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Invasive species and climate change

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BlueBRIDGE workshop: "Supporting Blue Growth with innovative applications based on EU e-infrastructures" - Brussels February 2018

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Invasive species and climate change

  1. 1. BlueBRIDGE receives funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 675680 www.bluebridge-vres.eu Invasive species and climate change Gianpaolo Coro ISTI-CNR gianpaolo.coro@isti.cnr.it Supporting Blue Growth with innovative applications based on EU e-infrastructures 14-15 February 2018, Brussels
  2. 2. "Supporting Blue Growth with innovative applications based on EU e-infrastructures”, 14-15 February 2018, Brussels 15/02/2018 2 Infra and VRE services Data Production and Representation Discovery of patterns in the data Ecological Modelling Discovery of patterns in Eco Models Assess effects on economy and society Reuse of data Reuse of processes From Virtual Research Environments to Open Science
  3. 3. "Supporting Blue Growth with innovative applications based on EU e-infrastructures”, 14-15 February 2018, Brussels 15/02/2018 3 Infra and VRE services
  4. 4. "Supporting Blue Growth with innovative applications based on EU e-infrastructures”, 14-15 February 2018, Brussels • Experiments on Big Data • Sharing inputs and results • Save the provenance of experiments • Supports R-R-R of experiments • Input/Out • Parameters • Provenance Cloud Computing Platform WPS REST NEW Workspace
  5. 5. "Supporting Blue Growth with innovative applications based on EU e-infrastructures”, 14-15 February 2018, Brussels Geospatial Interpolation From a set of punctual observations of a parameter in the sea To a uniform distribution of the parameter
  6. 6. "Supporting Blue Growth with innovative applications based on EU e-infrastructures”, 14-15 February 2018, Brussels Standard representation of geospatial data From a geospatial dataset To a standard representation
  7. 7. "Supporting Blue Growth with innovative applications based on EU e-infrastructures”, 14-15 February 2018, Brussels Presence/absence data Probab ility (1/ 0) 1. Depth mean 2. Depth Standard Deviation 3. Depth Maximum 4. Depth Minimum 5. Distance from Land 6. Ocean Area 7. Ice Concentration Annual Mean 8. PrimaryProduction Annual Mean 9. Sea SurfaceTemperature Standard Deviation 10. Sea SurfaceTemperature Maximum 11. Sea SurfaceTemperature Minimum 12. Sea SurfaceTemperature Range 13. Sea SurfaceTemperature Annual Mean 14. Sea Bottom Temperature Annual Mean 15. Salinity Minimum 16. Salinity Maximum 17. Salinity mean 18. Salinity bottom mean Ready-to-use Data Mining Algorithms • Weka • Rapid Miner • Knime • ISTI-CNR gCube Ecological Engine
  8. 8. "Supporting Blue Growth with innovative applications based on EU e-infrastructures”, 14-15 February 2018, Brussels WPS REST Geospatial data infra. Work- -space WMS WCS GeoTiff NetCDF OPeNDAP VRE • Data preparation • Ocean Currents • Parameters • Signal to noise estimation • Correlation analysis NetCDF file Provenance Metadata (Prov-O) Out. file Sharing Input User Other user OGC StandardsVisualisation Publication VRE Combining Multiple-Infrastructures
  9. 9. "Supporting Blue Growth with innovative applications based on EU e-infrastructures”, 14-15 February 2018, Brussels 15/02/2018 9 Data Production and Representation Infra and VRE services
  10. 10. "Supporting Blue Growth with innovative applications based on EU e-infrastructures”, 14-15 February 2018, Brussels 10 Time span: 1950, 2050, and 2100 at .5° degrees resolution. Parameters: Sea surface temperature, primary production, temperature at sea bottom level, sea surface salinity, salinity at sea bottom level, and ice concentration. Sources: IPSL weather forecast model adjusted using real observation data from The World Ocean Atlas, NOAA NCEP Climatology, SeaAroundUs, and the US National Snow and Ice Data Centres. Projection scenario: IPCC SRES A2 scenario - a future with independently operating, self-reliant nations, continuously increasing population and regionally oriented economic development. Availability: distributed in unstructured textual format via the Web site. Metadata described in a separate online-excel sheet. Global Forecast Data from 1950 to 2100 The AquaMaps Consortium NASA Earth Exchange platform NEX-GDDP Time span: daily forecasts from 1950 to 2100 at .25° resolution Parameters: minimum, maximum surface air temperature, precipitations. Sources: 21 models from the Coupled Model Intercomparison Project Phase 5 (CMIP5). Projection scenarios: medium mitigation (RCP 4.5) and high concentration (RCP 8.5) of greenhouse gasses. Availability: a Cloud service using the NetCDF standard that also embeds metadata.
  11. 11. "Supporting Blue Growth with innovative applications based on EU e-infrastructures”, 14-15 February 2018, Brussels AquaMaps data (600 MB): 1. Cleaned up and put in NetCDF format; 2. Distributions for 1950, 2050, and 2100 were extracted from the table; 3. A 2016 scenario was produced: real observations were adjusted with respect to the other scenarios (values were point-by-point automatically checked to be inside the boundaries of 1950 and 2050, not to go outside the expected maximum and minimum values etc.); 4. A 1999 scenario was produced: point-by-point backwards linear interpolation from 2016 (slopes in the interpolation were calculated based on the differences between 2050 and 1999 IPSL simulations). NASA data (200 GB): 1. The same five years of AquaMaps were selected; 2. The 21 models were averaged together and yearly; 3. Average surface air temperature was calculated as the average of min and max temperatures; 4. Resolution was downscaled to 0.5°; 5. Time series were produced for the RCP 4.5 and RCP 8.5 scenarios separately. Big Data Preparation 11  We used the DataMiner* Cloud computing system of the D4Science e-Infrastructure to process the data. This allows making all the experiments reproducible-repeatable-reusable, in compliance with Open Science directives.. *Coro, G., Panichi, G., Scarponi, P., & Pagano, P. (2017). Cloud computing in a distributed e‐infrastructure using the web processing service standard. Concurrency and Computation: Practice and Experience, 29(18).
  12. 12. "Supporting Blue Growth with innovative applications based on EU e-infrastructures”, 14-15 February 2018, Brussels Surface Air Temperature RCP 4.5 12 Sea Surface Temperature Surface Air Temperature RCP 8.5Sea Bottom Temperature Data Visualisation
  13. 13. "Supporting Blue Growth with innovative applications based on EU e-infrastructures”, 14-15 February 2018, Brussels 04-06 Dec. 2017 13 Sea Surface Salinity Salinity at Sea Bottom Primary ProductionIce Concentration Precipitations RCP 4.5 Precipitations RCP 8.5
  14. 14. "Supporting Blue Growth with innovative applications based on EU e-infrastructures”, 14-15 February 2018, Brussels Temperatures Differences Difference was calculated between the Surface Air Temperatures (SAT) in RCP 4.5 and RCP 8.5 and the Sea Surface Temperature (SST)  Highest discrepancy in 2100;  Covariate of sea level change: a small temperature difference likely indicates that there is no land or ice to isolate air from the sea. 04-06 Dec. 2017 14 SAT-SST RCP 4.5 SAT-SST RCP 8.5
  15. 15. "Supporting Blue Growth with innovative applications based on EU e-infrastructures”, 14-15 February 2018, Brussels Timeline and Linked Open Data 04-06 Dec. 2017 15 https://dlnarratives.eu/timeline/climate.html
  16. 16. "Supporting Blue Growth with innovative applications based on EU e-infrastructures”, 14-15 February 2018, Brussels 16 Data Production and Representation Discovery of patterns in the data Infra and VRE services
  17. 17. "Supporting Blue Growth with innovative applications based on EU e-infrastructures”, 14-15 February 2018, Brussels 17 Climate Change Patterns 17 Surface Air – Sea Surface Temperature RCP 4.5 Global Average Poles Equator Tropics North Atlantic Oc. South Atlantic Oc. Indian Oc. Pacific Oc. Oceania and Indonesia Mediterranean Sea Time series analysis per area: • [SAT-SST] in RCP 4.5 recovers in many areas, • [SAT-SST] in RCP 8.5 always decreases, • Overall sea level increase and ice melting. • Sea Surface Salinity increases globally but decreases locally; • No temperature recovery at the Poles even in low emission scenarios • Etc. Global Average Poles Equator Tropics North Atlantic Ocean South Atlantic Ocean Indian Ocean Pacific Ocean Oceania and Indonesia Mediterranean Sea Global Average 1.00 Poles 0.98 1.00 Equator 0.76 0.71 1.00 Tropics 0.98 0.93 0.77 1.00 North Atlantic Ocean 0.72 0.73 0.47 0.69 1.00 South Atlantic Ocean 0.80 0.76 0.76 0.80 0.49 1.00 Indian Ocean 0.95 0.90 0.82 0.98 0.63 0.80 1.00 Pacific Ocean 0.96 0.91 0.82 0.99 0.64 0.80 0.99 1.00 Oceania and Indonesia 0.85 0.80 0.84 0.88 0.56 0.70 0.91 0.91 1.00 Mediterranean Sea 0.41 0.40 0.34 0.43 0.72 0.24 0.42 0.42 0.39 1.00 Time series cross-correlation analysis: • The Poles reflect the global trend • The Mediterranean Sea is poorly correlated with other areas • Temperature is inverse correlated with Primary Production • Etc.
  18. 18. "Supporting Blue Growth with innovative applications based on EU e-infrastructures”, 14-15 February 2018, Brussels 20 Data Production and Representation Discovery of patterns in the data Ecological Modelling Infra and VRE services
  19. 19. "Supporting Blue Growth with innovative applications based on EU e-infrastructures”, 14-15 February 2018, Brussels Modelling the pufferfish invasion 04-06 Dec. 2017 21 1. Environmental Features are used to train different Species Distribution Models 2. The Models are merged together to estimate one habitat suitability model 3. Real observation are used to estimate potential geographical reachability 4. Forecasted environmental vars. are used to understand how the geographical distrib. changes in time and if it is a stable scenario
  20. 20. "Supporting Blue Growth with innovative applications based on EU e-infrastructures”, 14-15 February 2018, Brussels The puffer fish Lagocephalus sceleratus (Gmelin, 1789) is an invasive species for the Eastern Mediterranean Sea: • Entered through the Suez Canal; • Rapidly invaded the Eastern Mediterranean Sea reaching the western part of the basin; • A highly-toxic species that has an opportunistic behaviour: attacks fishes captured in the nets and lines, seriously damages fishing gears and catch, fast expanding, represents 4% of the weight of the total artisanal catches, very dangerous to humans.  Future expansion was calculated with respect to 2050;  Dynamic expansion and convergence was simulated;  Impact per area was calculated as density of high probability cells in the subdivisions;  The quality of the model was evaluated with respect to real observation and to published and grey literature*; Geographic reachability today Best convergence simulation: in 26 years *G. Coro, L. G. Vilas, C. Magliozzi, A. Ellenbroek, P. Scarponi, P. Pagano. 2017. Forecasting the ongoing invasion of Lagocephalus sceleratus in the Mediterranean Sea, Ecological Modelling (Elsevier)
  21. 21. "Supporting Blue Growth with innovative applications based on EU e-infrastructures”, 14-15 February 2018, Brussels 23 Data Production and Representation Discovery of patterns in the data Ecological Modelling Discovery of patterns in Eco Models Infra and VRE services
  22. 22. "Supporting Blue Growth with innovative applications based on EU e-infrastructures”, 14-15 February 2018, Brussels Quantity Description Mean Mean discrepancy between the probabilities Variance Variance of the discrepancies Number of errors Number of discrepant locations Number of comparisons Number of compared locations Accuracy Number of agreed locations divided by the number of compared locations Maximum error Maximum recorded discrepancy between two locations Relative error Average error divided by the maximum error Maximum error points List of the geographic areas of maximum discrepancy Cohens Kappa A value representing the agreement between the two maps with respect to agreement by chance Trend Expansion, contraction, or stationary label indicating if the second map in the comparison is more or less extended than the first Clusters Interpretation Cluster1 From small- to large-scale conservative distributions with localized moderate changes (40%) in one FAO Area Cluster2 From small- to medium- scale distributions with high (>=40%) habitat change in all the FAO Areas Cluster3 Conservative distributions with small localized change (from 10% to 20%) in one or two FAO Areas Cluster4 From small- and medium- scale distributions with moderate change (from 20% to 40%) in all the FAO Areas Cluster5 From small- and medium- scale distributions with low change (from 10% to 20%) in all the FAO Areas Cluster6 Medium-scale conservative distributions without sensible changes Cluster7 Small-scale conservative distributions, without sensible changes Global Patterns of Climate Change Effects on Species Distributions Discovered classes of change 90.13% agreement with expert assessment ** Coro, G., Magliozzi, C., Ellenbroek, A., Kaschner, K., & Pagano, P. (2015). Automatic classification of climate change effects on marine species distributions in 2050 using the AquaMaps model. Environmental and Ecological Statistics, 1-26. Cluster Analysis on the discrepancy Statistics** Calculated for 406 ASFIS-FAO species (100GB data) Heterodontus zebraMaps comparison statistics* * Coro, G., Pagano, P., & Ellenbroek, A. (2014). Comparing heterogeneous distribution maps for marine species. GIScience & remote sensing, 51(5), 593-611.
  23. 23. "Supporting Blue Growth with innovative applications based on EU e-infrastructures”, 14-15 February 2018, Brussels 25 Data Production and Representation Discovery of patterns in the data Ecological Modelling Discovery of patterns in Eco Models Assess effects on economy and society Infra and VRE services
  24. 24. "Supporting Blue Growth with innovative applications based on EU e-infrastructures”, 14-15 February 2018, Brussels Fisheries dependency on habitat and climate change 26 Alopias vulpinus Today 2050 • In a yield-biomass equilibrium scenario, abundancy shift may depend on the effects of Climate Change on habitat loss; • Catch-per-unit of effort is moderately proportional to habitat suitability for sustainable fisheries (low suitability->no CPUE); • Impact, calculated as density of habitat suitability in time, can be used in stock assessment predictions; • Clustering species’ Climate Change responses can help finding classes of impact on fisheries; • If an expert’s fisheries impact assessment were available for a certain area (e.g. FAO or EEZ), assessing Climate Change response similarities between the areas can help extending the expert’s assessment to other areas.
  25. 25. "Supporting Blue Growth with innovative applications based on EU e-infrastructures”, 14-15 February 2018, Brussels 27 Data Production and Representation Discovery of patterns in the data Ecological Modelling Discovery of patterns in Eco Models Assess effects on economy and society Reuse of data Infra and VRE services
  26. 26. "Supporting Blue Growth with innovative applications based on EU e-infrastructures”, 14-15 February 2018, Brussels 28 Reuse of Data Environmental Data Forecasts: http://thredds.d4science.org/thredds/catalog/public/netcdf/ClimateChange/catalog.html https://goo.gl/cVKuCb Species Distributions Data (AquaMaps Native Model): http://thredds.d4science.org/thredds/catalog/public/netcdf/AquamapsNative/catalog.html Species Distributions in 2050 Data (AquaMaps Native 2050 Model): http://thredds.d4science.org/thredds/catalog/public/netcdf/AquamapsNative2050/catalog.html Interactive Timeline – Linked Open Data: https://dlnarratives.eu/timeline/climate.html Pufferfish Invasion Data: https://goo.gl/vvleUG D4Science e-Infrastructure Catalogue: https://bluebridge.d4science.org/group/imarine-gateway/data-catalogue Cloud Computing Platform: https://wiki.gcube-system.org/gcube/Data_Mining_Facilities
  27. 27. "Supporting Blue Growth with innovative applications based on EU e-infrastructures”, 14-15 February 2018, Brussels 29 Data Production and Representation Discovery of patterns in the data Ecological Modelling Discovery of patterns in Eco Models Assess effects on economy and society Reuse of data Reuse of processes Infra and VRE services
  28. 28. "Supporting Blue Growth with innovative applications based on EU e-infrastructures”, 14-15 February 2018, Brussels 1 - Download the AquaMaps model from the e-Infrastructure: https://bluebridge.d4science.org/group/imarine-gateway/data-catalogue 2 - Produce presence and absence records in native env.: https://bluebridge.d4science.org/group/biodiversitylab/data- miner?OperatorId=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.PRESENCE_CELLS_GENERATION https://bluebridge.d4science.org/group/biodiversitylab/data- miner?OperatorId=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.ABSENCE_GENERATION_FROM_OBIS 3 - Collect environmental information used by AquaMaps: https://bluebridge.d4science.org/group/biodiversitylab/geo-visualisation Or directly: http://data.d4science.org/ctlg/BiodiversityLab/half-degree_cells_authority_file_-_hcaf 4 - Produce Neural Networks and MaxEnt models using the information above: https://bluebridge.d4science.org/group/biodiversitylab/data- miner?OperatorId=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.generators.AQUAMAPS_SUITABLE_NEURALNETWORK https://bluebridge.d4science.org/group/biodiversitylab/data- miner?OperatorId=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.MAX_ENT_NICHE_MODELLING 5 - Use SVMs as further model https://bluebridge.d4science.org/group/biodiversitylab/data- miner?OperatorId=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.SUPPORT_VECTOR_MACHINES_PROJECTOR https://bluebridge.d4science.org/group/biodiversitylab/data- miner?OperatorId=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.SUPPORT_VECTOR_MACHINES_MODELLING 6 - Merge and inverse weight – offline post-processing (integrated with the services) 7 - Display as a map using the e-Infrastructure: https://bluebridge.d4science.org/group/biodiversitylab/data- miner?OperatorId=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.SPECIES_MAP_FROM_POINTS 8 – Get reference points from GBIF and OBIS: https://bluebridge.d4science.org/group/biodiversitylab/species-discovery An Open Science workflow
  29. 29. "Supporting Blue Growth with innovative applications based on EU e-infrastructures”, 14-15 February 2018, Brussels Thank you 31

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