[Taxacom] Dispersal paradigm (was: Antarctic dispersal)

[Michael Heads]

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