-K to trace human evolution.
Note, some portion of HERV-K shows closer affinity of Pan and Gorilla as opposed to Pan/Homo. I don't think this falsifies Pan/Homo as a grouping because HERV-K is extremely active (there are novel integrations that are human specific..and presumably novel chimp, gorilla, etc. integrations), they tend to homogenize by gene conversion, and HERVs tend to excise themselves by recombination so that humans and gorillas may share a HERV whereas in the chimp lineage, it was deleted and the deletion fixed. So, I think you would have to look at the specific history of specific HERVs to be able to determine whether a specific association falsifies the current concepts of primate phylogeny or not (I have a paper in review on this which I will link to...if it gets accepted ).

This message is a reply to:
 Message 1 by Loudmouth, posted 10-19-2004 12:51 PM Loudmouth has replied

Replies to this message:
 Message 4 by Loudmouth, posted 10-20-2004 1:22 PM Mammuthus has replied

  
Mammuthus
Member (Idle past 6475 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 5 of 166 (151524)
10-21-2004 4:28 AM
Reply to: Message 4 by Loudmouth
10-20-2004 1:22 PM


Here is are reference to human specific HERVs (again supporting Pan/Gorilla)
Barbulescu M, Turner G, Seaman MI, Deinard AS, Kidd KK, Lenz J. Related Articles, Links
Many human endogenous retrovirus K (HERV-K) proviruses are unique to humans.
Curr Biol. 1999 Aug 26;9(16):861-8.
You are not barking up the wrong tree. The authors hypothesize that the proviral insertions were heterozygous and by chance disappeared in our lineage but became fixed in Pan and Gorilla. I guess the fact that such elements are rare (for inactive HERVs) supports this scenario i.e. as opposed to huge numbers of HERVs showing totally conflicting distribution patterns.
HERVs are difficult to study because they come in many different flavors. There are active HERVs like those of the HERV-K family which are still actively transposing around the genome. There are long dead ones even to the point of hardly being recognizable as HERVs anymore, there are HERVs that are serving critical function like syncytin so their evolution is much more highly conserved than one would expect, some have recombined to form novel elements, some have become homogenized by gene conversion, some are partially deleted because of recombination. The problem is HERVs are defined like cancer. One thinks of them as a single entity or locus as cancer is often thought of as a single disease. The fact is that HERVs make up about 10% of the genome which is far greater than the content of actual human genes. So it is millions of entities just as cancer referrs to a pantheon of diseases.
Then there is the issue of horizontal transfer. HERVs enter the genome by HGT. But then are transmitted vertically. Since different HERV groups entered the genome at different times and then transposed in (some cases) species specific ways, it makes studying their evolution challenging to say the least.

This message is a reply to:
 Message 4 by Loudmouth, posted 10-20-2004 1:22 PM Loudmouth has replied

Replies to this message:
 Message 6 by Loudmouth, posted 10-21-2004 1:13 PM Mammuthus has replied

  
Mammuthus
Member (Idle past 6475 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 7 of 166 (151879)
10-22-2004 5:12 AM
Reply to: Message 6 by Loudmouth
10-21-2004 1:13 PM


quote:
Studying ERV's in a single species would be difficult. Wouldn't you say that comparing ERV's in related species helps to elucidate insertion events and transpositions?
Yes, I would
http://www.ncbi.nlm.nih.gov/entrez/...
{Shortened display form of URL, to restore page width to normal - Adminnemooseus}
But in any case, that is a part of what I am doing in my research and what a large portion of the HERV community does i.e. Jens Mayer, Eugene Sverdlov, et al. The distributions however, tend to focus on HERV-K (with a bit of work on HERV-L to) but most other HERV's and their distributions are not known for non-human primates (until my paper gets accepted )
This message has been edited by Adminnemooseus, 10-22-2004 04:07 PM

This message is a reply to:
 Message 6 by Loudmouth, posted 10-21-2004 1:13 PM Loudmouth has replied

Replies to this message:
 Message 8 by Loudmouth, posted 10-22-2004 1:52 PM Mammuthus has replied

  
Mammuthus
Member (Idle past 6475 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 9 of 166 (152724)
10-25-2004 9:03 AM
Reply to: Message 8 by Loudmouth
10-22-2004 1:52 PM


Here is a brand spanking new example of a polymorphic HERV within a species, namely ours,
Genomics. 2004 Sep;84(3):596-599. Related Articles, Links
A rare event of insertion polymorphism of a HERV-K LTR in the human genome.
Mamedov I, Lebedev Y, Hunsmann G, Khusnutdinova E, Sverdlov E.
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya, 117997 Moscow, Russia.
Human endogenous retroviruses (HERVs), which constitute a significant part of the human genome, might have a serious impact on primate evolution. Over a hundred insertions of HERV-K(HML-2) family members distinguish the human genome from other primate genomes. However, only three cases of insertion polymorphisms have been reported so far, all for endogenous HERV-K proviruses. This suggests that some retroviral integrations occurred rather recently in human genome evolution. In this report, we describe a very rare case of true insertion polymorphism of a solitary HERV-K LTR in the human genome. Distribution of the LTR-containing allele was tested in 5 Africans and 83 individuals from three Russian populations. The allele frequency appeared to be relatively high in populations of both European and Asian origin. The detected polymorphic LTR could be a useful molecular genetic marker of the corresponding genomic region.
So it would appear it is a process that is still in action.

This message is a reply to:
 Message 8 by Loudmouth, posted 10-22-2004 1:52 PM Loudmouth has not replied

  
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