DOI: 10.5061/dryad.dz08kps77
title: Data from: Evaluating the role of frequency-dependent selection in controlling the expansion of clonal aggregations in the tropical forest's understory: Insights from a decade-long experiment.

description: Sexual reproduction, despite its associated costs and risks, is prevalent
 among many organisms, presumably to generate and maintain genetic
 diversity. This diversity is vital for adapting to environmental changes
 and combating natural enemies. Paradoxically, several clonal species also
 exhibit high genetic diversity. One theory for the maintenance of this
 genetic diversity is frequency-dependent selection, which favors rare
 genotypes over common ones, limiting the extent and dominance of a single
 clone, thereby preserving genetic diversity. Empirical evidence for this
 theory under natural conditions is sparse. Twelve years ago, we
 established in the forest fourteen genetically diverse plots where all
 plants had a unique genotype (rare genotypes) and paired with them clonal
 plots where all plants had the same genotype (common genotypes) to test
 whether common genotypes have a disadvantage and frequency-dependent
 selection is in action. Clones were created from cuttings from Piper
 cordulatum, a naturally clonally reproducing understory plant. We aimed to
 test if common genotypes are disadvantaged and if frequency-dependent
 selection is effective. Over the experiment's first ten years,
 herbivory, pathogen attacks, and plant size remained similar across both
 genotype categories. Intriguingly, clones exhibited superior survival
 during the initial five years. Survival rates equalize for rare and common
 genotypes by the decade's end. By year twelve, survival remained
 similar for rare and common genotypes. However, modeled survival
 projections based on the twelve-year-long trend suggest that common
 genotypes might experience increased mortality in the long run, consistent
 with the hypothesis of negative frequency-dependent selection. Moreover,
 plants in clonal plots exhibited lower fitness in terms of infructescence
 production at the plot level by the tenth year. Our findings suggest that
 having low genetic diversity in the neighborhood does not increase disease
 or herbivory susceptibility or reduce short-term survival. The impact of
 negative frequency-dependent selection is not immediate. However, it could
 eventually restrict the survival and reproduction of Piper clones in a
 tropical forest's understory, curbing the dominance of any single
 genotype and potentially enhancing population-wide genetic diversity.
description: Twelve years ago, we established fourteen experimental plots
 within a forest setting to investigate frequency-dependent selection among
 <em>Piper cordulatum</em>, a naturally clonally reproducing
 understory plant. Each plot was designated under one of two treatments:
 "All Clones," where all plants shared the same genotype, and
 "No Clones," where every plant possessed a unique genotype. This
 experimental design aimed to test the hypothesis that common genotypes,
 represented by the "All Clones" treatment, are at a disadvantage
 due to frequency-dependent selection, which might help preserve genetic
 diversity by limiting the dominance of any single clonal
 genotype. Data collection was carried out
 systematically over the course of the experiment. Initial measurements
 were taken at 0, 6, 12, and 18 months post-transplantation. Subsequent
 censuses were conducted at extended intervals—specifically at 30, 42, 60
 (5 years), and 120 months (10 years). In the final year, we harvested the
 above-ground parts of one focal plant per plot to measure the total leaf
 area, the extent of herbivory damage, and above-ground biomass
 (AGB). During each census, we documented the number of
 plants that were alive or dead. We also assessed the extent of damage from
 herbivores and pathogens, calculating the percentage of total plant
 damage. Furthermore, to determine whether plants with
 rare genotypes ("No Clones" treatment) exhibited higher
 reproductive success compared to those with common genotypes ("All
 Clones" treatment), we counted the total number of infructescences
 produced per plant and recorded the number of surviving plants in each
 plot during the reproductive season of the tenth year.
description: # Evaluating the role of frequency-dependent selection in controlling the
 expansion of clonal aggregations in the tropical forest's understory:
 insights from a decade-long experiment.
 [https://doi.org/10.5061/dryad.dz08kps77](https://doi.org/10.5061/dryad.dz08kps77) ## Description of the data and file structure **Summary of Experimental Efforts** This dataset originates from a 12-year experimental study conducted to investigate frequency-dependent selection in *Piper cordulatum*, a naturally clonally reproducing understory plant. The experiment was designed with 14 blocks, each containing two plots: one under the "All Clones" treatment where all plants shared the same genotype, and the other under the "No Clones" treatment where each plant had a unique genotype. The study aimed to assess whether common genotypes are at a disadvantage and if frequency-dependent selection helps preserve genetic diversity by limiting clonal dominance. ### Files and variables #### File: DataClonalPlots.xlsx **Description of File Structure and Contents** The dataset is structured into four worksheets within a single Excel file: 1. **Survival Data 12yrs**: Tracks the survival status of plants over 12 years. 2. **Leaf Area+Her+Pat**: Details on leaf area and damage from herbivores and pathogens at each census. 3. **Harvest Focal Plants 10yrs**: Contains measurements from the final harvest of focal plants after 10 years. 4. **Reproductive Effort**: Reports the reproductive output in the tenth year of the experiment. **Definitions of Variables, Abbreviations, and Units** * **Plant ID**: Unique identifier for each plant within the plots, facilitating tracking and analysis. Total of 560 plants, 20 on each plot. * **Block**: Identifier for the block of plots, each block containing two plots, one per treatment. Total of 14 blocks. * **Plot**: Identifier for each plot within a block. Total of 28 plots * **Genotype**: Identifier for the genotype of the plants within each plot. * **Treatment**: Indicates whether the plot is under the "All Clones" (common genotype) or "No Clones" (unique genotypes) treatment. * **Time:** Recorded as the number of years since the start of the experiment, used to reference the timing of data collection (e.g., 0, 0.5, 1, 1.5, 2.5, 3.5, 5, 10 years). Note: Only survival data was taken at the 12th year.  * **Censored**: Indicates the survival status; 0 = dead, 1 = alive. * **Leaf Area**: Measured in square centimeters (cm²). * **Herbivory Damage (%), Pathogen Damage (%), Combined Damage (%)**: Percentage of total leaf area affected. * **AGB (Above Ground Biomass)**: Measured in grams (g). * **Infructescences**: Count of reproductive structures per plant. **Data Entry conventions** **Handling Missing Data**: For dead or missing plants during the observed year, we use the word "null" instead of leaving the cell empty to maintain consistency and clarity in data presentation. # Code/software **Software Used to View Data:** **Microsoft Excel**: All datasets are formatted as Excel files (.xlsx), which can be easily opened and viewed using Microsoft Excel. **Workflow Description:** * Data were initially cleaned and organized in Microsoft Excel, where basic manipulations (e.g., filtering, sorting) were performed. * Detailed statistical analyses, including survival analysis and comparisons of growth metrics, were conducted in JMP 17.0.0 (JMP Statistical Discovery LLC). **Note on Code and Scripts:** * No specific scripts or code files are included with the dataset submission, as most analyses were performed interactively in JMP. Users wishing to replicate the analysis in other software should adapt the provided data and analysis descriptions to their chosen tools. ## Access information Data were independently collected as part of this study and are not derived from other sources.