DOI: 10.5061/dryad.0cfxpnw8p
title: Intraspecific plant-soil feedback in four tropical tree species is inconsistent in a field experiment

description: Soil microbes can influence patterns of diversity in plant communities via
 plant-soil feedbacks. Intraspecific plant-soil feedbacks occur when plant
 genotype causes variation in soil microbial composition, resulting in
 differences in the performance of seedlings growing near their maternal
 plants versus seedlings growing near non-maternal conspecific plants. How
 consistently such intraspecific plant-soil feedbacks occur in natural
 plant communities is unclear, especially under variable field conditions.
 We conducted an in situ experiment with four native tree species on Barro
 Colorado Island (BCI), Panama. Seedlings of each species were transplanted
 beneath their maternal tree or another conspecific tree in the BCI forest.
 Mortality and growth were assessed at the end of the wet season (~4 months
 post-transplant) and at the end of the experiment (~7 months
 post-transplant). Differences in seedling performance among field
 treatments were inconsistent among species and eroded over time. Effects
 of field environment were detected at the end of the wet season in two of
 the species: Virola surinamensis seedlings had higher survival beneath
 their maternal tree than other conspecific trees, while the opposite
 pattern was found in Ormosia macrocalyx. However, these differences
 disappeared by the end of the experiment. Our results suggest that
 intraspecific plant-soil feedbacks may not occur consistently under field
 conditions in tropical tree species and may have a limited role in
 determining seedling performance in tropical tree communities. Future
 studies are needed to elucidate the environmental and genetic factors that
 determine the incidence and direction of intraspecific plant-soil
 feedbacks in plant communities.
description: In an in-situ field experiment on Barro Colorado Island, Panama,
 we collected biomass, growth, and survival data on experimental seedlings
 of four tropical tree species.
description: # Intraspecific plant-soil feedback in four tropical tree species is
 inconsistent in a field experiment --- Here we present the data and R
 script used to produce the results described in our manuscript of the same
 name. This includes three elements: 1) data collected on seedlings of four
 tropical tree species during a field experiment conducted on Barro
 Colorado Island (BCI), Panama, 2) summary data formatted to enable easy
 plotting of the survival of seedlings in that same experiment, and 3) the
 R script that supported analysis of the experimental data. In brief, to
 test whether conspecific seedling performance was reduced near maternal
 conspecific trees relative to non-parent conspecific trees, we conducted
 an in situ experiment with four native tree species on Barro Colorado
 Island (BCI), Panama. Seedlings of each species were transplanted beneath
 their maternal tree or another conspecific tree in the BCI forest.
 Mortality and growth were assessed at the end of the wet season (~4 months
 post-transplant) and at the end of the experiment (~7 months
 post-transplant). Differences in seedling performance among field
 treatments were inconsistent among species and eroded over time. Effects
 of field environment were detected at the end of the wet season in two of
 the four species: Virola surinamensis seedlings had higher survival
 beneath their maternal tree than other conspecific trees, while the
 opposite pattern was found in Ormosia macrocalyx. However, these
 differences disappeared by the end of the experiment. ## Description of
 the data and file structure There are three relevant files: one data file
 containing data from the field experiment (field_experiment_data.txt), one
 data file containining data in a format for easy plotting of seedling
 survival (survival_plot_data.txt), and one code file containing script
 used for data analysis in R (R_code_for_analysis.R). More information
 about the data files and the variables it contains can be found below.
 More information about the code file and explanation can be found at the
 end of this README. Throughout the data file, NA cells represent either a)
 missing data for the variable or b) the variable is not applicable to the
 row. #### **field\_experiment\_data.txt** In this dataset, each row is one
 seedling individual from the field experiment. This dataset is
 tab-delimited and contains headers. All dates are reported in the format
 MM/DD/YYYY. Column explanations: * ID: The unique identifier for the
 seedling individual in the experiment. * species: The species of the
 seedling individual in the experiment. * seed.Acode: The unique identifier
 for the seed source adult individual. * soil.Acode: The unique identifier
 for the focal adult the seedling was planted near in the field. *
 mother.othercon: Which of the two field experimental treatments the
 seedling was grown in (maternal conspeecific tree or other conspecific
 tree). * plot: The ID of the specific plot beneath the focal adult the
 seedling was grown in. * n.seedlings.plot: The number of seedlings planted
 in that plot at the beginning of the experiment. * date.anyspecies.0: The
 date the first experimental seedling was transplanted into the field
 experiment. Used for calculating days since the beginning of the
 experiment. * date.0: The date the given experimental seedling was
 transplanted into the field experiment. Used for calculating days since
 transplant of the seedling. * exp.day: The number of days that had elapsed
 since the beginning of the experiment when the given seedling was
 transplanted. * ht.0: The stem height (in centimeters) of the seedling at
 the time of transplant. * lnum.0: The number of leaves on the seedling at
 the time of transplant. * la.0.ov: The estimated leaf area of the seedling
 (in centimeters squared) at the time of transplant. Calculated using
 species-specific allometric equations produced using measurements of the
 stem height, leaf number, leaf area, and dry biomass of a subset of
 potential experimental seedlings at the beginning of the experiment. *
 dry.wt.est.0.ht.lnum: The estimated dry biomass (in grams) of the seedling
 at the time of transplant based on it's ht.0 and lnum.0. Calculated
 using the allometric equation mentioned above. * dry.wt.est.0.ht.la: The
 estimated dry biomass (in grams) of the seedling at the time of transplant
 based on ht.0 and dry.wt.est.0.ht.lnum. Calculated using the allometric
 equation mentioned above. The following columns repeat for each census of
 the data. The census can be identified by .0, .1, .2, ... .h after the
 variable name. .0 Is the transplant/initial census. .h is the harvest
 census. Here it is written as .X to indicate repetition. * date.X: The
 date of the census. * time.X: The number of days that had elapsed since
 the first seedling of the seedling's species was transplanted. *
 time.in.trt.X: The number of days that had elapsed since the seedling was
 placed in the field treatment at the time of the census. Could be NA if
 the seedling died. * exp.day.X: The number of days that had elapsed since
 any seedling of any species was placed in the field experiment. *
 plot.ht.X: The height of the seedling (in cm), as measured once planted in
 the plot. * lnum.X: The number of leaves the seedling had at the census. *
 surv.X.01: Whether or not a seedling survived until the given census
 (binary variable, 0 = mortality, 1 = survival). * clipping.0.X.yn: Whether
 or not signs of clipping were present in the seedling at the given census
 (binary variable, y = yes, n = no). * dry.wt.est.X.ht.lnum: Estimated
 total dry biomass (in grams) of the seedling at the census, based on
 plot.ht.X and lnum.X. Calculated using the allometric equation mentioned
 above. The following harvest census data columns are unique (do not repeat
 for each census). * ht.h: The stem height (in centimeters) of the seedling
 at harvest (measured outside of the plot, so true height). * la.h: The
 measured total leaf area (in centimeters squared) of the seedling
 (measured using a leaf area scanner). * clipping.0.h.yn: Whether or not
 signs of clipping had ever been observed in the seeling during the
 experiment (binary variable, y = yes, n = no). * tot.dry.wt: The total dry
 biomass (in grams) of the seedling at harvest. * rgr.0.1.est.ht.lnum: The
 relative growth rate (i.e., rate of growth, in grams, per day) of the
 seedling between census 0 and 1, based on height and leaf number. *
 rgr.1.2.est.ht.lnum: The relative growth rate of the seedling (i.e., rate
 of growth, in grams, per day) between census 1 and 2, based on height and
 leaf number. * rgr.2.3.est.ht.lnum: The relative growth rate of the
 seedling (i.e., rate of growth, in grams, per day) between census 2 and 3,
 based on height and leaf number. * rgr.3.4.est.ht.lnum: The relative
 growth rate of the seedling (i.e., rate of growth, in grams, per day)
 between census 3 and 4, based on height and leaf number. *
 rgr.4.harvest.est.ht.lnum: The relative growth rate of the seedling (i.e.,
 rate of growth, in grams, per day) between census 4 and harvest, based on
 height and leaf number. #### survival\_plot\_data.txt In this dataset,
 each row is one census of one field treatment x species treatment
 combination. This summary data is intended for easy plotting of survival
 over time in the field experiment. It is derived from data included in
 field_experiment_data. This dataset is tab-delimited and contains headers.
 Column explanations: * survey: The census the data corresponds to. 0 =
 transplant, then 1, 2, ... 5 = harvest. * date.avg: The average date that
 the seedlings in each treatment combination were surveyed during this
 census. * exp.day.avg: The average number of days that had elapsed since
 the beginning of the experiment during this census for this combination of
 species and treatment. * time.in.trt.avg: The average number of days that
 had elapsed since the first seedling of this species was transplanted
 during this census for this combination of species and treatment. *
 species: The species that the census data corresponds to. *
 field.environment: The field treatment that the census data corresponds
 to. * alive: The number of seedlings that were alive in this species x
 field treatent combination during this census. * dead: The number of
 seedlings that had died in this species x field treatent combination
 during this census. * tot: The total number of seedlings that had been
 transplanted in this species x field treatent combination. * surv.rate:
 The survival rate (i.e., proportion) of the seedlings in the given species
 x field treatment combination during the given census. ## Sharing/Access
 information There are no other publicly accessible locations of the data.
 Data was derived only from first-hand collection by the listed authors. ##
 Code/Software The code file containing the R script used for data analysis
 is included (R_code_for_analysis.R). It is formatted for use with the R
 Statistical Software, which is freely available online. ####
 **R\_code\_for\_analysis.R** The R code file requires the data files
 (field_experiment_data.txt and survival_plot_data.txt) to run. Please make
 sure to set your working directory in R to a location that includes these
 files. The file contains all of the code used to produce the results and
 figures that appear in the relevant manuscript. Data analysis components
 (e.g., survival analysis versus growth analysis) are labelled using
 hierarchical subsection notation and headings. Data analysis was run with
 R version 4.2.2. The code requires installation and usage of the following
 packages: lme4, lmerTest, ggplot2, car, performance, interactions, tidyr.