Visualizing species distributions and

phylogeography using GenGIS

November 16, 2013

Kaila Lawton Alex Keddy

Daniel Ruzzante

Robert Beiko

Geography Environment

BiodiversityGenes &

Phylogeny

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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

What GenGIS Can Do

6

Hawaiian katydids: 2D / 3D phylogeny

Maximum Likelihood phylogramAlign tree to geographic axis(can be non-linear as well)

Haplotype geographic

(latitudinal) arrangement

Ruzzante et al., 2011PercichthysPhylogeography

Microbial beta-diversity

Diversity in the Human Microbiome

Data from Costello et al. (2009)

Ordination + Clustering

Python and R

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Animated flythroughsR libraries and visualizations

Analysis Plugins

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CCA / PEN

Regression and Mantel test

Beta-diversity networks

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

Single-species distributionsSource: GBIF query, “Liolaemus darwinii”

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: beiko@cs.dal.ca• 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)