[Taxacom] Taxacom Digest, Vol 185, Issue 14

Sun Sep 19 14:51:21 CDT 2021

Hi Brendon,

You say 'I set my fossil priors as the evidence-based stratigraphic range
for the given deposit or formation'.

That is, if the fossil is in a formation dated as extending from 10-20 Ma,
the group can be no older than 20 Ma. But why not? I don't see that the age
of the formation is relevant. It's like saying that if a fossil is in the
Cenozoic, it's group can't be Mesozoic, because that's a separate era. .

You're right, this technique ('bounding') isn't guesswork, but it seems
arbitrary and illogical. Why not just say that, based on the fossil record,
the fossil's group is *older than* the fossil by some unknown amount? This
is a valid and useful contribution, and data from other fields (e.g.
biogeography) can then be used to investigate further. I don't think you
can assess the accuracy of the fossil record by using data from the same
record.

Biogeographic-tectonic calibration  is now used quite widely (e.g. Ho et
al., 2015; De Baets et al., 2016; Landis, 2017; Gunter et al., 2018, Pett &
Heath, 2020).  As Landis (2020) argued, ‘Fossil and biogeographic dating
methods… should be regarded as complementary, not competing, strategies’.
This is the synthetic approach we take, using fossil-calibrated ages as
estimates of minimum clade age and biogeographic-tectonic calibrations as
estimates of actual clade age.

On Mon, Sep 20, 2021 at 3:52 AM Brendon E. Boudinot via Taxacom <
taxacom at mailman.nhm.ku.edu> wrote:

> Hello John!
>
> I disagree. In tip-dating analyses, I set my fossil priors as the
> evidence-based stratigraphic range for the given deposit or formation.
> Using this range, we can account for patterns of variation for both
> morphology and molecular data, given the estimated range of possible
> relationships and clades ages. The priors have strong affect when there is
> little information, such as at a root node. The main point is accounting
> for uncertainty regarding the most recent or oldest possible age for a
> fossil. Please explain, in this context, why that is a problem. I am here
> today because of curiosity in general; likewise, I am responding now
> because of specific curiosity. What alternatives should one make use of to
> combine genotypic, phenotypic, and stratigraphic ranges for estimating a
> possible set of relationships and ages?
>
> Noncombatively,
> Brendon
>
> On Sat, 18 Sep 2021, 19:05 <taxacom-request at mailman.nhm.ku.edu> wrote:
>
> > Daily News from the Taxacom Mailing List
> >
> > When responding to a message, please do not copy the entire digest into
> > your reply.
> > ____________________________________
> >
> >
> > Today's Topics:
> >
> >    1. Re: Snake garbage (John Grehan)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Fri, 17 Sep 2021 16:25:36 -0400
> > From: John Grehan <calabar.john at gmail.com>
> > To: taxacom <taxacom at mailman.nhm.ku.edu>
> > Subject: Re: [Taxacom] Snake garbage
> > Message-ID:
> >         <CADN0ud1-28JXFunp23V6=
> > v4evN7orEypWnxjf04t+TGoES5bEQ at mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > I wrote the original note in a bit of a hurry (should not do that) and
> > quite justifiably got castigated off list for not making sense. So below
> a
> > hopefully more coherent rant.
> >
> > This paper carries on the time honored scientific tradition of just
> > ignoring shortcomings of a method and ploughing on as if the ground was
> not
> > already falling away beneath. In this case the paper does this by
> > representing priors as some kind of empirically real source of estimating
> > fossil calibrated clade ages whereas it has been shown that fossil
> > calibrated ages cannot be anything but a minimum ages. Priors are just
> > personal guesses about how much older than the older fossil a taxon might
> > be (dressed up in numbers to look scientific). These authors just ignore
> > that. And they continue the temptation of using an automated biogeography
> > program as 'evidence' despite its inherent inability to distinguish
> between
> > vicariance and dispersal where either can generate the same biogeographic
> > pattern. In other words, they use a plug and play program that can render
> > artificial results and they have no way to know. But the authors carry on
> > the pretense that this is not the case.
> >
> > Cheers, John
> >
> > On Fri, Sep 17, 2021 at 10:20 AM John Grehan <calabar.john at gmail.com>
> > wrote:
> >
> > > "Evolution and dispersal of snakes across the Cretaceous-Paleogene mass
> > > extinction" (https://www.nature.com/articles/s41467-021-25136-y.pdf )
> > >
> > > This paper carries on the time honored scientific tradition of just
> > > ignoring shortcomings of a method and ploughing on as if the ground was
> > not
> > > already falling away beneath. In this case the representation or priors
> > as
> > > some kind of empirically real source of estimating fossil calibrated
> > clade
> > > ages as anything but a minimum ages, and the continued temptation of
> > using
> > > an automated biogeography program as 'evidence' despite its
> > > inherent inability to distinguish between vicariance and dispersal
> where
> > > either can generate the same biogeographic pattern. I have been
> attacked
> > > for calling this stuff 'garbage' but I have not come up with a more
> > > accurate term - yet.
> > >
> > > John Grehan
> > >
> >
> >
> > ------------------------------
> >
> > Subject: Digest Footer
> >
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> >
> > Nurturing nuance while assailing ambiguity for about 34 years, 1987-2021.
> >
> >
> > ------------------------------
> >
> > End of Taxacom Digest, Vol 185, Issue 14
> > ****************************************
> >
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> Nurturing nuance while assailing ambiguity for about 34 years, 1987-2021.
>

-- 
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>