Data from: Food quality, security, and thermal refuge influence use of microsites and patches by pygmy rabbits (Brachylagus idahoensis) across landscapes and seasons Dataset DOI: https://doi.org/10.7923/rk1c-jz69 Data re-use: License: CC-BY https://creativecommons.org/licenses/by/4.0/ Recommended Citation: Olsoy, P., Milling, C., Nobler, J. D., Camp, M. J., Shipley, L. A., Rachlow, J., & Thornton, D. H. (2022). Data from: Food quality, security, and thermal refuge influence use of microsites and patches by pygmy rabbits (Brachylagus idahoensis) across landscapes and seasons [Data set]. University of Idaho. https://doi.org/10.7923/RK1C-JZ69 Dataset published to support the following peer-reviewed manuscript: Title: Food quality, security, and thermal refuge influence use of microsites and patches by pygmy rabbits (Brachylagus idahoensis) across landscapes and seasons Journal: Ecology and Evolution DOI: https://doi.org/10.1002/ece3.8892 This dataset was derived from or used data products provided by the following datasets and manuscripts: Chemistry Data: Sorensen Forbey, J., Olsoy, P., Robb, B., Fremgen-Tarantino, M. R., & Nobler, J. D. (2022). Compiled Idaho sagebrush chemistry and plant herbivore interaction data [Data set]. University of Idaho. https://doi.org/10.7923/1JNH-Z422 License: CC-BY UAS Data: Olsoy, P., Burgess, M., Sorensen Forbey, J., Rachlow, J., Shipley, L., & Thornton, D. (2022). Unoccupied aerial systems imagery from Camas, Cedar Gulch and Rocky Canyon Idaho [Data set]. University of Idaho. https://doi.org/10.7923/EM9K-RD28 License: CC-BY PatchType Rasters: Olsoy, P., Sorensen Forbey, J., Shipley, L., Rachlow, J., Robb, B., Nobler, J., & Thornton, D. (2022). Data from: Mapping foodscapes and sagebrush morphotypes with unmanned aerial systems for multiple herbivores [Data set]. University of Idaho. https://doi.org/10.7923/6Z9M-WZ55 License: CC-BY Structural Data (Volume and Aerial Concealment): Olsoy, Peter J. et al. (2018), Data from: Unmanned aerial systems measure structural habitat features for wildlife across multiple scales, Dryad, Dataset, https://doi.org/10.5061/dryad.631q1 License: CC0 Thermal refuge data: Derived from Raw UAS data following methods and equations found in https://doi.org/10.1111/2041-210X.13008. Milling CR, Rachlow JL, Olsoy PJ, et al. Habitat structure modifies microclimate: An approach for mapping fine-scale thermal refuge. Methods Ecol Evol. 2018;9:1648–1657. https://doi.org/10.1111/2041-210X.13008 Data and Code Files: readme.txt DTR_Rasters: Data directory containing four GeoTIFFs of the diurnal temperature range (DTR) derived from UAS data, one each for Camas Summer, Camas Winter, Cedar Gulch Summer, and Cedar Gulch Winter (each comprised of 4 files, 16 total). Note: The Camas Idaho site is also referred to as the Magic Reservoir or MR site within data files and associated scripts within this study, as well as related ancillary projects. Camas == Magic Reservoir. Camas_MagicReservoir_DTR: data directory Camas_Summer_DTR.tif: 1-m pixel resolution Camas_Summer_DTR.tfw Camas_Summer_DTR.tif.aux.xml Camas_Summer_DTR.tif.xml Camas_Winter_DTR.tif: 1-m pixel resolution Camas_Winter_DTR.tfw Camas_Winter_DTR.tif.aux.xml Camas_Winter_DTR.tif.xml CedarGulch_DTR: data directory CedarGulch_Winter_DTR.tif: 1-m pixel resolution CedarGulch_Winter_DTR.tfw CedarGulch_Winter_DTR.tif.aux.xml CedarGulch_Winter_DTR.tif.xml CedarGulch_Summer_DTR.tif: 1-m pixel resolution CedarGulch_Summer_DTR.tfw CedarGulch_Summer_DTR.tif.aux.xml CedarGulch_Summer_DTR.tif.xml CedarGulch_DTR_Methods_Appendix.docx: Methods and equations Milling et al. 2018 (https://doi.org/10.1111/2041-210X.13008) on how to generate the Cedar Gulch DTR rasters. TabularData_Code: Data directory containing all tabular data and coding scripts needed to complete data analyses. CG_Patch_UAS_Cover_Temp_20211008.csv: UAS-derived variable data from Cedar Gulch used in the patch-scale models. Header Key: Patch: Patch type (i.e., microclimate or morphotype) of on-mound, off-mound or dwarf sagebrush UAS_Patch_AC: Average aerial concealment for the 3-m radius patch, calculated from the Olsoy et al. 2018 UAS dataset UAS_Patch_DTR_Sum: Average diurnal temperature range (DTR) in summer for the 3-m radius patch, calculated from CedarGulch_Summer_DTR.tif UAS_Patch_DTR_Win: Average diurnal temperature range (DTR) in winter for the 3-m radius patch, calculated from CedarGulch_Winter_DTR.tif UAS_Patch_Max_Height: Average maximum height for the 3-m radius patch, calculated from the Olsoy et al. 2018 UAS dataset UAS_Patch_Mean_Height: Average mean height for the 3-m radius patch, calculated from the Olsoy et al. 2018 UAS dataset UAS_Patch_Total_Volume: Average volume for the 3-m radius patch, calculated from the Olsoy et al. 2018 UAS dataset MR_Patch_UAS_Cover_Temp_20211008.csv: UAS-derived variable data from Camas used in the patch-scale models. Note: The Camas Idaho site is also referred to as the Magic Reservoir or MR site within data files and associated scripts within this study, as well as related ancillary projects. Camas == Magic Reservoir. Header Key: Patch: Patch type (i.e., microclimate or morphotype) of on-mound, off-mound or dwarf sagebrush UAS_Patch_AC: Average aerial concealment for the 3-m radius patch, calculated from the Olsoy et al. 2018 UAS dataset UAS_Patch_DTR_Sum: Average diurnal temperature range (DTR) in summer for the 3-m radius patch, calculated from Camas_Summer_DTR.tif UAS_Patch_DTR_Win: Average diurnal temperature range (DTR) in winter for the 3-m radius patch, calculated from Camas_Winter_DTR.tif UAS_Patch_Max_Height: Average maximum height for the 3-m radius patch, calculated from the Olsoy et al. 2018 UAS dataset UAS_Patch_Mean_Height: Average mean height for the 3-m radius patch, calculated from the Olsoy et al. 2018 UAS dataset UAS_Patch_Total_Volume: Average volume for the 3-m radius patch, calculated from the Olsoy et al. 2018 UAS dataset patch_use_matching_20191016.xlsx: These data are not utilized in the R analyses, but contain patch-scale use information that is referred to in R code comments (where some patches are assigned a "1" for use outside of the focal plants) pygmy_data_subset_20190828.csv: Data used in the plant-scale analysis. Header Key: [Column 1-NULL Header]: Integer based assignment for data organization GPS_Name: Point name from TopCon centimeter-grade GPS unit Site: Categorical assignment based on the site where plant sample was collected. Values: Camas: Camas/Magic Reservoir Idaho Cedar Gulch: Cedar Gulch Idaho Veg_type: Categorical assignment based on the type of patch (i.e., microclimate or morphotype) where the sample was collected Values: on: Sagebrush plants found on pygmy rabbit mima mounds (i.e., ~5m diameter mounds with deeper soils and denser sagebrush) off: Sagebrush plants found off of but within 8m of the center of pygmy rabbit mima mounds dwarf: Dwarf sagebrush plants found within micro-topographically unique patches near pygmy rabbit mima mounds Species: The species or nearest estimate of the collected plant, or composite of plants collected in a patch. These assignments were not confirmed genetically. Values: dwarf: Generic dwarf sagebrush, classified in the field according to relatively smaller morphological size and location of collection (i.e., nova: Black sagebrush, artemisia nova wyoming: Wyoming big sagebrush, artemisia tridentata ssp. wyomingensis NA: Null. No data collected. Northing: Plant location northing in reference to NAD83 UTM Zone 11N [Camas]/12N [Cedar Gulch] Easting: Plant location easting in reference to NAD83 UTM Zone 11N [Camas]/12N [Cedar Gulch] Elev: Plant location elevation in meters uav_mean_height: Mean height within a 0.5-meter radius of the plant, calculated from the UAS-derived canopy height model Bites_win: Number of bite marks by the associated herbivore counted on the sampled plant (winter sampling). Bites_sum: Number of bite marks by the associated herbivore counted on the sampled plant (summer sampling). Pellets_win: Number of fecal pellets from the associated herbivore counted near the sampled plant (winter sampling). Pellets_sum: Number of fecal pellets from the associated herbivore counted near the sampled plant (summer sampling). CP_Win: Percent (%) of crude protein quantified in the plant sample via combustion method used by Dairy One Forage Lab (winter sampling). CP_Sum: Percent (%) of crude protein quantified in the plant sample via combustion method used by Dairy One Forage Lab (summer sampling). Coum_Win: Concentration of total coumarins (scopoletin equivalents, umol/g dry weight) in the plant sample via a fluorescence assay (winter sampling). Coum_Sum: Concentration of total coumarins (scopoletin equivalents, umol/g dry weight) in the plant sample via a fluorescence assay (summer sampling). MT_Win: Concentration of total monoterpenes (area under the curve (AUC)/mg dry weight) in the plant sample via headspace gas chromatography. This includes total area for all known and unknown compounds (winter sampling). MT_Sum: Concentration of total monoterpenes (area under the curve (AUC)/mg dry weight) in the plant sample via headspace gas chromatography. This includes total area for all known and unknown compounds (summer sampling). Dist2Burrow: Distance in meters to nearest active pygmy rabbit burrow (locations taken from burrow census in the field) TerConc_win: Percent (0-100) terrestrial concealment from cover board photos taken in winter TerConc_sum: Percent (0-100) terrestrial concealment from cover board photos taken in summer AerConc_win: Percent (0-100) aerial concealment from cover board photos taken in winter AerConc_sum: Percent (0-100) aerial concealment from cover board photos taken in summer DTR_win_c: Diurnal temperature range (DTR) in winter, values were standardized by centering by the mean value for the sampling period DTR_sum_c: Diurnal temperature range (DTR) in summer, values were standardized by centering by the mean value for the sampling period MinT_win_c: Minimum temperature in winter, values were standardized by centering by the mean value for the sampling period MinT_sum_c: Minimum temperature in summer, values were standardized by centering by the mean value for the sampling period MaxT_win_c: Maximum temperature in winter, values were standardized by centering by the mean value for the sampling period MaxT_sum_c: Maximum temperature in summer, values were standardized by centering by the mean value for the sampling period BitesBinW: Binomial measure (0/1) of use by pygmy rabbit for bites in winter BitesBinS: Binomial measure (0/1) of use by pygmy rabbit for bites in summer PelletsBinW: Binomial measure (0/1) of use by pygmy rabbit for pellets in winter PelletsBinS: Binomial measure (0/1) of use by pygmy rabbit for pellets in summer Patch: Patch type (i.e., microclimate or morphotype) of on-mound, off-mound or dwarf sagebrush pygmy_rsf_micrositescale.R: R code script for microsite-scale analyses. Note: The Camas Idaho site is also referred to as the Magic Reservoir or MR site within data files and associated scripts within this study, as well as related ancillary projects. Camas == Magic Reservoir. pygmy_rsf_patchscale.R: R code script for patch-scale analyses. Note: The Camas Idaho site is also referred to as the Magic Reservoir or MR site within data files and associated scripts within this study, as well as related ancillary projects. Camas == Magic Reservoir. Resource URL: https://data.nkn.uidaho.edu/dataset/data-food-quality-security-and-thermal-refuge-influence-use-microsites-and-patches-pygmy Creator(s): 1. Peter Olsoy ORCiD: https://orcid.org/0000-0002-8785-0459/ Affiliation: Boise State University 2. Charlotte R. Milling ORCid: https://orcid.org/0000-0001-7466-4844 Affiliation: The Ohio State University 3. Jordan D. Nobler ORCid: NULL Affiliation: Boise State University 4. Meghan J. Camp ORCid: NULL Affiliation: Washington State University 5. Lisa A. Shipley ORCid: NULL Affiliation: Washington State University 6. Jennifer Sorensen Forbey ORCid: https://orcid.org/0000-0001-6069-4049/ Affiliation: Boise State University 7. Janet L. Rachlow ORCid: https://orcid.org/0000-0001-8810-9614/ Affiliation: University of Idaho 8. Daniel H. Thornton ORCid: https://orcid.org/0000-0002-2497-346X Affiliation: Washington State University Other Contributor(s): NA Title(s): Data from: Food quality, security, and thermal refuge influence use of microsites and patches by pygmy rabbits (Brachylagus idahoensis) across landscapes and seasons Description/Abstract: **Abstract** How intensely animals use habitat features depends on their functional properties (i.e., how the feature influences fitness) and the spatial and temporal scale considered. For herbivores, habitat use is expected to reflect the competing risks of starvation, predation, and thermal stress, but the relative influence of each functional property is expected to vary in space and time. We examined how a dietary and habitat specialist, the pygmy rabbit (Brachylagus idahoensis), used these functional properties of its sagebrush habitat—food quality, security, and thermal refuge—at two hierarchical spatial scales (microsite and patch) across two seasons (winter and summer). At the microsite and patch scales, we determined which plant functional traits predicted the number of bites (i.e., foraging) by pygmy rabbits and the number of their fecal pellets (i.e., general habitat use). Pygmy rabbits used microsites and patches more intensely that had higher crude protein and aerial concealment cover and were closer to burrows. Food quality was more influential when rabbits used microsites within patches. Security was more influential in winter than summer, and more at Cedar Gulch than Camas. However, the influence of functional properties depended on phytochemical and structural properties of sagebrush and was not spatiotemporally consistent. These results show function-dependent habitat use that varied according to specific activities by a central-place browsing herbivore. Making spatially explicit predictions of the relative value of habitat features that influence different types of habitat use (i.e., foraging, hiding, thermoregulating) will improve how we predict patterns of habitat use by herbivores and how we monitor and manage functional traits within habitats for wildlife. **Ancillary Data** This dataset was derived from or used data products provided by the following datasets and manuscripts: *Chemistry Data*: Sorensen Forbey, J., Olsoy, P., Robb, B., Fremgen-Tarantino, M. R., & Nobler, J. D. (2022). Compiled Idaho sagebrush chemistry and plant herbivore interaction data [Data set]. University of Idaho. https://doi.org/10.7923/1JNH-Z422 *UAS Data*: Olsoy, P., Burgess, M., Sorensen Forbey, J., Rachlow, J., Shipley, L., & Thornton, D. (2022). Unoccupied aerial systems imagery from Camas, Cedar Gulch and Rocky Canyon Idaho [Data set]. University of Idaho. https://doi.org/10.7923/EM9K-RD28 *PatchType Rasters*: Olsoy, P., Sorensen Forbey, J., Shipley, L., Rachlow, J., Robb, B., Nobler, J., & Thornton, D. (2022). Data from: Mapping foodscapes and sagebrush morphotypes with unmanned aerial systems for multiple herbivores [Data set]. University of Idaho. https://doi.org/10.7923/6Z9M-WZ55 *Structural Data (Volume and Aerial Concealment)*: Olsoy, Peter J. et al. (2018), Data from: Unmanned aerial systems measure structural habitat features for wildlife across multiple scales, Dryad, Dataset, https://doi.org/10.5061/dryad.631q1 *Thermal refuge data*: Derived from Raw UAS data following methods and equations found in https://doi.org/10.1111/2041-210X.13008 **Data Use** *License*: CC-BY *Recommended Citation*: Olsoy, P., Milling, C., Nobler, J. D., Camp, M. J., Shipley, L. A., Rachlow, J., & Thornton, D. H. (2022). Data from: Food quality, security, and thermal refuge influence use of microsites and patches by pygmy rabbits (Brachylagus idahoensis) across landscapes and seasons [Data set]. University of Idaho. https://doi.org/10.7923/RK1C-JZ69 Publisher: University of Idaho Publication Year: 2022 Language(s): American English Subject(s): 1. Natural Sciences 1.4 Chemical sciences 1.5 Earth and related Environmental sciences 1.6 Biological sciences 2. Engineering and technology 2.7 Environmental Engineering Keywords/Tags: food quality, functional properties, multi-scale habitat use, predation risk, security cover, thermal refuge Resource Type General: Dataset Dates: NA Date available for the public: 2022-04-30 Sizes: 36.4 MB Format(s): csv, tif, txt, r, xlsx Version: NA Funding References: US NSF OIA-1757324 RII Track-1: Linking Genome to Phenome to Predict Adaptive Responses of Organisms to Changing Landscapes https://www.nsf.gov/awardsearch/showAward?AWD_ID=1757324 DEB-1146368 Collaborative Research: Modeling the Tradeoffs within Food-, Fear-, and Thermal-Scapes to Explain Habitat Use by Mammalian Herbivores https://www.nsf.gov/awardsearch/showAward?AWD_ID=1146368 DEB-1146194 Collaborative Research: Modeling the Tradeoffs within Food-, Fear-, and Thermal-Scapes to Explain Habitat Use by Mammalian Herbivores https://www.nsf.gov/awardsearch/showAward?AWD_ID=1146194&HistoricalAwards=false IOS-1258217 Courtship Negotiation in a Life-history Context: Interaction between on- and off-lek Tactics in Sage-grouse https://www.nsf.gov/awardsearch/showAward?AWD_ID=1258217&HistoricalAwards=false OIA-1826801 RII Track-2 FEC: Genomics Underlying Toxin Tolerance (GUTT): Identifying Molecular Innovations that Predict Phenotypes of Toxin Tolerance in Wild Vertebrate Herbivores https://www.nsf.gov/awardsearch/showAward?AWD_ID=1826801&HistoricalAwards=false DEB-1146166 Collaborative Research: Modeling the Tradeoffs within Food-, Fear-, and Thermal-Scapes to Explain Habitat Use by Mammalian Herbivores https://www.nsf.gov/awardsearch/showAward?AWD_ID=1146166 Spatial/Geographical Coverage Location: Study Area Description: Idaho USA Site Point Locations: Magic Reservoir-Camas Idaho: -114.317528 43.242182 Cedar Gulch-Leadore Idaho -113.289869 44.699597 Geospatial Extent: West: -114.35388 East: -113.18686 North: 44.796898 South: 43.180083 Temporal Coverage: Start Date: 0214-01 End Date: 2015-06 License: Creative Commons Attribution (CC-BY) https://creativecommons.org/licenses/by/4.0/ Granularity of the Data: NULL Contact Info: Contact Name: Peter Olsoy Contact Email: peterolsoy@boisestate.edu Related Content: Associated Manuscript-Ecology and Evolution: https://doi.org/10.1002/ece3.8892 ### IN PRESS ### Ancillary Dataset-Chemistry Data: https://doi.org/10.7923/1JNH-Z422 Ancillary Dataset-UAS Data: https://doi.org/10.7923/EM9K-RD28 Ancillary Dataset-PatchType Rasters: https://doi.org/10.7923/6Z9M-WZ55 Ancillary Dataset-Structural Data: https://doi.org/10.5061/dryad.631q1 Related Manuscript-Methods in Ecology and Evolution | Thermal refuge: https://doi.org/10.1111/2041-210X.13008 Related Manuscript-Methods in Ecology and Evolution | Structural habitat features: https://doi.org/10.1007/s10980-020-00990-1