[Coral-List] interesting essay on the bird phylogenetic tree produced by DNA

[Austin Bowden-Kerby]

Sorry I mistyped-  the gene transfer is between species not within
species!

Again:  SOME SEA SNAKES HAVE CORAL GENES!  How cool is that?



On Fri, Jul 22, 2022 at 10:34 AM Austin Bowden-Kerby <abowdenkerby at gmail.com>
wrote:

> Re-posting with additions at the bottom, as I forgot to delete our logo,
> which I believe invalidates the post:
>
> Very interesting Doug,
> I have chickens that lay blue eggs, which has now been shown to result
> from a gene dragged in from another bird species by a bird virus (three
> variations- three times independently: in China, the South Pacific and
> South America).  I have other chickens with naked necks, presumably the
> result of vulture DNA being dragged in by a similar bird virus and inserted
> into the genome (in Romania a hundred years or more ago).  But chickens did
> not descend from black birds or vultures, they are all descended from red
> jungle fowl.
>
> Could viruses and gene transfer be responsible for this coral conundrum?
> If so it is not parallel evolution.  I suppose with a lot more genetic
> markers being discovered, that this will come out in time.
>
> More on this topic of gene exchange between species mediated by viruses
> and even bacteria can be found via abundant publications on the web.
>
> This article shows how the gene transfers can occur independent of viruses
> and bacteria during close contact during mass spawning!  With a vital
> antifreeze gene being transferred directly between two unrelated fish
> species.
>
> https://www.quantamagazine.org/dna-jumps-between-animal-species-no-one-knows-how-often-20210609/
>
>
> Also this amazing piece of information in the same article:
>
> "the olive sea snake (*Aipysurus laevis*)... has evidence of seven
> horizontal transfers (of genes) into the sea snake genome. .... the best
> matches were found in fish and, in one case, corals."  (Suspected to be via
> an unknown vector organism).
>
> SOME SEA SNAKES HAVE CORAL GENES!  How cool is that?
>
> My question is this:  are the people running these genetic tools trained
> geneticists, or are they mostly skilled lab technicians?  If they were
> the former then they would be aware of the widespread horizontal transfer
> of genes within species, especially those that coexist in the same
> environments and which are susceptible to the same disease vectors.
>
> Doug, I conclude that your perceptions are absolutely right!
>
> Stay safe everyone, there are many dangers out there!
>
> Austin
>
>
>
>>
>> On Mon, Jul 18, 2022 at 11:27 PM Douglas Fenner via Coral-List <
>> coral-list at coral.aoml.noaa.gov> wrote:
>>
>>>        The link to this essay is at the end of my message.  You can. if
>>> you
>>> wish, just skip all the stuff I've written below (as usual it is far too
>>> long, but for some it might provide some perspective and rationale for
>>> why
>>> this essay might be interesting for people working with corals or even
>>> other reef organisms.  I think it raises questions about the phylogeny of
>>> corals.  Anyhow, just look at the link at the end of my message if you'd
>>> like to go directly to it.  Cheers, Doug
>>>
>>> Many of you are likely aware that DNA sequencing (often referred to as
>>> "molecular" studies, but then H2O is a molecule too, and that's not what
>>> they are talking about) has produced results with corals that conflict in
>>> some families with the placement of genera into families produced by
>>> morphology, and in some cases which species go into which genera.  There
>>> are similar conflicts for other groups of organisms, I've read.
>>>         I get the distinct feeling that almost everyone thinks that "the
>>> DNA is right!"  And why wouldn't they?  Morphology has been used for
>>> classification since Linnaeus started the taxonomic system we still use
>>> for
>>> naming, in 1758, 264 years ago.  Everybody knows that trying to sort out
>>> and identify corals based on morphology is a nightmare, perhaps best
>>> documented in Veron's book "Corals in Space and Time."  All of its
>>> weaknesses have been laid out in great detail.  DNA, on the other hand,
>>> is
>>> incredible, it is objective fact, a physical reality, not subjective
>>> opinion like morphology, cutting edge science and technology, which has
>>> illuminated innumerable things.  No one can quibble with the fantastic
>>> science DNA sequencing has produced.  Fabulous things have been done with
>>> it, it is real science, and the methods being used today are always being
>>> improved, it is cutting edge science, such that I joke that DNA
>>> sequencers
>>> are using methods invented last Thursday, instead of over 250 years ago
>>> like morphology.  No wonder almost everybody automatically says "the DNA
>>> is
>>> right."  People who do the sequencing say that they have a
>>> "revolution."  I
>>> don't know hardly anything about DNA sequencing.  How can I evaluate it
>>> compared to morphology?  I have to assume it is correct.  Surely I'm not
>>> alone, do all coral reef biologists sequence DNA in their spare time?  I
>>> doubt it.  If you don't understand the details, how could you possibly
>>> argue with it??  No need to.  We can assume it is correct.
>>>         Still, there are a few things that are a bit hard to swallow.
>>> DNA
>>> says that Alveopora is in the Acroporaidae.  Some of the disc-shaped
>>> Fungia
>>> species are said by DNA to be in Lithophyllon.  The other Lithophyllon
>>> don't look remotely similar to Fungia, and those species that used to be
>>> put in Fungia look almost identical to other species that used to be in
>>> Fungia.  And one species each that were in Coscinaraea and Psammocora,
>>> were put into Cycloseris.  They don't look remotely like Cycloseris, many
>>> details are very different.  Many such puzzling results are explained
>>> away
>>> by DNA people as convergent evolution.  Convergent evolution is real, it
>>> is
>>> well documented.  There are cases like birds and bats both having wings
>>> and
>>> flying, or fish and whales swimming in water (or better yet, porpoises
>>> and
>>> plesiosaurs) in which the selection pressure that produced the
>>> similarities
>>> are obvious.  So it is a ready explanation for these strange things with
>>> corals.  But it is an after-the-fact explanation.  You could use that to
>>> explain anything.  Anything. including saying that frogs are most closely
>>> related to humans and toads most closely related to yeast, if the DNA
>>> said
>>> that.  It has no predictive power; because it could explain anything, it
>>> explains nothing.  The cases in which it has been invoked like bats and
>>> birds have obvious selection pressures that produced those convergences.
>>> But for the coral examples, I've never read or heard or thought of any
>>> hypothetical selection pressure that could produce the coral examples I
>>> quoted above.  None.  Yes, dimmer light in deeper water selects for
>>> corals
>>> to become more flattened.  But notice, it is still possible to tell that
>>> a
>>> flat Acropora and a flat Porites are in those genera, and aren't in the
>>> same genus due to the flat shape.  It's not only possible to tell them
>>> apart, it's easy and obvious, and it is obvious that they are not the
>>> same
>>> thing.  Like bats and birds, fish and whales.  It is quite possible that
>>> convergent evolution did produce those coral examples.  Or maybe not.
>>> But
>>> again, it is extremely weak evidence if it is evidence at all. It just
>>> makes people feel good.  Unless someone comes up with the selection
>>> pressure that produced it.
>>>         The problem is that not everybody is an expert on DNA sequencing
>>> that is able to evaluate all the evidence themselves, and so people have
>>> to
>>> decide who to trust,
>>>        So now I would like to point you to an article I just read about
>>> DNA
>>> sequencing and bird phylogeny.  It challenges the view that DNA
>>> sequencing
>>> reveals the "truth" about which species is related to which.  The results
>>> of DNA sequencing of corals are presented to us as reality, this is the
>>> way
>>> it is, morphology was wrong.  We assume that those results are correct,
>>> scientists in white coats who work with fancy machines and chemicals in
>>> laboratories tell us it is.  They are the experts, we have faith in them.
>>>       And that would predict that if different genes were used to produce
>>> the tree of coral life, they would produce the same answers.  Most of the
>>> DNA sequencing used to produce the current view of the coral tree of life
>>> were done using PCR, which can sequence just a relatively few genes
>>> (about
>>> 7?) out of maybe 30,000 in a coral.  Obviously, if other genes were
>>> tested,
>>> they'd say the same thing, wouldn't they?  In fact, a bunch of studies
>>> have
>>> done that, tested a gene in the mitochondria, and several in the cell
>>> nucleus, and they tell very similar stories.  There can be no more
>>> independent stretches of DNA than in the mitochondria and nucleus, can
>>> there?  That's replication.  Case closed, the DNA doesn't lie.   DNA
>>> results are true, morphology is unreliable, it misled us, it's just plain
>>> wrong.
>>>
>>>       The bird studies sequenced the complete genomes of many bird
>>> species.  To quote the essay:
>>>
>>> "When they told their tree-building software to focus only on regions of
>>> the genome that Prum’s team used, it produced a tree that looked like
>>> Prum’s. When they shifted focus to other regions, a very different tree
>>> emerged. When they divided their bird genomes into thousands of different
>>> parts and ran each through their software, they got thousands of
>>> different
>>> trees, and not one completely matched the “species tree” they had
>>> constructed from large portions of genomes. “Different parts of the
>>> genome
>>> have different stories,” Gilbert realized."
>>>
>>>       It seems that for birds, at least, different parts of the DNA don't
>>> always tell the same story.  If the different parts tell us different
>>> stories, which story is right?  Or is this just a science journalist who
>>> doesn't understand science and got it all wrong??  Or maybe it is just a
>>> problem with birds, it doesn't apply to corals??  (They argue it applies
>>> to
>>> humans.)  Or maybe our assumption that evolution was like a tree is
>>> wrong,
>>> there is hybridization that produces cross-links and instead of a tree at
>>> least parts of it are more like a net?  Or maybe they are just quibbling,
>>> the main parts of the tree are always the same, these arguments are just
>>> about a few of the branch tips?
>>>
>>> May I recommend the following essay?  It may be relevant for corals.
>>>
>>> The bizarre bird that's breaking the tree of life
>>>
>>> Darwin thought that family trees could explain evolution.  The hoatzin
>>> suggests otherwise.
>>>
>>>
>>> https://www.newyorker.com/science/elements/the-bizarre-bird-thats-breaking-the-tree-of-life
>>> ?
>>>
>>> open-access
>>>
>>> (actually, if I read it correctly, that bird did not break the tree.  It
>>> is
>>> not clear where that bird fits on the tree, but the problem is much
>>> deeper
>>> and probably more widespread than that.  See what you think.)
>>>
>>> Cheers, Doug
>>>
>>> --
>>> Douglas Fenner
>>> Lynker Technologies, LLC, Contractor
>>> NOAA Fisheries Service
>>> Pacific Islands Regional Office
>>> Honolulu
>>> and:
>>> Coral Reef Consulting
>>> PO Box 997390
>>> Pago Pago, American Samoa 96799-6298  USA
>>>
>>> A pass for polluting? Environmental groups, employees say EPA enforcement
>>> efforts lacking
>>>
>>> https://www.msn.com/en-us/news/us/a-pass-for-polluting-environmental-groups-employees-say-epa-enforcement-efforts-lacking/ar-AAXdYsL
>>>
>>> 1 in 6 deaths worldwide can be attributed to pollution, new review shows
>>>
>>> https://www.msn.com/en-us/health/medical/1-in-6-deaths-worldwide-can-be-attributed-to-pollution-new-review-shows/ar-AAXozQh
>>>
>>> UN: World on fast track to disaster, but we can avert it
>>> https://www.youtube.com/watch?v=9xBVD8r0aHQ
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>>
>>