A guide to generating geophylogenies

Evolution is fundamentally a spatio-temporal process – but how to visualize  it on a landscape? Geophylogenies are one elegant way to do just this, but as I’ve found out can be a little tricky to implement particularly if you have a particular base map in mind.

I had a lovely base map of southern California with  the national land cover % impervious surface overlaid but quickly ran into an issue. Unfortunately (for those folks that use ArcGIS) it looks like the arcGIS based geophylobuilder doesn’t install properly anymore – if anyone has a solution let me know. So the challenge then was to get this base map out of Arc and in to R or GenGIS to construct the geophylogeny.

I saved the map as a geoTIFF and tried GenGIS first. Importing the tiff file into GenGIS led to some weird coloration and it doesn’t quite look right even after playing around with the inbuilt features. I like this program though and it can be excellent if the basemap you want is from a different source.

Update: saving as a.jpeg with the world file added does a fine job.

Fig.1 : A fine example of what GenGIS can do.

Anyway, R can also do geophylogenies and I could get R to import the geoTIFF properly with the following code:

#basemap from arcGIS needs package raster
b <- brick(“urbanSoCal.tif”)

Then using Liam Revell’s brilliant phytools package:

tree = read.nexus(“TargetTree97”)
phylomorphospace(tree,cbind(long,lat), colors=setNames(“red”,1),node.by.map=TRUE,add=TRUE, label=”horizontal”)

This took  me a bit of mucking around so hopefully this makes someone else’s application of this cool tool a bit easier – particularly if you are having problems in ArcGIS/GenGIS.

Some links: GenGIS: http://kiwi.cs.dal.ca/GenGIS/Main_Page

Phytools: http://blog.phytools.org/2014/07/new-user-controls-in-phylotomap.html


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