1. Networks, pixels and smart devices Next gen ecology in a changing world Tim Brown, Postdoctoral Fellow Research school of biology Australian National University

2. More than 7 billion people on the planet for the next 100 years (Figure: Ezeh et al. The Lancet - 14 July 2012 3. At the same time the global climate will warm by 3-6 C This will greatly increase variability and severity of weather events Growing regions will probably shift by 600 900 km (150Km/C) We will need to produce 70% more food by 2050 to feed all these people1 Figure: Moritz & Agudo. 2013. Science 341 (6145), 504-508 1) Tester & LeGrange. 2010. Science:327(818) 4. Global climate will warm by 4-6 C by 2100 53% of Eucalyptus species will be out of their native ranges1 (Google Maps ) 1) Hughes et al. Climatic range sizes of Eucalyptus species in relation to future climate change. Global Ecology and Biogeography Letters (1996): 23-29. 5. If we believe what the science is telling us the next century will not be a pleasant one. The question is no longer How do we prevent this? it is: How do we minimize how bad things will get? 6. If we believe what the science is telling us the next century will not be a pleasant one. The question is no longer How do we prevent this? it is: How do we minimize how bad things will get? We no longer have the luxury of using low resolution ecological models 7. If we believe what the science is telling us the next century will not be a pleasant one. The question is no longer How do we prevent this? it is: How do we minimize how bad things will get? We no longer have the luxury of using low resolution ecological models We need to be tracking everything in the environment at high frequency for long periods of time. 8. If we believe what the science is telling us the next century will not be a pleasant one. The question is no longer How do we prevent this? it is: How do we minimize how bad things will get? We no longer have the luxury of using low resolution ecological models We need to be tracking everything in the environment at high frequency for long periods of time. TERN/ACEAS is uniquely positioned to facilitate this: Establishing long term continent-wide monitoring Pave the way for collaborative use of big data Data standards! 9. If we believe what the science is telling us the next century will not be a pleasant one. The question is no longer How do we prevent this? it is: How do we minimize how bad things will get? We no longer have the luxury of using low resolution ecological models We need to be tracking everything in the environment at high frequency for long periods of time. TERN/ACEAS is uniquely positioned to facilitate this: Establishing long term continent-wide monitoring Pave the way for collaborative use of big data Data standards! Near-surface remote sensing can vastly increase the temporal and spatial resolution of available environmental data. 10. Genotype x Environment = Phenotype Phenotype (and ecosystem function) emerges as a cross- scale interaction between genotypes and their environment 11. Genotype x Environment = Phenotype Phenotype (and ecosystem function) emerges as a cross- scale interaction between genotypes and their environment The degree to which we can measure G, E, P is the degree to which we can understand ecosystem function 12. Genotype x Environment = Phenotype Phenotype (and ecosystem function) emerges as a cross- scale interaction between genotypes and their environment The degree to which we can measure G, E, P is the degree to which we can understand ecosystem function Phenomics lets us we split out Traits the genetically heritable component of phenotype Plasticity the environmental component phenotype 13. Genotype x Environment = Phenotype Phenotype (and ecosystem function) emerges as a cross- scale interaction between genotypes and their environment The degree to which we can measure G, E, P is the degree to which we can understand ecosystem function Phenomics lets us we split out Traits the genetically heritable component of phenotype Plasticity the environmental component phenotype What is the scale and rate of local adaptation? 14. Genotype x Environment = Phenotype Phenotype (and ecosystem function) emerges as a cross- scale interaction between genotypes and their environment The degree to which we can measure G, E, P is the degree to which we can understand ecosystem function Phenomics lets us we split out Traits the genetically heritable component of phenotype Plasticity the environmental component phenotype What is the scale and rate of local adaptation? GxE=P lets us predict climate change impacts How brittle are specific ecosystems? 15. Current Work How do we capture what is going on in the environment, quantify it and provide it to scientists (and the public) in a format that they can use? 16. Current Work How do we capture what is going on in the environment, quantify it and provide it to scientists (and the public) in a format that they can use? (1) Lab phenomics Identifying the genetic basis of plant growth and development 17. Current Work How do we capture what is going on in the environment, quantify it and provide it to scientists (and the public) in a format that they can use? (1) Lab phenomics Identifying the genetic basis of plant growth and development (2) Field ecology High resolution monitoring of ecosystems 18. Current Work How do we capture what is going on in the environment, quantify it and provide it to scientists (and the public) in a format that they can use? (1) Lab phenomics Identifying the genetic basis of plant growth and development (2) Field ecology High resolution monitoring of ecosystems 19. Current Work How do we capture what is going on in the environment, quantify it and provide it to scientists (and the public) in a format that they can use? (1) Lab phenomics Identifying the genetic basis of plant growth and development (2) Field ecology High resolution monitoring of ecosystems How do we phenotype thousands of plants at high spatial and temporal resolution at low cost. 20. Lab phenotyping High precision measurements but low realism In the lab we can control environment and measure phenotype with high precision And we have to develop data pipelines to phenotype 2-3,000 plants continuously 21. Field phenotyping Realistic environment but low precision measurements In the field we have real environments but the complexity (and bad lighting!) reduces our ability to measure things with precision 22. NextGen Ecology Wheres my PCR? Ecology is like genetics before PCR and high throughput sequencing Remember back in the 80s & early 90s when people would get a PhD just sequencing a single gene? 23. NextGen Ecology Wheres my PCR? Ecology is like genetics before PCR and high throughput sequencing Remember back in the 80s & early 90s when people would get a PhD just sequencing a single gene? Humane Genome Project cost $2.7billion USD and took 13 years Now (20 years in) we buy sequencing machines on ebay and light sequence whole genomes for Genomics -> Phenomics 20 years of technical advances have turned genetics into genomics into phenomics and yielded the ability to address fundamental and very complex questions 25. Genetics -> Genomics -> Phenomics 20 years of technical advances have turned genetics into genomics into phenomics and yielded the ability to address fundamental and very complex questions Now state of the art phenomics is almost able to track everything all the time CSIRO High Resolution Plant Phenomics Center Glasshouse Capacity: Time-series hyperspectral and 3D imaging including Thermal & LIDAR 26. Genetics -> Genomics -> Phenomics 20 years of technical advances have turned genetics into genomics into phenomics and yielded the ability to address fundamental and very complex questions Now state of the art phenomics is almost able to track everything all the time CSIRO High Resolution Plant Phenomics Center Glasshouse Capacity: Time-series hyperspectral and 3D imaging including Thermal & LIDAR Generates: 3D time-lapse models of every plant growing with each pixel in all spectra mapped to the 3D data cube model of each plant 27. Genetics -> Genomics -> Phenomics 20 years of technical advances have turned genetics into genomics into phenomics and yielded the ability to address fundamental and very complex questions Now state of the art phenomics is almost able to track everything all the time CSIRO High Resolution Plant Phenomics Center Glasshouse Capacity: Time-series hyperspectral and 3D imaging including Thermal & LIDAR Generates: 3D time-lapse models of every plant growing with each pixel in all spectra mapped to the 3D data cube model of each plant Precision environmental controls 28. Genetics -> Genomics -> Phenomics 20 years of technical advances have turned genetics into genomics into phenomics and yielded the ability to address fundamental and very complex questions Now state of the art phenomics is almost able to track everything all the time CSIRO High Resolution Plant Phenomics Center Glasshouse Capacity: Time-series hyperspectral and 3D imaging including Thermal & LIDAR Generates: 3D time-lapse models of every plant growing with each pixel in all spectra mapped to the 3D data cube model of each plant Precision environmental controls Genome sequence for every plant 29. Genetics -> Genomics -> Phenomics 20 years of technical advances have turned genetics into genomics into phenomics and yielded the ability to address fundamental and very complex questions Now state of the art phenomics is almost able to track everything all the time CSIRO High Resolution Plant Phenomics Center Glasshouse Capacity: Time-series hyperspectral and 3D imaging including Thermal & LIDAR Generates: 3D time-lapse models of every plant growing with each pixel in all spectra mapped to the 3D data cube model of each plant Precision environmental controls Genome sequence for every plant Automated bioinformatics pipeline for trait extraction 30. Genetics -> Genomics -> Phenomics 20 years of technical advances have turned genetics into genomics into phenomics and yielded the ability to address fundamental and very complex questions Now state of the art phenomics is almost able to track everything all the time CSIRO High Resolution Plant Phenomics Center Glasshouse Capacity: Time-series hyperspectral and 3D imaging including Thermal & LIDAR Generates: 3D time-lapse models of every plant growing with each pixel in all spectra mapped to the 3D data cube model of each plant Precision environmental controls Genome sequence for every plant Automated bioinformatics pipeline for trait extraction But ecosystems are more complex than plants in growth chambers We need significantly higher resolution capacity in the field 31. TERN will be a multi-decade project NEON is 30-year project 30 years ago was ~1980 (everything was analog) New technology will enable NextGen ecology too 1.http://www.popsci.com/node/31716 2.http://modis.gsfc.nasa.gov/about/specifications.php 3.https://www.lte.vzw.com/AboutLTE/VerizonWirelessLTENetwork/tabid/6003/Default.aspx 32. TERN will be a multi-decade project NEON is 30-year project 30 years ago was ~1980 (everything was analog) The first space shuttle (1981) 1MB of RAM1 (your phone has 1000x this) New technology will enable NextGen ecology too 1.http://www.popsci.com/node/31716 2.http://modis.gsfc.nasa.gov/about/specifications.php 3.https://www.lte.vzw.com/AboutLTE/VerizonWirelessLTENetwork/tabid/6003/Default.aspx 33. TERN will be a multi-decade project NEON is 30-year project 30 years ago was ~1980 (everything was analog) The first space shuttle (1981) 1MB of RAM1 (your phone has 1000x this) 4G is the same bandwidth that MODIS uses to download a full satellite image of the earth every day (MODIS: 6.1Mbps avg; Verizon 4G: 5-12Mbps 2,3) New technology will enable NextGen ecology too 1.http://www.popsci.com/node/31716 2.http://modis.gsfc.nasa.gov/about/specifications.php 3.https://www.lte.vzw.com/AboutLTE/VerizonWirelessLTENetwork/tabid/6003/Default.aspx 34. TERN will be a multi-decade project NEON is 30-year project 30 years ago was ~1980 (everything was analog) The first space shuttle (1981) 1MB of RAM1 (your phone has 1000x this) 4G is the same bandwidth that MODIS uses to download a full satellite image of the earth every day (MODIS: 6.1Mbps avg; Verizon 4G: 5-12Mbps 2,3) When our kids grow up, what datasets can we have ready for them to use? New technology will enable NextGen ecology too 1.http://www.popsci.com/node/31716 2.http://modis.gsfc.nasa.gov/about/specifications.php 3.https://www.lte.vzw.com/AboutLTE/VerizonWirelessLTENetwork/tabid/6003/Default.aspx 35. Current capacity is very limited in most field work Typical field site: One weather station (temp, humidity, rain gauge, maybe soil moisture, sunlight) 36. Current capacity is very limited in most field work Typical field site: One weather station (temp, humidity, rain gauge, maybe soil moisture, sunlight) Much work is manual: hand measurements, subjective observations, etc. Manual measurements are often only for short time periods (e.g. 1-2 yrs) Repeat experiments to verify results are often at a different site by different observers 37. Current capacity is very limited in most field work Typical field site: One weather station (temp, humidity, rain gauge, maybe soil moisture, sunlight) Much work is manual: hand measurements, subjective observations, etc. Manual measurements are often only for short time periods (e.g. 1-2 yrs) Repeat experiments to verify results are often at a different site by different observers Some more advanced long term sites (e.g. TERN, NEON, fluxnet), but little phenotyping 38. Field site of the future Within 10 years we could have: 39. Field site of the future Within 10 years we could have: Time-series 3D model of every field site 40. Field site of the future Within 10 years we could have: Time-series 3D model of every field site Daily hyperspectral and thermal data layered over every plant with cm accuracy 41. Field site of the future Within 10 years we could have: Time-series 3D model of every field site Daily hyperspectral and thermal data layered over every plant with cm accuracy Every long lived species is sequenced so population genetics is known 42. Field site of the future Within 10 years we could have: Time-series 3D model of every field site Daily hyperspectral and thermal data layered over every plant with cm accuracy Every long lived species is sequenced so population genetics is known Microclimate mesh sensor networks provide growth and environmental data for every tree 43. Field site of the future Within 10 years we could have: Time-series 3D model of every field site Daily hyperspectral and thermal data layered over every plant with cm accuracy Every long lived species is sequenced so population genetics is known Microclimate mesh sensor networks provide growth and environmental data for every tree Advanced visualization tools let you fly into any site to look around, grab data from any location Slide back in time and watch any interaction for as long as there have been sensors Query field sites globally for matching or contrasting environments with the same data and all genetics available Back-end bioinformatics pipelines for automated data mining (cloud computing solutions) Generate snapshot and comparisons of data on the fly to share with colleagues 44. Field site of the future Within 10 years we could have: Time-series 3D model of every field site Daily hyperspectral and thermal data layered over every plant with cm accuracy Every long lived species is sequenced so population genetics is known Microclimate mesh sensor networks provide growth and environmental data for every tree Advanced visualization tools let you fly into any site to look around, grab data from any location Slide back in time and watch any interaction for as long as there have been sensors Query field sites globally for matching or contrasting environments with the same data and all genetics available Back-end bioinformatics pipelines for automated data mining (cloud computing solutions) Generate snapshot and comparisons of data on the fly to share with colleagues Start new research projects beginning with all the data previously collected at a site 45. Field site of the future Within 10 years we could have: Time-series 3D model of every field site Daily hyperspectral and thermal data layered over every plant with cm accuracy Every long lived species is sequenced so population genetics is known Microclimate mesh sensor networks provide growth and environmental data for every tree Advanced visualization tools let you fly into any site to look around, grab data from any location Slide back in time and watch any interaction for as long as there have been sensors Query field sites globally for matching or contrasting environments with the same data and all genetics available Back-end bioinformatics pipelines for automated data mining (cloud computing solutions) Generate snapshot and comparisons of data on the fly to share with colleagues Start new research projects beginning with all the data previously collected at a site In the field tablets, Google glass or similar augmented reality tools let you view high precision data mapped onto the actual plants you are looking at 46. Field site of the future Within 10 years we could have: Time-series 3D model of every field site Daily hyperspectral and thermal data layered over every plant with cm accuracy Every long lived species is sequenced so population genetics is known Microclimate mesh sensor networks provide growth and environmental data for every tree Advanced visualization tools let you fly into any site to look around, grab data from any location Slide back in time and watch any interaction for as long as there have been sensors Query field sites globally for matching or contrasting environments with the same data and all genetics available Back-end bioinformatics pipelines for automated data mining (cloud computing solutions) Generate snapshot and comparisons of data on the fly to share with colleagues Start new research projects beginning with all the data previously collected at a site In the field tablets, Google glass or similar augmented reality tools let you view high precision data mapped onto the actual plants you are looking at So how do we do this? 47. Gigapixel Imaging 48. Gigapixel Imaging - Golfer, 7km distant 49. (Single 15MP image) Area: ~7ha Area: ~1m2 The Gigapan and Gigavision systems allow you to capture hundreds or thousands of zoomed-in images in a panorama. Images are then Stitched into a seamless panorama. The super-high resolution of the final panorama lets you monitor huge landscape areas in great detail. Gigapixel Imaging How it works 50. Gigavision: Gigapixel time-lapse camera 2008 - TimeScience (my company) & U Chicago (Borevitz Lab) Capture timelapse of every leaf on every tree within a few hectares 51. Gigavision: Gigapixel time-lapse camera 2008 - TimeScience (my company) & U Chicago (Borevitz Lab) Capture timelapse of every leaf on every tree within a few hectares ~1-2 billion pixels / panorama = Avg. resolution of ~1-2 pixel / cm over 7 hectares (~600 million > MODIS resolution) Solar powered; wireless/cellular Data management and extraction are a challenge 52. Gigavision: Gigapixel time-lapse camera 2008 - TimeScience (my company) & U Chicago (Borevitz Lab) Capture timelapse of every leaf on every tree within a few hectares ~1-2 billion pixels / panorama = Avg. resolution of ~1-2 pixel / cm over 7 hectares (~600 million > MODIS resolution) Solar powered; wireless/cellular Data management and extraction are a challenge The Future Standardized control software (AXIS VAPIX protocols and PelcoD) would enable almost ANY cheap PTZ camera to become a gigapixel timelapse camera Cloud solution for data processing -> Just buy a camera and plug it in and post- processing is automatic < $6,000 for complete wifi, solar gigapixel system 53. Unmanned Aerial Systems (UAV/UAS) Tech is very new Getting much easier & cheaper VERY quickly Current regs are restrictive But anyone can get started now for