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1. Active restoration increases tree species richness and recruitment of large-seeded taxa after 16-18 years

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

   Schubert, Spencer; Zahawi, Rakan; Oviedo-Brenes, Federico; Rosales, Juan Abel; Holl, Karen (January 2025, Dryad)

   {"Abstract":["Tropical forest restoration presents a potential lifeline to mitigate\n climate change and biodiversity crises in the Anthropocene. Yet, the\n extent to which human interventions, such as tree planting, accelerate the\n recovery of mature functioning ecosystems or redirect successional\n trajectories towards novel states remains uncertain due to a lack of\n long-term experiments. In 2004-2006, we established three 0.25-ha plots at\n ten sites in southern Costa Rica to test three forest restoration\n approaches: natural regeneration (no planting), applied nucleation\n (planting in patches), and plantation (full planting). In a comprehensive\n survey after 16-18 years of recovery, we censused >80,000\n seedlings, saplings, and trees across 26 restoration plots (9 natural\n regeneration, 9 applied nucleation, 8 plantation) and six adjacent\n reference forests to evaluate treatment effects on recruitment patterns\n and community composition. Both applied nucleation and plantation\n treatments resulted in significantly elevated seedling and sapling\n establishment and more predictable community composition compared to\n natural regeneration. Similarity of vegetation composition to reference\n forest tended to scale positively with treatment planting intensity.\n Later-successional species with seeds ≥5 mm had significantly greater\n seedling and sapling abundance in the two planted treatments, and\n plantation showed similar recruitment densities of large-seeded (≥10 mm)\n species to reference forest. Plantation tended towards a lower abundance\n of early-successional recruits than applied nucleation. Trees (≥5 cm DBH)\n in all restoration treatments continued to be dominated by a few\n early-successional species and originally transplanted individuals.\n Seedling recruits of planted taxa were more abundant in applied nucleation\n than the other treatments though few transitioned into the sapling layer.\n Overall, our findings show that active tree planting accelerates the\n establishment of later-successional trees compared to natural regeneration\n after nearly two decades. While the apparent advantages of higher density\n tree planting on dispersal and understory establishment of larger-seeded,\n later-successional species recruitment is notable, more time is needed to\n assess whether these differences will persist and transition to the more\n rapid development of a mature later-successional canopy. Results\n underscore the need for ecological restoration planning and monitoring\n that targets biodiversity recovery over multiple decades."],"TechnicalInfo":["# Active restoration increases tree species richness and recruitment of\n large-seeded taxa after 16-18 years\n [https://doi.org/10.5061/dryad.s7h44j1gc](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](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](https://www.tropicos.org)) * Genus: String; genus classification following the nomenclature of Tropicos ([https://www.tropicos.org](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](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](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](https://www.tropicos.org)) * Genus: String; genus classification following the nomenclature of Tropicos ([https://www.tropicos.org](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](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](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"]} 

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2. Data from: Restoration fosters later-successional seed rain, yet large seeds remain scarce after two decades

   https://doi.org/10.5061/dryad.cc2fqz6mt  

   San-José, Miriam; Werden, Leland; Holl, Karen; Rosales, Juan; Zahawi, Rakan (January 2026, Dryad)

   {"Abstract":["These datasets contain seed rain and fruiting trees data collected from a\n long-term tropical forest restoration experiment in southern Costa Rica.\n Seed sampling was conducted across seven experimental sites, each\n including three restoration treatments (natural regeneration, applied\n nucleation, and plantation), as well as four nearby reference forest\n sites. Within each plot, 16 seed traps (0.5 m², 1 mm mesh) were installed\n and monitored over a two-year period (March 2021–February 2023), with\n seeds collected twice monthly. All seeds ≥1 mm were counted and identified\n to the lowest possible taxonomic level using a reference collection,\n resulting in 142,501 seeds from 104 later-successional species across 41\n families. For each record, associated information includes trap identity\n and coordinates, site and treatment, species identity, dispersal mode,\n growth form, and seed size. Species were classified into successional\n categories (mid- or late-successional), and seed size was recorded or\n categorized. Additional data include observations of fruiting trees within\n plots to assess potential local versus external seed sources."],"TechnicalInfo":["# Data from: Restoration fosters later-successional seed rain, yet large\n seeds remain scarce after two decades Dataset DOI:\n [10.5061/dryad.cc2fqz6mt](https://doi.org/10.5061/dryad.cc2fqz6mt) ##\n Description of the data and file structure These datasets contain seed\n rain and fruiting trees data collected from a long-term tropical forest\n restoration experiment near Agua Buena, Puntarenas, Costa Rica. See the\n Islas Project for more information\n ([http://www.holl-lab.com/islas-project.html](http://www.holl-lab.com/islas-project.html)) Seed sampling was conducted across seven experimental sites, each site contained three 0.25-ha areas with a tree plantation, natural regeneration, and an applied nucleation restoration plot. Additionally, four mature forests nearby the restoration sites are used as reference forest. Within each plot, 16 seed traps (0.5 m², 1 mm mesh) were installed and monitored over a two-year period (March 2021–February 2023), with seeds collected twice monthly. All seeds ≥1 mm were counted and identified to the lowest possible taxonomic level using a reference collection, resulting in 142,501 seeds from 104 later-successional species across 41 families. For each record, associated information includes trap identity and coordinates, site and treatment, species identity, dispersal mode, growth form, and seed size. Species were classified into successional categories (mid- or late-successional), and seed size was recorded or categorized. Tree species’ successional stage was determined based on the expert opinion of two taxonomists who have each worked in the region for >20 years, herbarium specimens at Las Cruces, and literature resources (Chazdon et al. 2011 A novel statistical method for classifying habitat generalists and specialists. Ecology 92, 1332–1343. De Souza, 2001. Seed size, seed germination, and seedling survival of Brazilian tropical tree species differing in successional status. Biotropica 33, 447–457. Werden et al. 2020 Effects of dispersal- and niche-based factors on tree recruitment in tropical wet forest restoration. Ecol. Appl. 30, e02139). Finally, we recorded data on which trees were flowering or fruiting in restoration plots from January 2021 to April 2023. Observations were made during seed collection fieldwork and during bird surveys (4 times per year). ### Files and variables #### File – Seed_rain_data.csv Primary dataset containing seed counts at the trap level. Each row represents a sampling event for a given seed trap. It also contains the species-level trait dataset used to assign ecological categories. Key variables include: *Site* Two-letter identifier of the 7 restoration sites used in the study. At four of them (*), a nearby mature forest was selected as a reference forest. These acronyms are mostly based on the original landowner names: BB = Bambu EC = El Cenizo JG = Julio Gonzalez* LL = Loma Linda* MM = Melissa's Meadow* OM = Omar* SG = San Gabriel *Treatment* Restoration treatment: NR = natural regeneration AN = applied nucleation PL = plantation RF = reference forest *Trap* Number of the trap where the seeds were collected (1 to 16) *Species* Species name 6-letter code: first three letters for genus, followed by the three first letters of the species (GEN_SPP). *succ_stage* Early- mid- or late-successional species according to expert opinion, herbarium specimens at Las Cruces, and literature resources. *disp_mode* Dispersal syndrome: ZOO = animal-dispersed WIND = wind-dispersed GRAV = barochory EXPL = explosive dispersal *grow_form* Growth form of the seed species: UP = understory palm CP = canopy palm ET = emergent tree CT = canopy tree UT = understory tree Shrub Liana Epiphyte *Forbs were not taken into account due to the height of our traps (>1 m from the ground) *seed_size* Size classes according to seed width: 1: <5 mm 2: 5 < 10 mm 3: 10 - 15 mm 4: >15 mm *seed_width* Seed size in mm measured or assigned based on the literature *seed_sum* Sum of the number of seeds recorded in each trap along two sampling years. Missing values are indicated as "NA". **File – Fruiting_tree_data.csv** Records of fruiting individuals within plots are used to infer potential local seed sources. Key variables include: *Date* Date of observation dd-month-yy *Site* Two-letter identifier of the 7 restoration sites used in the study. At four of them (*) a nearby mature forest was selected as a reference forest. These acronyms are mostly based on the original landowner names: BB = Bambu EC = El Cenizo JG = Julio Gonzalez* LL = Loma Linda* MM = Melissa's Meadow* OM = Omar* SG = San Gabriel *Treatment* Restoration treatment: NR = natural regeneration AN = applied nucleation PL = plantation RF = reference forest *Species* Species name 6-letter code: first three letters for genus followed by the three first letters of the species (GEN_SPP). *Family* Taxonomical family of the species *Genus* Taxonomical genus of the species *Specific.Epithet* Epithet of the species *Authority* Author(s) of the species name *grow_form* Growth form of the seed species: UP = understory palm CP = canopy palm ET = emergent tree CT = canopy tree UT = understory tree Shrub Liana Epiphyte *Forbs were not taken into account due to the height of our traps (>1 m from the ground) *disp_mode* Dispersal syndrome: ZOO = animal-dispersed WIND = wind-dispersed GRAV = barochory EXPL = explosive dispersal *succ_stage* Early- mid- or late-successional species according to expert opinion, herbarium specimens at Las Cruces, and literature resources. *seed_size* Size classes according to seed width: 1: <5 mm 2: 5 < 10 mm 3: 10 - 15 mm 4: >15 mm *seed_width*_mm Missing values are indicated as "NA". **File – Trap_location.csv** *Site* Two-letter identifier of the 7 restoration sites used in the study. At four of them (*) a nearby mature forest was selected as a reference forest. These acronyms are mostly based on the original landowner names: BB = Bambu EC = El Cenizo JG = Julio Gonzalez* LL = Loma Linda* MM = Melissa's Meadow* OM = Omar* SG = San Gabriel *Treatment* Restoration treatment: NR = natural regeneration AN = applied nucleation PL = plantation RF = reference forest *Trap* Number of the trap where the seeds were collected (1 to 16) *Latitude*, *Longitude*: Geographic coordinates of each trap in decimal degrees (WSG86/UTM zone 17 N) ## Code/software Excel (Microsoft Office 2016) Data processing involved several steps to prepare the dataset for analysis. Early-successional species and selected taxonomically ambiguous groups were excluded to focus on mid- and late-successional species relevant to forest recovery. Seed deposition rate (SDR) was calculated at the seed-trap level as the total number of seeds divided by trap area and sampling duration (seeds m⁻² yr⁻¹), and values were log-transformed to account for high variance in seed counts. Species were grouped by successional stage and seed size (small <5 mm; large ≥5 mm), and dispersal modes and growth forms were assigned based on previously published trait databases. Spatial coordinates were used to calculate distances among traps and account for spatial autocorrelation in subsequent analyses. Species-by-trap matrices were constructed for diversity and composition analyses, and additional datasets were merged (e.g., fruiting tree records) to classify seeds as locally produced or externally dispersed at the plot (treatment within a site) level."]} 

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3. Restoration Method Influences Spatial Patterns of Tree Seedling and Sapling Recruitment in the Second Decade of Tropical Forest Recovery

   https://doi.org/10.1111/avsc.70058  

   Schubert, Spencer C; Zahawi, Rakan A; Oviedo‐Brenes, Federico; Rosales, Juan Abel; Holl, Karen D (January 2026, Applied Vegetation Science)

   ABSTRACT AimsFine‐scale floristic heterogeneity is a hallmark of mature tropical forests. Restoring such patterns in degraded habitats should produce more resilient and biodiverse systems, yet these end‐goals are rarely compared across multiple restoration scenarios. We analyzed fine‐scale spatial tree recruitment patterns in a long‐term tropical forest restoration experiment. LocationCoto Brus County in southern Costa Rica, 1100–1430 m above sea level. MethodsWe censused seedlings and saplings in 26 experimental restoration plots (0.25 ha) after 16–18 years and six reference forests. Restoration treatments included the following: (1) plantation—four tree species planted in rows; (2) applied nucleation—six tree nuclei of varying sizes planted with the same four species; and (3) natural regeneration—no trees planted. In 2022, we censused all tree stems ≥ 20 cm and mapped each to 3 × 3 m grid cells. ResultsMean local species density of seedlings (per 6 × 6 m quadrat) was significantly greater in plantation (10.9; 95% CI = 10.0–11.9) and applied nucleation (8.4; 95% CI = 7.7–9.3) than in natural regeneration subplots (5.0; 95%CI = 4.5–5.5), as the latter commonly had quadrats with no recruits. Within‐plot Bray–Curtis dissimilarity was highest in natural regeneration, intermediate in applied nucleation, and lowest in plantations. Differences arose primarily from variation in seedling abundance, rather than from species turnover, but did not differ in sapling communities. Recruits of large‐seeded, later‐successional species were significantly less clustered and established more frequently in plot interiors of planted treatments than of natural regeneration. ConclusionsAfter nearly two decades, the extent of initially planted trees did not substantially influence the fine‐scale heterogeneity of recruit community composition beyond spatial variation in seedling density. However, both applied nucleation and plantation restoration approaches resulted in a more even spatial distribution of large‐seeded recruits, highlighting the importance of tree planting for facilitating the recovery of dispersal‐limited species. 

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4. Data from: Lower-intensity restoration interventions drive greater seedling establishment for later-successional tree species

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

   Joyce, Francis H; Zahawi, Rakan A; Holl, Karen D (January 2025, Dryad)

   Recovery of tree community composition in restored tropical forests relies on successful recruitment of later-successional species. However, the long-term effects of different restoration interventions on establishment success of arriving seeds are poorly understood. We evaluated the effects of three restoration treatments on the seed-to-seedling transition for later-successional tree species in a fragmented agricultural landscape in southern Costa Rica. Restoration plots (0.25 ha) were established in a block design nearly two decades prior and spanned a gradient of intervention intensity: natural regeneration (not planted), applied nucleation (planted tree clusters), and plantation (fully planted). We conducted seed addition experiments from 2021-2023 using eight species at seven replicate restoration sites and in four nearby remnant forests. Study region We conducted this study from June 2021 to September 2023 in southern Costa Rica near Las Cruces Biological Station. The forests in this region are at the boundary between Tropical Premontane Wet and Rain Forest zones (Holdridge et al., 1971), and the study sites range from ~1100 to 1200 m in elevation. Soils are volcanic in origin, mildly acidic (pH ~5.5), low in P, and high in organic matter. Mean annual temperature is ~21°C, and annual precipitation is between 2700 and 5000 mm, with a dry season from December to March. The landscape was largely deforested between 1960 and 1980 and is now a fragmented mosaic of remnant forest, secondary forest, cattle pastures and agricultural fields. Design of long-term restoration experiment We used seven restoration sites set up in 2004-2006 (Figure 1), a subset of the 15 sites described in Holl et al. (2020). All sites were previously used for ≥ 18 years for grazing or coffee production, and most are steeply sloped (15-35º). Minimum distance between sites is 700 m. Each restoration site had three 50 × 50 m (0.25 ha) plots: natural regeneration, applied nucleation, and plantation. Natural regeneration plots were not planted, whereas applied nucleation and plantation plots were planted with seedlings of four tree species: Erythrina poeppigiana (Walp.) Skeels, Inga edulis Mart., Terminalia amazonia (J.F. Gmel.) Exell, and Vochysia guatemalensis Donn. Sm. E. poeppigiana and I. edulis are naturalized, fast-growing N-fixers commonly used in agricultural intercropping, whereas T. amazonia and V. guatemalensis are native timber species. In applied nucleation plots trees were planted in six nuclei or patches, two each of 4 × 4, 8 × 8, and 12 × 12 m, whereas plantation plots were planted uniformly throughout; the number of trees planted in applied nucleation plots was 27% of the total in plantation plots. Four sites also have paired remnant forest (2 to >300 ha) located 5-50 m from restoration plots, which serve as a reference system for comparing the conditions and ecological processes of restoration plots. On average, percent canopy cover was lower and cover of exotic pasture grasses was much greater in natural regeneration than planted treatments (Kulikowski et al., 2023). Seed addition experiment We selected eight tree species (Table 1; Figure S1) for seed addition experiments, based on: (a) their later-successional status, categorized by expert opinion as occurring exclusively in late-successional forest or both early- and late-successional forest (Schubert et al., 2025); (b) a continuum of seed sizes; and (c) regional availability of seeds (>700) for the experiment. Study species were all animal-dispersed and ranged from 2.4 to 24.8 mm seed width. We collected seeds from at least three mother trees per species, encountered in conditions that differed by species: (1) mature fruits/nuts from the ground (Pseudolmedia mollis, Quercus benthamii, Trophis mexicana, and some Erythroxylum macrophyllum and Otoba novogranatensis), (2) seeds with pulp already removed by birds from the ground (Ocotea puberula and some O. novogranatensis), and (3) ripe fruit directly from trees (Lacistema aggregatum, Palicourea padifolia, some E. macrophyllum). We manually removed any fruit pulp from seeds and briefly submerged all seeds in water to check for insect damage. Seeds that floated were assumed to be non-viable and not used. We measured fresh mass and width for ≥50 seeds per species (Table 1; Figure S1). We thoroughly mixed conspecific seeds to avoid bias in seed source or quality among sites or habitat types (hereafter ‘treatments’). We conducted concurrent germination trials to confirm that no species completely failed to germinate in a nursery setting. Within each restoration plot and remnant forest, we established four sets (hereafter ‘stations’) of three 1-m² quadrats separated by ≥15 m. In natural regeneration, plantation, and reference forest plots, one station was located in each quarter of the plot (Figure 2a). In applied nucleation plots, stations were systematically distributed with one station at each of four positions relative to the initial planting design (Figure 2b): (1) within a large nucleus; (2) at the edge of a medium nucleus; (3) between two nuclei, and (4) far from any nucleus. Nuclei have spread considerably beyond the planted area due to crown expansion and natural recruitment; however, these positions spanned a representative range of microsite conditions. Two quadrats per station were used for seed additions to accommodate all eight species, and one non-sown control quadrat was surveyed to assess background abundance of naturally recruited seedlings of the study species (Figure 2c). Each control quadrat was located 2 m from a seed addition quadrat and on the uphill side if on a slope. We placed quadrats to avoid large tree trunks but did not remove existing vegetation or leaf litter. At each station, we sequentially added seeds of three species (P. mollis, O. novogranatensis, and O. puberula) to one quadrat (26 total seeds m⁻²) and five species (Q. benthamii, E. macrophyllum, L. aggregatum, T. mexicana, and P. padifolia) to the second quadrat (47 total seeds m⁻²) as seeds of each species became available between July 2021 and August 2022. The number of seeds added per quadrat ranged from 7 to 11 seeds per species (Table 1) because of varying seed availability. Realized densities of total added individuals were lower than the cumulative densities because of (a) temporal staggering of additions by species and (b) seed mortality. We placed seeds on top of the litter or soil to simulate how seeds would naturally be deposited from primary dispersal, slightly pressing down to minimize rolling on steeper slopes. We secured a roll of fine mesh ~5 cm high on the downhill side of each seed addition quadrat to catch seeds washed downslope by runoff. Seeds were placed in rows with 10-20 cm minimum spacing and assigned an identifier based on grid position. For the five smallest-seeded species, locations were marked with popsicle sticks to facilitate monitoring. We monitored seedling emergence, survival, and height (to nearest 0.5 cm) for each species at least four times. Census intervals were timed to: (a) to capture seedling emergence approximately 1-2 months post seed addition and every 2-4 months thereafter, and (b) measure the first-year survival percentage of emerged seedlings 12-15 months after seed addition. Because some seedlings may have emerged and died between censuses or prior to the first census, we may have underestimated emergence and overestimated seedling survival. This uncertainty was mitigated by our observations of obviously dead seeds (indicating failure to emerge) or dead seedlings (indicating emergence but subsequent mortality). For the four larger-seeded species for which ungerminated seeds could be reliably re-found, missing seeds were interpreted as pre-emergence mortality. Assuming that missing seeds were predated was reasonable because a companion study found that almost all seeds removed by vertebrates were eventually predated (Joyce et al., 2024). Variable durations of the “first year” period are typical in tropical tree seed addition experiments involving multiple species with differing phenologies (e.g. Svenning & Wright, 2005). One of the seven sites where we added seeds in 2021 was then cleared by the landowner, so in 2022 we added seeds of the remaining six species to an alternate site. The other six sites were used for the duration of the study. Accordingly, P. mollis and Q. benthamii, were tested at six sites rather than seven. We did not tag seedlings but were able to distinguish between natural recruits and seedlings that recruited from added seeds based on the location of seedlings relative to the grid and the size of seedlings compared to the experimental cohort. We sampled the non-sown control quadrat at each station at a single timepoint (July 2023) for seedlings similarly sized to our added individuals. References Holdridge, L. R., Grenke, W. C., Hatheway, W. H., Liany, T., & Tosi Jr, J. A. (1971). Forest environments in tropical life zones: A pilot study. Pergamon Press. 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 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, 56(6), e13381. https://doi.org/10.1111/btp.13381 Kulikowski, A. J., Zahawi, R. A., Werden, L. K., Zhu, K., & Holl, K. D. (2023). Restoration interventions mediate tropical tree recruitment dynamics over time. Philosophical Transactions of the Royal Society B: Biological Sciences, 378(1867), 20210077. https://doi.org/10.1098/rstb.2021.0077 Schubert, S. C., Zahawi, R. A., Oviedo-Brenes, F., Rosales, J. A., & Holl, K. D. (2025). Active restoration increases tree species richness and recruitment of large-seeded taxa after 16–18 years. Ecological Applications, 35(1), e3053. https://doi.org/10.1002/eap.3053 Svenning, J.-C., & Wright, S. J. (2005). Seed limitation in a Panamanian forest. Journal of Ecology, 93(5), 853–862. https://doi.org/10.1111/j.1365-2745.2005.01016.x # Data from: Lower-intensity restoration interventions drive greater seedling establishment for later-successional tree species Dataset DOI: [10.5061/dryad.cfxpnvxjp](10.5061/dryad.cfxpnvxjp) ## Description of the data and file structure Data from a field experiment in which seeds of eight later-successional tree species were added to restoration plots and remnant forests in southern Costa Rica to assess barriers to seedling establishment.   ### Files and variables #### File: canopy\_cover.csv **Description:** canopy cover above each seed addition quadrat, calculated from four densiometer measurements ##### Variables * plot_id: (character) Unique identifier for each plot, combining site and treatment (see below). * site: (character) two-letter code identifying each study site * treatment: (character) two-letter code for treatment. NR = natural regeneration, AN = applied nucleation, PL = plantation, RF = reference forest * station: factor (integer 1-4) identifying the set of plots (“station”) within each plot. * station_id: (character) uniquely identifying each station; combination of site, treatment, and station. * quadrat: character variable identifying the quadrat within each station * quadrat_id: (character) unique identifier for each seed addition quadrat * densi_1 to densi_4 : Four numeric variables with raw densiometer measurements (number of densiometer points not open sky, range 0-96). * mean_densi: (numeric) mean of densi_1, densi_2, densi_3, and densi_4 * canopy_cover: mean_densi measurement converted to percent canopy cover (mean_densi/96*100), rounded to 1 decimal point #### File: litter\_depth.csv **Description:** leaf litter (or thatch) depth in each seed addition quadrat ##### Variables * plot_id: (character) Unique identifier for each plot, combining site and treatment (see below). * station_id: (character) Unique identifier for each station * quadrat_id: (character) unique identifier for each seed addition quadrat * site: (character) two-letter code identifying each study site * treatment: (character) two-letter code for treatment. NR = natural regeneration, AN = applied nucleation, PL = plantation, RF = reference forest * station: factor (integer 1-4) identifying the set of plots (“station”) within each plot. * quadrat: character variable (A or B) identifying the quadrat within each station. * date: date of measurement; format is YYYY-MM-DD * pt1-pt5: litter depth in cm at each of 5 points laid out in an X-shaped pattern within each 1-m quadrat, measured using a marked pin-flag (nearest 0.5 cm). * quadrat_mean_depth: mean of 5 depth measurements in each quadrat (pt1-pt5) #### File: natural\_recruit\_frequency.csv **Description:** Summary of naturally recruiting seedlings of study species recorded in non-seeded quadrats at each station. Each row is a combination of study species and treatment. ##### Variables * treatment: (character) two-letter code for treatment. NR = natural regeneration, AN = applied nucleation, PL = plantation, RF = reference forest * species: (character) 6-letter code for species * quads_with_recruits: (integer) number of sampled non-seeded quadrats with natural recruits of the specified species * n_quads: (integer) total number of non-seeded quadrats that were sampled for each species and treatment combination * freq: relative frequency of natural recruits within sampled non-seeded quadrats. Equals quads_with_recruits divided by n_quads. #### File: seedling\_emergence.csv **Description:** summary of seedling emergence, where each row is a combination of study species and station ##### Variables * species: (character) 6-letter code for species. Corresponding study species are as follows: * PAL_PAD = *Palicourea padifolia* * TRO_MEX = *Trophis mexicana* * LAC_AGG = *Lacistema aggregatum* * ERY_MAC = *Erythroxylum macrophyllum* * OCO_PUB = *Ocotea puberula* * OTO_NOV = *Otoba novogranatensis* * QUE_BEN = *Quercus benthamii* * PSE_MOL = *Pseudolmedia mollis* * plot_id: (character) Unique identifier for each plot, combining site and treatment (see below). * site: character) two-letter code identifying each study site * treatment: (character) two-letter code for treatment. NR = natural regeneration, AN = applied nucleation, PL = plantation, RF = reference forest * station: integer (1-4) identifying the set of plots (“station”) within each plot. * station_id: (character) uniquely identifying each station; combination of site, treatment, and station. * added_seeds: (integer) number of conspecific seeds added to each quadrat * live_stems: (integer) number of recorded seedlings that emerged within the quadrat * failed: (integer) number of seeds that failed to emerge. Equal to difference between added_seeds and live_stems. * prop_emerged: proportion of added seeds that emerged. Equal to live_stems/added_seeds. #### File: seedling\_heights.csv **Description:** median seedling height for seedlings of each species surviving to one year in each station ##### Variables * species: (character) 6-letter code for species * site: (character) two-letter code identifying each study site * treatment: (character) two-letter code for treatment. NR = natural regeneration, AN = applied nucleation, PL = plantation, RF = reference forest * station: integer (1-4) identifying the set of plots (“station”) within each plot. * station_id: (character) uniquely identifying each station; combination of site, treatment, and station. * median_height_cm: (numeric) median height of conspecific seedlings that survived to the end of the 1-year experimental period. NA = not available (used when sample_size = 0; i.e., when no seedlings survived). * sample_size: (integer) number of seedlings that survived to the end of the 1-year period; n for calculation of median_height_cm. #### File: seedling\_survival.csv **Description:** proportion of seedlings surviving to one year for each combination of species and station. ##### Variables * species: (character) 6-letter code for species. * plot_id: (character) Unique identifier for each plot, combining site and treatment (see below). * site: (character) two-letter code identifying each study site * treatment: (character) two-letter code for treatment. NR = natural regeneration, AN = applied nucleation, PL = plantation, RF = reference forest * station: integer (1-4) identifying the set of plots (“station”) within each plot. * station_id: (character) uniquely identifying each station; combination of site, treatment, and station. * germ_seeds: (integer) number of added seeds that emerged * survived_seedlings: (integer) number of seedlings that survived to the end of the ~1-year experimental period. * dead_seedlings: (integer) number of emerged seedlings that died * prop_surv: proportion of emerged seedlings that survived to the end of the ~1-year experimental period, rounded to two decimal places. Equal to survived_seedlings/germ_seeds. ## Code/software Any software capable of opening csv files. ## Access information Other publicly accessible locations of the data: * NA Data was derived from the following sources: * NA 

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5. Lower‐intensity restoration interventions drive greater seedling establishment for later‐successional tree species

   https://doi.org/10.1111/1365-2664.70116  

   Joyce, Francis H; Zahawi, Rakan A; Holl, Karen D (September 2025, Journal of Applied Ecology)

   Abstract Recovery of tree community composition in restored tropical forests relies on successful recruitment of later‐successional species. However, the long‐term effects of different restoration interventions on establishment success of arriving seeds are poorly understood.We evaluated the effects of three restoration treatments on the seed‐to‐seedling transition for later‐successional tree species in a fragmented agricultural landscape in southern Costa Rica. Restoration plots (0.25 ha) were established in a block design nearly two decades prior and spanned a gradient of intervention intensity: natural regeneration (not planted), applied nucleation (planted tree clusters) and plantation (fully planted). We conducted seed addition experiments from 2021 to 2023 using eight species at seven replicate restoration sites and in four nearby remnant forests. We defined the seed‐to‐seedling transition as two stages: seedling emergence and post‐emergence survival.Seedling emergence was highest in natural regeneration (48%), intermediate in applied nucleation (37%) and lowest in plantation (25%) and remnant forests (27%), with high variability across species. First‐year survival of emerged seedlings was greater in applied nucleation than in plantation and was lower in remnant forest than in all restoration treatments. On average, seedlings grew slightly taller in natural regeneration compared to the other treatments.Despite seed mass spanning four orders of magnitude among the eight species, this trait did not explain variation in seedling emergence or survival.Synthesis and applications: Taken together, results suggest that after ~15 years, applied nucleation and natural regeneration plots may provide more favourable conditions for establishment of later‐successional trees than do plantation plots. When the seed‐to‐seedling transition is not a major barrier for the recruitment of later‐successional tree species in restoration plots, practitioners should focus on increasing seed arrival for these species. Seed addition could be a viable strategy to introduce later‐successional species that fail to colonize restoration sites, particularly in restoration sites with low intensity interventions (i.e. natural regeneration or applied nucleation). 

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