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

JF Mate aphodiinaemate at gmail.com
Sun Dec 27 07:58:57 CST 2020


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
>>>> >>> >
>>>> >>> >
>>>> >>> >
>>>> >>>
>>>> ----------------------------------------------------------------------------------------------------------------------------
>>>> >>> >
>>>> >>> >
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>>>> >>
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>>>> Nurturing nuance while assaulting ambiguity for about 33 years,
>>>> 1987-2020.
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>>>> Taxacom Mailing List
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>>>>
>>>>


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