DOI: 10.5061/dryad.05qfttfb9
title: Data from: Vertebrate seed predation can limit recruitment of later-successional species in tropical forest restoration

description: The effects of vertebrate seed predation on the regeneration of restored
 forests are not well understood because most past studies have focused on
 seed predation within the first few years after restoration and have
 measured seed removal without quantifying subsequent seedling
 establishment of seeds that avoid predation. Quantifying the establishment
 of seeds that escape predation in restored forests at later stages of
 regrowth is crucial for anticipating longer-term recovery trajectories.
 Here, we evaluated the potential role of vertebrate seed predators in
 limiting recruitment of later-successional tree species in nine forests
 actively restored ≥15 years prior and in four paired remnant forest
 fragments embedded in an agricultural landscape in southern Costa Rica. We
 conducted seed addition experiments with four tree species inside and
 outside vertebrate exclosures and used camera trapping to detect seed
 predators. To determine the fate of seeds that avoided predation, we also
 measured seedling establishment after 1 year, given that other mortality
 factors may compensate in the absence of vertebrate seed predation. We
 detected two species of birds and five species of granivorous mammals
 removing seeds. Seed tagging indicated that most removal resulted in
 predation. For three of the four tree species tested, vertebrate seed
 predation reduced seedling establishment. The magnitude of this effect
 depended on species' susceptibility to other causes of mortality
 during the seed-to-seedling transition. Our study demonstrates that
 vertebrate seed predators can substantially reduce later-successional
 seedling recruitment in restored forests and should be considered
 alongside dispersal limitation and microsite conditions as factors slowing
 forest recovery.
description: # Data from: Vertebrate seed predation can limit recruitment of
 later-successional species in tropical forest restoration
 [https://doi.org/10.5061/dryad.05qfttfb9](https://doi.org/10.5061/dryad.05qfttfb9) ## Description of the data and file structure ### General Information Name of data set: Islas Seed Predation Experiment This repository contains data from a study on the influence of vertebrate seed predation on the seedling establishment of four later-successional tree species within a long-term forest restoration experiment in southern Costa Rica. Data files: (1) seed_removal.csv (2) seedling_establishment.csv (3) seed_predator_detections.csv (4) seed_tagging.csv (5) litter_depth.csv Date the data set was last modified: 12 July 2024 Funder: U.S. National Science Foundation How to cite data: Joyce, Francis H. et al. (2024). Vertebrate seed predation can limit recruitment of later-successional species in tropical forest restoration [Dataset]. Dryad. [http://doi.org/10.5061/dryad.05qfttfb9](https://doi.org/10.5061/dryad.05qfttfb9). Primary article: Joyce, F. H., Ramos, B. M., Zahawi, R. A., & Holl, K. D. (2024). Vertebrate seed predation can limit recruitment of later-successional species in tropical forest restoration. *Biotropica,* e13381. [https://doi.org/10.1111/btp.13381](https://doi.org/10.1111/btp.13381) ### Data Collection Methodology for data collection: described in primary article: Joyce, F. H., Ramos, B. M., Zahawi, R. A., & Holl, K. D. (2024). Vertebrate seed predation can limit recruitment of later-successional species in tropical forest restoration. *Biotropica,* e13381. [https://doi.org/10.1111/btp.13381](https://doi.org/10.1111/btp.13381) Data collectors: Francis Joyce (exclosure experiment), Brianna Ramos (seed tagging). Dates of data collection: July 2021 to September 2023. Contact for project: Francis H. Joyce ([fjoyce@ucsc.edu](mailto:fjoyce@ucsc.edu); [fhjoyce@gmail.com](mailto:fhjoyce@gmail.com)) ### Data entry Software used to prepare data set: Microsoft Excel (16.83), R v3.0.1-4.2.2 People who entered data: Francis Joyce, Brianna Ramos People who proofed data: Francis Joyce Contact for questions: F. H. Joyce ([fjoyce@ucsc.edu](mailto:fjoyce@ucsc.edu); [fhjoyce@gmail.com](mailto:fhjoyce@gmail.com)) ### File: seed\_removal.csv variables -species: six-letter code identifying focal tree species: OCO_PUB = Ocotea puberula, OTO_NOV = Otoba novogranatensis, PSE_MOL = Pseudolmedia mollis, QUE_BEN = Quercus benthamii.    -site: two-letter code identifying the site. Codes are consistent with Holl et al. (2020).  -trt: factor describing the forest type. Values are "Restored" (plantation) or "Remnant" (reference forest) -station: integer between 1 and 4 identifying the set of seed addition quadrats within a particular restored or remnant forest -exclosure: factor describing the exclosure treatment. Values are "caged" or "exposed." -seeds_total: integer describing the total number of conspecific seeds added per station. Values are 7, 8, or 11. -seeds_remaining: integer describing the number of seeds remaining in the quadrat at the end of the removal monitoring period.  -seeds_missing: integer describing the number of seeds missing (removed) from the quadrat at the end of the removal monitoring period. ### File: seedling\_establishment.csv variables -species: six-letter code identifying focal tree species. Values same as above. -site: two-letter code identifying the site -trt: factor describing the forest type. Values are "Restored" (plantation) or "Remnant" (reference forest) -station: integer between 1 and 4 identifying the set of seed addition quadrats within a particular restored or remnant forest -seeds_total: integer describing the total number of conspecific seeds added per station. Values are 7, 8, or 11. -seeds_established: integer describing the number of added seeds that were established seedlings at the end of the one-year monitoring period. -seeds_failed: integer describing the number of added seeds that failed to establish at the end of the one-year monitoring period  ### File: seed\_*predator*\_detections.csv -site: two-letter code identifying the site -trt: factor describing the forest type. Values are "Restored" (plantation) or "Remnant" (reference forest) -focal_species: six-letter code identifying focal tree species. Values same as above. -binomial_name: binomial name of seed predator species -presence: binary variable indicating whether or not the seed predator species was detected during the camera deployment -independent_observations: number of independent observations (&gt;30 minutes apart) -nights_elapsed: the duration of the camera trap deployment in number of nights ### File: seed\_tagging.csv -species: six-letter code identifying focal tree species. Values same as above. -day_of_experiment:  number of days since experimental seeds were added -site: two-letter code indicating site. Values are LL or JG. -trt: factor describing the forest type. Values are "Restored" (plantation) or "Remnant" (reference forest) -quadrat: string describing the seed addition quadrat within the restoration or remnant forest plot (five per plot). -seed_id: integer from 1 to 10 for PSEMOL or 1 to 4 for QUE_BEN, identifying each seed within each quadrat. -present: binary variable describing whether each added seed was still present (1) or absent (0) at the seed addition quadrat. -intact: binary variable describing whether present seeds were undamaged (1) or damaged (0). -distance_m: distance in meters seeds (intact or damaged) were found from the quadrat where they were initially placed, measured to the nearest 0.1 m. -notes: any comments elaborating on the seed's condition. ### File: litter\_depth.csv date: date when data were collected in format yyyy-mm-dd -Site: two-letter code indicating site -Trt: factor describing the forest type. Values are "Restored" (plantation) or "Remnant" (reference forest) -station: -station: integer between 1 and 4 identifying the set of seed addition quadrats within a particular restored or remnant forest -cage_treatment: factor describing the exclosure treatment. Values are "caged" or "exposed." -quadrat: factor identifying the seed addition quadrat (one of three) within each station. Each station has one "caged" quadrat. The remaining two exposed quadrats per station are coded as  "Oto_nov_exp," "small-seeded," "Pm_exp", or "Qb_exp." -depth_X: columns (from 1:5) for individual depth measurements with numeric values of litter depth to the nearest 0.5 cm.    -Notes: comments specific to that quadrat's depth measurements. ### References Holl, K. D., Reid, J. L., Cole, R. J., Oviedo-Brenes, F., Rosales, J. A., & Zahawi, R. A. (2020). Applied nucleation facilitates tropical forest recovery: Lessons learned from a 15-year study. Journal of Applied Ecology, 57(12). [https://doi.org/10.1111/1365-2664.13684](https://doi.org/10.1111/1365-2664.13684) ### Comments Note that the number of observations in seedling_establishment.csv (352) is less than in seed_removal.csv (368)  because 16 quadrats (2 species, 2 exclosure treatments, 4 stations per plot) were not monitored through the seedling phase at site HB, which was lost in January 2022 when land ownership changed.  Litter depth was not collected at site HB, nor at two quadrats where there was a wasp nest. ### Files and variables #### See readme file.