The impact of shade on whole-plant carbon allocation in an East African tree sapling
Data files
Jul 30, 2025 version files 520.81 KB
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Acdr_GasExchange.csv
20.91 KB
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Acdr_shade_isotope_all_2.csv
38.20 KB
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Acdr_shade_isotope_all_2.xlsx
60.48 KB
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Acdr_shade_isotope_all.csv
137.38 KB
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Acdr_shade_isotope_all.xlsx
188.78 KB
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Mizell_etal_AoBP_2025.R
27.44 KB
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README.md
10.63 KB
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sapling_biomass.csv
22 KB
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sapling_shade_NSC_all.csv
14.20 KB
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shade_lma_treatments.csv
780 B
Abstract
Plasticity in resource allocation can be beneficial for plants under stress. In savannas, tree-grass competition forces tree saplings growing in the grass layer to compete for water, nutrients, and light. Savanna tree saplings are also vulnerable to fire and herbivory, which may favor investment in storage belowground to support regrowth aboveground. It is unclear if carbon (C) limitation from grass shading similarly favors allocation belowground. Further, investigating how light reduction changes allocation by juvenile trees to above- and belowground biomass, storage, and defense can help us understand juvenile tree allocation strategies during ubiquitous C limitation. Using a screenhouse experiment, we evaluated the effects of shade on carbon allocation and leaf physiology in saplings of a dominant ant-acacia, Acacia (Vachellia) drepanolobium. We hypothesized that shade would induce greater belowground allocation by saplings to root growth and storage. Indeed, we found that shaded saplings had higher root mass fractions and higher concentrations of starch in their roots than plants in full sunlight. Plants in full sunlight, meanwhile, invested more in aboveground growth, with higher stem mass fractions than shaded plants. Shade did not affect leaf mass fraction, but plants in the shade had a lower leaf mass per area, higher stomatal conductance, and a higher maximum photosynthetic rate, indicating leaf-level adjustments that increased carbon capture under light limitation. These responses are consistent with possible adaptive allocation strategies that buffer the impacts of fire and herbivory, underscoring the essential role of belowground reserves for regrowth.
Dataset DOI: 10.5061/dryad.bvq83bknb
Description of the data and file structure
Date of data collection (single date, range, approximate date): 2022-07-01 - 2023-07
Geographic location of data collection: 0°15’35.44”N, 36°53’53.36”E, Mpala Research Centre, Kenya
DATA & FILE OVERVIEW
File List:
sapling_biomass.csv - data for whole plant biomass and mass fractions of stems, roots, and leaves
Acdr_shade_isotope_all.csv - delta 13C data for control and labeled plants that includes all plant samples
Acdr_shade_isotope_all.xlsx - same as .csv version, but also shows calculations
Acdr_shade_isotope_all_2.csv - data for isotope mass fractions for leaves, stems, and roots
Acdr_shade_isotope_all_2.xlsx - same as .csv versio,n but also shows calculations
sapling_shade_NSC_all.csv - data for stem and root starch
shade_lma_treatments.csv - leaf mass per area measurements
Acdr_GasExchange.csv - leaf gas exchange data. Includes photosynthesis, stomatal conductance, and transpiration measurements.
METHODOLOGICAL INFORMATION
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Description of methods used for the collection/generation of data:
See article in AoB PLANTS: The impact of shade on whole-plant carbon allocation in a dominant East African tree sapling
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Methods for processing the data:
All data processing is documented in the associated .xlsx files and R script.
The raw data we received from UC Davis Stable Isotope Facility included the delta 13C values. This file was widened to include a new column for each experimental treatment. Columns that were not used in our analyses (e.g., total C and total N in each sample) were removed.
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People involved with sample collection, processing, analysis, and/or submission:
Gabriella Mizell, Elizabeth Pringle, John Lemboi, John Mosiany
Files and variables
DATA-SPECIFIC INFORMATION FOR: sapling_biomass.csv
- Number of variables: 17
- Number of cases/rows: 177
- Variable List:
- Plant.id - a unique code for each individual plant. Included in the code when plant was harvested (hours or days) after pulse-labeling
- Timepoint - the number of days after pulse labeling that the plant was harvested
- shade.treatment - the experimental light level assigned to each plant. Ns = no shade (sun), ss = soil shade (not used in this analysis), and fs = full shade.
- Group - the pulse-labeling group each plant was assigned to (1,2, or 3).
- days.in.treatment - the number of days each plant was in their assigned shade treatment before harvesting
- leaves- the biomass in grams of the leaves
- stems - the biomass in grams of the stems
- roots - the biomass in grams of the roots
- spines - the biomass in grams of the spines
- domatia - the biomass in grams of the domatia
- total.biomass - the biomass in grams of all plant material
- rootshoot.ratio - the stem biomass divided by the root biomass
- lmf - leaf mass ratio. The biomass of leaves divided by total biomass
- smf - stem mass ratio. The biomass of the stem divided by total biomass
- rmf - root mass ratio. The biomass of roots divided by total biomass
- domatia.mf - domatia mass fraction. The biomass of domatia divided by total biomass
- spine.mf - spine mass fraction. The biomass of spines divided by total biomass
- Missing data codes: na - data was not collected
DATA-SPECIFIC INFORMATION FOR: Acdr_shade_isotope_all.csv and Acdr_shade_isotope_all.xlsx
- Number of variables: 18
- Number of cases/rows: 1063
- Variable List:
- SampleID - the unique sample identifier for isotope analysis. Includes descriptive information about plant ID and harvest date
- Material - the part of the plant that the sample comes from
- Time.point - the day after pulse-labeling that the plant that the sample comes from was harvested.
- days.in.treatment - the number of days the plant that the sample comes from was in its shade treatment before harvest
- Label.treatment - 13C pulse-labeling treatment. Either control or label
- Shade.treatment - the experimental light level that the plant was in. Either ns, ss, or fs.
- delta.13C - the delta. 13C of each sample. This data comes from UC Davis SIF.
- Total.C.ug. the total amount of carbon in the sample in micrograms. This data comes from UC Davis SIF.
- at.pt.13C - the atom percent 13C. This data comes from UC Davis SIF.
- SIF.group - the batch that each sample was sent in for analysis. Either 1 or 2.
- machine - the specific machine the isotope analysis was run on at UC Davis SIF. Either A or H.
- sample.weight.mg - the sample weight in milligrams sent to UC Davis SIF
- ug.13C.in.sample - the micrograms of 13C in the sample. Calculation shown in .xlsx version.
- g.13C.in.sample - the grams of 13C in the sample. Calculation shown in .xlsx version.
- sample.weight.g - the sample weight scaled to g
- prop.13C.sample - the proportion of 13C in the sample. Calculation shown in .xlsx version.
- pool.biomass - the biomass of the plant material that the sample comes from. For example, if it's a leaf sample, the total biomass of leaves for that plant.
- g.13C.pool - the estimated grams of 13C in the whole pool (leaves, stems, roots, etc.) for the plant that the sample came from. Calculation shown in .xlsx version.
- Missing data codes: na - data not available because either the pool weights or samples weights were not recorded.
DATA-SPECIFIC INFORMATION FOR: Acdr_shade_isotope_all_2.csv and Acdr_shade_isotope_all_2.xlsx
- Number of variables: 21
- Number of cases/rows: 254
- Variable List:
- SampleID - the unique sample identifier that includes information about the plant it came from and day after pulse-labeling that it was sampled
- Material - plant material of the sample (either leaf, root, or twig)
- Time.point.d - the number of days after pulse-labeling that the sample was collected
- Label.treatment - indicates all samples came from labeled plants
- Shade.treatment - thee experimental light level that the plant was in
- days.in.treatment - the number of days the plant was in the light treatment before harvesting
- delta.13C - the delta 13C value for the sample. Data comes from UC Davis SIF
- Total.C.ug. the total amount of carbon in the sample in micrograms. This data comes from UC Davis SIF.
- at.pt.13C - the atom percent 13C. This data comes from UC Davis SIF.
- SIF.group - the batch that each sample was sent in for analysis. Either 1 or 2.
- machine - the specific machine the isotope analysis was run on at UC Davis SIF. Either A or H.
- sample.weight.mg - the sample weight in milligrams sent to UC Davis SIF
- ug.13C.in.sample - the micrograms of 13C in the sample. Calculation shown in .xlsx version.
- g.13C.in.sample - the grams of 13C in the sample. Calculation shown in .xlsx version.
- sample.weight.g - the sample weight scaled to g
- prop.13C.sample - the proportion of 13C in the sample. Calculation shown in .xlsx version.
- pool.biomass - the biomass of the plant material that the sample comes from. For example, if it's a leaf sample, the total biomass of leaves for that plant.
- g.13C.pool - the estimated grams of 13C in the whole pool (leaves, stems, roots, etc.) for the plant that the sample came from. Calculation shown in .xlsx version.
- g.13C.allpools - the total grams of 13C for the plant. Leaf, root, and twig 13C pool values were added together for the same plant ID to estimate total 13C in whole plant.
- isotope.fraction - the proportion of the total plant 13C in each pool. Grams 13C pool divided by grams 13C all pools.
- Missing data codes: NA - data not collected/available
DATA-SPECIFIC INFORMATION FOR: sapling_shade_NSC_all.csv
- Number of variables: 12
- Number of cases/rows: 177
- Variable List:
- sample.name - the unique sample identifier that includes information about the plant ID, material, and harvest time
- plant.material - where the sample came from on the plant. Either root or twig
- label.treatment - the 13C pulse-labeling treatment of the plant. Either control or label
- shade.treatment - the experimental light treatment that the plant was in. Either ns = no shade, ss = soil shade (not used in this analysis) or fs = full shade.
- harvest.date - when the plant was harvest/the sample was collected.
- NSC.group - the batch that the sample was analyzed in, either 1, 2, or 3
- sugar - the sugar that was analyzed. Either glucose, sucrose, or starch
- percent.sugar - the concentration of sugar in the sample.
- total.pool.biomass - the total biomass in grams of the plant part (pool or sink) that was analyzed.
- total.sugar.g - the total amount of sugar in grams scaled to pool size. Percent sugar multiplied by total pool biomass
- total.sguar.mg - total sugar in g converted to milligrams
- total.plant.sugar - the total amount of sugar in the plant. The twig and root total sugar g values added together for each plant.
- Missing data codes: Total plant sugar only for starch because that is the focus of the analysis. Blank cells because total pool biomass not available for all plants
DATA-SPECIFIC INFORMATION FOR: shade_lma_treatments.csv
- Number of variables: 3
- Number of cases/rows: 38
- Variable List:
- treatment - the experimental light treatment the plant was in. Either fs = full shade or ns = no shade
- lma - leaf mass per area
- tree tag - the unique identifier for each plant
- Missing data codes: No missing data
DATA-SPECIFIC INFORMATION FOR: Acdr_GasExchange.csv
- Number of variables: 14
- Number of cases/rows: 311
- Variable List:
- Msmt - measurement. Either A (photosynthesis) or Rd (dark respiration). Only A is used in the analysis.
- ExcelTime - the date that the measurement was taken
- plant.id - unique plant identifier
- PARi - internal (chamber) photosynthetic active radiation during measurements
- Tamb - ambient temperature during measurement
- Tcuv - cuvette temperature during measurement
- Tleaf - leaf temperature during measurement
- RH - relative humidity
- Gs - stomatal conductance
- VPD - vapor pressure deficit
- A - photosynthetic rate
- E - transpiration
- WUE - water use efficiency
- Missing data codes: No missing data
Code/software
R code is in the file: Mizell_etal_AoBP_2025.R: The version used is 4.1.1. All necessary packages are included at the top of the R script.
Biological samples were collected at Mpala Research Centre by Grabriella Mizell, John Mosiany, and John Lemboi. Plant biomasses were dried weighed by John Mosiany and John Lemboi at Mpala Research Centre, plant samples were analyzed for 13C content at the University of California, Davis Stable Isotope Facility starch analysis was done at the University of Nevada, Reno. Gabriella Mizell and Elizabth Pringle conducted data analyses at the University of Nevada, Reno. No other processing was done beyond transformations and manipulations outlined in the data files, R script, and associated article.