A short illustration of some of the features of GenGIS, including geophylogeny, statistical analysis, and automated data retrieval.

1. Visualizing species
distributions and
phylogeography using GenGIS
Robert Beiko
Daniel Ruzzante
Kaila Lawton
November 16, 2013
Alex Keddy

3. Geography
Environment
Worldclim.org
webmap.ornl.gov
data from gbif.org
Biodiversity
data from NCBI
Infuenza Database
GenGIS
Genes &
Phylogeny

4. GenGIS v1 overview
GUI (wxPython)
Core
application
(C++)
Output
Saved image files
Scripting interface
(Python, R)
Data
Map – raster formats (GDAL)
Samples – CSV
“Sequences” – CSV
Trees - Newick
Crossing minimization + statistical test
Supported platforms: Windows XP, Vista, 7; OS X 10.4, 10.5, 10.6
Open source: Creative Commons Attribution – Share Alike 3.0
GenGIS v1: Parks et al (2009) Genome Res

5. what's new in v2
GUI (wxPython)
Core
application
(C++)
Scripting interface
(Python, R)
Python plugins
Data retrieval
Data analysis
Output
Saved image files
Save / restore
sessions
Data
Map – raster + vector
Samples – CSV
“Sequences” – CSV
Trees - Newick
External files (e.g., distance matrices)
Stability improvements, various things now work properly on the Mac
Interface updates (legends, data visualizations)
Linear axes analysis
GenGIS v2: Parks et al (2013) PLoS ONE

6. What GenGIS Can Do
6

7. Hawaiian katydids:
2D / 3D phylogeny

8. Percichthys
Phylogeography
Ruzzante et al., 2011
Haplotype geographic
(latitudinal) arrangement
Maximum Likelihood phylogram
Align tree to geographic axis
(can be non-linear as well)

9. Microbial
beta-diversity

10. Diversity in the Human Microbiome
Data from Costello et al. (2009)

11. Ordination + Clustering

12. Python and R
R libraries and visualizations
Animated flythroughs
12

13. Analysis Plugins
CCA / PEN
Beta-diversity networks
Regression and Mantel test
13

14. Troncoso-Palacios J, F. Garin C (2013)
doi:10.3897/zookeys.294.4399
Liolaemus

15. Single-species distributions
Source: GBIF query, “Liolaemus darwinii”

16. Distributions of four Liolaemus
species
CCA (Environmental data from BioClim)
Occurrences (retrieved from GBIF)
PEN

17. 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: beiko@cs.dal.ca
• Help with technical problems, data workup, etc.

18. GenGIS developers
Donovan Parks
Mike Porter
Timothy Mankowski
Brett O'Donnell
Kathryn Dunphy
Sylvia Churcher
Mike Porter
Suwen Wang
Harman Clair
Greg Smolyn
Stephen Brooks
Christian Blouin
Jacqueline Whalley
(Auckland U Tech)