Dataset DOI: 10.5061/dryad.ns1rn8q72

Description of the data and file structure

The data were collected from a series of experiments designed to evaluate seed germination, fruit traits, and fruit removal across different species and developmental stages. Germination experiments quantified germination percentage and timing under controlled conditions. Additional datasets include fruit color measurements (RGB), multivariate trait data (germination percentage, MGT, and GSI) used in principal component analyses (PCA), and field-based removal experiments assessing fruit removal. Together, these data support analyses of how fruit traits and display characteristics influence germination patterns and removal by dispersal agents.

Files and variables

File: germination.zip

Description: This directory contains datasets and scripts associated with germination analyses and artificial fruit experiments.

Folder structure:

• script/ – R scripts used for data analysis
• data/ – datasets used in the analyses
• germination_project.Rproj

Subfolders (inside Data/):

• TXT_time/ – Dataset used to analyze germination over time (Figures 4 and 5)
  • ca_time.txt - Germination time (in days) for seeds of Campomanesia aromatica.
  • cd_time.txt - Germination time (in days) for seeds of Campomanesia dichotoma.
  • e_ast_time.txt - Germination time (in days) for seeds of Eugenia astringens.
  • e_az_time.txt - Germination time (in days) for seeds of Eugenia azeda.
  • el_time.txt - Germination time (in days) for seeds of Eugenia luschnathiana.
  • ep_time.txt - Germination time (in days) for seeds of Eugenia punicifolia.
  • eu_time.txt - Germination time (in days) for seeds of Eugenia uniflora.
  • mb_time.txt - Germination time (in days) for seeds of Myrcia bergiana.
  • mg_time.txt - Germination time (in days) for seeds of Myrcia guianensis.
  • mm_time.txt - Germination time (in days) for seeds of Myrcia multiflora.
  • ms_time.txt - Germination time (in days) for seeds of Myrcia sylvatica.
  • pg_time.txt - Germination time (in days) for seeds of Psidium guineense.
    • Variables:
      • ord - Unit identifier
      • genus – Genus name of the species.
      • epiteth - Specific epithet of the species.
      • sp – Species name.
      • stage – Fruit maturation stage (e.g., immature, intermediate, mature).
      • days – Time (in days) since the beginning of the experiment (sowing).
      • germi_day – Number of seeds that germinated on a given day.
      • ger_cumu – Cumulative number of germinated seeds over time.
      • ger_perc – Germination percentage (%), calculated based on the total number of seeds.
      • MGT – Mean germination time (in days).
      • GSI – Germination speed index.
• glm/ – Dataset used to analyze germination percentage and probability of germination (Figures 2 and 3). This folder contains data used in generalized linear models (GLMs) to evaluate germination outcomes.
  • ca.txt - Germination percentage for seeds of Campomanesia aromatica.
  • cd.txt - Germination percentage for seeds of Campomanesia dichotoma.
  • e_ast.txt - Germination percentage for seeds of Eugenia astringens.
  • e_az.txt - Germination percentage for seeds of Eugenia azeda.
  • el.txt - Germination percentage for seeds of Eugenia luschnathiana.
  • ep.txt - Germination percentage for seeds of Eugenia punicifolia.
  • eu.txt - Germination percentage for seeds of Eugenia uniflora.
  • mb.txt - Germination percentage for seeds of Myrcia bergiana.
  • mg.txt - Germination percentage for seeds of Myrcia guianensis.
  • mm.txt - Germination percentage for seeds of Myrcia multiflora.
  • ms.txt - Germination percentage for seeds of Myrcia sylvatica.
  • pg.txt - Germination percentage for seeds of Psidium guineense.
    • Variables:
      • sp – Species name.
      • code – Abbreviated code assigned to each species for use in principal component analysis (PCA).
      • genus – Genus name of the species.
      • display – Fruit display type or experimental treatment related to fruit presentation (unicolored or multicolored).
      • rep – Replicate number.
      • stage – Fruit maturation stage (e.g., immature, intermediate, mature).
      • n_seed – Total number of seeds used in the experimental unit.
      • MGT – Mean germination time (in days).
      • GSI – Germination speed index.
      • ger_perc – Germination percentage (%).
• PCA/ – Dataset used for principal component analysis (PCA) (Figure 6).
  • pca.txt
    • Variables:
      • sp – Species name.
      • code – Abbreviated code assigned to each species for use in principal component analysis (PCA).
      • genus – Genus name of the species.
      • display – Fruit display type or experimental treatment related to fruit presentation (unicolored or multicolored).
      • stage – Fruit maturation stage (e.g., immature, intermediate, mature).
      • MGT – Mean germination time (in days).
      • GSI – Germination speed index.
      • ger_perc – Germination percentage (%).
• removal/ – data from the removal experiment (Figure 7)
  • Data from the artificial fruit removal experiment used for generalized linear model (GLM) analyses.
    • Variables:
      • ord – Observation or experimental unit identifier.
      • shrub – Identifier of the focal shrub (plant individual).
      • display – Fruit display type or experimental treatment related to fruit presentation (unicolored or multicolored).
      • color – Fruit color category used in the experiment.
      • Nfruit_marked – Number of marked fruits.
      • Nfruit_removed – Number of removed fruits.
      • Nfruit_wt_marked – Number of unmarked fruits.
      • Total_detected – Total number of fruits detected.
      • Total_fruits_shrub – Total number of fruits per shrub.
      • perc_0_1 – Fruit removal proportion (0–1 scale).
      • perc_100 – Fruit removal percentage (0–100 scale).

• RGB/ – Dataset containing RGB color data used in linear discriminant analysis (LDA) (Figures S4 and S5)
  • ca_rgb.txt - RGB color values for fruits of Campomanesia aromatica.
  • cd_rgb.txt - RGB color values for fruits of Campomanesia dichotoma.
  • e_ast_rgb.txt - RGB color values for fruits of Eugenia astringens.
  • ea_rgb.txt - RGB color values for fruits of Eugenia azeda.
  • el_rgb.txt - RGB color values for fruits of Eugenia luschnathiana.
  • ep_rgb.txt - RGB color values for fruits of Eugenia punicifolia.
  • eu_rgb.txt - RGB color values for fruits of Eugenia uniflora.
  • mb_rgb.txt - RGB color values for fruits of Myrcia bergiana.
  • mg_rgb.txt - RGB color values for fruits of Myrcia guianensis.
  • mm_rgb.txt - RGB color values for fruits of Myrcia multiflora.
  • ms_rgb.txt - RGB color values for fruits of Myrcia sylvatica.
  • pg_rgb.txt - RGB color values for fruits of Psidium guineense.
    • Variables:
      • ord – Observation or sample identifier.
      • color – Fruit color category.
      • red – Raw red channel intensity value obtained from image analysis.
      • green – Raw green channel intensity value obtained from image analysis.
      • blue – Raw blue channel intensity value obtained from image analysis.
      • R+G+B – Sum of red, green, and blue channel intensities.
      • R – Relative contribution of the red channel to total RGB (R / [R+G+B]).
      • G – Relative contribution of the green channel to total RGB (G / [R+G+B]).
      • B – Relative contribution of the blue channel to total RGB (B / [R+G+B]).
      • LM – Long–medium wavelength component derived from color space transformation.
      • S – Short wavelength component derived from color space transformation.

Code/software

All analyses were conducted using R software (version 4.4.3).

Users should set the working directory to the “germination” folder to access scripts and datasets.

Subfolders (inside Scripts/):

• germination/ – Scripts for germination analyses and generation of graphical outputs by species.
• pca/ – Script used for principal component analysis (PCA) and associated graphical outputs.
• removal/ – Script used for analyses of the artificial fruit removal experiment and associated graphical outputs.

The following R packages are required to run the analyses:

• ggplot2
• hrbrthemes
• viridis
• rstatix
• devtools
• MASS
• tidyverse
• caret
• ggord
• FactoMineR
• factoextra
• ggthemes
• plotly
• lme4
• emmeans