How old are complex retroviruses? At least 400 million years old!!!

Posted by ERV on August 27, 2012
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Paleovirology seems to work the opposite of the way the Creationist want.  The more information we have, the further back the timeline shifts, not vice versa.

For example, we used to think HIV-1 started in humans ~1930, but after we found more ‘old’ HIV sequences, the clock got pushed back to 1902-1921.

We used to think Simian Immunodeficiency Virus emerged 1266-1685, but after we found more ‘old’ SIV sequences, the clock got pushed back 76,794 years.

After a recent finding in fish, the evolutionary history of retroviruses got pushed back… 400 million years.

An Endogenous Foamy-like Viral Element in the Coelacanth Genome

They found an endogenous retrovirus in a fishy genome.  But not just any ol ERV… a foamy virus ERV.  Foamy viruses are complex, and only found in land mammals, thus assumed to be relatively recent inventions of nature.

But here is a foamy virus, plopped in the middle of a fishy genome, itself about 19 million years old.

When they compared the fishy foamy ERV to mammalian foamy viruses, and lots of different kinds of exogenous and endogenous retroviruses, they found:

… the most parsimonious explanation of this phylogenetic pattern is that foamy viruses infecting land mammals originated ultimately from a prehistoric virus circulating in lobe-finned fishes.

… The common ancestor of coelacanths and tetrapods must have existed prior to the earliest known coelacanth fossil, which is 407–409 million years old.

This means that complex retroviruses are at least ~400 million years old (how old are the simple ones??? HA!).  They followed us out of the water, and onto the land.

Its like every great event in our evolutionary history, we were walking hand-in-hand with our retroviruses… footprints in the sand…

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Comments

  1. #1 Optimus Primate
    August 27, 2012

    But, umm… what does it mean when there’s only one set of footprints?

  2. #2 Burden to the NWO
    August 27, 2012

    Means you are not being followed by the FEDs.

  3. #3 Bob Powers
    August 27, 2012

    Fortunately, to anyone who’s paying attention, there are not only more than one set of footprints– there are many, many sets.

    Evolution does not work on single individuals. It only works at the species level and beyond.

    Thus, there are a multiplicity of footprints….

  4. #4 Jake
    August 27, 2012

    Awww sh*t, 5-star post Abbie! I’m going to have to read this paper…

  5. #5 Hugo
    August 28, 2012

    Good god. That is old. Have you by any chance seen Nick Lane’s theory that microorganisms basically never go extinct?

  6. #6 harold
    United States
    August 28, 2012

    It depends on what you mean by “old”. There have probably been living cells for over three billion years. I’m sure viruses, broadly defined, can’t be all that much younger.

    Nitpick/request for more information – a certain collaborative online encyclopedia says that spumaviruses are ds DNA viruses. Is it fair to call the ERVs, or are they just EVs?

  7. #7 ERV
    August 28, 2012

    Spumas are definitely retroviruses– they have the usual LTR-gag-pol-env-LTR genomic structure, plus some accessory genes (its a complex retrovirus, not simple), integrates into the genome, etc. It just plays the retrovirus game a little differently than the others, and reverse transcribes itself more before it is ever packaged, rather than after it is released into the new host cell :)

  8. #8 windy
    August 28, 2012

    Amazing. Seems a bit unlikely that the viruses would infect coelacanths and mammals, but not any other tetrapods besides mammals? Maybe they have, and the traces haven’t been found yet. They should test a lungfish genome for those things, too.

  9. #9 Ken
    Orlando
    August 30, 2012

    Not all creationists believe in a 6000 year creative timeline so it really does’t matter when science says something existed. The truth is, nobody knows how long a creative day was. A day with God is like 1000 years with man. Before you go calculating like a scientists, focus on the phrase “like”.

  10. #10 Tommykey
    http://anexeciseinfutility.blogspot.com
    August 30, 2012

    Shorter Ken from Orlando: We might as well not even waste our time trying to study anything.

  11. #11 dr duke
    September 2, 2012

    You’ve made one error. Finding the virus in one fish and no other vertebrate yet argues against it integrating into a common ancestor 400 Mya. Most likely a foamy virus was exogenous in the sea and integrated into this fish lineage less than 40Mya.

  12. #12 windy
    September 2, 2012

    dr duke: neither Abbie nor the authors of the study claim it integrated 400 Mya, but because of the phylogenetic congruence it’s likely that the viruses have co-evolved with their hosts for long periods before integration. The authors have addressed this possibility:

    “Given that there is strong evidence that placental mammals were already being infected with foamy viruses by about 100 million years ago [9], the distinctness of the coelacanth virus suggests that it would have to have crossed from some other unidentified host, one whose foamy-like virus was already hundreds of millions of years divergent from the mammalian viruses. This seems highly unlikely.”

  13. #13 Brian Foley
    September 3, 2012

    Abbie may not have stated that this foamy virus integrated 400 Mya but her title sort of implies that it did. The discovery of this foamy virus in a fish genome does not prove that retroviruses are more than 400 million years old. It does perhaps prove they have existed for more than 30 or 40 million years, but that is more dependant on comparing the two LTRs in integrated copies in the genome of the fish, to estimate the date of the integration event. The two LTR copies of an integrating genome are identical at the time of integration, and diverge over time at the rate of noncoding DNA in the host genome after that point.

  14. #14 windy
    September 3, 2012

    “Abbie may not have stated that this foamy virus integrated 400 Mya but her title sort of implies that it did.”

    No, the paper argues that this group of viruses has existed at least 400 my, not that they found a 400 my old integration event (that would probably be too degraded to detect anyway!). The paper (if we can call epubs “papers”) is open access, so you can easily check their reasoning for the age estimate.

  15. #15 David Edwards
    February 19, 2013

    Indeed, the authors checked various possibilities before erecting the conclusion that they did. Indeed, in the paper, they asked themselves the question, could this coelacanth ERV be the result of a more recent infection from a foamy virus of mammalian origin? This is discounted on the basis that [1] the other foamy viruses currently known are confined to terrestrial mammals (namely gorilla, chimpanzee, macaque, vervet monkey, spider monkey, cow, horse, cat and sloth, with a recent find in the aye-aye to add to the mix), whilst the coelacanth is a deep-water ocean dweller, separated from terrestrial mammals by 1,000 feet or more of ocean depth.

    In the meantime, whilst posting about this (including an exposition of the paper for the other forum members), I ended the post with this comment, which BBC TV viewers in the UK will probably smile at:

    “I think Abbie should present a TV show – Walking With Retroviruses.“

  16. #16 David Edwards
    February 19, 2013

    Oops, forgot to provide a link to the ,a href=”http://www.rationalskepticism.org/creationism/nested-hierarchy-and-predictions-t37733.html#p1632930″>post in the above. :)

  17. #17 David Edwards
    February 19, 2013

    Oh for crying out loud, I hate this keyboard … let’s try that again …

    link to post

    Abbie, any chance of a preview button on your blog, so I can deal with such errors at source? :)