Friday, May 26, 2006

TreeBASE meets Google Earth





Bill Piel has created a cool tool for creating KMZ files of phylogenies for Google Earth. From the web site:

One of the components of the CIPRES project is the development of TreeBASE II — a robust, scalable, and versatile re-design and re-engineering of TreeBASE. As part of this project, we are exploring other ways of browsing and visualizing trees. Google Earth is a fantastic 3-D browser for exploring geographic resources and has the potential to be a useful and fun tool for delivering biological information with a geographic component.


Google Earth (available for Windows and Mac OS X) is opening up all sorts of possibilities for biodiversity informatics (ants being one of the first examples). What is cool about Bill's work is that it departs from simple locality records.

As always, after pausing to say "wow", there are all sorts of things that one could think of adding. For example, some trees are clearer than others, due to how well the geography and trees match. I wonder if this could be used as a measure of how well geography "explains" the tree. For example, simple vicariance or serial dispersal would have few cross-overs, a history of dispersal (or an old pattern with extinction, or if geography has changed) might be messier. Perhaps there is a metric that could be developed for this. It strikes me as similar in spirit to trees for tandem duplications -- there's a nice spatial (albeit it linear) order in a tree if the sequences are tandem duplications.

If the trees had dated nodes (i.e., were "chronograms"), presumably this could be used to compute node heights, so you'd be able to have chronograms. Sort of a reverse onion, the layers getting older as you go out. People could then see whether biogeographic patterns were of a similar age. This adds a spatial dimension to chronograms (see an earlier post on the analogy between genome browsers and chronograms).

As an aside, and because I was once a panbiogeography enthusiast, why haven't panbiogeographers leap on Google Earth as a tool to display "tracks"? If ever there was an opportunity to drag that movement out of the doldrums, this is it.

5 comments:

Fiona said...

What an excellent idea... will be really useful for studies of human population history. Cheers!

Mauro Cavalcanti said...

As of your comment on the use of Google Earth to display panbiogeographic tracks, surely this idea would be welcome, provided the necessary tool for computing minimum-spanning trees and representing them in the required format is available.

And just as an aside, Panbiogeography is alive and quicking - see the continuous flow of publications by John Grehan, Michael Heads (both your former colleagues in NZ), Juan Morrone, and others (myself included), in the Journal of Biogeography and elsewhere.

Grehan, Morrone, and Malte Ebach manage a discussion list on Biogeography (in general), as well as an electronic bulletin (Biogeografia) where there are frequent discussions of the panbiogeographic method and synthesis. The list and the bulletin can be reached at http://www.sebasite.org/.

Cheers!

Mr. LoRtZ said...

Sad to see you labeled yourself as "WAS " once a panbiogeography enthusiast. Well, maybe it is the washbrain of molecular enthusiasts. Hope one day you can open up your eyes to the REAL future. We really admire you ... at once.

Cheers!

Brad McFall said...

Cheers,

I have expressed my opinion as to why this idea may not work so well to leaven the quickening of panbiogeography at
http://axiompanbiog.com/method.aspx

One only knows all too well that, I, may be wrong. I hope to have time the summer to spell out all of the details so that there is no confusion over what I am trying to get in communication with panbiogeographers with/over.

It is odd that Grehan and or Ebach have kept me from posting on their discussion list. They have not told me why.

It may be however that I AM correct and this may explain why Page moved away from Panbiog to more mainline pursuits. The MST seems a bit too contrived to be precisely what Croizat had in mind, fully. But I can not disuade myself from finding that MSTs can not be used when ordinating collection localities TO or AWAY from proposed water/land boundaries over the face of the globe. Morrone's recent use of the baseline concept within the mainland shows how difficult it is to out live panbiogeography.

There is no doubt that high-tech is going to bring panbiogeography up against so-called standard evolutionary theory, but seeing how Gould frames geographic range in his "Structure of Evolutionary Theory" book there are still some "juices" to be stewed as Leon wrote on, about Stephen Gould.

Brad McFall

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