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[Taxacom] Dispersal paradigm (was: Antarctic dispersal)

JF Mate aphodiinaemate at gmail.com
Tue Jun 17 16:52:47 CDT 2014 

This doesn?t really answer my key complaint.
You could avoid the circularity by not testing tectonics with
geologically dated phylogenies. A pity and a real loss of potentially
useful data but surmountable. A bigger issue is the fact that tectonic
"dates" are a range which can be very wide. So when you say "... if
the phylogenetic break was caused by a spatially coincident tectonic
feature, and this is dated at x million years old, then the
phylogenetic break is also x million years old;..." you are ignoring
two very important facts. Firstly, that geological dates are a range,
from first opening to last connection (and I am ignoring the
uncertainty in determining each of those dates, so there are ranges to
each of your endpoints). Secondly, that taxa will vary in their
response to the barrier emerging. Some will be cut off immediately,
others will be able to cross it for a while, while others may have
populations right around the barrier. With such complex scenarios the
idea that you can collapse multiple splitting dates into a single
common one is just not possible. The current iterative method, albeit
imperfect, serves better the purpose of crosschecking (our differing
opinions on dispersal not withstanding).

Best

Jason

On 17 June 2014 00:19, Michael Heads <m.j.heads at gmail.com> wrote:
> Hi Jason,
>
> You say: '...phylogenies calibrated with vicariance are useless for testing
> relative times due to inherent circularity'.
>
> This follows Kodandaramaiah (2011), who argued that a ?major drawback of
> vicariant calibrations is the problem of circular reasoning when the
> resulting
> estimates are used to infer ages of biogeographic events...?. Yet the use of
> vicariance events to provide dates is based on a simple deduction: if the
> phylogenetic break was caused by a spatially coincident tectonic feature,
> and
> this is dated at x million years old, then the phylogenetic break is also x
> million
> years old; there is no circular reasoning here, whether or not particular
> cases of tectonic-vicariance calibration are incorrect. If a model of
> vicariance
> caused by tectonics is adopted, deductions about the age of a break can be
> tested against each other and other events. This follows a normal process of
> investigation based on the proposal of hypotheses, testing of predictions
> deduced from the hypotheses, and the framing of new hypotheses.
>
>
>
>
> On Tue, Jun 17, 2014 at 9:44 AM, JF Mate <aphodiinaemate at gmail.com> wrote:
>>
>> Dear John and Michael,
>>
>> I was not aware that there was an implicit time limit. I travel a lot
>> and drop in and out of Taxacom as time allows so if you require
>> immediate answers please keep this in mind. Also, to give Michael the
>> benefit of the doubt, I decided to reread his 2011 paper and at least
>> a few of the papers contained within to refresh my mind. The essence
>> of Michael?s paper boils down to this statement: ?But if a single
>> tectonic event related to a node that is distant in phylogeny and
>> space can be used to date the overall phylogeny of a group, presumably
>> separate tectonic events can be used to date many individual nodes
>> within the group itself. This approach involves a de- tailed,
>> systematic engagement of biology with tectonics at many levels, ...
>> this approach combines the best of molecular biology (the clades and
>> their distributions) with hard-rock geology (rather than stratigraphy
>> and fossils) and avoids the many problems of fossil calibration. ?
>> ;geographic distribution has turned out to be the ?character of
>> characters? for molecular phylogeny in general.?
>>
>> Tectonic events are subject to the same uncertainties as any other
>> temporal data source. You are not breaking a biscuit. Some areas will
>> separate first and partial connections (islands, etc) may act as a
>> filter. Can you account for partial filtering as the barrier emerges
>> or  due to disruptions along the barrier (river valleys in mountain
>> ranges, land bridges or connecting islands between separating
>> continents? Your idea sounds like it involves collapsing multiple
>> splitting dates into one ?educated guess?. The patterns may look the
>> same but not the dates.
>>
>> On a more practical note, phylogenies calibrated with vicariance are
>> useless for testing relative times due to inherent circularity. You
>> will still need ?outside? data (fossils, independentl calibrated
>> genetic distances) to corroborate your dating.
>>
>> Rocks on their own do not have inherent solidity. Even you exploit
>> this idea when you say that islands can be older than the sampled
>> surface material implies. Having said that, I could invoke your trump
>> card of (selective) variable divergence rates and simply say that they
>> coincide perfectly. I just need to make the rate that much faster and
>> presto.
>>
>> Regarding Ho & Phillips (2009), your citation is not quite in the
>> spirit of the article. I had to check as it has been a while and as I
>> thought, their opinion of exponential priors is that ?..., it can also
>> be used when there is strong expectation that the oldest fossil lies
>> very close to the divergence event being represented by the node,
>> relative to a distant, soft maximum. ? Otherwise they recommend a
>> lognormal as this can take into account the ambiguity of temporally
>> placing a fossil along the stem group. So if you disagree on an
>> author?s taxonomic guess and have reasons other than pattern fitting,
>> then go ahead and criticize. For me the major take-home message from
>> Ho & Phillips was to use whenever possible multiple calibration points
>> and increased matrix size. That is, lots of data to reduce the
>> uncertainty caused by poor prior choice. This is the point that
>> Richard mentioned and I agree with it. Reducing the choice of data to
>> the ?character of characters? goes against their very sound advice.
>>
>> Finally, John, keeps drumming on the ?dispersal from the centers of
>> origin?. I guess you are fixated on Hennig?s interpretation, and since
>> I am neither partial to his definition nor I care, I stand to one side
>> on that one.
>>
>> Best
>>
>> Jason
>>
>> On 13 June 2014 15:12, Richard Zander <Richard.Zander at mobot.org> wrote:
>> > If the prior affects the posterior probability too much, then the
>> > exercise fails. The whole idea of Bayesian analysis is to update previous
>> > estimates with new information. If there is not much of an update (use Bayes
>> > factors) then Bayes is not the way to go. You can use the simple joint
>> > probability distribution instead, and maybe a likelihood ratio. Any info on
>> > this?
>> >
>> > -----Original Message-----
>> > From: taxacom-bounces at mailman.nhm.ku.edu
>> > [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of John Grehan
>> > Sent: Friday, June 13, 2014 7:55 AM
>> > To: Michael Heads
>> > Cc: taxacom at mailman.nhm.ku.edu
>> > Subject: Re: [Taxacom] Dispersal paradigm (was: Antarctic dispersal)
>> >
>> > Ken and Jason,
>> >
>> > I was hoping to see either of you explain your positions with respect to
>> > the points published by Mike, but Mike has kindly summarize his findings
>> > again and so now I look forward to to seeing how you regard the points
>> > raised.
>> >
>> > John Grehan
>> >
>> >
>> > On Thu, Jun 12, 2014 at 11:24 PM, Michael Heads <m.j.heads at gmail.com>
>> > wrote:
>> >
>> >> Hi Ken,
>> >>
>> >> All the Bayesian dating studies I've seen use very tight priors (see
>> >> my review in J Biogeog 37: 1749. 2011, also my 2014 book). In other
>> >> words, they stipulate, before any analysis, that the clade age can
>> >> only be a little older than the oldest fossil of the group (e.g. 2
>> >> million years).
>> >> This generates 'evidence' that the group is young, and so vicariance
>> >> is ruled out and dispersal is 'revealed'. Many studies use exponential
>> >> priors (which stipulate that the probability of earlier clade ages
>> >> decreases very rapidly), and cite Ho as support for this (even though
>> >> Ho specifically warned against this). Many studies stipulate that the
>> >> clade age can be no older than the base of the geological formation
>> >> that the oldest fossil is from (typically just a few million years) -
>> >> again, there is no logical basis for this, but it generates the desired
>> >> results.
>> >>
>> >> A few authors apart from myself have pointed out the problem of the
>> >> priors.
>> >> Berbee and Taylor (2010) found that 'Different priors for node ages
>> >> had a striking effect on our results....?, but ?Whether or not it is
>> >> possible to select reasonable priors is a serious concern in Bayesian
>> >> analysis (Felsenstein, 2004). Parham et al. (2012: 352) observed:
>> >> ?Most studies use a Bayesian framework for estimating divergence dates
>> >> with probability curves between minimum and maximum bounds? but there
>> >> is presently no practical way to estimate curve parameters [i.e.
>> >> priors]?. One review of recent studies showed that the parameters are
>> >> usually not justified (Warnock et al., 2012). Another review noted
>> >> that ?current practice often consists of little more than educated
>> >> guesswork? (Lee and Skinner, 2011:
>> >> 540). Parham et al. (2012) wrote: ?the fact that a widely applied
>> >> methodology is subjected to such ambiguous assumptions that have a
>> >> major impact on results? is a major limitation of molecular divergence
>> >> dating studies? (p. 352).
>> >>
>> >>    Wilkinson et al. (2011: 28) also criticized the current approach,
>> >> as adopted in studies on primates (Chatterjee et al., 2009). They
>> >>
>> >> wrote the young age estimated for the main divergence in primates
>> >> (strepsirrhines vs. haplorhines):
>> >>
>> >>
>> >>
>> >> may be due to the use of two exponential distributions? These
>> >> distributions? implicitly assume that the true age is
>> >>
>> >> close to the minima [i.e. oldest fossil age] and unlikely to be much
>> >> older than those minima. This assumption, we feel, is unlikely to be
>> >> warranted, as it does not take account of the sizable gaps that exist
>> >> in the primate fossil record.
>> >>
>> >>
>> >>
>> >>
>> >> On Fri, Jun 13, 2014 at 1:54 PM, Ken Kinman <kinman at hotmail.com> wrote:
>> >>
>> >> > John,        I found Jason's critiques to be quite insightful.  I
>> >> > would
>> >> be
>> >> > particularly interested in a straightforward response from you to
>> >> > his question about phylogeny calibration using priors (as follows):
>> >> > ?Anyway, you contend that ?... the point here is that the
>> >> > misrepresentation of minimal ages as actual or maximal has led to
>> >> erroneous
>> >> > results.? I am sure that you are aware that phylogeny calibration
>> >> > allows for priors to be used and that this is common practice to use
>> >> > log priors
>> >> to
>> >> > accommodate not just for the uncertainty in the stratigraphy of
>> >> > fossils
>> >> but
>> >> > also for origination uncertainty. So is your complaint against
>> >> > someone in particular who used a very tight prior or about
>> >> > calibrations in general??
>> >> > -------------------------------------------------------------------
>> >> > _______________________________________________
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>> >> > The Taxacom Archive back to 1992 may be searched at:
>> >> > http://taxacom.markmail.org
>> >> >
>> >> > Celebrating 27 years of Taxacom in 2014.
>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >> Dunedin, New Zealand.
>> >>
>> >> My recent books:
>> >>
>> >> *Molecular panbiogeography of the tropics.* 2012. University of
>> >> California Press, Berkeley.
>> >> www.ucpress.edu/book.php?isbn—80520271968
>> >>
>> >> *Biogeography of Australasia:  A molecular analysis*. 2014. Cambridge
>> >> University Press, Cambridge. www.cambridge.org/9781107041028
>> >> _______________________________________________
>> >> Taxacom Mailing List
>> >> Taxacom at mailman.nhm.ku.edu
>> >> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>> >> The Taxacom Archive back to 1992 may be searched at:
>> >> http://taxacom.markmail.org
>> >>
>> >> Celebrating 27 years of Taxacom in 2014.
>> >>
>> > _______________________________________________
>> > Taxacom Mailing List
>> > Taxacom at mailman.nhm.ku.edu
>> > http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>> > The Taxacom Archive back to 1992 may be searched at:
>> > http://taxacom.markmail.org
>> >
>> > Celebrating 27 years of Taxacom in 2014.
>> > _______________________________________________
>> > Taxacom Mailing List
>> > Taxacom at mailman.nhm.ku.edu
>> > http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>> > The Taxacom Archive back to 1992 may be searched at:
>> > http://taxacom.markmail.org
>> >
>> > Celebrating 27 years of Taxacom in 2014.
>>
>> _______________________________________________
>> Taxacom Mailing List
>> Taxacom at mailman.nhm.ku.edu
>> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>> The Taxacom Archive back to 1992 may be searched at:
>> http://taxacom.markmail.org
>>
>> Celebrating 27 years of Taxacom in 2014.
>
>
>
>
> --
> Dunedin, New Zealand.
>
> My recent books:
>
> Molecular panbiogeography of the tropics. 2012. University of California
> Press, Berkeley. www.ucpress.edu/book.php?isbn—80520271968
>
> Biogeography of Australasia:  A molecular analysis. 2014. Cambridge
> University Press, Cambridge. www.cambridge.org/9781107041028

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