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 Visualizing Phylogeography in 3D

10/12/2012

5 Comments

 
Picture
When we want to visualize biogeographical distributions we usually create maps. When we want to visualize phylogenetics we often build taxonomic trees. What if we want to visualize phylogeography? Typically we use maps and phylogenetic trees side-by-side. There is a relatively new tool called GeoPhyloBuilder that joins the two. It is available in ArcGIS 9.3 and later versions and was created by David Kidd and Xianhua Liu of The National Evolutionary Synthesis Center (2008).  GeoPhyloBuilder builds a 3D spatiotemporal, phylogenetic GIS data model by attaching the phylogenetic tree tips to the geographical locations of the samples. The geographical locations can be points, lines, or polygons. The 3D dimension comes from the node depths of the phylogenetic tree.  Longer, older branches are elevated further above the map.  The model can be visualized in 2D or 3D in ArcMap, ArcScene, or other Earth Browsers. Examples of images and movies as well as the download are available at: https://www.nescent.org/sites/evoviz/GeoPhyloBuilder.  Although some of these images make the phylogenetic tree look like spaghetti hanging over a map, you can color code different branches to see how they relate geographically. You can also visualize the 3D images in a movie, rotating the image so that you can get varying perspectives. Passing information on is easiest when you have powerful visuals and this may be helpful for some phylogeographical results.

Lisa Marrack

Phylogenies of the freshwater fish family Goodienae: (purple; Webb et al., 2004) and genera Poeciliopsis (green; Mateos et al., 2002) and Notropis (blue; Schonhuth & Doadrio, 2003) with modern elevation and drainage. Pliocene and Miocene drainage and palaeolakes from de Cserna & Alvarez (1995). [In Kidd and Ritchie (2006): Journal of Biogeography].


 

5 Comments
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8/13/2013 10:30:37 pm

In 3D it is very easy to understand the map. I use Matlab for produce such type of Simulink. CAD is one of the best option.

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9/1/2013 05:11:00 pm

Ideally, converting a photo in 3D requires two separate images processed together to provide three-dimensional depth. These stereo photos are "almost identical" left and right photos that are shot simultaneously with cameras that are in short distance from each other.

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10/30/2013 06:52:01 am

Very Useful information , this is both good reading for, have quite a few good key points, and I learn some new stuff from it too, thanks for sharing your information.

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Raul
2/14/2016 06:59:43 am

Thanks for this post. Can you show how the input tree and lat/long data looks like for the GeoPhyloBuilder?

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