[Taxacom] Dispersal paradigm (was: Antarctic dispersal)

[John Grehan]

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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>
>
>
> --
> 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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>
> Celebrating 27 years of Taxacom in 2014.
>