rob's gengis presentation at ibs special meeting (montreal 2013)
TRANSCRIPT
Visualizing species distributions and
phylogeography using GenGIS
November 16, 2013
Kaila Lawton Alex Keddy
Daniel Ruzzante
Robert Beiko
Geography Environment
BiodiversityGenes &
Phylogeny
web
map
.orn
l.gov
Wo
rld
clim
.org
data fro
m gb
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ata
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Dat
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GenGIS
DataMap – raster formats (GDAL)Samples – CSV“Sequences” – CSVTrees - Newick
GenGIS v1 overview
Core application
(C++)Scripting interface
(Python, R)
GUI (wxPython)
OutputSaved image files
Open source: Creative Commons Attribution – Share Alike 3.0
Supported platforms: Windows XP, Vista, 7; OS X 10.4, 10.5, 10.6
Crossing minimization + statistical test
GenGIS v1: Parks et al (2009) Genome Res
DataMap – raster + vectorSamples – CSV“Sequences” – CSVTrees - Newick
what's new in v2
Core application
(C++)Scripting interface
(Python, R)
GUI (wxPython)
OutputSaved image files
Save / restore sessions
Python pluginsData retrievalData analysis
Stability improvements, various things now work properly on the Mac
Linear axes analysis
Interface updates (legends, data visualizations)
External files (e.g., distance matrices)
GenGIS v2: Parks et al (2013) PLoS ONE
Maximum Likelihood phylogramAlign tree to geographic axis(can be non-linear as well)
Haplotype geographic
(latitudinal) arrangement
Ruzzante et al., 2011PercichthysPhylogeography
Troncoso-Palacios J, F. Garin C (2013)doi:10.3897/zookeys.294.4399 Liolaemus
Distributions of four Liolaemusspecies
Occurrences (retrieved from GBIF)
CCA (Environmental data from BioClim)
PEN
Finding GenGIS
• http://kiwi.cs.dal.ca/GenGIS• Current version: 2.1.1
• Release candidate 2.2 going up very soon
• Bleeding edge: https://github.com/beiko-lab/gengis
• GenGIS announcements: @rob_beiko on Twitter
• Support: [email protected]• Help with technical problems, data workup, etc.
GenGIS developers
Donovan ParksMike PorterTimothy MankowskiBrett O'DonnellKathryn DunphySylvia ChurcherMike PorterSuwen WangHarman ClairGreg SmolynStephen BrooksChristian BlouinJacqueline Whalley
(Auckland U Tech)