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S. Joost et al. 2010. GEOME. Towards an integrated web-based landscape genomics platform 668 GEOME Towards an integrated web-based landscape genomics platform Stéphane Joost 1* , Michael Kalbermatten 1 & Nicolas Ray 2 1 GIS Research Laboratory (LASIG), Institute of Environmental Engineering (IIE), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland 2 EnviroSPACE Laboratory, Institute for environmental Sciences (ISE), University of Geneva, Switzerland Abstract The aim of the GEOME project is to develop a WebGIS-based platform for the integrated analysis of environmental, ecological and molecular data through the implementation of an original set of combined databases, spatial analysis and population genetics tools, in a High Performance Computing context. GEOME will support tasks of landscape ecologists and resource conservation managers who increasingly have to use geo-referenced data but are not trained to efficiently use Geographical Information Systems together with appropriate geoenvironmental information and spatial analysis approaches. Preliminary developments (three first applications) are already available here: http://lasigpc8.epfl.ch/geome/ Keywords: landscape genomics, geocomputation, environmental data, adaptation, GIS 1. Introduction Since 2000, we are witnessing a progressive integration of the fields of ecology, evolution and population genetics (Lawry 2010). The combination of landscape ecology with population genetics led to the advent of landscape genetics whose goal is to understand how geographical and environmental features structure genetic variation in living organisms (Manel 2003). Recently, landscape genomics (Luikart 2003; Joost 2007; Lawry 2010) emerged as a research field at the interface of genome sciences, environmental resources analysis and spatial statistics. The combination of these fields permits to assess the level of association between specific genomic regions and environmental factors to identify loci responsible for adaptation to different habitats (Lawry 2010). Henceforth, knowledge of geo-environmental data and skills in GIS are a necessity to develop research or management activities in these landscape sciences. To favor the use of landscape genomics and to facilitate access to necessary geo-environmental data, GIS and spatial analysis tools, the development of a robust and efficient computer infrastructure is required. Therefore, GEOME will constitute a robust, easy-to-use and powerful internet platform based on High Performance Computing (HPC), able to handle and process very large genome and environmental data sets, and offering facilities for the statistical and (geo)visual analysis of results (http://lasigpc8.epfl.ch/geome/). The GEOME platform will support access to free geo-environmental data (database) and provide dedicated GIS tools to scientists and professional users (e.g. landscape ecologists or resource conservation managers) who often do not have a background nor a training in * Corresponding author. Tel.:+41216935782 - Fax:+41216935790 Email address: stephane.joost@epfl.ch Forest Landscapes and Global Change-New Frontiers in Management, Conservation and Restoration. Proceedings of the IUFRO Landscape Ecology Working Group International Conference, September 21-27, 2010, Bragança, Portugal. J.C. Azevedo, M. Feliciano, J. Castro & M.A. Pinto (eds.) 2010, Instituto Politécnico de Bragança, Bragança, Portugal.
S. Joost et al. 2010. GEOME. Towards an integrated web-based landscape genomics platform 669 GIScience (Geographic Information Systems and spatial analysis), and do not have time to acquire them. To be able to carry out their investigations, these users need support to i) find appropriate geo-referenced environmental data sets to address their research problematics, ii) integrate their own data sets (e.g. presence/absence of genotypes, of species) with the geoenvironmental information mentioned here above, iii) benefit from specific analytical tools implemented within a simple GIS environment. Several web-based platforms already exist in the domain of genomics or other genetic topics (population genetics, phylogenetics). An interesting example is the BIOPORTAL platform (http://www.bioportal.uio.no), a web-based service platform developed at University of Oslo for phylogenomic analysis, population genetics and high-throughput sequence analysis. BIOPORTAL is the largest publicly available computer resource with 300 dedicated computational cores in a cluster named TITAN. Currently, applications in chemistry and economics have been integrated, but other applications will be added along the way. Another example is GeneGrid, a web-based collaborative industrial grid computing solution developed in the United Kingdom. It was initiated by the Belfast e-Science Centre (BeSC) under the UK e- Science programme and supported by the UK Department of Trade & Industry (DTI). This platform gives access to collective resources, skills, experiences and results in a secure, reliable and scalable manner through the creation of a “Virtual Bioinformatics Laboratory”. GeneGrid provides seamless integration of a series of heterogeneous applications and data sets that span multiple administrative domains and locations across the globe, and presents these to the scientist through a simple user friendly interface (Kelly et al. 2005). It has to be noted that no existing Web-based platform includes the combination of services to be implemented within GEOME. This combination will permit to address the issue of local adaptation through the complementary implementation of a theoretical approach in population genomics (Foll and Gaggiotti 2008) and of a spatial analysis approach (Joost et al. 2007). 2. Main issue addressed: local adaptation In the present context of rapid global climate change, ecologists and evolutionists show a renewed interest to study adaptation (Holderegger et al. 2008). Local adaptation in particular is an important issue in conservation genetics. For example, this process has to be better understood in order to correctly consider the effects of transfers of individuals between populations, which is often a technique proposed to replenish genetic variation and to reduce negative effects of low genetic diversity. The study of local adaptation is also likely to provide objective and unambiguous criteria to characterize conservation areas – in combination with models of predictive habitat or Species Distribution Models (SDMs, Guisan and Thuiller 2005) – which are the most worthwhile preserving. In parallel, development of low impact sustainable agriculture as well as husbandry based on adapted breeds is of priority to most countries in the world, and is of key importance to emerging countries in particular. The genetic basis and the level of adaptation of livestock breeds to their environment has to be investigated, in order to reach better understanding of the relationship between environment and the adaptive fitness of livestock populations, and to favor sustainable production systems based on adapted breeds. During the last decade, “tremendous advances in genetic and genomic techniques have resulted in the capacity to identify genes involved in adaptive evolution across numerous biological systems” (Lowry 2010). There is now an important need to provide tools allowing the acceleration of the study of how landscape-level geographical and environmental features are involved in the distribution of functional adaptive genetic variation, as highlighted by recent publications (Lowry 2010). A few years ago, Holderegger and Wagner (2008) already stated that “Novel approaches linking spatially explicit environmental analysis with molecular genetics could offer effective means to study the spread of adaptive genes across landscapes”. Forest Landscapes and Global Change-New Frontiers in Management, Conservation and Restoration. Proceedings of the IUFRO Landscape Ecology Working Group International Conference, September 21-27, 2010, Bragança, Portugal. J.C. Azevedo, M. Feliciano, J. Castro & M.A. Pinto (eds.) 2010, Instituto Politécnico de Bragança, Bragança, Portugal.
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Landscapes Forest and Global Change
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The contributions to this volume ha
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Table of contents Foreword Preface
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Fine-scale mapping of High Nature V
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Characterization of a Maculinea alc
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Urban tree inventory and socio-econ
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xiii Foreword Twenty years ago, Dr.
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Section 1 Scaling in landscape anal
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V. Cortes et al. 2010. Environmenta
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D. S. de Ron et al. 2010. Habitat s
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B. Bożętka 2010. Recent relations
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S.F. Chen et al. 2010. A physiotope
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N.S. Evseeva & Z.N. Kvasnikova 2010
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S. Frank et al. 2010. A regionally
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M. García et al. 2010. The effect
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M. García et al. 2010. The effect
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S. Gholami et al. 2010. Spatial pat
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P. Matos et al. 2010. Can lichen fu
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E.S. Meier et al. 2010. Projections
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E.S. Meier et al. 2010. Projections
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H. Moutahir et al. 2010. Applicatio
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H. Moutahir et al. 2010. Applicatio
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C. Palaghianu 2010. The use of Voro
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G. Zhelezov 2010. Evaluation of the
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Section 3 Disturbances in changing
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A. Altamirano et al. 2010. Human-ca
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A. Altamirano et al. 2010. Human-ca
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T. Curt & J. Pausas 2010. Are chang
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R.A Fleming et al. 2010. Forest man
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R.A Fleming et al. 2010. Forest man
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P.C. Goebel et al. 2010. How import
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L.R. Iverson et al. 2010. Merger of
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T.-C. Lin et al. 2010. Immediate ef
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K. L. Martin & P.C. Goebel 2010. Im
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G.M. Pastur et al. 2010. Indirect e
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E.W Saragih et al. 2010. Effects of
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L.R.P. Williamson et al. 2010. Anth
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N. Zurbriggen et al. 2010. Modeling
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Section 4 Biodiversity conservation
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Akbarzadeh et al. 2010. Ecotourism
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Akbarzadeh et al. 2010. Ecotourism
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C. Carvalho-Santos 2010. Fine-scale
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I. Catalano et al. 2010. Wood macro
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R.A. Diaz-Varela et al. 2010. Asses
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P.A.E. Diogo & J. Aranha 2010. GIS
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P.A.E. Diogo & J. Aranha 2010. GIS
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V. Etemad & N. Avani 2010. Investig
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A.E. Eycott et al. 2010. The impact
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E. Fernández-Núñez et al. 2010.
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J. Hartter et al. 2010. Fortresses
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M.B. Horta et al. 2010. Landscape S
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Sara Marques et al. 2010. Impact of
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M.G.C. Martins & J. Aranha 2010. El
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M.C. Rodrigues et al. 2010. Charact
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J. Gaspar et al. 2010. Visibility a
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A. Matos et al. 2010. Economic valu
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A. Migliozzi et al. 2010. Land-use
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M.L Porto et al. 2010. Naturalness
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M.L Porto et al. 2010. Naturalness
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M. Rehor & V. Ondracek 2010. Applic
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J. Russell et al. 2010. Developing
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Section 7 Management and sustainabi
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J.M. Rey Benayas 2010. Restoration
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IUFRO Unit 8.01.02 Landscape Ecolog
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