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[Taxacom] Dispersal paradigm (was: Antarctic dispersal)

Michael Heads m.j.heads at gmail.com
Tue Jun 17 22:54:05 CDT 2014 

Hi Jason,

You wrote that: 'Tectonic events are subject to the same uncertainties as
any other
temporal data source'.

Radiometric dating means that many geological events are very well-dated.

Estimating the age of a clade from its oldest fossil is much more
problematic. Just
how much older is a clade than its oldest fossil? One million years? 20?
50? Most
authors pick something like 2-10? What do you think?


On Wed, Jun 18, 2014 at 9:52 AM, JF Mate <aphodiinaemate at gmail.com> wrote:

> 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??
> >> >> > -------------------------------------------------------------------
> >> >> > _______________________________________________
> >> >> > 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
> >> >> _______________________________________________
> >> >> 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
>
> _______________________________________________
> 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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