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Biogeoinformatics
Stéphane JOOSTLab of Geographic Information Systems (LASIG)
Ecole Polytechnique Fédérale de Lausanne
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GIS Lab EPFL
Computational Landscape Genetics Group‐ Joost‐Widmer‐ Leempoel‐ Duruz‐ Rochat‐ Cesconeto
• GIS application design• Spatial Decision Support Systems• Geospatial data infrastructures• GIS for urban studies and design
• Spatial statistics and analysis
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Research goals
• Make use of GIScience methods and geodatato contribute to :
– The elaboration of efficient decision‐makingsupport approaches to favor the conservation of plant/animal genetic diversity
– The advancement of our understanding of mechanisms controlling the evolution of species(adaptation to local environment in particular)
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GIScience as insider
• Since 2001, immersion in the evolutionarybiology community
• Close collaboration with biologists, geneticists, vets, etc.
• Transdisciplinarity vs interdisciplinarity• A real appropriation of the research field• Members of the team are biologists• Projects submitted to life sciencedivisions
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A key function
Spatial coincidence
Geographic coordinatesX, Y
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Conservation and monitoring of Farm animal Genetic Resources
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FAnGR conservation
• Management and conservation of livestock genetic resources imply breed prioritization, and therefore decision making
• Decision making rests on the simultaneous analysis of several criteria…
• … in order to identify and to favour sustainable breeding conditions
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Data categories
1. Population and evolutionary genetics2. Animal husbandry practices3. Socio‐economic and socio‐demographic data in the
regions where animals are bred4. Environmental information: climatic and geophysical
characteristics of the places where animals are bred5. Political and administrative boundaries: geographical
units where policies have to be applied
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Data integration
SamplingGenetic data
Environmental data:topography, climate,soil, etc.
Administrative boundariesSocio‐Economic dataSocio‐demographic data
QuestionnairesHusbandry praticesGISGIS
Geographic coordinatesX, Y
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FAnGR monitoring
• FAO Global plan (2007) requires countries to monitor their FAnGR
• Countries like Austria, Germany, Great Britainhave developed a monitoring system
• GenMon prototype under development in Switzerland (Duruz 2014)
• The system uses geographic information to assess endangerment
• And to communicate information bymeans of thematic maps
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• Breed, demography, biology, population genetics
• Geodata (sampling design, geocoordinates) • Communication skills, thematic mapping• Database, spatial database, web protocols, web design
• GIS software, programming languages, data processing
• Computer science
Geointelligence
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Understanding of mechanisms controlling the
evolution of species
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Science, 2010
Landscape genomics
• Correlative approaches and spatial statistics
Genome‐wide information• Paradigm shift and transition phase
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GEO
GENETICS
Genetic data
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GENETICS ENVIRONMENTGEO
Environmental data characterizingsampling locations
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Logistic regression
Multiple parallel logistic regressions
Individuals Genetic markers Environmental variables
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http://lasig.epfl.ch/sambada
Computation time (in hours) Spatial statistics
23 environmental variables
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• Breed, biology, population genetics, genomics
• Geodata (sampling design, geocoordinates) • Communication skills, thematic mapping• GIS software, programming languages• Spatial statistics, High Performance Computing(HPC) for data processing
• Computer science
Geointelligence
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Limit
• An important problems we need to overcome for effective livestock genomic resources conservation
• to enforce the recording of geographical coordinates of any sampled animal as a standard rule
• so that we can fully benefit from the power of biogeoinformatics
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Report on PEDs for FAnGR in 2008
• Edited by FAO & WAAP
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Recommendation X,Y
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Conclusion
• In both cases, an original combination of skills including molecular biology, computer science and geographic information science is necessary
• New knowledge will be extracted from the present data tsunami (large molecular, environmental, and socio‐economic datasets)
• … only if we train a new generation of students/scientists able to develop innovative transdisciplinary and efficient geocomputingtools
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Thank you for your attention !