DOI: 10.5061/dryad.bvq83bknb
title: The impact of shade on whole-plant carbon allocation in an East African tree sapling

description: 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.
description: 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.
description: # The impact of shade on whole-plant carbon allocation in an East African
 tree sapling Dataset DOI:
 [10.5061/dryad.bvq83bknb](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 1. 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 2. 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. 3. 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 1. Number of variables: 17 2. Number of cases/rows:
 177 3. 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 4. Missing data codes: na - data was not
 collected **DATA-SPECIFIC INFORMATION FOR: Acdr_shade_isotope_all.csv and
 Acdr_shade_isotope_all.xlsx** 1. Number of variables: 18 2. Number of
 cases/rows: 1063 3. 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. 4. 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** 1. Number
 of variables: 21 2. Number of cases/rows: 254 3. 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. 4. Missing data codes: NA -
 data not collected/available **DATA-SPECIFIC INFORMATION FOR:
 sapling_shade_NSC_all.csv** 1. Number of variables: 12 2. Number of
 cases/rows: 177 3. 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. 4. 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** 1.
 Number of variables: 3 2. Number of cases/rows: 38 3. 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 4. Missing data codes: No missing data
 **DATA-SPECIFIC INFORMATION FOR: Acdr_GasExchange.csv** 1. Number of
 variables: 14 2. Number of cases/rows: 311 3. 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 4.
 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.