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Peromyscus?

WiYC quotes:
“We have identified two hot spots for SINE insertion within mys-9 and at each hot spot have found that two independent SINE insertions have occurred at identical sites. These results have major repercussions for phylogenetic analyses based on SINE insertions, indicating the need for caution when one concludes that the existence of a SINE at a specific locus in multiple individuals is indicative of common ancestry. Although independent insertions at the same locus may be rare, SINE insertions are not homoplasy-free phylogenetic markers.”
“An ancient retrovirus-like element contains hot spots for SINE insertion.”
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1461688

I don't think that anyone has brought up a case for common ancestry bases solely on a SINGLE SINE at A SPECIFIC locus. In the whale instance, we have eight SINES in the chimp/human we have eight (so far). Homoplasy would be extremely unlikely in a single instance. The odds against it with seven or eight SINES is atronomical. Besides, who was talking about deer mice.

Read the paper. This is science providing new tools to refine our understanding.

WiYC quoted Kriegs, Churakov, Kiefmann, Brosius and Schmitz:

“Recently, Bashir et al. [ 44] published a purely computational method for reconstructing the phylogenetic relationships between mammals by automatically scanning for the presence and/or absence of transposed elements in mammalian sequences. However, this use of pure bioinformatics is fraught with pitfalls. The available sequence information is often not reliable, sequence drift makes identifying orthologous insertions extremely difficult, and full sequences are available for only a limited number of species. Extreme care must be taken to conclusively verify that supposedly homoplasmic insertions belong to the same class of transposons and are integrated at orthologous positions. For high-quality, reliable phylogenetic inferences it is essential to individually characterize the nature of each insertion as well as its integration site, a process not amenable to high-throughput computational searches and incomplete species sampling. “
“Retroposed Elements as Archives for the Evolutionary History of Placental Mammals”
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1395351

Yes, there are short-comings to the application of some methods in some circumstances as the quotation states. However, the caution to use care does not mean using SINES are useless. Note that they criticize the method used in another study and offer a way to better analyze phylogeny. At the same time, the paper acknowleges that analyzing relationships on the basis of molecular sampling has corrected earlier cladistic misgroupings based on morphology.

"Reconstruction of the placental mammalian (eutherian) evolutionary tree has undergone diverse revisions, and numerous aspects remain hotly debated. Initial hierarchical divisions based on morphology contained many misgroupings due to features that evolved independently by similar selection processes. Molecular analyses corrected many of these misgroupings and the superordinal hierarchy of placental mammals was recently assembled into four clades."

Science becomes more powerful as alternative tools and methods are developed to test conclusions. This team is using retrotransposons to test relationships between mammal species. There strategies and refinements will strengthen this kind of analysis. This paper doesn't undermine the use of genetic markers to analyze phylogeny, it supports it. As there paper said discussing retroposed elements.

"Retroposed elements provide an exceptionally informative source of rare genomic changes. They are a virtually ambiguity-free approximation of evolutionary history [ 24, 25]. The nearly homoplasy-free character and innate complexity of retroposed elements in mammalian species, coupled with their high abundance, enables phylogenetic reconstructions based on a variety of alternative markers."

Moving the goalposts when you can't respond to ERV evidence for evolution

WiYC said:
"1. Explain in detail a hypothetical genetic step-by-step scenario of the evolution of the first virus."

The question at hand was whether or not you could respond to the evidence for evolution that is provided by ERVs. This has nothing to do with that. You obviously can't respond.

How retroviruses evolved billions of years ago does not change the fact that genetic evidence shows that they did infect the common ancestors of all great apes (including us) a few million years ago.

Re: Moving the goalposts when you can't respond to ERV evidence for evolution

For feather thread:

Will you stop deleting my links to articles already! Deleting them doesn't make them non-existant!

1. I said no such thing. I said that there is too much that we do not know about genes.

2. Here are the links to articles you continue to delete on teh subject of feather evolution.
http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WX0-4N3GFRW-1&_user=5908723&_coverDate=04%2F30%2F2007&_alid=621592783&_rdoc=2&_fmt=summary&_orig=search&_cdi=7144&_sort=d&_docanchor=&view=c&_ct=41&_acct=C000050221&_version=1&_urlVersion=0&_userid=5908723&md5=66c0d86bf513d97494a0bd402ca30539
http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WDG-4N2KTJD-5&_user=5908723&_coverDate=05%2F01%2F2007&_alid=621592783&_rdoc=1&_fmt=summary&_orig=search&_cdi=6766&_sort=d&_docanchor=&view=c&_ct=41&_acct=C000050221&_version=1&_urlVersion=0&_userid=5908723&md5=79a81a12564e8c8a534426c17693d492
http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRW-4M4KK5D-1&_user=5908723&_coverDate=12%2F31%2F2006&_alid=621592783&_rdoc=3&_fmt=summary&_orig=search&_cdi=6245&_sort=d&_docanchor=&view=c&_ct=41&_acct=C000050221&_version=1&_urlVersion=0&_userid=5908723&md5=6930394eb57ddf3bf04d3ec604921ccd

Now either acknowledge that they exist or stoip acting high and mighty.

Goalpost argument

In regard to your comment:

"WiYC said:
"1. Explain in detail a hypothetical genetic step-by-step scenario of the evolution of the first virus."

The question at hand was whether or not you could respond to the evidence for evolution that is provided by ERVs. This has nothing to do with that. You obviously can't respond."


Discussing how and why viruses ‘evolved’ (retroviruses in particular) in addition to the continued evolution of viruses is critical to the argument:

"Clearly, properly understanding the nature of SINE retroposons and how they evolve is fundamental to their intelligent application as phylogenetic tools."
“SINE Evolution, Missing Data, and the Origin of Whales”
http://209.85.165.104/search?q=cache:O7yDdmkPl1cJ:www.ulb.ac.be/sciences/ueg/pdf_files/shedlock%26al_00.pdf+hillis+9980+sine+evolution&hl=en&ct=clnk&cd=1&gl=us


2. In regard to your comment:

"How retroviruses evolved billions of years ago does not change the fact that genetic evidence shows that they did infect the common ancestors of all great apes (including us) a few million years ago."


Retrovirus 'infection' does NOT prove common descent.

Please provide your 'genetic evidence.'

You need to understand what they are talking about.

WiYC:
Discussing how and why viruses ‘evolved’ (retroviruses in particular) in addition to the continued evolution of viruses is critical to the argument:

"Clearly, properly understanding the nature of SINE retroposons and how they evolve is fundamental to their intelligent application as phylogenetic tools."
“SINE Evolution, Missing Data, and the Origin of Whales”
http://209.85.165.104/search?q=cache:O7yDdmkPl1cJ:www.ulb.ac.be/sciences/ueg/pdf_files/shedlock%26al_00.pdf+hillis+9980+sine+evolution&hl=en&ct=clnk&cd=1&gl=us

You really should read the article. They are talking about changes in SINES not retroviruses. SINES are the remnants of an earlier infection. If you read the section just after what is quoted, they explain how SINES are effected by subsiquent evolution of the host.

If you would actually read what I posted about your questions and the links I provided, you would understand this issue. From the very article you quote, the authors support the use of SINES to establish artyodactyl descent for whales. They criticize the Lucket and Hong for not understanding how SINES evolve.

"In there recent assessment of morphological and molecular evidence for inferring cetacean ancestry, Luckett and Hong (1998) badly miscontrue how SINEs evolve, misinterpret how they are used for phylogeny inference, and incorrectly dismiss evidence from SINEs that conclusively demonstrate paraphyly of the Artiodacyla. We believe this is a serious problem that is counterproductive to advancing an accurate understanding of cetacean evolution and unfortunately promotes a negative view regarding the value of molecular data that goes well beyond the current debate about whale origins."

Note that the paper talks about the evolution of SINEs (Short Interspersed Elements) are not retroviruses. Although they are one of the four classes of retrotransposons. SINE insertions are also evidence of common descent. They are much shorter segments of code than ERVs. "These are approximately 300 bp long and do not encode any protein sequence. The recent DNA sequence analysis of the human genome found about 1.1 million Alus, comprising 10.6% of the DNA (Nature 409:860, 2001)."
http://www.talkorigins.org/faqs/molgen/

ERVs are much longer and more complex. They were noted after intensive studies retroviruses because they are structured like them.

"Soon after the discovery of infections retroviruses, scientists noticed that similar sequences were present in the DNA of many mammalian species, including humans; these copies are called endogenous retroviruses, and presumably represent the consequences of ancient retroviral infections of germline cells. In human DNA there are about 8 different classes of endogenous retroviruses with members of each class varying in number from one or two to more than 50 copies. Essentially all of these endogenous retroviruses contain mutations that would disrupt the function of their genes, as would be expected if they inserted millions of years ago with no selective pressure to maintain the function of the genes. In addition, the duplicated LTR sequences represent potential targets for "homologous recombination" events that delete the DNA between the corresponding region of the LTRs, leaving only a single composite LTR sequence; many more copies of these isolated LTR fragments exist in the DNA than complete retroviral copies."
http://www.talkorigins.org/faqs/molgen/

ERVs are no longer active viruses either. They have become artifacts in the DNA of the host species. To conclude, understanding how SINEs or ERVs evolve within the host is indeed important to understanding how to use them to determine phylogenetic sequences. However, neither would require an understanding of the origin of retroviruses. SINEs never were viruses and ERVs are no longer active viruses. Both do evolve within the host, but because neither are functional there is no selective pressure which allows them to continue to change. This is why ERVs are so effective for determining phylogeny.

First you deleted the post providing evidence for ERVs supporting common descent.

WiYC said:
"Retrovirus 'infection' does NOT prove common descent.

Please provide your 'genetic evidence.'"

I provided the evidence in an earlier post addressing one of your four questions.