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1. Marked tree demographic variation along subtle elevation differences partially explains species' habitat associations in an Amazonian forest

   https://doi.org/10.1111/1365-2745.70132  

   Jaramillo, Paola A; Russo, Sabrina E; Duque, Alvaro; Castaño, Nicolás; Zuleta, Daniel (October 2025, Journal of Ecology)

   It is widely recognized that large‐scale topographic variation affects the distribution of tree diversity, yet the effects of topography at smaller scales are less appreciated but can be no less consequential. We evaluated how small‐scale topographic variation affects tree demography and diversity in a hyperdiverse Amazonian forest where species distributions respond strongly to elevation differences as small as 22 m. For topographically structured species distributions to arise, species should grow and survive (perform) better in the topographic habitat they are associated with, and they should outperform other species that are found, but not strongly aggregated, in that habitat. Here, we tested these demographic hypotheses using data on the growth and mortality of 79,911 trees (352 species) among three topographic habitats (valleys, slopes and ridges) in the 25‐ha Amacayacu Forest Dynamics Plot.Despite the small variation in elevation, there was significant community‐level variation in growth and mortality among topographic habitats: trees growing in valleys, where soil moisture is higher, had significantly higher growth and mortality rates than those growing on slopes and ridges. However, tree growth rates did not depend on, and mortality rates varied inconsistently with, species' habitat association. Our results partially support the resident‐advantage hypotheses for valley‐associated species, which grew best in their home habitat (valleys) than elsewhere and had lower mortality there compared to slope‐associated or generalist species (foreigners). For slope‐ and ridge‐associated species, our results did not support these hypotheses at the community level. Species‐specific analyses revealed that 73 out of the 352 species analysed at the community level supported either hypothesis. Our findings show that even small differences in elevation can lead to biologically meaningful variation in resource access that translates into significant differences in tree growth and survival. However, resource access could not fully explain the patterns of topographically driven demographic variation we observed. While certain species may still exhibit home and resident advantages in specific habitats, even when community‐level averages partially reflect this pattern, alternative hypotheses are likely driving the patterns observed at the community level. 

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2. Long-term growth, mortality and regeneration of trees in permanent vegetation plots in the Pacific Northwest, 1910 to present

   https://doi.org/10.6073/pasta/8b40e3edb538a253b24ae235b1cee8a7  

   Franklin, Jerry F; Bell, David M; Remillard, Suzanne M; Pabst, Robert J; Bluhm, Andrew; Powers, Matt (January 2025, Environmental Data Initiative)

   A network of more than 130 permanent vegetation plots provides long-term information on patterns and rates of forest succession in most of the major forest zones of the Pacific Northwest. The plot network extends from the coast to the Cascades in western Oregon and Washington and east to ponderosa pine forests in the Oregon Cascades. Most of the permanent plots were established during two intervals: from 1910 to 1948, and from 1970 to 1989. The earlier plots were established by U.S. Forest Service researchers to quantify timber growth in young stands of important commercial species and to help answer other applied forestry questions. The more recent period of plot establishment began under the Coniferous Forest Biome program of the International Biological Program during the 1970s, and continued under the Long-term Ecological Research program. A broader set of objectives motivated plot establishment since 1970, especially quantification of composition, structure, and population and ecosystem dynamics of natural forests. Plots have one of three spatial arrangements: (1) contiguous rectangles subjectively placed within an area of homogeneous forest; (2) circular plots subjectively placed within an area of homogeneous forest; and (3) circular plots systematically located on long transects to sample an entire watershed, ridge, or reserve. Rectangular study areas are mostly 1.0 ha or 0.4 ha (1.0 ac) in size (slope-corrected). Circular plots are 0.1 ha (0.247 ac), not corrected for slope. The tree stratum is the focus of work in closed-forest study areas. All trees larger than a minimum diameter (5 cm for most areas) are permanently tagged. Plots are censused every 5 or 6 years. Attributes measured or assessed at each census include tree diameter, tree vigor, and the condition of the crown and stem. The same attributes are recorded for trees (ingrowth) that have exceeded the minimum diameter since the previous census. In many plots tree locations are surveyed to provide a plot-specific x-y location. A mortality assessment is done for trees that have died since the previous census. The assessment characterizes rooting, stem, and crown condition, obvious signs of distress or disturbance, and the apparent predisposing and proximate causes of tree death. 

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3. Long-term growth, mortality and regeneration of trees in permanent vegetation plots in the Pacific Northwest, 1910 to present

   https://doi.org/10.6073/pasta/dc4be3db15934e0e5eb4820f56e5d569  

   Franklin, Jerry F; Bell, David M; Remillard, Suzanne M; Pabst, Robert J; Bluhm, Andrew; Powers, Matt (January 2025, Environmental Data Initiative)

   A network of more than 130 permanent vegetation plots provides long-term information on patterns and rates of forest succession in most of the major forest zones of the Pacific Northwest. The plot network extends from the coast to the Cascades in western Oregon and Washington and east to ponderosa pine forests in the Oregon Cascades. Most of the permanent plots were established during two intervals: from 1910 to 1948, and from 1970 to 1989. The earlier plots were established by U.S. Forest Service researchers to quantify timber growth in young stands of important commercial species and to help answer other applied forestry questions. The more recent period of plot establishment began under the Coniferous Forest Biome program of the International Biological Program during the 1970s, and continued under the Long-term Ecological Research program. A broader set of objectives motivated plot establishment since 1970, especially quantification of composition, structure, and population and ecosystem dynamics of natural forests. Plots have one of three spatial arrangements: (1) contiguous rectangles subjectively placed within an area of homogeneous forest; (2) circular plots subjectively placed within an area of homogeneous forest; and (3) circular plots systematically located on long transects to sample an entire watershed, ridge, or reserve. Rectangular study areas are mostly 1.0 ha or 0.4 ha (1.0 ac) in size (slope-corrected). Circular plots are 0.1 ha (0.247 ac), not corrected for slope. The tree stratum is the focus of work in closed-forest study areas. All trees larger than a minimum diameter (5 cm for most areas) are permanently tagged. Plots are censused every 5 or 6 years. Attributes measured or assessed at each census include tree diameter, tree vigor, and the condition of the crown and stem. The same attributes are recorded for trees (ingrowth) that have exceeded the minimum diameter since the previous census. In many plots tree locations are surveyed to provide a plot-specific x-y location. A mortality assessment is done for trees that have died since the previous census. The assessment characterizes rooting, stem, and crown condition, obvious signs of distress or disturbance, and the apparent predisposing and proximate causes of tree death. 

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4. 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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5. Nonnative tree invaders lead to declines in native tree species richness

   https://doi.org/10.1073/pnas.2424908122  

   Liu, Yunpeng; Scheiner, Samuel M; Hogan, J Aaron; Thomas, Matthew B; Soltis, Pamela S; Guralnick, Robert P; Soltis, Douglas E; Lichstein, Jeremy W (April 2025, Proceedings of the National Academy of Sciences)

   Biological invasions are profoundly altering Earth’s ecosystems, but generalities about the effects of nonnative species on the diversity and productivity of native communities have been elusive. This lack of generality may reflect the limited spatial and temporal extents of most previous studies. Using >5 million tree measurements across eastern US forests from 1995 to 2023, we quantified temporal trends in tree diversity and biomass. We then analyzed community-level changes in native tree diversity and biomass in relation to nonnative tree invasion and native species colonization. Across the entire eastern United States, native tree species richness decreased over time in plots where nonnatives occurred, whereas nonnative species richness and the biomass of both natives and nonnatives increased over time. At the community scale, native richness tended to decline following nonnative invasion, whereas native biomass and richness-independent measures of trait and phylogenetic diversity tended to remain stable. These patterns can be explained by the rarity of the displaced native species and their functional and phylogenetic similarity to native species that survived nonnative invasions. In contrast, native survivors tended to be functionally distinct from nonnative invaders, suggesting an important role for niche partitioning in community dynamics. Colonization by previously absent native species was associated with an increase in native richness (beyond the addition of native colonizers), which contrasts with declines in native richness that tended to follow nonnative invasion. These results suggest a causal role for nonnative species in the native richness decline of invaded communities. 

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