[Taxacom] Dispersal paradigm (was: Antarctic dispersal)

Mon Jun 16 16:44:51 CDT 2014

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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>> >
>> > 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
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>> http://taxacom.markmail.org
>>
>> Celebrating 27 years of Taxacom in 2014.
>>
> _______________________________________________
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>
> Celebrating 27 years of Taxacom in 2014.
> _______________________________________________
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> 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.