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

[Kenneth Kinman]

Thank you Jason,
        You present an excellent critique of "CP" panbiogeographers arguments.   Almost always the same old rigmarole of cherry-picking, quoting out of context, sophistry, circular argumentation, and other methods of muddying the waters.  And it is often cloaked within a barrage of other verbiage, so I agree that it is important to warn newcomers.

________________________________
From: Taxacom <taxacom-bounces at mailman.nhm.ku.edu> on behalf of JF Mate via Taxacom <taxacom at mailman.nhm.ku.edu>
Sent: Saturday, January 2, 2021 12:35 AM
To: Taxacom <taxacom at mailman.nhm.ku.edu>
Subject: Re: [Taxacom] Molecular evidence (in 2017) supports my 2014 theory about rafting killifish

I think that Rob was on the right track but not precise enough. It is not
that panbiogeography is akin to creationism, it is that the defence John
and Michael are mounting is reminiscent of creationists. I may be wrong in
your intention but the arguments I hear are cherry-picking, sophistry,
circular argumentation and in general muddying the waters so as to create a
gap for a "Panbiogeography of the gaps". This, however, is a mistake and
has left you holding an untenable arcane view of biogeography whilst
ignoring the last 60 years of advances in phylogenetics. The debate
strategy seems to me to be a kafkaesque attempt to neutralize any
possibility of criticizing Croizat or panbiogeography by labelling as
suspect all other contenders, molecular phylogenetics (you call it
phenetics), fossil calibration (using minimum age as a the fine edge of the
wedge to push arguments such as confusing point calibration with log
distributions), molecular clocks (your definition is "strict clock" from
the 1960´s but you don´t care), and generally weaponizing the widely
acknowledged limitations of all of these and more fields.

John, you asked me to argue why I said that your position on Croizatian
Panbiogeography (CP) was untenable. Succinctly, because of two main
reasons. Firstly because Croizat quite simply rejected cladistics, and if
you accept cladistics you are a vicariance cladist by definition and
arguing otherwise is rejecting reality Secondly, because CP rejects
dispersal (“Interestingly it is dispersalism that invokes miracles and
mysteries.”) in spite of evidence that demonstrates that, however
infrequently, it happens. Trying to relabel cases of dispersal as "range
expansion" is sophistry aimed at making panbiogeography unfalsifiable.

This pattern of muddying the waters is particularly noticeable when you
selectively quote, for example with Donoghue and De Baets. From the same
2016 publication: "Biogeographic and fossil calibrations are complementary,
not competing, approaches to constraining molecular clock analyses,
providing alternative constraints on the age of clades that are vital to
avoiding circularity in investigating the role of biogeographic mechanisms
in shaping modern biodiversity." (2016). I don´t think any biogeographer
would disagree with this statement, but it is anathema with CP because, as
John has said: “If molecular clock models incorporating a tectonic
correlation result in unacceptable results, that does not invalidate the
tectonic correlation. But it does raise questions about the molecular
model. Nothing ridiculous about it at all.”  The unfalsifiability of CP in
all its glory. If something disagrees with CP, CP is not at fault because
it is perfect. Other examples of cherry-picking involve the numerous out of
context quotes of researchers acknowledging the caveats of phylogenetics
and calibration as evidence of the inferiority and mendaciousness of non CP
researchers (“magic”, “dark art”, “lies”, etc).

This pattern is so extensive it is tiring pointing out the examples:

“...keep in mind that some molecular systematists are recognizing that
fossil calibration only provides minimum ages and are looking to tectonic
correlates instead - which is another way of saying that they have adopted
this panbiogeographic method.” ML or Bayesian models do not assume point
dates but a probability distribution into the past. Please stop confusing
the terms.


“The idea that there has to be a constant molecular clock throughout the
phylogenetic history of a group is not an empirical finding. It is a model
of evolution that may not be true. … Like priors, molecular clocks are also
theoretical models (and there are different models) and open to question or
refutation. I would like to see you, Ken, show how a constant molecular
clock” A molecular clock model does not assume monotonic (constant) rates
within genes or within lineages nor are clocks assumed a priori.  This is a
straw man argument. Nobody assumes the strict clock a priori except in very
specific cases like viruses and even then after testing. I can´t believe
that this is a mistake when you guys selectively quote dos Reis et al 2016:
“Thus, while the clade ages generated in Bayesian studies are extremely
precise and have excellent statistical support, because 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.” Cherry
picked quote: “Errors in the time prior and in the rate prior can lead to
very precise but grossly inaccurate time estimates. Great care must always
be taken in the construction of fossil calibrations and in the
specification of priors on times and on rates in a dating analysis.” Not
quite the same meaning, in particular with the added sentence ending “tens
or hundreds of millions of years…”. That is a misquote if I ever saw one.

“We see this in the morphological aspect of molecular genetics where
different groups separated or dislocated by a tectonic feature show
different levels of morphological divergence (for example with the NZ
Alpine fault dislocation where correlated distributions may be conspecific
or species level differences even after more than 20 million years. So the
panbiogeographic implication of tectonic correlation is that this provides
an approximation of age for the correlated groups.”
You are assuming as axiomatic that the taxa on either side of the fault
have been unable to cross since the tectonic event.

“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’.”

Again, cherry-picked, out of context quote. It is followed by: “If the
importance of vicariance in the course of the Gondwanan breakup is to be
evaluated via the pragmatic criterion of mismatch between age estimates and
geological history, the priors defining the molecular dating analyses have
to be solid. As those are predominantly influenced by fossil attribution
(Magallón, 2014; Pirie, Litsios, Bellstedt, Salamin, & Kissling, 2015; Shen
et al., 2016), taxonomy and phylogeny of the study group are of crucial
importance. Consequently, taxonomically resolved groups with a rich fossil
record should constitute ideal model groups, because they are more likely
to uncover accurate age estimates (e.g., Favre et al., 2016; Muellner‐Riehl
et al., 2016).”
And what did the authors find?
“Results: Our biogeographic analyses illustrate that the ziziphoid lineage
was influenced by both long‐distance dispersal and Gondwanan breakup
vicariance events. Yet, these vicariance events cannot explain all
divergence events at the backbone of this lineage.” Shocker, they find both
mechanisms at play. I can´t wait to see how you ignore this part of the
paper whilst using the bits that you agree with (usually the necessary
acknowledgement of study limitations).

This is a pattern. I have kept correspondence for the last 10 years on
these exchanges and it is always the same rigmarole. But I still bite
because it is important to warn newcomers.

Happy New Year everyone.

Jason

On Sat, 2 Jan 2021 at 09:03, John Grehan via Taxacom <
taxacom at mailman.nhm.ku.edu> wrote:

> p.s. keep in mind that some molecular systematists are recognizing that
> fossil calibration only provides minimum ages and are looking to tectonic
> correlates instead - which is another way of saying that they have adopted
> this panbiogeographic method.
>
> John Grehan
>
> >
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