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

Thu Jul 21 11:23:18 UTC 2022

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 (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 here:

https://www.pnas.org/doi/10.1073/pnas.1909030116

New research shows gene exchange between viruses and hosts drives evolution
https://www.sciencedaily.com/releases/2022/01/220105111420.htm

And this one shows how the gene transfers can occur independent of viruses
and bacteria during close contact during mass spawning!
https://www.quantamagazine.org/dna-jumps-between-animal-species-no-one-knows-how-often-20210609/

Stay safe everyone!

Austin

Austin Bowden-Kerby, PhD
Corals for Conservation
P.O. Box 4649 Samabula, Fiji Islands

https://www.corals4conservation.org
*https://reefresilience.org/case-studies/south-pacific-restoration/
<https://reefresilience.org/case-studies/south-pacific-restoration/>*
https://www.globalgiving.org/projects/emergency-response-to-massive-coral-bleaching/
<https://www.globalgiving.org/projects/emergency-response-to-massive-coral-bleaching/>

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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