Data from: High-resolution thermal imagery reveals how interactions between crown structure and genetics shape plant temperature DOI: 10.7923/B68T-2S83 Data, code and/or products within this dataset support the following manuscript: Manuscript Title: High-resolution thermal imagery reveals how interactions between crown structure and genetics shape plant temperature Journal: Remote Sensing in Ecology and Conservation DOI: https://doi.org/10.1002/rse2.359 Description/Abstract: Understanding interactions between environmental stress and genetic variation is crucial to predict the adaptive capacity of species to climate change. Leaf temperature is both a driver and a responsive indicator of plant physiological response to thermal stress, and methods to monitor it are needed. Foliar temperatures vary across leaf to canopy scales and are influenced by genetic factors, challenging efforts to map and model this critical variable. Thermal imagery collected using unoccupied aerial systems (UAS) offers an innovative way to measure thermal variation in plants across landscapes at leaf-level resolutions. We used a UAS equipped with a thermal camera to assess temperature variation among genetically distinct populations of big sagebrush (Artemisia tridentata), a keystone plant species that is the focus of intensive restoration efforts throughout much of western North America. We completed flights across a growing season in a sagebrush common garden to map leaf temperature relative to subspecies and cytotype, physiological phenotypes of plants, and summer heat stress. Our objectives were to: (1) determine whether leaf-level stomatal conductance corresponds with changes in crown temperature; (2) quantify genetic (i.e., subspecies and cytotype) contributions to variation in leaf and crown temperatures; and (3) identify how crown structure, solar radiation, and subspecies-cytotype relate to leaf-level temperature. Stomatal conductance was negatively, non-linearly correlated with crown-level temperature derived from UAS. Subspecies identity best explained crown-level temperature with no difference observed between cytotypes. However, structural phenotypes and microclimate best explained leaf-level temperature. These results show how fine-scale thermal mapping can decouple the contribution of genetic, phenotypic, and environmental factors on leaf temperature dynamics. As climate-change-induced heat stress becomes prevalent, thermal UAS represents a promising way to track plant phenotypes that emerge from gene-by-environment interactions. **Data Use** *License* Creative Commons Attribution ([CC-BY 4.0](https://creativecommons.org/licenses/by/4.0)) *Recommended Citation* Olsoy, P., Zaiats, A., Delparte, D., Roop, S., Roser, A., & Caughlin, T. T. (2022). Data from: High-resolution thermal imagery reveals how interactions between crown structure and genetics shape plant temperature [Data set]. University of Idaho. https://doi.org/10.7923/B68T-2S83 **Funding** US National Science Foundation and Idaho EPSCoR: OIA-1757324 US National Science Foundation and Idaho EPSCoR: OIA-1826801 US National Science Foundation: 2207158 USDA Forest Service Rocky Mountain Research Station: Great Basin Native Plant Project Resource URL: https://data.nkn.uidaho.edu/dataset/data-high-resolution-thermal-imagery-reveals-how-interactions-between-crown-structure-and Creator(s): 1. Peter Olsoy Unique identifier: https://orcid.org/0000-0002-8785-0459 Affiliation(s): Boise State University 2. Andrii Zaiats Unique identifier: https://orcid.org/0000-0001-8978-4152 Affiliation: Boise State University 3. Donna Delparte Unique identifier: https://orcid.org/0000-0002-9107-5117 Affiliation(s): Idaho State University 4. Spencer Roop Unique identifier: NULL Affiliation: Idaho State University 5. Anna V. Roser Unique identifier: https://orcid.org/0000-0002-5184-2916 Affiliation(s): Boise State University 6. T. Trevor Caughlin Unique identifier: https://orcid.org/0000-0001-6752-2055 Affiliation(s): Boise State University Other Contributor(s): 1. Andrew Wright Child Role: Data manager Unique identifier: https://orcid.org/0000-0001-6666-0739 Affiliation(s): University of Idaho Publisher: University of Idaho Publication Year: 2023 Language(s): American English Subject(s): 1 Natural Sciences 1.6 Biological Sciences Ecology 2 Engineering and Technology 2.7 Environmental Engineering Remote Sensing Keywords/Tags: adaptive capacity; Artemisia tridentata; common garden experiment; leaf temperature; sagebrush; stomatal conductance; thermal imagery; unoccupied aerial imagery Resource Type General: Dataset Date available for the public: 2023-06-26 Sizes: 790.6MB Format(s): .tif, .txt, .r, .kml, .tfw, tif.aux.xml, tif.ovr, .tif.xml, .cpg, .dbf, .prj, .shp, .shx, .shp.xml, .sbn, .sbx, .rdata, .rds Version: NULL Funding References: National Science Foundation Idaho EPSCoR Award: OIA-1757324 Title: RII Track-1: Linking Genome to Phenome to Predict Adaptive Responses of Organisms to Changing Landscapes URL: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1757324 National Science Foundation Award: OIA-1826801 Title: RII Track-2 FEC: Genomics Underlying Toxin Tolerance (GUTT): Identifying Molecular Innovations that Predict Phenotypes of Toxin Tolerance in Wild Vertebrate Herbivores URL: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1826801 National Science Foundation Award: BIO-2207158 Title: EAGER: Scaling Up Plant Demographic Rates with Imagery from Unoccupied Aerial Systems URL: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2207158&HistoricalAwards=false USDA Forest Service Rocky Mountain Research Station Great Basin Native Plant Project Spatial/Geographical Coverage Location: Orchard Common Garden Idaho USA Polygon: [-115.9981414739816,43.32237007699626],[-115.9986042885067,43.32190287132909],[-115.9982776172424,43.32171788561769],[ -115.9978185806674,43.32218031878294],[-115.9981414739816,43.32237007699626] Geospatial Extent: Easting: -115.9978185806674 Westing: -115.9986042885067 Northing: 43.32237007699626 Southing: 43.32171788561769 Temporal Coverage: Start Date: 2019-06-05 End Date: 2019-08-28 Granularity of the Data: NULL Contact Info: Contact Name: Peter Olsoy Contact Email: peterolsoy@boisestate.edu Related Content: Peer Reviewed Manuscript-Remote Sensing in Ecology and Conservation | https://doi.org/10.1002/rse2.359 Data/Code Files: A. rgb: Sub-directory containing RGB infrared orthomosaic imagery data in tif format for each date analyzed. 1. Orchard_20190605_RGB_IDTM_clipped.tif a. Orchard_20190605_RGB_IDTM_clipped.tfw b. Orchard_20190605_RGB_IDTM_clipped.tif.aux.xml c. Orchard_20190605_RGB_IDTM_clipped.tif.ovr d. Orchard_20190605_RGB_IDTM_clipped.tif.xml 2. Orchard_20190711_RGB_IDTM_clipped.tif a. Orchard_20190711_RGB_IDTM_clipped.tfw b. Orchard_20190711_RGB_IDTM_clipped.tif.aux.xml c. Orchard_20190711_RGB_IDTM_clipped.tif.ovr d. Orchard_20190711_RGB_IDTM_clipped.tif.xml 3. Orchard_20190828_RGB_IDTM_clipped.tif a. Orchard_20190828_RGB_IDTM_clipped.tfw b. Orchard_20190828_RGB_IDTM_clipped.tif.aux.xml c. Orchard_20190828_RGB_IDTM_clipped.tif.ovr d. Orchard_20190828_RGB_IDTM_clipped.tif.xml B. chm: Sub-directory containing canopy height model (CHM) data in tif format for each date analyzed. 1. Orchard_CHM_20190605_IDTM_clip.tif 2. Orchard_CHM_20190711_IDTM_clip.tif 3. Orchard_CHM_20190828_IDTM_clip.tif C. dsm: Sub-directory containing digital surface model (DSM) data in tif format for each date analyzed. 1. Orchard_DSM_20190605_IDTM.tif a. Orchard_DSM_20190605_IDTM.tif.aux.xml b. Orchard_DSM_20190605_IDTM.tfw c. Orchard_DSM_20190605_IDTM.tif.ovr 2. Orchard_DSM_20190711_IDTM_clip.tif a. Orchard_DSM_20190711_IDTM_clip.tfw b. Orchard_DSM_20190711_IDTM_clip.tif.aux.xml c. Orchard_DSM_20190711_IDTM_clip.tif.ovr d. Orchard_DSM_20190711_IDTM_clip.tif.xml 3. Orchard_DSM_20190828_IDTM_clip.tif a. Orchard_DSM_20190828_IDTM_clip.tfw b. Orchard_DSM_20190828_IDTM_clip.tif.aux.xml c. Orchard_DSM_20190828_IDTM_clip.tif.ovr d. Orchard_DSM_20190828_IDTM_clip.tif.xml D. poly-shape-files: Sub-directory containing polygon shapefiles used during analysis. 1. Orchard_garden_boundary.shp a. Orchard_garden_boundary.cpg b. Orchard_garden_boundary.dbf c. Orchard_garden_boundary.prj d. Orchard_garden_boundary.sbn e. Orchard_garden_boundary.sbx f. Orchard_garden_boundary.shx 2. orchard_ground_poly.shp a. orchard_ground_poly.prj b. orchard_ground_poly.sbn c. orchard_ground_poly.sbx d. orchard_ground_poly.shx 3. orchard_sagebrush_outlines_2019_august.shp a. orchard_sagebrush_outlines_2019_august.cpg b. orchard_sagebrush_outlines_2019_august.dbf c. orchard_sagebrush_outlines_2019_august.prj d. orchard_sagebrush_outlines_2019_august.sbn e. orchard_sagebrush_outlines_2019_august.sbx f. orchard_sagebrush_outlines_2019_august.shp.xml g. orchard_sagebrush_outlines_2019_august.shx 4. orchard_sagebrush_outlines_2019_july.shp a. orchard_sagebrush_outlines_2019_july.cpg b. orchard_sagebrush_outlines_2019_july.dbf c. orchard_sagebrush_outlines_2019_july.prj d. orchard_sagebrush_outlines_2019_july.sbn e. orchard_sagebrush_outlines_2019_july.sbx f. orchard_sagebrush_outlines_2019_july.shp.xml g. orchard_sagebrush_outlines_2019_july.shx 5. orchard_sagebrush_outlines_2019_june.shp a. orchard_sagebrush_outlines_2019_june.cpg b. orchard_sagebrush_outlines_2019_june.dbf c. orchard_sagebrush_outlines_2019_june.prj d. orchard_sagebrush_outlines_2019_june.shx E. rds: Sub-directory containing R data files (.Rds and .RData) to go along with R code. 1. august_split.Rdata: Random sample of 120 pixels from each plant for training and testing of the pixel-level model for August 2019. See pixel_temperature_model_final.R for code to generate the samples. Header Key: CHM_2019: vegetation height for the given pixel in meters (from Orchard_CHM_20190828_IDTM_clip.tif). Radiation_2019: solar radiation on the given pixel calculated using the "insol" R package on Orchard_DSM_20190828_IDTM_clip.tif AREA: plant-level variable for the size of the plant in m^2. DistToPlantCenter: Euclidean distance from the pixel to the center of the plant polygon in meters. plantID: unique identifier for the plant (also called "Tag" in other files). ploidy: ploidy level of the plant (2n or 4n). ssp: subspecies of the plant (T: tridentata; V: vasyena; W: wyomingensis). plantType: combination of ploidy and subspecies (e.g., 2n_T = 2n tridentata; 4n_V = 4n vaseyana). Temp: pixel temperature from August UAS flight. 2. july_split.Rdata: Random sample of 120 pixels from each plant for training and testing of the pixel-level model for July 2019. See pixel_temperature_model_final.R for code to generate the samples. Header Key: CHM_2019: vegetation height for the given pixel in meters (from Orchard_CHM_20190711_IDTM_clip.tif). Radiation_2019: solar radiation on the given pixel calculated using the "insol" R package on Orchard_DSM_20190711_IDTM_clip.tif AREA: plant-level variable for the size of the plant in m^2. DistToPlantCenter: Euclidean distance from the pixel to the center of the plant polygon in meters. plantID: unique identifier for the plant (also called "Tag" in other files). ploidy: ploidy level of the plant (2n or 4n). ssp: subspecies of the plant (T: tridentata; V: vasyena; W: wyomingensis). plantType: combination of ploidy and subspecies (e.g., 2n_T = 2n tridentata; 4n_V = 4n vaseyana). Temp: pixel temperature from July UAS flight. 3. june_split_20220517.Rdata: Random sample of 120 pixels from each plant for training and testing of the pixel-level model for June 2019. See pixel_temperature_model_final.R for code to generate the samples. Header Key: CHM_2019: vegetation height for the given pixel in meters (from Orchard_CHM_201900605_IDTM_clip.tif). Radiation_2019: solar radiation on the given pixel calculated using the "insol" R package on Orchard_DSM_20190605_IDTM_clip.tif AREA: plant-level variable for the size of the plant in m^2. DistToPlantCenter: Euclidean distance from the pixel to the center of the plant polygon in meters. plantID: unique identifier for the plant (also called "Tag" in other files). ploidy: ploidy level of the plant (2n or 4n). ssp: subspecies of the plant (T: tridentata; V: vasyena; W: wyomingensis). plantType: combination of ploidy and subspecies (e.g., 2n_T = 2n tridentata; 4n_V = 4n vaseyana). Temp: pixel temperature from June UAS flight. 4. mAugust_final_10000iter_lasso_priors.Rdata: brmsfit object, see pixel_temperature_model_final.R for model code and out-of-sample validation. 5. mJuly_final_6000iter_lasso_priors.Rdata: brmsfit object, see pixel_temperature_model_final.R for model code and out-of-sample validation. 6. mJune_final_6000iter_lasso_priors_20220517.Rdata: brmsfit object, see pixel_temperature_model_final.R for model code and out-of-sample validation. 7. orchard2019_thermal_variance_stomatal_conductance.Rds: Data used in generating Figure 2 in the paper and analysis of the relationship between crown-level temperature and stomatal conductance. Header Key: ID: unique identifier for the plant (also called "Tag" or "plantID" in other files). subspp: subspecies and ploidy of the plant, also called plantType in other files (e.g., T2n = 2n tridentata; V4n = 4n vaseyana). Season: month associated with the UAS crown-level temperatures (June, July, August). Stts_QC: plant status in the Orchard common garden as of summer 2019 (Living, Dead, Recently Dead). X_IDTM: x coordinate of plant (Easting, meters, Idaho Transverse Mercator projection) Y_IDTM: y coordinate of plant (Northing, meters, Idaho Transverse Mercator projection) AREA: plant-level variable for the size of the plant in m^2. UAS_Thermal: mean crown-level temperature from UAS thermal imagery centered by the average ground pixel temperature (Mean_Plant_Temp - ground), also called Mean_Plant_Temp_Centered in other files. Variance_Plant_Temp: variance of crown-level temperature from UAS thermal imagery in units of (degrees C)^2. Cond: leaf ecophysiology measurement of stomatal conductance from a Licor instrument. 8. TempModelStack_August2019.Rds: Full pixel-level data frame of all vegetation pixels in August, which is sampled from to generate august_split.Rdata Header Key: x: x coordinate of pixel (Easting, meters, Idaho Transverse Mercator projection) y: y coordinate of pixel (Northing, meters, Idaho Transverse Mercator projection) Temp_2019: pixel temperature from August UAS flight in digital number (convert to Celsius with [Temp_2019*0.04 - 273]). CHM_2019: vegetation height for the given pixel in meters (from Orchard_CHM_20190828_IDTM_clip.tif). Radiation_2019: solar radiation on the given pixel calculated using the "insol" R package on Orchard_DSM_20190828_IDTM_clip.tif Tag: unique identifier for the plant (also called "plantID" in other files). Sbssp_P: Plant-level source population for seed in common garden includes State and subspecies (e.g., ID'W = Idaho, wyomingensis; NVT = Nevada, tridentata). ssp: subspecies of the plant (T: tridentata; V: vasyena; W: wyomingensis). ploidy: ploidy level of the plant (2n or 4n). Stts_QC: plant status in the Orchard common garden as of summer 2019 (Living, Dead, Recently Dead). AREA: plant-level variable for the size of the plant in m^2. Centroid_X: x coordinate of the plant center, used to calculate DistanceToPlantCenter. Centroid_Y: y coordinate of the plant center, used to calculate DistanceToPlantCenter. Flight_Date: month the UAS data was collected (August). DistToPlantCenter: Euclidean distance from the pixel to the center of the plant polygon in meters. 9. TempModelStack_July2019.Rds: Full pixel-level data frame of all vegetation pixels in July, which is sampled from to generate july_split.Rdata Header Key: x: x coordinate of pixel (Easting, meters, Idaho Transverse Mercator projection) y: y coordinate of pixel (Northing, meters, Idaho Transverse Mercator projection) Temp_2019: pixel temperature from July UAS flight in digital number (convert to Celsius with [Temp_2019*0.04 - 273]). CHM_2019: vegetation height for the given pixel in meters (from Orchard_CHM_20190711_IDTM_clip.tif). Radiation_2019: solar radiation on the given pixel calculated using the "insol" R package on Orchard_DSM_20190711_IDTM_clip.tif Tag: unique identifier for the plant (also called "plantID" in other files). Sbssp_P: Plant-level source population for seed in common garden includes State and subspecies (e.g., ID'W = Idaho, wyomingensis; NVT = Nevada, tridentata). ssp: subspecies of the plant (T: tridentata; V: vasyena; W: wyomingensis). ploidy: ploidy level of the plant (2n or 4n). Stts_QC: plant status in the Orchard common garden as of summer 2019 (Living, Dead, Recently Dead). AREA: plant-level variable for the size of the plant in m^2. Centroid_X: x coordinate of the plant center, used to calculate DistanceToPlantCenter. Centroid_Y: y coordinate of the plant center, used to calculate DistanceToPlantCenter. Flight_Date: month the UAS data was collected (July). DistToPlantCenter: Euclidean distance from the pixel to the center of the plant polygon in meters. 10. TempModelStack_June2019.Rds: Full pixel-level data frame of all vegetation pixels in June, which is sampled from to generate june_split_20220517.Rdata Header Key: x: x coordinate of pixel (Easting, meters, Idaho Transverse Mercator projection) y: y coordinate of pixel (Northing, meters, Idaho Transverse Mercator projection) Temp_2019: pixel temperature from June UAS flight in Celsius. CHM_2019: vegetation height for the given pixel in meters (from Orchard_CHM_20190605_IDTM_clip.tif). Radiation_2019: solar radiation on the given pixel calculated using the "insol" R package on Orchard_DSM_20190605_IDTM_clip.tif Tag: unique identifier for the plant (also called "plantID" in other files). Sbssp_P: Plant-level source population for seed in common garden includes State and subspecies (e.g., ID'W = Idaho, wyomingensis; NVT = Nevada, tridentata). ssp: subspecies of the plant (T: tridentata; V: vasyena; W: wyomingensis). ploidy: ploidy level of the plant (2n or 4n). Stts_QC: plant status in the Orchard common garden as of summer 2019 (Living, Dead, Recently Dead). AREA: plant-level variable for the size of the plant in m^2. Centroid_X: x coordinate of the plant center, used to calculate DistanceToPlantCenter. Centroid_Y: y coordinate of the plant center, used to calculate DistanceToPlantCenter. Flight_Date: month the UAS data was collected (June). DistToPlantCenter: Euclidean distance from the pixel to the center of the plant polygon in meters. 11. fig3.Rds: Data used in generating Figure 3 in the paper and analysis of crown-level temperature by month and sagebrush type (subspecies and ploidy). Header Key: Tag: unique identifier for the plant (also called "plantID" in other files). subspp: subspecies and ploidy of the plant, also called plantType in other files (e.g., T2n = 2n tridentata; V4n = 4n vaseyana). X_IDTM: x coordinate of plant (Easting, meters, Idaho Transverse Mercator projection) Y_IDTM: y coordinate of plant (Northing, meters, Idaho Transverse Mercator projection) Mean_Plant_Temp: mean crown-level temperature from UAS thermal imagery in Celsius. Season: month associated with the UAS crown-level temperatures (June, July, August). Mean_Plant_Temp_Centered: mean crown-level temperature from UAS thermal imagery centered by the average ground pixel temperature (Mean_Plant_Temp - ground). F. thermal: Sub-directory containing thermal imagery data in tif format for each date analyzed. 1. Orchard_Thermal_20190605_F3_IDTM_clip_ground_normalized.identifier Orchard_Thermal_20190605_F3_IDTM_clip_ground_normalized.tfw Orchard_Thermal_20190605_F3_IDTM_clip_ground_normalized.tif.aux.xml Orchard_Thermal_20190605_F3_IDTM_clip_ground_normalized.tif.xml 2. Orchard_Thermal_20190711_IDTM_clip_ground_normalized.tif Orchard_Thermal_20190711_IDTM_clip_ground_normalized.tfw Orchard_Thermal_20190711_IDTM_clip_ground_normalized.tif.aux.xml Orchard_Thermal_20190711_IDTM_clip_ground_normalized.tif.xml 3. Orchard_Thermal_20190828_IDTM_clip_ground_normalized.tif Orchard_Thermal_20190828_IDTM_clip_ground_normalized.tfw Orchard_Thermal_20190828_IDTM_clip_ground_normalized.tif.aux.xml Orchard_Thermal_20190828_IDTM_clip_ground_normalized.tif.xml G. code: Sub-directory with non-novel code for analysis and figure generation. 1. conductance_temp_model.R: R code for analysis and figure generation (Fig. 2) on the relationship between crown-level temperature and stomatal conductance. 2. crowntemperature_month_sagebrushtype.R: R code for analysis and figure generation (Fig. 3) related to crown-level temperature by month and sagebrush type (subspecies and ploidy). 3. pixel_temperature_model_final.R: R code for pixel-level temperature (June, July, and August) and out-of-sample cross-validation. 4. ridge_plot_thermal.R: R code for Figures 4-6 showing the fixed effects, random intercept, and random slope results of the pixel-level models. H. orchard-common-garden-uas-extent: KML file outlining unoccupied aerial systems (UAS) flight area of interest. I. readme.txt J. metadata.xml: project level metadata in ISO 19115-2 standardized format