This readme.txt file was generated on 2020/05/14 by Erin O'Connell and Jessica Savage ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset Maximum carbon assimilation model for understory wood plants growing at Bagley Nature Area in Duluth, MN 2. Author Information Principal Investigator Contact Information Name: Jessica A. Savage Institution: University of Minnesota Address: 1035 Kirby Drive, 207 Swenson Science Building, Duluth, MN 55812 Email: jsavage@d.umn.edu ORCID: 0000-0002-7756-7166 First Author Contact Information Name: Erin O'Connell Institution: University of Minnesota Address: 1035 Kirby Drive, 207 Swenson Science Building, Duluth, MN 55812 Email: oconn877@d.umn.edu ORCID: 0000-0002-7983-7959 3. Date of data collection (single date, range, approximate date) 2017/02/16-2018/11/11 4. Geographic location of data collection (where was data collected?): Bagley Nature Area, Duluth, MN 5. Information about funding sources that supported the collection of the data: National Science Foundation (IOS:1656318), the University of Minnesota – Duluth, and the Integrated Biosciences Graduate Program -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: Manuscript copyright held by Biological Invasions. 2. Links to publications that cite or use the data: O'Connell, E. and Savage, J. (2020). Extended leaf phenology has limited benefits for invasive species growing at northern latitudes. Biological Invasions 22(10): 2957-2974. https://doi.org/10.1007/s10530-020-02301-w 3. Links to other publicly accessible locations of the data: None 4. Links/relationships to ancillary data sets: None 5. Was data derived from another source? If yes, list source(s): No 6. Recommended citation for the data: O'Connell, Erin and Savage, Jessica A. (2020). Maximum carbon assimilation model for understory wood plants growing at Bagley Nature Area in Duluth, MN. Retrieved from the Data Repository for the University of Minnesota. https://doi.org/10.13020/t9bg-vr86 --------------------- DATA & FILE OVERVIEW --------------------- 1. File List A. Filename: Maximum_Carbon_Assimilation_Model.R Short description: This program models maximum seasonal carbon assimilation for 8 species (6 plants/species) growing in a 50-year-old mixed forest at Bagley Nature Area in Duluth, MN based on understory light availability on sunny days, carbon dioxide assimilation rates, and leaf area over time. B. Filename: Carbon_gain_input Short description: This file contains individual plant numbers included in the model, plant height, stem count, leaf count, average leaf area, and total leaf area. C. Filename: Spring_leaf_expansion_2017 Short description: This file contains weekly leaf area measurements of 6-15 scanned leaves for 48 individuals in spring 2017. D. Filename: Fall_leaf_phenology_2017 Short description: This file contains weekly observations of leaf drop, leaf color change, and leaf senescence in fall 2017. E. Filename: Photosynthetic_light_response_curves Short description: This file contains raw output data from a LiCOR-6400 XT measuring photosynthetic light response curves of young and mature leaves in summer 2017. F. Filename: Understory_light_monthly Short description: This file contains data on monthly understory light availability above the study plants. G. Filename: Understory_light_daily Short description: This file contains data on daily understory light availability above the study plants logged every fiften minutes during six months. 2. Relationship between files: All of these files are data collected during a two year project at Bagley Nature Area, Duluth MN investigating phenology, growth, freezing tolerance, and carbon gain of invasive and native shrubs. 3. Additional related data collected that was not included in the current data package. N/a 4. Are there multiple versions of the dataset? yes/no Yes, data in the files "Carbon_gain_input," "Fall_leaf_phenology_2017," and "Photosynthetic_light_response_curves" are also summarized in the data package: O'Connell, E. and Savage, J. (2020). Plant phenology, growth, freezing damage, and carbon gain data observed from 2017 to 2018 on wood plants growing at Bagley Nature Area in Duluth, MN. Retrieved from the Data Repository for the University of Minnesota. https://doi.org/10.13020/5dp7-5a20 And data in the files "Understory_light_monthly" and "Understory_light_daily" are also included in the data package: O'Connell, Erin and Savage, Jessica A. (2020). Understory light environment measured in 2017 and 2018 at Bagley Nature Area in Duluth, MN. Retrieved from the Data Repository for the University of Minnesota. https://doi.org/10.13020/mwhd-jy06 -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: See descriptions under "Variable Lists" below and publication for details. A. Maximum_Carbon_Assimilation_Model.R None B. Carbon_gain_input Total stems per plant were counted for six plants per species in May 2018. Leaf area was measured on 6-15 fully expanded leaves for ten plants per species in summer 2017. Leaves were scanned and measured using imageJ. Total number of leaves were estimated for six plants per species in August 2017. C. Spring_leaf_expansion_2017 6-15 leaves from ten plants per species were collected weekly in spring/summer 2017. Leaf area was measured on scanned leaves using imageJ. D. Fall_leaf_phenology_2017 Fall leaf senescence (leaf drop, color change, or photosystem function loss) was monitored weekly on ten plants per species in 2017. E. Photosynthetic_light_response_curves Light response curves were measured on six plants per species for immature/expanding leaves in early June and for mature leaves in mid-August 2017. Measurements were made on sun leaves between 8am and 2pm during sunny days using a portable gas exchange system (6400, LI-COR, Lincoln, NE) with a red-blue light source (6400-02B). The auto program LightCurve was used with 10 light levels between 0 and 2000 μmol photons s-1 m-2. F. Understory_light_monthly Percent light transmittance on cloudy days was measured above ten plants per species in May, July, September, and October 2018. Each measurement is the ratio of the light level above the plant to the light level recorded simultaneously in the open. G. Understory_light_daily Temperature and light were measured at 15-minute intervals on 11-30 days per month (May, July, August, September, October, and November 2018) using lux sensors mounted at the top of six plants per month. 2. Methods for processing the data: All data was processed in the R script (Maximum_Carbon_Assilimation_Model.R). Understory light levels (Understory_Light_Monthly) were converted from lux (lumens s-1) to PPFD (µmol photons m-2 s-1) based on seasonal calibrations in each month (created from Understory_light_monthly). Light levels were then multiplied by carbon assimilation rates (Photosynthetic_light_response_curves) from corresponding light levels for young and mature leaves. The resulting daily carbon gain was multiplied by total leaf area (from Carbon_gain_input) and corrected in the spring for expanding leaves (Spring_leaf_expansion_2017) and in the fall for senescing leaves (Fall_leaf_phenology_2017). Daily carbon gain was finally partioned into seasonal carbon gain based on overstory canopy openness. See descriptions under "Variable Lists" below and publication (Fig 2) for details. 3. Instrument- or software-specific information needed to interpret the data: R (version 3.4.1 or later) 4. Standards and calibration information, if appropriate: NA 5. Environmental/experimental conditions: Measurements in the file "Photosynthetic_light_response_curves" were made between 8am and 2pm on sunny days. The auto program LightCurve was used with 10 light levels between 0 and 2000 μmol photons s-1 m-2. The following conditions were maintained: leaf temperature = 20°C, CO2 concentration = 400 μmol mol-1, water content = 12-15 mmol, and flow rate = 50 – 200 μmol s-1. 6. Describe any quality-assurance procedures performed on the data: All data entry was double checked. 7. People involved with sample collection, processing, analysis and/or submission: Erin O'Connell, Jessica Savage, Alex Peichel, Natalie McMann, Collin Monette, Kennedy Mosher, Thomas Kiecker, Max Bonfig, Shauna Blake, Sydney Hudzinski, Rishika Quick-Singh, and Nihaar Joshi ---------------------------------------------------------------- DATA-SPECIFIC INFORMATION FOR: Maximum_Carbon_Assimilation_Model ---------------------------------------------------------------- See R file for details. ------------------------------------------------ DATA-SPECIFIC INFORMATION FOR: Carbon_gain_input ------------------------------------------------ 1. Number of variables: 10 2. Number of cases/rows: 47 3. Missing data codes: Code/symbol: NA Definition: Data not available. 4. Variable List A. Name: Plant_ID Description: Unique number given to each plant included in the model. B. Name: Species Description: Species code based on the first two letters of the genus and the first two letters of the species. BETH = Berberis thunbergii, COCO = Corylus cornuta, COSE = Cornus sericea, FRAL = Frangula alnus, LOBE = Lonicera x. bella, RHCA = Rhamnus cathartica, RUID = Rubus idaeus, VILE = Viburnum lentago. C. Name: Species_scientific Description: Scientific name of the species [Genus_species]. D. Name: Genus Description: Genus corresponding to each species included in the model. E. Name: Status Description: Origin of the species. Species native to North America are designated as "native," and species native to Europe or Asia and invasive in North America are designated as "invasive." F. Name: Plant_height Description: Plant height [cm] measured during fall 2018 using transect tape. G. Name: Stem_count Description: Number of stems counted in spring of 2017. H. Name: Leaf_count Description: Number of leaves per plant counted in August 2017. I. Name: Ave_leaf_area Description: Average leaf area [cm^2] of 6-15 fully expanded leaves per plant collected summer 2017. Individual leaf area was measured in imageJ from scanned leaves. J. Name: Total_leaf_area Description: Total leaf area [m^2] per plant; the product of Leaf_count multiplied by Ave_leaf_area and converted to square meters. --------------------------------------------------------- DATA-SPECIFIC INFORMATION FOR: Spring_leaf_expansion_2017 --------------------------------------------------------- 1. Number of variables: 20 2. Number of cases/rows: 485 3. Missing data codes: Code/symbol: NA Definition: Data not available. 4. Variable List A. Name: Date Description: Date when leaves were collected [MM/DD/YYYY]. B. Name: Date_J Description: Julian date when leaves were collected [119-195]. C. Name: Species Description: Species code based on the first two letters of the genus and the first two letters of the species. BETH = Berberis thunbergii, COCO = Corylus cornuta, COSE = Cornus sericea, FRAL = Frangula alnus, LOBE = Lonicera x. bella, RHCA = Rhamnus cathartica, RUID = Rubus idaeus, VILE = Viburnum lentago. D. Name: Plant_ID Description: Unique number given to each plant observed. E. - S. Name: Leaf_1 - Leaf_15 Description: Leaf area [cm^2] of a single leaf collected in summer 2017. Each column (Leaf_1 - Leaf_15) includes the area of a single leaf. Individual leaf area was measured in imageJ from scanned leaves. A minimum of six leaves were collected from smaller plants with fewer leaves. T. Name: Ave_leaf_area Description: Average leaf area [cm^2] of 6-15 leaves per plant (Leaf_1 - Leaf_15) per collection date in summer 2017. ------------------------------------------------------- DATA-SPECIFIC INFORMATION FOR: Fall_leaf_phenology_2017 ------------------------------------------------------- 1. Number of variables: 8 2. Number of cases/rows: 836 3. Missing data codes: Code/symbol: NA Definition: Data not available. 4. Variable List A. Name: Date Description: Date when when leaf phenology was observed [MM/DD/YYYY]. B. Name: Date_J Description: Julian date when leaf phenology was observed [224 - 344]. c. Name: Species Description: Species code based on the first two letters of the genus and the first two letters of the species. BETH = Berberis thunbergii, COCO = Corylus cornuta, COSE = Cornus sericea, FRAL = Frangula alnus, LOBE = Lonicera x. bella, RHCA = Rhamnus cathartica, RUID = Rubus idaeus, VILE = Viburnum lentago. D. Name: Plant_ID Description: Unique number given to each plant obesrved. E. Name: Percent_leaf_drop Description: Percent of total leaves dropped from the plant. RUID observations are an average of first and second year growth. F. Name: Percent_leaf_color_change Description: Percent of leaves remaining on the plant that are not green. RUID observations are an average of first and second year growth. G. Name: Percent_leaf_senescence Description: Percent of total leaves that have senesced, assuming dropped leaves and non-green leaves still on the plant have senesced. Calculated according to the following equation: Percent_leaf_senescence = (100 - Percent_leaf_drop) * (Percent_leaf_color_change / 100) + Percent_leaf_drop. H. Name: Notes Description: Additional field notes. ------------------------------------------------------------------- DATA-SPECIFIC INFORMATION FOR: Photosynthetic_light_response_curves ------------------------------------------------------------------- 1. Number of variables: 64 2. Number of cases/rows: 950 3. Missing data codes: Code/symbol: NA Definition: Data not available. 4. Variable List This file is the raw output from the LiCOR 6400 XT Light Response Curve autoprogram. The two variables used on the model (Photo and PARi), as well as aditional variables not included in the output (A-D) are described below. For descriptions of the other 58 variable outputs, see LiCOR 6400 XT manual. A. Name: Date Description: Date when measurement was taken [MM/DD/YYYY]. B. Name: Species Description: Species code based on the first two letters of the genus and the first two letters of the species. BETH = Berberis thunbergii, COCO = Corylus cornuta, COSE = Cornus sericea, FRAL = Frangula alnus, LOBE = Lonicera x. bella, RHCA = Rhamnus cathartica, RUID = Rubus idaeus, VILE = Viburnum lentago. C. Name: Plant_ID Description: Unique number given to each plant measured. D. Name: Month Description: Month (MMM) during which the measurement was taken. Measurements taken in JUN are on young leaves and measurements taken in AUG are on mature leaves. I. Name: Photo Description: Carbon assimilated by sun leaves [umol CO2 m^-2 s^-1] at a given light level (PARi). AC. Name: PARi Description: Photosynthetically active radiation (PAR) inside the leaf chamber [umol photons m^-2 s^-1]. ------------------------------------------------------- DATA-SPECIFIC INFORMATION FOR: Understory_light_monthly ------------------------------------------------------- 1. Number of variables: 11 2. Number of cases/rows: 327 3. Missing data codes: Code/symbol: NA Definition: Data not available. 4. Variable List A. Name: Species Description: Scientific name of the species [Genus_species]. B. Name: Plant_ID Description: Unique number given to each plant observed in the study. C. Name: Date Description: Date measurement was taken [MM/DD/YYYY]. D. Name: Time Description: Time of measurement [HH:MM:SS]. E. Name: Month Description: Month measurement was taken. F. Name: Season Description: Season measurement was taken. "Season" corresponds with "Month" as follows: "May" = "Spring," "Jun" = "SummerI," "Aug" = "SummerII," "Sep" = "Fall." G. Name: PPFD_plant Description: Photosynthetic photon flux density (PPFD) measured above each study plant [umol photons m^-2 s^-1], averaged over 15 seconds. Measurements were taken simultaneously with LUX_plant and LUX_full_sun. H. Name: LUX_plant Description: Light level measured above each study plant [lumens m^-2], averaged over 15 seconds. Measurements were taken simultaneously with PPFD_plant and LUX_full_sun. I. Name: LUX_full_sun Description: Light level measured in an open area with no canopy cover [lumens m^-2], averaged over 15 seconds. Measurements were taken simultaneously with PPFD_plant and LUX_plant. J. Name: LUX_percent Description: Percent light transmittance measured above each plant. LUX_percent = (LUX_plant / LUX_full_sun) * 100. K. Name: Bin Description: Catergorical bin numbers [1 - 6] assigned to each plant based on LUX_percent values within each season. There are six bins per season. ----------------------------------------------------- DATA-SPECIFIC INFORMATION FOR: Understory_light_daily ----------------------------------------------------- 1. Number of variables: 9 2. Number of cases/rows: 65897 3. Missing data codes: Code/symbol: NA Definition: Data not available. 4. Variable List A. Name: Logger_No Description: Numbers 1-6 assigned to each logger unit (HOBO Pendant Temp/Light, 8k, UA-002-08, Onset Computer Corporation, Bourne, Massachusetts USA). B. Name: Species Description: Scientific name of the species [Genus_species] above which the sensor was mounted. C. Name: Plant_ID Description: Unique number of the plant above which the sensor was mounted. D. Name: Month Description: Approximate month measurement was taken. Measurements are grouped into four months: May – open canopy, July – closed canopy and long daylength, September – closed canopy and short daylength, and October – open canopy. E. Name: Date Description: Date measurement was taken [MM/DD/YYYY]. F. Name: Time Description: Time of measurement [HH:MM:SS]. G. Name: Temperature Description: Temperature logged above each study plant every fifteen minutes [degrees Celcius]. H. Name: LUX Description: Light level logged above each study plant every fifteen minutes [lumens m^-2]. I. Name: Weather Description: Days were designated as "sunny" or "cloudy" based on light measurements. Only data from sunny days were included in the carbon assimilation model.