Beiko gen gis2-share

Rob Beiko

New approaches to understand the geography of our microbial world

GenGIS 2

Donovan Parks

Mike Porter

Brett O`Donnell

Timothy Mankowski

demo: the GenGIS environment

GenGIS v1: Parks et al (2009) Genome Res2-24

DataMap – many formats (GDAL)Samples – CSVSequences – 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

DataMap – many formats (GDAL)Samples – CSVSequences – CSVTrees - Newick

what's new in v2

Core application

(C++)Scripting interface

(Python, R)

GUI (wxPython)

OutputSaved image files

Save / restore sessions

Python plugins

Stability improvements, various things now work properly on the Mac

Linear axes analysis

Interface updates (legends, data visualizations)

External files

bringing map data into GenGIS

• Maps:

– MapMaker (included application)

– Digital elevation data (Geobase.ca, NASA Shuttle Topography data, etc.)

– Images (.png, .tif, etc.)

three views of the LineP transect

Original data: Jody Wright, Steven Hallam

diversity and depth

clustering based on Canberrabeta-diversity

relative abundance of SUP05

demo: plugins and R scripts

Original data:

Costello et al. Science 326:1694-1697

Linear regression of group frequencies

Heatmap RPy2 script

10-29

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?

• 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

Wood Buffalo National Park

biomonitoring 2.0what 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.)

biomonitoring 2.0replication results – 2010 trial

• fjej

biomonitoring 2.0sampling 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

biomonitoring 2.0our 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

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!

the long-term goal

Local data

Online data sources

with APIs

+Automated dataset

generation /

visualization

Analysis:

-Geo gradients

-Diversity vs. habitat

-Diversity networks

-Functional models

acknowledgments

GenGIS developers (Dal)

Donovan ParksMike PorterTimothy MankowskiBrett O'DonnellKathryn DunphySylvia ChurcherMike PorterSuwen WangHarman ClairGreg SmolynStephen BrooksChristian BlouinJacqueline Whalley

(Auckland U Tech)

LineP (UBC)

Jody Wright

Steven Hallam

Bio2.0

Mehrdad Hajibabaei (Guelph)

Donald Baird, Wendy Monk (UNB)

Brian Golding (McMaster)

Jeff Shatford (Parks Canada)

Marske et al. Mol Ecol (2009)

Data shown in GenGIS

New Zealand fungus beetle (Agyrtodes labralis)

COI phylogenyEcological niche modelling suggests several glacial refugia, phylogenies suggest transalpine migration

map

locations

sequence summaries

tree vs geography

axes test

body site data

linear regression

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tmap

su

sin

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