[Taxacom] Molecular evidence (in 2017) supports my 2014 theory about rafting killifish

Michael Heads m.j.heads at gmail.com
Sun Dec 27 13:26:26 CST 2020


'...not a magical black box'.

No, it's definitely a magical black box. You can get any date you want.
Here's a section from a recent manuscript:

*The problem of the priors*

In the Modern Synthesis approach, ‘Fossils record the origins and
disappearance of organisms’ (Herrera, 2017). However, a clade’s actual age
is older than its oldest fossil’s age by an unknown amount of time. In most
studies, clade ages are calculated from fossil-calibrated molecular-clock
analyses. However, fossil calibrated studies on their own can provide only
minimum ages. In Bayesian analyses, these *fossil* ages are converted into
estimates of absolute (not minimum) *clade* ages by imposing priors that
stipulate how much older than its oldest fossil a clade is. Naturally, the
estimates of clade age are extremely sensitive to the time priors (Warnock *et
al*., 2015).

The problem is that the choice of the priors is left up to the author, and
the priors that are chosen are invariably very narrow; in other words, a
clade used for calibration is assumed to be not much older (often <10 Myr) than
its oldest fossil. This use of very narrow priors represents the formal
imposition of an old belief – that fossil age more or less equals clade age.

Choosing priors is ‘highly arbitrary’ (Pirie and Doyle, 2012), ‘...often
subjective…’ (Ho & Duchêne, 2014), ‘invariably established without
justification’ (Warnock *et al*., 2015) and, in sum, ‘could be considered a
dark art’ (De Baets *et al*., 2016). Thus, while the clade ages generated
in Bayesian studies are extremely precise and have excellent statistical
support, becaue of the problem of the priors they can be ‘grossly
inaccurate’ (dos Reis *et al*., 2016) and could be tens or even hundreds of
millions of years too young. As Hauenschild *et al.* (2018) observed, clade
ages that are too young may be calculated ‘based on too narrowly set
priors, and vicariance thereby may be erroneously ruled out’.

On Mon, Dec 28, 2020 at 2:59 AM JF Mate via Taxacom <
taxacom at mailman.nhm.ku.edu> wrote:

> John, you are not discussing the points nor answering the questions but
> simply repeating "twaddle" in an attempt to rescue a point of view
> (Croizatian Panbiogeography) which is simply untenable nowadays. All
> biogeographers consider vicariance and dispersal, and their definition of
> dispersal does not depend on accepting Panbiogeography.
>
> As for node calibration, exponential and lognormal bounds are not maximum
> ages but probability curves which extend the "minimum" node age into the
> past as a first step. The model then works the best fit based on the data
> at hand and gives you estimated ages with ranges. That is a transparent
> model, not a magical black box as you are claiming.
>
> It is fair to argue if the model parameters are adequate, if the fossils
> used are properly interpreted, or to reanalyze the data. These are all
> limitations, but simply using them to disregard studies out of hand because
> they don't support your point of view is not helpful.
>
> Best
>
> Jason
>
>
>
> On Sat, 26 Dec 2020, 01:57 John Grehan, <calabar.john at gmail.com> wrote:
>
> >
> > Jason – thank you for elaborating on the defense of minimums
> > misrepresented as maximums. Comment below:
> >
> > “0.5 SD on the fossil's age seems a reasonable and conservative range”
> >
> > 'reasonable or not' it's still just made up out of thin air. It is magic.
> >
> > “Are you arguing for a minimum hardbound and if so what is your
> > justification? “
> >
> > Yes, although not sure what you mean by 'hardbound'.  A minimum is a
> > minimum so it is hardbound in that respect. Justification is simple,
> > fossils provide minimum ages and no data on potential older ages of
> origin
> > for the taxon in question.
> >
> > “why not use lognormal or exponential for both points and maybe some
> > sensitivity analysis in regards to this but other than that I wouldn't
> call
> > it twaddle”
> >
> > You are welcome to use anything you like, but it's still magic and the
> > result is twaddle. A minimum cannot be turned into a maximum. That is the
> > reality. The rest is an invention of the imagination.
> >
> > “This argument is at best specious. Molecular calibrations have been
> using
> > soft calibrations for well over a decade now to account for the
> > uncertainties that you mention “
> >
> > Wrong, the molecular calibrations misrepresent minimum ages as maximum.
> >
> > “ majority use either lognormal or exponential bounds “
> >
> > So what? They are both inventions of the mind – magical transformation of
> > minimum into maximum.
> >
> > “In other words, there is already the acknowledgement that known fossils
> > may not be the oldest exemplars of a taxon, but you have to work with
> what
> > you have
> >
> > of course. But if fossils may not be the oldest exemplars then the
> > molecular extrapolations may not be either. To say otherwise is to
> invoke a
> > magical transformation - not science as I understand it.
> >
> > “ and, when new fossil evidence is discovered, corrections will be made.”
> >
> > Corrections to what? Corrections to a maximum that never was in the first
> > place?
> >
> > “What you are asking for is the legal equivalent of proving someone's
> > innocence.”
> >
> > Rubbish. I am asking that the empirical reality be recognized – that
> > fossil calibrated molecular divergence dates be recognized as minions
> that
> > cannot falsify earlier origins or biogeographic correlations that may
> > suggest earlier origins.
> >
> > Molecular transformations of minimums into maximums is perhaps the only
> > modern case of magic being used in science that I am aware of (other than
> > perhaps some political inventions with COVID). Just to be sure that there
> > is no misunderstanding (as has happened in the literature),
> > panbiogeographic approaches do not ignore or disregard molecular
> divergence
> > ages, but accept and incorporate those findings as MINIMUM ages only.
> That
> > is science.
> >
> > Cheers,
> >
> > John Grehan
> >
> >
> > On Fri, Dec 25, 2020 at 7:01 AM JF Mate <aphodiinaemate at gmail.com>
> wrote:
> >
> >> Michael, regarding the calibration method used: "It corresponds to the
> >> origin of the crown European cyprinodontoid clade [39], which was
> estimated
> >> to have occurred at least 33 Ma on the basis of the oldest identifiable
> >> clade member, the
> >> fossil Prolebias stenoura Sauvage, 1874 from the Lower Stampien (Lower
> >> Oligocene) of Puy-
> >> de-Dome, France [40] (prior setting: lognormal distribution, mean = 33
> >> and standard devia-
> >> tion = 0.5). ( [40] Costa WJEM. Oligocene killifishes (Teleostei:
> >> Cyprinodontiformes) from southern France: relationships, taxonomic
> >> position, and evidence of internal fertilization. Vertebr Zool. 2012;
> 62:
> >> 371–386.)
> >>
> >> John:
> >> 0.5 SD on the fossil's age seems a reasonable and conservative range,
> >> with a lognormal distribution for the node. My only quibble is why not
> use
> >> lognormal or exponential for both points and maybe some sentivity
> analysis
> >> in regards to this but other than that I wouldn't call it twaddle. Are
> you
> >> arguing for a minimum hardbound and if so what is your justification?
> >>
> >> "But I have not seen any published refutation of the empirical fact that
> >> fossils can only give mimiums with no direct information on upper age
> >> limits of taxa and that molecular extrapolations are in the same boat."
> >> This argument is at best specious. Molecular calibrations have been
> using
> >> soft calibrations for well over a decade now to account for the
> >> uncertainties that you mention, and the majority use either lognormal or
> >> exponential bounds. In other words, there is already the acknowledgement
> >> that known fossils may not be the oldest exemplars of a taxon, but you
> have
> >> to work with what you have and, when new fossil evidence is discovered,
> >> corrections will be made. What you are asking for is the legal
> equivalent
> >> of proving someone's innocence.
> >>
> >> Merry Xmas
> >>
> >> On Fri, 25 Dec 2020, 14:14 John Grehan, <calabar.john at gmail.com> wrote:
> >>
> >>> Ken, thanks for specifying that your support for their paper as
> evidence
> >>> comes from your acceptance of the time calibrated phylogeny in the
> article.
> >>> So naturally the question arises, as Heads stated, how was the time
> >>> calibrated? Costa et al say they use:
> >>>
> >>> “a normal uncorrelated relaxed clock model, which emphasizes the
> minimum
> >>> age and has been considered appropriate for fossil calibration points”
> >>>
> >>> OK that is fine, fossil calibration points are minimum dates. But (and
> >>> there is always a but in this stuff) they then say:
> >>>
> >>> “A Yule speciation process for the tree prior (Gernhard, 2008) was
> used”
> >>>
> >>> This 'prior was presented as follows:
> >>>
> >>> “origin of the crown European cyprinodontoid clade (Pohl et al., 2015),
> >>> which was estimated to have occurred at least 33 Mya on the basis of
> the
> >>> oldest identifiable clade member”
> >>>
> >>> “at least' is fine and factual, but then the oil gets applied with:
> >>>
> >>> “prior setting: exponential distribution, mean = 33 and standard
> >>> deviation = 0.5).”
> >>>
> >>> In other words, as if by magic, they have decided that the oldest upper
> >>> limit lies within a standard deviation of 0.5. Where on earth does this
> >>> come from? Well, not from earth as we know it. Its pure magic (I
> challenge
> >>> anyone to demonstrate otherwise). Its a sort of game – go on, pick a
> prior,
> >>> any prior will do. And all it produces is twaddle dressed up in fancy
> >>> algorithms and techniques.
> >>>
> >>> Similarly for their second calibration point:
> >>>
> >>> “where Aphanius and Valencia diverge, corresponding to the most ancient
> >>> record with recognisable synapomorphies of Aphanius, the fossil
> Aphanius …
> >>> with 17 Mya (prior setting: exponential distribution, mean = 17 and
> >>> standard deviation = 0.5.)
> >>>
> >>> Same magic, same twaddle.
> >>>
> >>> So when they say:
> >>>
> >>> “Divergence time estimates indicate that the Neotropical aplocheiloid
> >>> clade diverged from its sister group comprising Old World aplocheiloids
> >>> in the Early Eocene (50 Mya, 95% HDP: 39–63 Mya).”
> >>>
> >>> its really a sort of fraud as minimums are represented as a value with
> >>> maximum upper limits that are not much older. Its pure garbage, like
> >>> presenting lead as gold. A minimum is a minimum is a minimum. Twaddle,
> >>> twaddle, waddle all the day.
> >>>
> >>> OK so I am rather blunt about it. But I have not seen any published
> >>> refutation of the empirical fact that fossils can only give mimiums
> >>> with no direct information on upper age limits of taxa and that
> molecular
> >>> extrapolations are in the same boat. Claims to the contrary therefore
> come
> >>> across as misrepresentations of the evidence, and misrepresentations
> are
> >>> fraudulent. Again, I am open to discussion with any expert on this list
> >>> who can present evidence to the contrary.
> >>>
> >>> It appears that Ken believes in priors as authoritative when invoked by
> >>> molecular technologists and I have no problem with that. We are all
> >>> entitled to believe whatever we want. But in science one does look for
> an
> >>> empirical basis and it appears that Ken and others with the same
> >>> viewpoint cannot or are unwilling to give that – at least so far.
> >>>
> >>> With respect Kryptolebias being capable of surviving out of water and
> >>> spending much of their time in logs and cavities of trees – that is
> fine as
> >>> an ecological quality. But it has no automatic connection with the
> origin
> >>> of allopatric taxa. Ironically it is biogeographic analysis that might
> give
> >>> some insight into understanding the role of ecological means of
> >>> dispersal rather than the other way around.
> >>>
> >>> Taxacom might be the only place this issue is directly discussed. Good
> >>> to see. It's what makes Taxacom exceptional.
> >>>
> >>> John Grehan
> >>>
> >>>
> >>>
> >>> On Thu, Dec 24, 2020 at 9:35 AM Kenneth Kinman via Taxacom <
> >>> taxacom at mailman.nhm.ku.edu> wrote:
> >>>
> >>>> Hi Jason,
> >>>>          Thanks for the input Jason.   Yes, the time calibrated
> >>>> phylogeny (from molecular sequences) in the article.  And also
> >>>> early-branching Kryptolebias known to be capable of surviving out of
> water
> >>>> for up to 66 days and spending much of their time while out of the
> water in
> >>>> logs and cavities of trees (plenty of those in such rafts).  And I
> was even
> >>>> more convinced by their unusual reproductive abilities
> (hermaphroditism and
> >>>> even self-fertilization).  Seems like the best of all vertebrate
> candidates
> >>>> for trans-Atlantic dispersal in the Eocene-Oligocene time frame.
> >>>>                          --------------Ken
> >>>>
> >>>> ________________________________
> >>>> From: Taxacom <taxacom-bounces at mailman.nhm.ku.edu> on behalf of JF
> >>>> Mate via Taxacom <taxacom at mailman.nhm.ku.edu>
> >>>> Sent: Wednesday, December 23, 2020 10:54 PM
> >>>> To: John Grehan <calabar.john at gmail.com>; Taxacom <
> >>>> taxacom at mailman.nhm.ku.edu>
> >>>> Subject: Re: [Taxacom] Molecular evidence (in 2017) supports my 2014
> >>>> theory about rafting killifish
> >>>>
> >>>> I can't speak for Ken nor be sure that my interpretation is correct,
> >>>> but if
> >>>> I had to guess, then I would say that in the case of the killifish,
> the
> >>>> evidence for postvicariance dispersal would be in the time calibrated
> >>>> phylogeny and the pattern being consistent with previous studies
> >>>> detecting
> >>>> a similar pattern and timing. If am wrong in your interpretation Ken
> >>>> please
> >>>> let me know.
> >>>>
> >>>> Best and Merry Christmas to all
> >>>>
> >>>> Jason
> >>>>
> >>>> On Wed, 23 Dec 2020, 01:50 John Grehan, <calabar.john at gmail.com>
> wrote:
> >>>>
> >>>> > Jason,
> >>>> >
> >>>> > Thanks for the paper. I would be happy to do that, but first I need
> >>>> Ken to
> >>>> > specify what in the paper he sees as constituting evidence.
> Otherwise
> >>>> I am
> >>>> > just left guessing. Once Ken specifies what particular items
> >>>> presented in
> >>>> > the paper constitute evidence I would be happy to comment. I have
> >>>> noticed
> >>>> > that Ken tends to cite papers as evidence for is views, but rarely
> >>>> > specifies what within qualifies as evidence. I hope in this case he
> >>>> will do
> >>>> > that for the purposes of discussion.
> >>>> >
> >>>> > Cheers,
> >>>> >
> >>>> > John Grehan
> >>>> >
> >>>> > On Tue, Dec 22, 2020 at 9:37 AM JF Mate <aphodiinaemate at gmail.com>
> >>>> wrote:
> >>>> >
> >>>> >> Here is a copy John. Your line of argumention would be more
> >>>> constructive
> >>>> >> if you could provide a critique of their work and why you think
> their
> >>>> >> conclusions are wrong. That way it would be easier to understand
> your
> >>>> >> perspective.
> >>>> >>
> >>>> >> Best
> >>>> >>
> >>>> >> Jason
> >>>> >>
> >>>> >> On Tue, 22 Dec 2020, 07:07 John Grehan via Taxacom, <
> >>>> >> taxacom at mailman.nhm.ku.edu> wrote:
> >>>> >>
> >>>> >>> Hi Ken. See below
> >>>> >>>
> >>>> >>>  They say: "Our estimates indicate that divergence between the
> >>>> clades
> >>>> >>> comprising New World and Old World aplocheiloids occurred during
> the
> >>>> >>> Eocene, about 50 Mya, much more recent than the Gondwanan
> >>>> fragmentation
> >>>> >>> scenario assumed in previous studies."
> >>>> >>>
> >>>> >>> So they say. But what is the evidence? Ken, all you ever seem to
> do
> >>>> is
> >>>> >>> post
> >>>> >>> assertions, never specifying the evidence.
> >>>> >>>
> >>>> >>>  The molecular evidence in 2017 supports my theory.
> >>>> >>>
> >>>> >>> What is the molecular evidence?
> >>>> >>>
> >>>> >>> Cheers,
> >>>> >>>
> >>>> >>> John Grehan
> >>>> >>>
> >>>> >>>
> >>>> >>>
> >>>> >>> On Mon, Dec 21, 2020 at 3:40 PM Kenneth Kinman via Taxacom <
> >>>> >>> taxacom at mailman.nhm.ku.edu> wrote:
> >>>> >>>
> >>>> >>> > Hi All,
> >>>> >>> >       Rivulidae (a.k.a. Cynolebiini) are New World killifish
> once
> >>>> >>> thought
> >>>> >>> > to have arisen in the Cretaceous before South America fully
> >>>> separated
> >>>> >>> from
> >>>> >>> > Africa.  However, molecular evidence in 2017 indicates they
> arose
> >>>> in
> >>>> >>> the
> >>>> >>> > Eocene.   They say: "Our estimates indicate that divergence
> >>>> between the
> >>>> >>> > clades comprising New World and Old World aplocheiloids occurred
> >>>> >>> during the
> >>>> >>> > Eocene, about 50 Mya, much more recent than the Gondwanan
> >>>> fragmentation
> >>>> >>> > scenario assumed in previous studies. This estimation is nearly
> >>>> >>> synchronous
> >>>> >>> > to estimated splits involving other South American and African
> >>>> >>> vertebrate
> >>>> >>> > clades, which have been explained by transoceanic dispersal
> >>>> through an
> >>>> >>> > ancient Atlantic island chain during the Palaeogene."
> >>>> >>> >       This makes me quite happy since I brought up this
> >>>> possibility
> >>>> >>> back
> >>>> >>> > in 2014, in a post here on Taxacom entitled: transoceanic
> >>>> "rafting"
> >>>> >>> fish
> >>>> >>> > (great candidate).
> >>>> >>> >       The early branching genus Kryptolebias just happens to be
> a
> >>>> great
> >>>> >>> > candidate for a fish that could disperse on a raft of vegetation
> >>>> from
> >>>> >>> > Africa to South America:   (1) It's not only very tolerant of
> salt
> >>>> >>> water,
> >>>> >>> > but also and more importantly (2) it can survive out of water
> for
> >>>> >>> weeks at
> >>>> >>> > a time (66 days in one case).  (3) And guess where Kryptolebias
> >>>> >>> marmoratus
> >>>> >>> > spends much of its time while out of the water----in logs and
> >>>> cavities
> >>>> >>> of
> >>>> >>> > trees (which would be the main structural components of a large
> >>>> >>> > transoceanic raft).
> >>>> >>> >          Those are the three things I thought of offhand which
> >>>> pointed
> >>>> >>> to
> >>>> >>> > possible trans-Atlantic dispersal.  But then I began wondering
> >>>> about
> >>>> >>> yet
> >>>> >>> > another strange thing about Kryptolebias fish.  They often
> exhibit
> >>>> >>> various
> >>>> >>> > types of hermaphroditism, and even its most extreme form
> >>>> >>> > (self-fertilization, which is apparently absent in vertebrates
> >>>> except
> >>>> >>> for
> >>>> >>> > Kryptolebias).  So just a few of these fish (or even a single
> >>>> >>> individual)
> >>>> >>> > could have established a population on another continent.   The
> >>>> >>> molecular
> >>>> >>> > evidence in 2017 supports my theory.
> >>>> >>> >
> >>>> >>>
> >>>>
> https://www.sciencedirect.com/science/article/abs/pii/S1055790317300386?casa_token=ONKSbcnOLNEAAAAA:roWXxXgD1F0NqnWh9fozphZ4BbyAngOtCQwxXkyr552h7rNz1M366R2yniah-HK5hDFbRaaV
> >>>> >>> >
> >>>> >>> >                                   ------------------Ken
> >>>> >>> >
> >>>> >>> >
> >>>> >>> >
> >>>> >>>
> >>>>
> ----------------------------------------------------------------------------------------------------------------------------
> >>>> >>> >
> >>>> >>> >
> >>>> >>> > _______________________________________________
> >>>> >>> > Taxacom Mailing List
> >>>> >>> >
> >>>> >>> > Send Taxacom mailing list submissions to:
> >>>> taxacom at mailman.nhm.ku.edu
> >>>> >>> > For list information; to subscribe or unsubscribe, visit:
> >>>> >>> > http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
> >>>> >>> > You can reach the person managing the list at:
> >>>> >>> > taxacom-owner at mailman.nhm.ku.edu
> >>>> >>> > The Taxacom email archive back to 1992 can be searched at:
> >>>> >>> > http://taxacom.markmail.org
> >>>> >>> >
> >>>> >>> > Nurturing nuance while assaulting ambiguity for about 33 years,
> >>>> >>> 1987-2020.
> >>>> >>> >
> >>>> >>> _______________________________________________
> >>>> >>> Taxacom Mailing List
> >>>> >>>
> >>>> >>> Send Taxacom mailing list submissions to:
> >>>> taxacom at mailman.nhm.ku.edu
> >>>> >>> For list information; to subscribe or unsubscribe, visit:
> >>>> >>> http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
> >>>> >>> You can reach the person managing the list at:
> >>>> >>> taxacom-owner at mailman.nhm.ku.edu
> >>>> >>> The Taxacom email archive back to 1992 can be searched at:
> >>>> >>> http://taxacom.markmail.org
> >>>> >>>
> >>>> >>> Nurturing nuance while assaulting ambiguity for about 33 years,
> >>>> >>> 1987-2020.
> >>>> >>>
> >>>> >>
> >>>> _______________________________________________
> >>>> Taxacom Mailing List
> >>>>
> >>>> Send Taxacom mailing list submissions to: taxacom at mailman.nhm.ku.edu
> >>>> For list information; to subscribe or unsubscribe, visit:
> >>>> http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
> >>>> You can reach the person managing the list at:
> >>>> taxacom-owner at mailman.nhm.ku.edu
> >>>> The Taxacom email archive back to 1992 can be searched at:
> >>>> http://taxacom.markmail.org
> >>>>
> >>>> Nurturing nuance while assaulting ambiguity for about 33 years,
> >>>> 1987-2020.
> >>>> _______________________________________________
> >>>> Taxacom Mailing List
> >>>>
> >>>> Send Taxacom mailing list submissions to: taxacom at mailman.nhm.ku.edu
> >>>> For list information; to subscribe or unsubscribe, visit:
> >>>> http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
> >>>> You can reach the person managing the list at:
> >>>> taxacom-owner at mailman.nhm.ku.edu
> >>>> The Taxacom email archive back to 1992 can be searched at:
> >>>> http://taxacom.markmail.org
> >>>>
> >>>> Nurturing nuance while assaulting ambiguity for about 33 years,
> >>>> 1987-2020.
> >>>>
> >>>>
> _______________________________________________
> Taxacom Mailing List
>
> Send Taxacom mailing list submissions to: taxacom at mailman.nhm.ku.edu
> For list information; to subscribe or unsubscribe, visit:
> http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
> You can reach the person managing the list at:
> taxacom-owner at mailman.nhm.ku.edu
> The Taxacom email archive back to 1992 can be searched at:
> http://taxacom.markmail.org
>
> Nurturing nuance while assaulting ambiguity for about 33 years, 1987-2020.
>


-- 
Dunedin, New Zealand.

My books:

*Biogeography and evolution in New Zealand. *Taylor and Francis/CRC, Boca
Raton FL. 2017.
https://www.routledge.com/Biogeography-and-Evolution-in-New-Zealand/Heads/p/book/9781498751872


*Biogeography of Australasia:  A molecular analysis*. Cambridge University
Press, Cambridge. 2014. www.cambridge.org/9781107041028


*Molecular panbiogeography of the tropics. *University of California Press,
Berkeley. 2012. www.ucpress.edu/book.php?isbn=9780520271968


*Panbiogeography: Tracking the history of life*. Oxford University Press,
New York. 1999. (With R. Craw and J. Grehan).
http://books.google.co.nz/books?id=Bm0_QQ3Z6GUC
<http://books.google.co.nz/books?id=Bm0_QQ3Z6GUC&dq=panbiogeography&source=gbs_navlinks_s>


More information about the Taxacom mailing list