GenGIS (http://kiwi.cs.dal.ca/GenGIS) presentation given by Rob Beiko at Canadian Society of Microbiologists meeting June 21, 2012

1. GenGIS 2
New approaches to understand the
geography of our microbial world
Rob Beiko

2. Donovan Parks
Timothy Mankowski
Mike Porter
Brett O`Donnell

3. demo: the GenGIS environment
2-24 GenGIS v1: Parks et al (2009) Genome Res

4. GenGIS v1 overview
GUI (wxPython)
Core Output
application Saved image files
(C++)
Scripting interface
(Python, R)
Data
Map – many 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

5. what's new in v2
GUI (wxPython)
Core Output
application Saved image files
(C++) Save / restore
Scripting interface sessions
(Python, R)
Data
Map – many formats (GDAL)
Samples – CSV
Sequences – CSV
Python plugins Trees - Newick
External files
Stability improvements, various things now work properly on the Mac
Interface updates (legends, data visualizations)
Linear axes analysis

6. bringing map data into GenGIS
• Maps:
– MapMaker (included application)
– Digital elevation data (Geobase.ca, NASA Shuttle
Topography data, etc.)
– Images (.png, .tif, etc.)

7. three views of the LineP transect
Original data: Jody Wright, Steven Hallam

8. diversity and depth

9. clustering based on Canberra
beta-diversity

10. relative abundance of SUP05

11. demo: plugins and R scripts
Linear regression of group frequencies
Heatmap RPy2 script
Original data:
10-29 Costello et al. Science 326:1694-1697

12. clustering of fecal samples
Female subjects: F1 – F3
Male subjects: M1 – M3
Two sampling methods:
- TP
- Direct from feces
Two time points
= 4 samples per individual. Do these
samples cluster with each other?

14. Wood Buffalo National Park
• Canada’s largest National Park
• UNESCO World Heritage status (Boreal Forest)
• Threatened by encroaching development
– Oil Sands mining (Alberta)
– Metal mining (NWT)
– Hydro-electric dams (Peace River, BC)
• Natural resources sustain traditional use by Métis and
First Nations peoples
Photos: D Baird

15. biomonitoring 2.0
what is being collected
• Benthic invertebrates (COI, 28S) – kick sample
• Water (16S, 18S, 28S) – 1L volume
• Soil (16S, COI, ITS, 18S, 28S, RbcL) - cores
• Terrestrial arthropods (COI, 28S) – malaise / pitfall traps
• All samples replicated 3 times
• 5 time points in initial study
• Lots of metadata (soil chemistry,
flooding, etc.)

16. biomonitoring 2.0
replication results – 2010 trial
• fjej

17. biomonitoring 2.0
sampling progress
• August 2011
• Samples collected, starting analysis of sequences
• 'traditional' taxonomy where applicable (arthropods
si, bacteria no)
• June 2012
• Samples collected
• Future sampling: August 2012, June – August 2013

18. biomonitoring 2.0
our three-year mission (and beyond)
• Develop robust sampling techniques for sequence-
based biomonitoring
• Develop and apply different approaches for
assessing biodiversity (taxon-based and taxon-
free), and compare their performance on WBNP data
• Identify whether “reference conditions” can be
established against which future samples can be
compared

19. call for collaborators
• Currently underway:
– Combined axis tests (Many trees, one optimal gradient)
– Regional tests of diversity
– Canonical correlation analysis and related
– Bio2.0 analysis
• Goals:
– Integrate with online data sources
– Support more data types (especially vector data)
– More plugins!

20. the long-term goal
Online data sources Analysis:
with APIs -Geo gradients
Automated dataset -Diversity vs. habitat
+ generation / -Diversity networks
Local data visualization -Functional models

22. acknowledgments
GenGIS developers
(Dal)
Donovan Parks
Mike Porter LineP (UBC)
Timothy Mankowski Jody Wright
Brett O'Donnell Steven Hallam
Kathryn Dunphy
Bio2.0
Sylvia Churcher
Mike Porter Mehrdad Hajibabaei (Guelph)
Suwen Wang Donald Baird, Wendy Monk (UNB)
Harman Clair Brian Golding (McMaster)
Greg Smolyn Jeff Shatford (Parks Canada)
Stephen Brooks
Christian Blouin
Jacqueline Whalley
(Auckland U Tech)

24. New Zealand fungus beetle
(Agyrtodes labralis)
COI phylogeny
Ecological niche modelling suggests
Marske et al. Mol Ecol (2009)
several glacial refugia, phylogenies Data shown in GenGIS
suggest transalpine migration

25. map

26. locations

27. sequence summaries

28. tree vs geography

29. axes test

30. body site data

31. linear regression

32. heatmaps using R