Distance decay of fungivores

Just had a quick read a really interesting paper by Kobayashi and Sota just out in Ecosphere that used genetic data to reveal if dispersal limitation could be the driver of community change in fungivores. They used really cool techniques used to find an interesting pattern (or lack there of).

Here is the link: http://onlinelibrary.wiley.com/doi/10.1002/ecs2.1358/full


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

Experimental parasite community ecology

Are experimental approaches a useful way at looking at community assembly of parasites? The answer is obviously yes after you read the neat paper by Banesh and Kalbe that just came out in Animal Ecology.  I really like their blend of semi-field ( fish in cages exposed to natural parasites) and lab experiments, and how they compared low/high growth populations. A nice and simple parasite community with a neat experimental design with some nice results – a great way to start Friday morning.