ReadMe for "Age-dependent leaf function and consequences for crown-scale carbon uptake during the dry season in an Amazon evergreen forest" AUTHORS: Loren P. Albert, Jin Wu, Neill Prohaska, Plinio Barbosa de Camargo, Travis E. Huxman, Edgard S. Tribuzy, Valeriy Y. Ivanov, Rafael S. Oliveira, Sabrina Garcia, Marielle N. Smith, Raimundo Cosme Oliveira Junior, Natalia Restrepo-Coupe, Rodrigo da Silva, Scott C. Stark, Giordane A. Martins, Deliane V. Penha, and Scott R. Saleska JOURNAL: New Phytologist YEAR: 2018 DOI: 10.1111/nph.15056 Date: January 18, 2018 This readme file describes the data files and supplementary files accompanying the above publication. Unless otherwise stated, all data was collected in the Tapajos National Forest near the K67 eddy covariance tower in the state of Pará Brazil (54°580W, 2°510S). For any questions please contact Loren Albert: loren_albert@brown.edu; lalbert@email.arizona.edu The following files are included: ############################################## 1) "Albert_et_al_2018_TNF_leaf_chem_trait_data.csv" ################ DESCRIPTION ################# This is leaf chemistry and leaf trait data for leaves of different ages for six trees near K67 collected during the dry season in 2012 and 2013. Leaves were dried for at least 72 hours at ~60 ºC in a drying oven. Leaf carbon and nitrogen composition were determined in a combustion analyzer coupled to a mass spectrometer for carbon isotopic analysis at the Centro de Energia Nuclear na Agricultura (CENA-USP), Piracicaba, Brazil. A standard of known isotopic content was run every 11 samples. Standard deviation of these standard samples was less than .041 for percent nitrogen, and less than 1.67% for percent carbon. This data is shown in Fig. 5d and 5e of Albert et al. 2018. This file has 688 rows (not including row of headers) and 20 columns. Empty cells (missing data) are denoted with 'NA'. ------------- COLUMN DESCRIPTIONS ------------- match_leaf_chem_ID: This is a code that helped us match leaves between datasets when leaves had multiple measurements made. Date: Date format is MMDDYYYY. For example, 10082012 means October 08, 2012. Transect: This is the transect number from the tree species inventory (Pyle et al. 2008 Figure 1a). Each tree tag is associated with a transect. Transect number is useful for finding the trees used for this dataset, and cross-referencing with species inventories for this site. Species_name: Species identification for trees. Note the synonymns and other notes in supporting information Table S1 of Albert et al. 2018. Family: Plant family Unique_Tree_ID: The unique ID for the tree. Note that the tree with the ID 'Caferana' was not yet tagged in 2012 (DBH than 10) but it is a mid-canopy Coussarea tree near the tree with tag #9 in transect 1. Unique_Branch_ID: This is the unique ID for the tree followed by '_' and then another code. Possibilities are _SU for 'sun branch' in a crown; _SH for 'shade branch' in a crown; _LO for low sample in a mid-canopy tree crown _HI high sample in a mid-canopy tree. Then the code could be followed by _B# where # referred to the sample number of the branch that day. Branch_Light_Environment: Categories describing light environment typically experienced by the sampled branch. Shade ="SH"; Sun = "SU"; Understory = "US" Leaf_number: The leaf number given to each leaf. The combination of Unique.Branch.ID and leaf number created a unique leaf number. LICOR_leaf: This column has a '1' for leaves that had also had gas exchange measurements. Branch_Height: Height of sampled branch measured with meter tape by a tree-climber and a helper on the ground. Maximum_Canopy_Height: Height of the tree measured with meter tape by a tree-climber and a helper on the ground. Dry_weight_grams: The weight of each leaf in grams after drying in oven for at least 72 hours. Leaf_Area: Leaf area in cm^2 estimated using ImageJ with RGB scanned images of leaves and compiled by Jin Wu. SLA_JW: Specific leaf area (leaf area divided by leaf dry weight) in cm^2/g. Mass_for_chemistry: Dry mass of sample of leaf used for leaf carbon and nitrogen composition in XXXmg? percent_N: Percent nitrogen percent_C: Percent carbon C_N_ratio: The carbon to nitrogen ratio Leaf_Age_for_Analysis: Leaf age category. Young leaf = 'Y'; Mature leaf = 'M', Old leaf = 'O'. ############################################# 2) Albert_et_al_2018_TNF_leaf_chlorophyll_data.csv ################ DESCRIPTION ################ For chlorophyll a, b, and total (a+b) content of leaves, approximately 0.5 g (fresh weight) of each leaf was macerated in 7 ml 80% acetone, and then filtered. The filtrate volume was increased to a total of 20 mL. The supernatant was removed and absorbance was measured at 663nm and 647nm, for chlorophyll a and b, respectively, using a spectrophotometer (NOVA Instruments, 3300 UV) and absorbance was used to estimate chlorophyll content following Lichtenthaler (1987). In the file, each row corresponds to one leaf, with columns presenting information about the leaf (see column descriptions below). This data is shown in Fig. 5b and 5c of Albert et al. 2018. The file has 53 rows (not including row of headers) and 13 columns. Empty cells (missing data) are denoted with 'NA'. ------------- COLUMN DESCRIPTIONS ------------- Date: Date format is MMDDYYYY. For example, 10082012 means October 08, 2012. Unique_Tree_ID: The unique ID for the tree. Note that the tree with the ID 'Caferana' was not yet tagged in 2012 (DBH than 10) but it is a mid-canopy Coussarea tree near the tree with tag #9 in transect 1. Species_name: Species identification for trees. Note the synonymns and other notes in supporting information Table S1 of Albert et al. 2018. Family: Plant family Leaf_label: Label given to leaf. Light_Environment: Canopy light environment where leaf was collected. chlorophyll_a_ug_g_leaf.mass: Chlorophyll a concentration in ug/g. chlorophyll_b_ug_g_leaf.mass: Chlorophyll b concentration in ug/g. Total_chlorophyll: Chlorophyll a plus chlorophyll b concentrations in ug/g. Canopy_height_m: Height from ground for where leaves were sampled in the canopy. Canopy_height_notes: Notes about canopy height Chlorophyll_a_to_b_ratio: ratio of chlorophyll a concentration to chlorophyll b concentration. Leaf_age: Age class of leaf. ############################################# 3) Albert_et_al_2018_TNF_leaf_demo_data.csv ################ DESCRIPTION ################ Leaf demographic surveys were performed by categorizing all leaves on ~1 meter branches as either young, mature, or old. This file contains the leaf demographic surveys, including multiple ~1 m branches from the same tree, sampling date, and light environment that were averaged together before the analysis in the manuscript. (The file Albert_et_al_2018_TNF_leaf_demo_data_means.csv is the version of the data used in the analysis.) The reason to share this file is that it contains information about data quality (FLAG) and height of branch sample when available (Branch.Height..m.) which may be useful for future research. This file has 137 row (not including row of headers) and 9 columns. Empty cells (missing data) are denoted with 'NA'. ------------- COLUMN DESCRIPTIONS ------------- Unique_Tree_ID: The unique ID for the tree. Note that the tree with the ID 'Caferana' was not yet tagged in 2012 (DBH than 10) but it is a mid-canopy Coussarea tree near the tree with tag #9 in transect 1. MDDYY: Date of leaf demographic survey in month/day/year format. LE: light environment (sun or shade) typically experienced by the branch sample. Branch.Height..m.: Height in meters of branch sample used for demographic survey. Y.num: Number of young leaves on branch. M.num: Number of mature leaves on branch. O.num: Number of old leaves on branch. total.Number: Total number of leaves on branch. FLAG: Data quality flag. A 1 flag indicates data for which we have high confidence. A 2 glag indicates data that we may have had some issue such as lack of scans or images to reference after the fieldwork was complete, or the count may have been an outlier. A 2.5 indicates lower confidence because a correction to the leaf counts may have been applied later based on scanned images of the leaves, or we had some doubt about that particular survey. A 3 indicates that we thought the data should be excluded (and these data are not included in this dataset, and were not included in our analysis in Albert et al. 2018). We included this Flag so that we and others could see if analysis results were sensitive to data quality. For future uses of this data, we recommend trying analyses with different flags included (e.g. only including 1, including 1 and 2, etc) to see if results are affected. ############################################# 4) Albert_et_al_2018_TNF_leaf_demo_data_means.csv ################ DESCRIPTION ################ Leaf demographic surveys were performed by categorizing all leaves on ~1 meter branches as either young, mature, or old. This file contains the leaf demographic surveys, where multiple ~1 m branches from the same tree, sampling date, and light environment were averaged together before the analysis in the manuscript (so this file results from Albert_et_al_2018_TNF_leaf_demo_data.csv after this averaging). This data corresponds to Figure 6a through Figure 6i. The file has 74 rows and 9 columns. Empty cells (missing data) are denoted with 'NA'. ------------- COLUMN DESCRIPTIONS ------------- Unique_Tree_ID: The unique ID for the tree. Note that the tree with the ID 'Caferana' was not yet tagged in 2012 (DBH than 10) but it is a mid-canopy Coussarea tree near the tree with tag #9 in transect 1. MDDYY: Date of leaf demographic survey in month/day/year format. LE: light environment (sun or shade) typically experienced by the branch sample. mean_Y_num: The number young leaves on branch, as an average if there were multiple branches sampled from the same tree x date x light environment. mean_M_num: The number mature leaves on branch, as an average if there were multiple branches sampled from the same tree x date x light environment. mean_O_num: The number old leaves on branch, as an average if there were multiple branches sampled from the same tree x date x light environment. total.Number: The total number leaves on branch, as an average if there were multiple branches sampled from the same tree x date x light environment. DOY: Day of year early_or_late: Categorical assignment of early or late in dry season. ############################################# 5) Albert_et_al_2018_TNF_gas_exchange_parameters.csv ################ DESCRIPTION ################ Parameters from A/Ci curves using LI-6400 gas exchange systems at K67 in the Tapajos National Forest, Brazil. Prior to gas exchange measurements, branches were cut, gently lowered to the ground with ropes, and re-cut under water within 15 minutes. For each branch, leaves were then classified into age categories (young, mature, or old). We fitted the photosynthesis model developed by Farquhar et al. in Planta (1980), with triose phosphate use limitation (Harley and Sharkey PC&E 1992), to the A/Ci response curve data using a curve fitting routine in R based on the minimum least-squares routine from Domingues et al. in PC&E (2010). This file includes the parameters estimated at the temperature of the measurement as well as parameter estimates normalized to 25 ºC using the temperature dependencies summarized in Sharkey et al. in PC&E (2007). A note to modelers: we highlight that different curve-fitting methods can result in different parameters, as has been described in other publications (e.g. Miao et al. PC&E 2009). In our data exploration, the leaf age-dependency was similar for different curve-fitting methods that we tried, but the parameters themselves did shift somewhat. For this reason, we include the cleaned A/Ci response curve data so that others can fit photosynthesis models to the data using the software and algorithms of their choice, or otherwise explore the data. (See item #7 below for cleaned A/Ci response curve data: Albert_et_al_2018_Clean_LICOR_files_for_upload.zip) The A/Ci parameters in this file correspond to Fig 4a through 4c. The file has 97 rows (not including row of headers) and 23 columns. Empty cells (missing data) are denoted with 'NA'. ------------- COLUMN DESCRIPTIONS ------------- code_for_matching: Internal code for matching with other datasets. Filename: Filename of LI-6400 txt output with A/Ci curve. R.Date: Date of measurement formatted as YYYY-MM-DD. tree_number: Tree tag number from KM 67 tree inventory (most trees were along transect 1). This corresponds to the Unique_Tree_ID in other datasets by adding 'TR' before the tag number. Note that the tree with the ID 'Caferana' was not yet tagged in 2012 (DBH than 10) but it is a mid-canopy Coussarea tree near the tree with tag #9 in transect 1. leaf_number: Leaf number (should be unique for a given tree and date). Leaf_ID: Internal code for matching with other datasets. Sun.or.Shade: light environment (sun or shade) typically experienced by the branch that the leaf was on. Leaf_age: Age class of leaf. QC_code: Quality control for each file based on LiCOR meta-data and/or visual examination of the curve and/or notes from the field made during the curve measurement. Analysis in article included data with codes 1 through 3. Codes are as follows: 1=OK 2=maybe exclude 3=probably exclude 4=always exclude (not included in dataset). mean.PARi: Mean PAR (μmol m^-2 s^-1) measured by quantum sensor in the chamber during A/Ci curve. Used for quality control. std.PARi: Standard deviation of PAR (μmol m^-2 s^-1) measured by quantum sensor in the chamber during A/Ci curve. Used for quality control. mean.LeafT: Mean leaf temperature (°C) during A/Ci curve. Used for quality control. std.LeafT: Standard deviation of leaf temperature (°C) during A/Ci curve. Used for quality control. Vcmax_Tleaf: Maximum carboxylation capacity (µmol CO2 m^-2 s^-1) parameter from fitting A/Ci curves using the data without temperature standardization. Jmax_Tleaf: Electron transport rate (µmol CO2 m^-2 s^-1) parameter from fitting A/Ci curves using the data without temperature standardization. TPU_Tleaf: Triose phosphate utilization (µmol CO2 m^-2 s^-1) parameter from fitting A/Ci curves using the data without temperature standardization. Rd_Tleaf: Respiration under light (µmol CO2 m^-2 s^-1) parameter from fitting A/Ci curves using the data without temperature standardization. T25_Doming_Vcmax: Maximum carboxylation capacity (µmol CO2 m^-2 s^-1) parameter normalized to 25 °C using the parameter temperature dependencies summarized in Sharkey et al. PC&E (2007). T25_Doming_Jmax: Electron transport rate (µmol CO2 m^-2 s^-1) parameter normalized to 25 °C using the parameter temperature dependencies summarized in Sharkey et al. PC&E (2007). T25_Doming_TPU: Triose phosphate utilization (µmol CO2 m^-2 s^-1) parameter normalized to 25 °C using the parameter temperature dependencies summarized in Sharkey et al. PC&E (2007). T25_Doming_Rd: Respiration under light (µmol CO2 m^-2 s^-1) parameter normalized to 25 °C using the parameter temperature dependencies summarized in Sharkey et al. PC&E (2007). Photo_350: Net assimilation with reference cell CO2 set to 350 (μmol CO2 mol^-1). Cond_350: Conductance with reference CO2R at 350 (μmol CO2 mol^-1). ############################################# 6) Albert_et_al_2018_TNF_Gs_porometer.csv ################ DESCRIPTION ################ Stomatal conductance of the abaxial surface of leaves was measured in situ in the canopy using a steady-state leaf porometer from Decagon Devices. Five trees were measured early in the dry season (prior to October 15), and nine trees were measured late in the dry season (from October 15 to the end of the dry season). Note that there were multiple measurements per leaf on the same day, and these were averaged before the meta-analysis presented in the publication in tables and Figure 5a and Table S9. The file has 688 rows (not including row of headers) and 14 columns. Empty cells (missing data) are denoted with 'NA'. ------------- COLUMN DESCRIPTIONS ------------- Tree: Tree tag number from KM 67 tree inventory (most trees were along transect 1). This corresponds to the Unique_Tree_ID in other datasets by adding 'TR' before the tag number. Note that the tree with the ID 'Caferana' was not yet tagged in 2012 (DBH than 10) but it is a mid-canopy Coussarea tree near the tree with tag #9 in transect 1. Date: Date of measurement formatted as D/MM/YY. Measurement_time: Time of day of measurement. AM.or.PM: Whether measurement time was AM or PM. Twenty.four.hour.time: Time of day of measurement in twenty-four hour format. Conductance: Stomatal conductance (mmol m^-2 s^-1) from porometer. Temperature: Temperature measurement from porometer. Sample.ID: Leaf sample ID created during measurement (used internally and can be ignored). Leaf.number: Leaf identification, which was unique within each tree. Height: Height off the ground that stomatal conductance was measured in tree. Light.environment: Light environment (sun or shade) typically experienced by the branch that the leaf was on. Notes: Notes about measurements that were used in quality control, etc. Leaf_age: Age class of leaf. early.or.late: Categorical assignment of early or late in dry season. ############################################# 7) Albert_et_al_2018_Clean_LICOR_files_for_upload.zip ################ DESCRIPTION ################ This folder contains the gas exchange measurements from the LI-6400 in the Tapajos National Forest, Brazil, that were used for estimation of the parameters given in file Albert_et_al_2018_TNF_gas_exchange_parameters.csv (see #5 in this README file). The column descriptions below are for custom columns that we added to LI-6400 output. See LI-6400 manual (Using the LI-6400 version 6) chapter 14 for information about the system variables output by the LI-6400. ------------- COLUMN DESCRIPTIONS ------------- tree_ or tree_number: Tree tag number from KM 67 tree inventory (most trees were along transect 1). This corresponds to the Unique_Tree_ID in other datasets by adding 'TR' before the tag number. Note that the tree with the ID 'Caferana' was not yet tagged in 2012 (DBH than 10) but it is a mid-canopy Coussarea tree near the tree with tag #9 in transect 1. sun_or_shade: Light environment (sun or shade) typically experienced by the branch that the leaf was on. leaf_age: Age class of leaf. Note that young/mature (or Y/M) indicates that the leaf was transitioning between the young and mature classes, and since we used three age classes in our analysis these were re-assigned as either young or mature based on RGB scans and/or pictures of the leaves. leaf_no or leaf_number: Leaf number (should be unique for a given tree and date). column_for_Exclude_pts: As part of quality control points were excluded if field notes suggest that there was a problem during the measurement or if the measurement was an outlier compared the the rest of the curve. An 'OK' entry in this column meant that measurement was included in curve-fitting for parameter estimation, as is the case for the points in these files.