Data from: Biomass production of tropical trees across space and time: The shifting roles of diameter growth and wood density
Data files
Aug 12, 2025 version files 3.24 MB
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cedrela_biomass_dataset.txt
3.22 MB
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climate_soil_dataset.txt
3.35 KB
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metadata.txt
1.88 KB
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README.md
6.13 KB
Abstract
Woody biomass in tropical trees contributes significantly to global carbon stocks; however, these stocks are increasingly affected by climate and land-use changes. Understanding the growth mechanisms driving woody biomass production is essential for assessing the short- and long-term contributions to carbon stocks and dynamics in tropical forests. Trees accumulate biomass by increasing their size (wood volume) and/or tissue density (wood density). However, estimates of tree biomass production are often based solely on size increment through measurements of stem diameter growth, overlooking the potential spatial and temporal variation in wood density within trees. Tree-ring analysis can be applied to reconstruct past tree volume growth and wood density variations, allowing the quantification of their relative contributions when reconstructing past woody biomass production. Here, we studied trees of the widespread Neotropical genus Cedrela (C. fissilis, C. odorata, and C. montana) along an environmental (climate and soil) gradient to address two key questions: 1) How does temporal variation in tree diameter growth and wood density affect biomass production? 2) To what extent do these relationships vary along the environmental gradient? We examined long-term (ontogenetic, variation from pit to bark) and short-term (annual, interannual variation) variations in diameter growth and wood density, covering eighteen sites in the Amazon rainforest, Atlantic Forest, Cerrado savanna, and Caatinga dry forest. We found that diameter growth and wood density drive short- and long-term biomass production dynamics. Interestingly, diameter growth patterns predominantly explained short-term variability in biomass production at all sites, whereas wood density explained ontogenetic biomass patterns mainly at humid sites. These results highlight the importance of accounting for both short- and long-term variation, including climatic and ontogenetic drivers, to increase the accuracy of biomass estimations in tropical trees, particularly in humid forest ecosystems such as the Amazon.
Diameter growth is an important and good indicator of forest carbon production. However, size-related changes in wood density, which are usually neglected, are critical for accurate short- and long-term carbon assessments, especially in tropical humid sites.
Dataset DOI: 10.5061/dryad.1g1jwsv9b
Description of the data and file structure
This dataset was collected as part of a study on trees of the widespread Neotropical genus Cedrela (C. fissilis, C. odorata, and C. montana), sampled across eighteen sites spanning diverse biomes, including the Amazon rainforest, Atlantic Forest, Cerrado savanna, and Caatinga dry forest. The research aimed to address two main questions:
1) How does temporal variation in tree diameter growth and wood density affect biomass production?
2) To what extent do these relationships vary along the environmental gradient?
To answer these questions, we measured both long-term (ontogenetic, from pith to bark) and short-term (annual to interannual) variations in diameter growth and wood density. Biomass estimates were derived using the pantropical allometric equation from Chave et al. (2014), enabling the assessment of productivity patterns about environmental heterogeneity.
Files and variables
File: metadata.txt
Description:
Variables
- ID_area: Identifier for the study area or site.
- local_descr: Description of the location (e.g., private area, concession)
- lat: Latitude of the site , Decimal degrees
- long: Longitude of the site , Decimal degrees
- biome: Biome classification (e.g., Amazon, Cerrado, Atlantic Forest)
- veget: Vegetation type (e.g., dry forest)
- specie: Scientific name of the studied tree species (CF = Cedrela fissilis, CO = Cedrela odorata, CM = Cedrela montana)
- position: Position on the tree where the sample was taken (e.g., DBH, base)
File: climate_soil_dataset.txt
Description:
Variables
- ID_area: Identifier for the study area or site.
- CWD: Climatic Water Deficit in mm fromChavee et a,l 2014
- E: Environmental stress factor affecting tree allometry, as defined in Chave et al. (2014) , Unitless
- PETt: Mean annual Potential Evapotranspiration in mm from TerraClimate (1990–2000 mean)
- MAPt: Mean Annual Precipitation in mm from TerraClimate (1990–2000 mean)
- SRADt: Mean annual Solar Radiation in MJ/m²/day or W/m² from TerraClimate (1990–2000 mean)
- TMAXt Mean annual Maximum Temperature °C from TerraClimate (1990–2000 mean)
- TMINt Mean annual Minimum Temperature °C from TerraClimate (1990–2000 mean)
- VPDt: Mean annual Vapor Pressure Deficit in kPa from TerraClimate (1990–2000 mean)
- MAPqmax: Precipitation in the wettest quarter in mm from TerraClimate (1990–2000 mean)
- MAPqmin: Precipitation in the driest quarter in mm from TerraClimate (1990–2000 mean)
- phh2o: Soil pH measured in water solution, unitless from SoilGrids
- soc_gkg: Soil Organic Carbon content in g/kg from SoilGrids
- clay_g100g: Clay content of the soil in g/100g from SoilGrids
- cec_cmolc_kg: Soil Cation Exchange Capacity, reflecting soil fertility potential in cmol(+)/kg from SoilGrids
- lat_site: Latitude of the site , Decimal degrees
- long_site: Longitude of the site , Decimal degrees
File: cedrela_biomass_dataset.txt
Description:
Variables
- ID_area: Identifier for the study area or site.
- ID_tree: Unique identifier for each sampled tree.
- ID_radii: Identifier for the specific tree core or radius sampled.
- ID_full: Composite identifier combining multiple IDs (e.g., area, tree, and core) for full traceability.
- age_pith_to_bark: Estimated age (years) from the pith (center) to the bark (outer edge) of the tree core.
- rw_mm: Ring width in millimeters; annual radial growth.
- rd_gcm3: Apparent wood density, g/cm³.
- rd_filter: Apparent wood density excluding rd above 1.2 and below 0.2, we need to use it to remove from the final analysis
- rd_pred_bas_gcm3: basic wood density calculated considering rd
- rd_pond_gcm3: rd_pred_bas_gcm3 weighted by basal area, used only to calculate biomass
- diam_cum_cm: Cumulative diameter (in centimeters) of the tree, measured from pith to bark.
- diam_inc_cm: Annual diameter increment (in centimeters), representing the increase in stem diameter over one year.
- ba_m2: Cumulative basal area (in square meters), calculated from the diameter and representing the cross-sectional area of the tree trunk at breast height.
- bai_m2: Basal area increment (in square meters), showing the annual increase in basal area.
- bio_cum_kg: Cumulative aboveground biomass (in kilograms), representing the total biomass accumulated by the tree up to a given year.
- bio_incr_kg: Annual biomass increment (in kilograms), indicating the amount of biomass produced in a single year.
- bio_incr_div_kg: Relative change in biomass per year by dividing the ABP from the present year by the total biomass from the previous year (ABPP = ABPt/Bt-1) to reduce the size-ABP relationship bias.
Code/software
This dataset is provided in a tab-delimited text format (.txtand can be accessed using either R or Python. Below is a description of the software environment and packages used for the analysis:
Software environment: R version 4.3.2 (2023-10-31), RStudio version 2024.04.2+761
Packages: dplyr to make tabular data manipulation easier, and tidyverse to enable swift conversion between different data formats. Example of how to install packages in RStudio:
install.packages(c("tidyverse", "dplyr"))
Access information
Other publicly accessible locations of the data:
- The full dataset is also available upon request by contacting the first author, Bruna Hornink (email: bhornink@gmail.com).
Data was derived from the following sources:
- The environmental data in
"climate_soil_dataset.txt"Were derived from publicly available global datasets:- Climate data: Extracted from TerraClimate (Abatzoglou et al., 2018), using long-term means from 1991 to 2020.
- Soil data: Obtained from SoilGrids (Poggio et al., 2021), which provides gridded predictions of global soil properties at 250 m resolution.
Sample collection
Samples were collected from eighteen forest sites across Brazil and Peru, covering a range of forest types and environmental characteristics. The study sites included national, state, and municipal parks and private forests located in tropical and subtropical regions. These sites represent ecosystems from the Amazon Rainforest, Atlantic Forest, Brazilian Cerrado savanna, and Caatinga dry forest. Samples from sites in the Amazon were collected in sustainable-use conservation units (National and State Forests), where legal forest management operations are conducted. In these areas, samples were obtained by collecting cross-sectional wedges from felled trees as part of authorized logging activities. In the remaining areas, samples were collected from state, municipal, and private forests where forest management is not legally authorized. In these cases, non-destructive coring methods were used to extract wood samples. Each population was sampled in different years for various dendrochronological applications. We included only samples that spanned from the pith to the bark, contained the pith, or were close enough to estimate the distance to the pith. At each location, the number of trees we used ranged from eight to eighteen, due to the availability of samples with complete pith and sufficient material for wood density analysis.
Sample preparation and wood density analysis
We selected one radius from each tree to perform the analysis. All the cores were previously polished and scanned at high resolution (1,200-2,400 dpi), and tree rings were marked following the marginal parenchyma bands associated with semi-porous or porous xylem. To measure the growth rate and wood density, cores were sectioned transversely into radial sections of 0.5-2 cm wide and 1.5 mm thick, while wedges were cut into sections of 2 cm wide and 1.5 mm thick. Wood density was determined following the protocol established by Quintilhan et al. (2021) and Tomazello et al. (2009). Radial sections were conditioned in a climatic chamber at 20°C and 60% relative humidity until they reached a stable moisture content of 12%. All samples were scanned in an X-ray densitometry chamber (Faxitron X-Ray, Illinois, USA) equipped with a measurement unit scale and a cellulose acetate calibration wedge for wood density calibration. Digital X-ray images of the radial section samples (96 dpi, .tiff) were analyzed with WinDendro Density 2017a® software (Regent Instruments Inc., Canada) to obtain the tree-ring width (TRW) and tree-ring wood density at 12% moisture content (WDU12%) per year. Sample preparation, X-ray imaging, and wood density measurements were performed at the Tree-Ring and Wood Anatomy Laboratory of the University of São Paulo (Piracicaba, São Paulo, Brazil). Data processing and data analysis were conducted at the Dendroecology and Wood Biology Laboratory at the State University of São Paulo (Campinas, São Paulo, Brazil).
Diameter reconstruction and biomass estimation
For each tree, the cumulative diameter (D) and cumulative basal area (BA) during the year of ring formation were reconstructed by summing the previous tree-ring widths, assuming a circular growth pattern. For tree-ring samples without a visible pith, we estimated the distance based on the concentric circle method, using CDendro and CooRecorder® software (Cybis Electronic, 2013).
To calculate the aboveground biomass production per year, we first reconstructed the total historical aboveground biomass per year (B) using the pantropical equation described by Chave et al. (2014) (equation 1). Not all sites had tree height data available; therefore, we used the pantropical equation that included a diameter–height allometric model. This model has a stress factor (E, Table S2) that represents the environmental conditions of the site where the trees grow. Chave et al. (2014) demonstrated that factor E is strongly dependent on the diameter-height allometry relationship and is particularly useful for improving model accuracy in the absence of tree height data.
For each tree and year, biomass was estimated based on D and a tree-level weighted average wood density (WDWA). The WDWA value was obtained from the weighted average of the WDU12% values by the basal area increment of each year (Equation 2). This calculation was designed to prevent the influence of the wood proportion near the pith (Williamson and Wiemann, 2010). Before weighing, WDU12% was transformed into basic wood density (WD) by multiplying WDU12% by 0.838 (Vieilledent et al., 2018). The absolute ABP was obtained by subtracting the total biomass from the present year minus the total biomass of the previous year (ABP = Bt-Bt-1). We also calculated the relative change in biomass per year by dividing the ABP from the present year by the total biomass from the previous year (ABPP = ABPt/Bt-1) to reduce the size-ABP relationship bias.
Equation 1:
B = exp[-18.03 – 0.976E + 0.976 ln(WDWA) + 2.673 ln(D) – 0.0299 [ln(D)2]
Where B is the historical aboveground biomass (kg); D is the total diameter of each tree per year reconstructed by the accumulated tree-ring width increment (cm); WDWA is the average basic wood density-weighted by basal area increment (g/cm³); E is the environmental stress factor unitless for each site obtained from the raster file available in Chave et al. (2014).
Equation 2:
WDWA = (BAIt * WDt)/BAt
Where WDWA is the weighted average wood density (g/cm³); BAIt is the basal area increment in year t (m²); WD is the basic wood density (g/cm³), obtained from WDU12% * 0.838 in year t; BAt is the total basal area in year t (m²).
