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

[Douglas Fenner]

       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

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