Data and code from: Decoupled carbon assimilation and growth responses to aridity in temperate deciduous oaks
Data files
Jun 04, 2026 version files 384.50 MB
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r_markdown.zip
384.48 MB
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README.md
16.92 KB
Abstract
The magnitude of the terrestrial carbon sink remains a key uncertainty in future climate projections, in part due to poorly understood links between carbon uptake and its allocation to woody biomass in vegetation. Here, we show that photosynthesis and above-ground growth occur asynchronously across diel to seasonal scales in eight North American oak species. Across 137 tree-ring sites, current-year annual growth was insensitive to climate variability after mid-summer, despite 26-36% of annual gross primary productivity (GPP) occurring during this period. Hourly GPP flux and growth measurements at four sites spanning seven site-years further demonstrate that wood formation ceases earlier than photosynthesis and is restricted to periods of low atmospheric aridity and temperature. This photosynthesis-growth decoupling intensifies with inter-annual variability in vapour pressure deficit (r=0.86, p<0.05), suggesting that by assuming tight coupling between photosynthesis and woody biomass, current earth system models may overestimate long-term carbon sequestration in forests.
DOI: 10.5061/dryad.m63xsj4h4
Last date updated, May 22 2026, by Rao MP.
The dataset (r_markdown.zip) contains tree growth, carbon flux, and environmental data for different oak sites across North America
This includes 4 high-resolution monitoring sites in the USA, which include (See Supplementary Figure 1)
- Morton Arboretum, IL, USA 41.82°N, 88.07°W
- Point dendrometers
- Phenocams
- SIF derived GPP data (computed from Turner et al 2021)
- Environmental data
- Lamont Sanctuary, NY, USA 41°N, 73.90°W
- Point dendrometers
- Phenocam - https://phenocam.nau.edu/webcam/sites/ldeocam/
- SIF derived GPP data (computed from Turner et al 2021)
- Xylogenesis/Wood Anatomy data
- Leaf level chlorophyll fluorescence data using a Jr. Pam instrument
- Environmental data
- Pace Forest, VA, USA 78°N, 33°W
- Point dendrometers
- Phenocam
- In-situ eddy covariance and environmental data
- Tonzi Ranch, CA, USA 38.43°N, 120.96°W
- Point dendrometers
- Phenocam - https://phenocam.nau.edu/webcam/sites/tonzi/
- In-situ eddy covariance and environmental data - https://ameriflux.lbl.gov/sites/siteinfo/US-Ton
Also included are raw (cross-dated) tree ring measurements from 137 oak sites across North America (134 - USA & 3 - Canada)
Sharing/Access information
You may contact the lead author Mukund Palat Rao mukund@ldeo.columbia.edu or mukund24rao@gmail.com for assistance in interpreting and using the data. Please also cite the original publication if these data or codes are used.
Rao MP et al (2026), Decoupled carbon assimilation and growth responses to aridity in temperate deciduous oaks, Science Advances, DOI: 10.1126/sciadv.ady7139
Links to other publicly accessible locations of the data: The data are available directly through the manuscript
Code/Software
Files in this folder can be read using R (.Rmd), and included code can be used to read these data and replicated all analysis included in the papers.
Files 1-4 read in dendrometer, PhenoCam, flux, or remote sensing, and environmental data
for the 4 high-resolution monitoring sites to compare the phenology and environmental sensitivity of growth vs gross primary productivity (GPP)
- IL_Morton_Dendro-GPP-Pheno_20260126.Rmd
- CA_Tonzi_Dendro-GPP-Pheno_20260208.Rmd
- VA_Pace_Dendro-GPP-Pheno_20260218.Rmd
- NY_Lamont_Dendro-GPP-Pheno_20260222.Rmd
Files 5-6 are specific to Lamont-NY for leaf-level chlorophyll fluorescence data (using a Jr. PAM) and wood anatomy data
- jrPAM_lamont_20240522.Rmd
- NY_woodanatomy_20240401.Rmd
File 7. Evaluates environmental data at all 4 sites and evaluates the environmental driver of the 'offset' variable
- env_cv_vs_growth_gpp_20260223.Rmd
File 8. Evaluates the environmental drivers of growth at 137 tree-ring sites
- dendro_sensitivity_20240506.Rmd
- climcorr_20260221.R is an embedded dependent function for the climate-growth response analysis
File 9. Evaluates the phenology of Gross Primary Productivity (GPP) across all 137 tree-ring sites based on the
Turner et al (2021) data set using solar-induced chlorophyll fluorescence (SIF). https://doi.org/10.3334/ORNLDAAC/1875
Note that the code directly reads in downloaded data just for the 137 sites; however, commented code is included that would read in data from the original NETCDF files
In this case, the user needs to download the Turner et al. data by themselves first.
- turner_gpp_sites_20241104.R
These files have been tested on R version 4.4.2.
In each file, the working directory will need to be changed to your working directory in the first section.
All required packages and dependencies will be auto-installed (if unavailable locally)
Knit HTML versions of each file are also included
These files are HTML versions that show code and embedded figures in a web browser without needed to run the code
- IL_Morton_Dendro-GPP-Pheno_20260126.html (from IL_Morton_Dendro-GPP-Pheno_20260126.Rmd)
- NY_Lamont_Dendro-GPP-Pheno_20260222.html (from NY_Lamont_Dendro-GPP-Pheno_20260222.Rmd)
- VA_Pace_Dendro-GPP-Pheno_20260218.html (from VA_Pace_Dendro-GPP-Pheno_20260218.Rmd)
- CA_Tonzi_Dendro-GPP-Pheno_20260208.html (from CA_Tonzi_Dendro-GPP-Pheno_20260208.Rmd)
- jrPAM_lamont_20240522.html (from jrPAM_lamont_20240522.Rmd)
- NY_woodanatomy_20240401.html (from NY_woodanatomy_20240401.Rmd)
Data
This includes files included inside the data folder that are read into R
- CRU
- CRU Ts v 4.06 downloaded on Jan 18, 2023
- These data are used to compute the climate sensitivity of tree ring data in dendro_sensitivity_20240506.Rmd
- Instructions to download data are provided inside the readme.text within the Data/CRU/ts.4.06/ folder.
- tree-rings
- Includes tree ring data in Tucson Format organised by US State (two letter code) and Canada (CAN). More information on each site is provided in Supplementary Table 1
- ITRDB_readme.txt - includes information on codes used to download tree ring data from the International Tree Ring Data Bank (ITRDB).
- See Brewer et al 2011 for more information on the Tucson Format
https://bioone.org/journals/tree-ring-research/volume-67/issue-2/2010-12.1/Tricycle--A-Universal-Conversion-Tool-For-Digital-Tree-Ring/10.3959/2010-12.1.full
- US_CA_Tonzi
- phenocam - data downloaded from Phenocam Website, see https://phenocam.nau.edu/webcam/tools/summary_file_format/ for descriptions of each column
- dendrometers - Dendrometer data on site -
US_CA_TON_20240125_clean.csv includes the following columns- time (local time in California, UTC-8)
- year
- tree (codes from TON1 to TON5)
- species (4-letter species code, QUDO - Quercus douglasii),
- val (change in tree radius in micrometers based on point dendrometer)
- gr (tree radial growth in micrometers based on the zero-growth model)
- battery (dendrometer battery voltage)
- flux - data downloaded from the Ameriflux website, see README_AmeriFlux_BASE.txt for information on headers and data interpretation
Information on column names is also available here https://fluxnet.org/data/aboutdata/data-variables/
Note that we cannot provide these data directly, as they use to CC-BY-4.0 (By ATTRIBUTION). Instructions on how to download Ameriflux data are provided in data/US_CA_Tonzi/flux/20251124/AMF_US-Ton_BASE-BADM_25-5 in the readme.txt. Once data are downloaded, we use the following columns
File name AMF_US-Ton_BASE_HH_25-5.csv
Columns that are used
- TIMESTAMP_START - start time of measurement
- TIMESTAMP_END - end time of measurement
- GPP_PI_F_1_1_1 - Gross Primary Productivity based on nightime method for the tall tower μmol/(m^2.s)
- GPP_PI_F_1_2_1 - Gross Primary Productivity based on nightime method for the tall tower μmol/(m^2.s)
- TA_PI_F_1_1_1 - Photosynthetic Photon Flux Density mol photons/(m2.s)
- SWC_PI_F_1_2_1 SWC_PI_F_2_2_1, SWC_PI_F_3_2_1 SWC_PI_F_4_2_1, WC_PI_F_5_1_1, SWC_PI_F_6_3_1 SWC_PI_F_7_3_1 - Soil Water Content (m3 water/m3 soil), the numbers indicate horizontal, vertical, and repetitions H_V_R (Horizontal_Vertical_Replicate), ere each measurement is in a different horizontal location 1-7.
- US_IL_Morton
- sif - data on solar induced chlorophyll fluorescence (SIF) and SIF-Derived GPP around Morton Arboretum, as calculated by turner_gpp_sites_20241104.R
Morton_Arborutum_Turner_SIF_GPP_2019_2021.csv includes the following columns- Year
- Month (month from 1-12)
- Day (day of month)
- SIF (mW m−2 sr−1 nm−1)
- GPP (in gC/(m2.day))
- phenocam - Phenological Camera information
OakPhenology2019-2022.csv includes the following columns- Plot (4 plots for different species)
- Datetime (Local datetime in Ilinois, USA, Central Time Zone UTC-6)
- Date (date in yyyy-mm-dd)
- Year (calendar year)
- Day (Day of Year)
- Jday (Julian Day)
- Hour (Hour of Day)
- Minute
- Red (reflectance in red band in an 8-bit colour system from 0-255 for the region of interest - ROI)
- Green (reflectance in green band in an 8-bit colour system from 0-255 for the region of interest - ROI)
- Blue (reflectance in blue band in an 8-bit colour system from 0-255 for the region of interest - ROI)
- gcc (Green Chromatic Coordinate - Green/(Red+Green+Blue)
- ROI (Region of Interest, 3 per plot)
- environmental - micrometeorological data at Morton Arboretum
Please see the README weather_processe.docx within the same folder for description of the column names - dendrometers - Contains dendrometer data organised by Plot and Tree in micrometers
in the file US_IL_MORTON_202103-202302_clean.csv
Columns are defined as:- ts (Local datetime in Ilinois, USA, Central Time Zone UTC-6)
- Series (unique code for 20 different trees monitored using dendrometers with codes for species, plot, and tree number within the plot)
- Year (year)
- Plot (code for Plot ID, 4 plots "QUAL-E" "QUBI-E" "QUBI-W" "QUPA-W")
- Tree (tree number within plot)
- val (change in tree radius in micrometers based on point dendrometer)
- val_growth (tree radial growth in micrometers based on the zero-growth model)
- US_NY_Lamont
- phenocam - data downloaded from Phenocam Website, see https://phenocam.nau.edu/webcam/tools/summary_file_format/ for descriptions of each column
- anatomy - wood anatomical data at Lamont Sanctuary Forest, NY in 2021 based on xylogenesis sampling
- For Column definitions, please see the embedded ROXAS_column_dictionary.xlsx file
- This includes definitions for each column
- Columns that are used in analyses are
- RCTA - Relative Conductive Area Over Time
- DOY - Day of year
- dendrometers - dendrometer data on Lamond-Doherty Earth Observatory campus (site name Lamont Sanctuary-NY)
File name hourly_dendro_env_20240401.csv with columns- variable ("dendro" for dendrometer, "airT" - for air temperature in degree C,"soilT" - for soil temperature in deg. C, "VPD" - for Vapour Pressure Deficit in kPa "VWC" - for volumetric water content at -10 cm)
- tree (tree code for 8 trees with dendrometers, "oak1", "oak2", "oak3", "oak4", "redoak1", "redoak2", "redoak3", "whiteoak")
- year (calendar year)
- date (calendar date)
- time (Local datetime in New York, USA, Central Time Zone UTC-4)
- val (change in tree radius in micrometers based on point dendrometer)
- battV (battery voltage 4 * 1.5V batteries, not used in analysis)
- environmental - micrometeorological data on a campus
Five different files with environmental data spanning different periods- 06-02000(06-02000)-Configuration 1-1710495780.0390148.csv
- 06-02000(06-02000)-Configuration 2-1710495780.0390148.csv
- 06-02000(06-02000)-Configuration 3-1710495780.0390148.csv
- 06-02000(06-02000)-Configuration 4-1710495780.0390148.csv
- 06-02000(06-02000)-Configuration 5-1710495780.0390148.csv
Column definitions are
"TA" = "degree_C Air Temperature",
"TS" = "degree_C Soil Temperature",
"VPD" = "kPa VPD - Vapour Pressure Deficit",
"VP" = "kPa Vapor Pressure",
"PA" = "kPa Atmospheric Pressure",
"SWC" = "m3/m3 Water Content"
- JrPAM - leave-level chlorophyll fluorescence data collected from a Jr. PAM on 3 trees between October-November 2021
Please see the Walz Jr. Pam handbook for a detailed explaination of all columns
Available at https://www.walz.com/products/junior-pam/
Column names are
"F" = "1:F",
"Fmp" = "1:Fm'",
"PAR" = "1:PAR", Photosynthetically Active Radiation, Photosynthetic Photon Flux Density (PPFD), μmol/m2/s
"Temp" = "1:Temp", Leaf temperature in degrees C.
"YII" = "1:Y (II)", Effective quantum yield. Measures the proportion of light absorbed by PSII that is used for photochemistry in the light.
"ETR" = "1:ETR", electron Transport Rate. Estimates the rate of electrons transported through the photosynthetic chain
"FoP" = "1:Fo'",
"ETRmf"= "1:ETR-F.",
"qP" = "1:qP", Photochemical/Non-photochemical Quenching Coefficients.
"qN" = "1:qN", Photochemical/Non-photochemical Quenching Coefficients.
"qL" = "1:qL", Photochemical/Non-photochemical Quenching Coefficients.
"NPQ" = "1:NPQ", Non-Photochemical Quenching.
"Y_NO" = "1:Y (NO)", Quantum yield of non-regulated energy dissipation (energy lost as heat and fluorescence without being safely regulated).
"Y_NPQ"= "1:Y (NPQ)", Quantum yield of regulated, light-induced energy dissipation (heat loss).
"Fo" = "1:Fo", Minimal fluorescence. The baseline fluorescence level emitted when all Photosystem II (PSII) reaction centers are fully "open" (oxidized) after dark-adaptation.
"Fm" = "1:Fm", Maximum fluorescence. The peak signal when a saturating flash of light temporarily closes all PSII reaction centers.
"FvFm" = "1:Fv/Fm" Maximum quantum yield of Photosystem II - sif - data on solar induced chlorophyll fluorescence (SIF) and SIF-Derived GPP around Morton Arboretum, as calculated by turner_gpp_sites_20241104.R
Turner_SIF_GPP_2019_2021.csv includes the following columns- Year
- Month (month from 1-12)
- Day (day of month)
- SIF (mW m−2 sr−1 nm−1)
- GPP (in gC/(m2.day))
- US_VA_Pace
- phenocam - Green Chromatic Coordinate is calculated by Fluospec2 spectrometer on site as GCC = (green/(red+green+blue))
two files, Pace_GCC_2023_nostablefilter.txt & Pace_GCC_2023.txt
Columns are- t_10min (local standard tiem in Pace Forest, Virgina, USA)
- GCC_10min (green chromatic coordinate)
- dendrometers - Dendrometer data on site
US_VA_Pace_20251121.csv- time (Local time)
- Tree (Tree code from Pace 1 to 5)
- Species (which species, Quercus falcata, Pinus virginiana, Quercus alba, Quercus rubra)
- Genus (Pine or oak)
- val (change in tree radius in micrometers based on point dendrometer)
- flux - data downloaded from Ameriflux website, see README_AmeriFlux_BASE.txt for information on headers and data interpretation
Information on column names is also available here https://fluxnet.org/data/aboutdata/data-variables/
File name FLX_US-Pac_FLUXNET_FULLSET_HH_2023_beta-5.csv
Columns that are used- TIMESTAMP_START - start time of measurement
- TIMESTAMP_END - end time of measurement
- GPP_NT_VUT_REF - Gross Primary Productivity based on nightime method, μmol/(m^2.s)
- GPP_DT_VUT_REF - Gross Primary Productivity based on daytime method, μmol/(m^2.s)
- NEE_VUT_REF - Net Primary Productivity based on daytime method, μmol/(m^2.s)
- PPFD_IN - Photosynthetic Photon Flux Density mol photons/(m2.s)
- USTreeAtlas-main
- Shapefiles for major tree species in the United States, see embedded README.md for more information
data used for this study include shapefiles for study species - included in the shp folder.
We use the following subfolders, querdoug, querrubr, queralba, querpalu, quercocc, querfalc, querprin
for Quercus douglasii, Q. rubra, Q. alba, Q. palustris, Q. falcata, Q. coccinea, Q. prinus (now montana)
- results
- These results are generated from the intermediate files
- Each line here comes from one of
- IL_Pace_Dendro-GPP-Pheno_20260126.Rmd
- CA_Tonzi_Dendro-GPP-Pheno_20260208.Rmd
- VA_Pace_Dendro-GPP-Pheno_20260218.Rmd
- NY_Lamont_Dendro-GPP-Pheno_20260222.Rmd
Columns include- No - Serial Number; site - which site; year - which year
- los.nd - length of season in number of days
- off1.nd - offset during phase I in number of days (see table 1)
- off2.nd - offset during phase II in number of days (see table 1)
- Gr.Fr - Growth fraction in Phase I
- Gr.P - Percent length of Phase I relative to active season (Phase I+II+III)
- GPP.Fr - GPP fraction in Phase III
- GPP.P - Percent length of Phase III relative to active season (Phase I+II+III)
- Offset.N - Offset fraction as (Phases I+III)/Phase I + II + III
- Remaining columns for micrometeorological variables at each site and eyar
- Tmp - temperature in degrees Celcius
- Tmp.K - temperature in degrees Kelvin
- VPD - Vapour Pressure Deficit in kPa
- Pr - Precipitation (mm)
- SD - Standard Deviation
- CV - Coefficient of Variation
- QCV - Quartile CV