[Taxacom] Hedges/Kumar (eds) The Timetree of Life

John Grehan jgrehan at sciencebuff.org
Mon May 23 07:31:39 CDT 2011



-----Original Message-----
From: Sergio Vargas [mailto:sevragorgia at gmail.com] 

> I meant, I have not read the book... I have read the literature,
though. 
> I know what a track is and how you can draw one, and my point was 
> precisely that since you can link the localities using a nearest 
> neighbor criterion you don't need a phylogeny for the group you are 
> working with.

True, you don't need a phylogeny for the group. But that is different
from saying that panbiogeography ignores phylogeny or does not include
phylogeny which is the usually gist of claims made about that.



> As I mentioned in an earlier posting, a beginner paper posted on my
> website that covers various approaches although I do not go into
> quantitative algorithms as its not my forte.
>
http://www.sciencebuff.org/research/current-research-activities/john-gre
>
han/evolutionary-biography/panbiogeographic-publications/grehan-publicat
> ions/
>
> well, I have been trying for years now to get panbiogeography's 
> algorithms. Aside from Page (1987) and Henderson (1989) I've had 
> troubles finding any. That's why I used Track compatibility analysis
as
>  proposed by Craw. In doing this I've found that the method is not 
> spatial at all, and its results are maximum vicariance. I've seen
papers 
> using PAE to find generalized tracks in an unexplained way: I still 
> don't know how to turn a steiner tree into a minimun spanning tree; I 
> think this is not possible at all, but there are published papers
using 
> PAE to derive generalized tracks... You also have, of course, the 
> classic "by eye"...

Yes there is a lot to do in the quantitative area.

 >Please cite the publications illustrating the frequent use of clique

Publications using track compatibility analysis...

I admit my ignorance here - that track compatibility anaslysis is clique
analysis. But thanks for the examples. At least one of these is titled
'constructing area cladograms' which is not panbiogeographic method.
I'll take a closer look and comment in more detail later.

> looking at the literature, it seems that PAE became more popular as a 
> panbiogeographic technique at some point. Again, how you turn the 
> results of PAE into a generalized tracks remains (at least to me) 
> unexplained.

Agreed. I do not see PAE as a panbiogeographic method for constructing
tracks. Others might argue differently of course.

> The original email I send to Jason was not a critique to 
> panbiogeography. I criticized the use of track compatibility for 
> determining generalized tracks, the method is wrong even from a 
> panbiogeographic perspective, and I gave specific applications and 
> reasons why the method is wrong. I wrote "There is another problem
with 
> panbiogeography...", ok, sorry, please read: there is a problem with
the 
> application of track compatibility analysis for discovering
generalized 
> tracks...

ok. No worries. You may or may not be right about that assertion. When
you publish on it I will take a closer look at your argument.

> I also mentioned that because you can use a nearest neighbor criterion

> to draw the tracks panbiogeography was used as an escape when you want

> to do historical biogeography and don't have cladograms to do BPA for 
> instance. I still think most people do this, at least in Latin America

> where you have many species and not too many cladograms or money to
work 
> on them...

Ah, so now it comes out - that panbiogeography using the nearest
neighbor criterion is an escape from using cladograms (presumably you
mean biological cladograms). Well, perhaps it does not really matter as
the panbiogeographic method (which is more than just drawing tracks of
course) works and gets results that are informative about earth and
life, and even produces results not anticipated by competing research
programs. I am happy to use something that works so well in this regard.

Thank you for taking the time to express your thoughts on this.

John Grehan

sergio





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