https://doi.org/10.5061/dryad.s7h44j1gc

Description of the data and file structure

STUDY AREA AND BACKGROUND ON EXPERIMENT
Data collection occurred Jun-Jul 2022 in Coto Brus county of southern Costa Rica near Las Cruces Biological Station. The data represent full censuses of 26 plots from 10 restoration sites and six plots sampled from mature reference forests in adjacent areas at six of these locations. Restored areas were designed to have an area of 0.25 ha with either 48x48 m or 42x54 m dimensions with a ≥5-m buffer. Restoration experiments initiated in 2004-2006, when each plot received one of three randomized treatments: natural regeneration n = 9 plots, applied nucleation n = 9, or plantation n = 8. Some of the sites were missing one or two treatments due to their being destroyed or heavily damaged by this point in the study, and so were not censused. Plantations were uniformly planted with tree seedlings. Applied nucleation treatment was planted with six tree islands of three sizes: two each of 4×4, 8×8, and 12×12 m. Planted seedling spacing was kept constant (~2.8 m) in the plantation and applied nucleation treatments; 313 trees were planted in the plantation, 86 in the applied nucleation, and none in natural regeneration plots (see Holl et al. 2011 for further details). All plots (including natural regeneration) were cleared to ground level by machete at ~3-month intervals for the first 2.5 years to allow planted tree seedlings to grow above existing vegetation. We planted seedlings (20-30 cm tall) of four tree species; these included two native late-successional species, Terminalia amazonia (J.F. Gmel.) Exell (Combretaceae) and Vochysia guatemalensis Donn. Sm. (Vochysiaceae), and two naturalized early-successional species, Erythrina poeppigiana (Walp.) Skeels and Inga edulis Mart. (both Fabaceae) that are used widely in intercropping systems in Central America. By the time of the surveys presented here, a majority of the planted softwoods had died (mean survival and standard deviation: E. poeppigiana 34.5 ± 28.5%; I. edulis 22.9 ± 18.5%). Survival of the other two species remained high (V. guatemalensis 82.8 ± 18.4%; T. amazonia 82.1% ± 17.8%). At six sites, we also sampled adjacent remnant forests to serve as references. These reference forests ranged in size from 2-320 ha and showed no evidence of clearing in the last 75 years since aerial photographs have been available (Zahawi et al. 2015b). All have been impacted to some extent by human disturbance, as “pristine” forests are not present in our study area (Clement and Horn 2001). 

DATA COLLECTION

16-18 years after establishing plots, we censused all naturally recruiting trees ≥20 cm height (hereafter “recruits”) throughout each restoration treatment plot. We mapped individual recruits to a grid of 3×3 m quadrats and counted the number of seedlings >=20 cm but <1 cm diameter at breast height (DBH) of each species within each quadrat. We measured DBH for all recruits >=1 cm and categorized each into sapling (1-<5 cm DBH) or tree (>=5 cm DBH) size classes. If an individual had multiple stems, we based our size classification on the largest stem. Individual restoration plots were mostly 48×48 m (256 3×3 m quadrats), but in some cases, plots were 42×54 m (252 quadrats) due to constraints in the landscape at initial plot setup. In a few cases, a smaller plot area was sampled primarily due to extensive anthropogenic damage to a section of the plot (Table S1). The layout of the reference forest plots was slightly different and consisted of four 21×21 m plots (196 quadrats) at five sites and three 21×21 m plots (147 quadrats) at one site. Tree recruits were identified to the lowest operational taxonomic unit following the nomenclature of Tropicos (https://www.tropicos.org).

Citations: 
Clement, R. M., and S. P. Horn. 2001. Pre-Columbian land-use history in Costa Rica: a 3000-year record of forest clearance, agriculture, and fires from Laguna Zoncho. The Holocene 11:419–426.
Holl, K. D., R. A. Zahawi, R. J. Cole, R. Ostertag, and S. Cordell. 2011. Planting seedlings in tree islands versus plantations as a large-scale tropical forest restoration strategy. Restoration Ecology 19:470–479.
Zahawi, R. A., G. Duran, and U. Kormann. 2015b. Sixty-seven years of land-use change in southern Costa Rica. PloS One 10:e0143554.

Files and variables

File: ECOLAPPS_final_Schubert.et.al.2024.csv

Description: The data presented here have been redacted slightly from the original survey spreadsheets. Namely, we have removed columns for data that were recorded for purposes beyond the scope of the manuscript (e.g., presence/cover of herbaceous plants, plaque numbers of trees part of smaller permanently monitored quadrats, descriptive comment columns). Several calculated columns have been added to classify stem sizes based on maximum diameter. Furthermore, our inclusion of data from planted tree species comes from a separate, distinct survey protocol to document the survival of the original 4 planted species. This latter protocol documented survival of all planted stems, but measured diameter from only a subset. For this reason, we have extrapolated size estimates for unmeasured stems such that a fixed diameter measurement is assigned (i.e., 0, 1, 5). The assignment was made such to preserve the relative ratio of seedling, sapling, and tree size classes for each plot-species based on the empirical measurements. These extrapolations were made for approximately 35% of the planted stems in plantation plots and less than 1% in applied nucleation plots.

Persons responsible for data entry and proofing
Botanical Identification Person Initials: ARO,FOB,JAR,JF,KDH,RAZ
Data Entry/Proofing Person Initials: BR,CB,FOB,JOP,KDH,MSJ,SCS,THL,VRM

Number of variables: 18

Number of cases/rows: 67046

Variables

• Especie: String; taxonomic codes for each distinguishable taxonomic unit, "ND" denotes "Quadrante" sampling units where no stems were present
• Sitio: String; two-letter site codes corresponding to 10 locations described in Table S1 of Schubert et al. 2024
• Trat: String; two-letter codes indicating forest type or treatment, NR - Natural Regeneration, AN - Applied Nucleation, PL - Plantation, RF - Reference Forest
• Parcela: Numeric; numbers from 1-78 indicating the 6x6 m grid cell from each restoration plot. Standard 48x48 m plots have parcela numbers up to 64. Rectangular 42x54 m has numbers up to 78
• Quadrante: String; letter codes for the four subdivisions (each 3x3 m) of a 6x6 m grid cell
• No..indiv.: Numeric; recorded number of individuals of each species, each class in each 3x3 "Quadrante" sampling unit
• Altura: Numeric; height in centimeters of a stem reported "seedling" stems that do not reach 1 cm in diameter at breast height, values represent the medians of binned categories from the census protocol where 35 = 20-<50 cm, 75 = 50-<100 cm, 125 = 100-<150 cm, 175 = 150-<200 cm, 201 = >=200 cm, larger size classes are recorded as NA
• DAPmax: Numeric; stem diameter at breast height in centimeters, representing the largest stem in cases where multiple stems corresponded to a single individual
• Origin: String; code indicating the origin of a recorded individual, distinguishing between: Recruit - naturally established individual, Planted - an individual that was originally planted in a restoration plot
• Measured: String; code indicating how individual measurements were produced: Empirical - direct measurement of individuals during the census, Extrapolated - applies to a subset of surviving planted stems whose approximate size was estimated based on a subset of individuals measured empirically
• Class: String; description distinguishing the three size classes of recorded individuals: seedling - individuals with stems <1 cm, sapling - individuals with stems 1-<5 cm, tree - individuals with stems >=5 cm
• Family: String; family classifcation following the nomenclature of Tropicos (https://www.tropicos.org)
• Genus: String; genus classification following the nomenclature of Tropicos (https://www.tropicos.org), NA is given for taxa identified only to family level
• Specific.Epithet: String; specific epithet classification following the nomenclature of Tropicos (https://www.tropicos.org), NA is given for taxa identified to only family or genus level
• Authority: String; naming authority following the nomenclature of Tropicos (https://www.tropicos.org), NA is given for taxa identified to only family or genus level
• disp_mode: String; codes for dispersal mode, ZOO - zoochory, GRAV - gravity, WIND - anemochory, EXPL - ballistic
• succ_stage: String; codes for successional stage at which taxa are most represented, Early - early successional, Mid - mid successional, Late - late successional, UNK - successional stage uncertain
• seed_size: String; numeric codes for seed size based on width, 1 - seeds <5 mm, 2 - 5-<10 mm, 3 - >=10 mm

File: PlotQuadrantes.csv

Description: A supplementary data file used to calculate the sampled area in each plot based on the total number of 3x3 m quadrats.

Number of variables: 2

Number of cases/rows: 33

Variables

• Site.Treat: String; codes for all 33 of the sample plots, first two letters are derived from "Sitio" in the main file, second two letters are derived from "Trat" in the main file
• N.Quad: Total number of 3x3 m "Quadrante" (main file) sample units recorded from each plot

File: FinalAnalysis_ECOLAPP_Schubert.et.al.R

Description: R code to reproduce the figures and statistical analyses in the manuscript, as well as tables/figures in the supporting information section.

[12 Dec 2025 -- THIS README DESCRIPTION HAS BEEN UPDATED TO INCLUDE DATA & DESCRIPTIONS FOR A NEW ANALYSIS FROM MANUSCRIPT ACCEPTED FOR PUBLICATION IN JOURNAL OF APPLIED VEGETATION SCIENCE]

Restoration method influences spatial patterns of tree seedling and sapling recruitment in the second decade of tropical forest recovery

Files and variables

File: IslasMaster_abbreviated2025.csv

Description: Taxonomic information and attributes for all of the operational taxonomic units (OTUs) in the tree survey data set. Most recent revisions and proofing were completed by FOB in July 2025.

Number of variables: 8

Number of cases/rows: 256

Variables

• Especie: String; taxonomic codes for each distinguishable taxonomic unit
• Family: String; family classifcation following the nomenclature of Tropicos (https://www.tropicos.org)
• Genus: String; genus classification following the nomenclature of Tropicos (https://www.tropicos.org), NA is given for taxa identified only to family level
• Specific.Epithet: String; specific epithet classification following the nomenclature of Tropicos (https://www.tropicos.org), NA is given for taxa identified to only family or genus level
• Authority: String; naming authority following the nomenclature of Tropicos (https://www.tropicos.org), NA is given for taxa identified to only family or genus level
• disp_mode: String; codes for dispersal mode, ZOO - zoochory, GRAV - gravity, WIND - anemochory, EXPL - ballistic
• succ_stage: String; codes for successional stage at which taxa are most represented, Early - early successional, Mid - mid successional, Late - late successional, UNK - successional stage uncertain
• seed_size: String; numeric codes for seed size based on width, 1 - seeds <5 mm, 2 - 5-<10 mm, 3 - >=10 mm

File: Cartesian.Standard.Meters.csv File: Cartesian.Long.Meters.csv File: Cartesian.Reference.Meters.csv

Description: Three analogous files to assist with translating the spatial information of Parcela and Quadrante information for each plot. Distances are presented as X and Y, specifying the distance of the central point of the quadrat from the plot center as origin.

Number of variables: 4-5

Number of cases/rows: up to 256

Variables

• Section: String; letter codes indicating up to four replicate 21 x 21 m grids for reference plots, some sections were adjoining if reference patches were sufficiently large and contiguous. In some sites, reference plot sections were scattered to suit the shape of the forest available in the landscape. Sections for restored plots are defined in the code file based on individual plot maps from the site.
• Parcela: Numeric; numbers from 1-78 indicating the 6x6 m grid cell from each restoration plot. Standard 48x48 m plots have parcela numbers up to 64. Rectangular 42x54 m has numbers up to 78
• Quadrante: String; letter codes for the four subdivisions (each 3x3 m) of a 6x6 m grid cell
• X: Numeric; distance in meters from the sub-quadrat (i.e., Parcela-Quadrante) from the plot center as origin. "Plot West" is indicated by negative numbers. "Plot East" is indicated by positive numbers.
• Y: Numeric; distance in meters from the sub-quadrat (i.e., Parcela-Quadrante) from the plot center as origin. "Plot South" is indicated by negative numbers. "Plot North" is indicated by positive numbers.

File: FinalAnalysis_AVS_Schubert.et.al.R