Rob's GenGIS presentation at IBS Special Meeting (Montreal 2013)

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

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Rob's GenGIS presentation at IBS Special Meeting (Montreal 2013)

  1. 1. Visualizing species distributions and phylogeography using GenGIS Robert Beiko Daniel Ruzzante Kaila Lawton November 16, 2013 Alex Keddy
  2. 2. Geography Environment Worldclim.org webmap.ornl.gov data from gbif.org Biodiversity data from NCBI Infuenza Database GenGIS Genes & Phylogeny
  3. 3. 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
  4. 4. 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
  5. 5. What GenGIS Can Do 6
  6. 6. Hawaiian katydids: 2D / 3D phylogeny
  7. 7. Percichthys Phylogeography Ruzzante et al., 2011 Haplotype geographic (latitudinal) arrangement Maximum Likelihood phylogram Align tree to geographic axis (can be non-linear as well)
  8. 8. Microbial beta-diversity
  9. 9. Diversity in the Human Microbiome Data from Costello et al. (2009)
  10. 10. Ordination + Clustering
  11. 11. Python and R R libraries and visualizations Animated flythroughs 12
  12. 12. Analysis Plugins CCA / PEN Beta-diversity networks Regression and Mantel test 13
  13. 13. Troncoso-Palacios J, F. Garin C (2013) doi:10.3897/zookeys.294.4399 Liolaemus
  14. 14. Single-species distributions Source: GBIF query, “Liolaemus darwinii”
  15. 15. Distributions of four Liolaemus species CCA (Environmental data from BioClim) Occurrences (retrieved from GBIF) PEN
  16. 16. 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.
  17. 17. 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)

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