About

Daniel J. Johnson is an Associate Professor in the School of Forest, Fisheries, and Geomatics Sciences at the University of Florida's Institute of Food and Agricultural Sciences. His research focuses on addressing gaps in knowledge about how forests function and respond to change, whether natural or anthropogenic. He seeks to understand the outcomes of forest dynamics to inform sustainable management practices. His work spans local to global scales and utilizes data from various sources to inform forecasting, management, and policy. Johnson employs both experimental and observational data sets to analyze spatial and temporal forest change, with research interests including forest dynamics, forest regeneration, production ecology, tree survival, and forest health.

Research topics

• Biology
• Ecology
• Geography
• Environmental science
• Environmental resource management
• Botany
• Geology
• Climatology
• Agroforestry

Selected publications

• Higher-order interactions enhance the latitudinal tree diversity gradient

  Nature · 2026-04-29

  articleOpen access

  Abstract The global decrease in species diversity from low to high latitudes is among the most robust biogeographic patterns 1,2 . There is continuing debate on the contribution of conspecific negative density dependence (CNDD) to the latitudinal diversity gradient evident for trees 3,4 . Theory suggests that CNDD based on pairwise interactions alone is not sufficient to explain the intricacies of diverse communities, because higher-order interactions (HOIs) may greatly modify these interactions 5,6 . However, there has been a lack of empirical studies investigating how HOIs intertwine with pairwise interactions and how they may contribute to the latitudinal tree diversity gradient. Here we examined both pairwise interactions and HOIs across 32 large permanent forest plots, most in the northern hemisphere. We detected evidence of HOIs in 40% of the 1,543 species–plot combinations for tree growth, and 23% of the 1,340 such combinations for tree survival, with the strength of these interactions declining with latitude. HOIs were found to benefit rare species but disadvantage common species, suggesting a potential mechanism promoting species diversity. This stabilizing effect weakened towards higher latitudes, consistent with the latitudinal tree diversity gradient. Our findings reveal an important interplay between pairwise interactions and HOIs in promoting the latitudinal tree diversity gradient and help to clarify the contribution of CNDD to this biogeographic pattern.

  PublisherDOI

• Tree diversity–soil organic carbon relationships strengthen under colder and more arid conditions

  New Phytologist · 2026-05-08

  article

  Soil organic carbon (SOC) plays an essential role in carbon sequestration and climate change mitigation in forest ecosystems. While experimental studies have shown that plant diversity usually increases SOC, it remains unclear whether this positive relationship holds in natural ecosystems across varying climatic conditions. Using a global dataset of 15 large and long-term monitored natural forest sites spanning a wide latitudinal range, we assess the relationship between tree diversity and SOC within and across sites in temperate, subtropical, and tropical regions. We found an overall positive relationship between tree taxonomic diversity and SOC. The relationships between tree taxonomic or functional diversity and SOC became stronger under colder and more arid conditions. Additionally, tree functional composition was linked to SOC only within a subset of sites in more arid climates. These findings suggest that warmer and more humid conditions increase decomposition, offsetting diversity-driven carbon inputs, while colder and more arid conditions enhance SOC through low decomposition and increased inputs through abiotic facilitation and biotic interactions in high-diversity communities. Our findings indicate that conserving plant diversity is critical for enhancing carbon sequestration and mitigating the effects of climatic conditions, particularly in cold climates and regions facing an increase in arid conditions.

  PublisherDOI

• Continental-scale mapping of forest tree density in North America using remote sensing and deep learning with uncertainty quantification

  Forest Ecosystems · 2026-04-09

  articleOpen access

  Accurate, spatially consistent estimates of tree density remain elusive at continental scales, limiting our ability to assess forest structure, carbon stocks, and biodiversity. Existing global assessments have relied on simplified statistical models and sparse, heterogeneous ground data that are insufficient to capture nonlinear ecological interactions and spatial variability. To address these limitations, we integrated more than 600,000 harmonized ground-based forest inventory plots with satellite-derived vegetation indices, climate surfaces, soil properties, and topographic covariates to develop a deep learning framework for high-resolution mapping of tree density across North America. We evaluated four modeling approaches—generalized linear models (GLMs), ridge regression (RR), random forest (RF), and a feedforward neural network (FFNN). Among all models tested, the FFNN achieved the highest predictive accuracy (RMSE = 344.8; R 2 = 39.53%), and was used to produce a wall-to-wall tree density map at 3 km resolution for the continent. We estimated that the total number of forest trees with diameter at breast height (DBH) ≥ 10 cm across North America ranges from 339 to 514 billion, substantially lower than the widely cited estimate of 603 billion trees reported by Crowther et al. (2015). When smaller stems were included (no DBH threshold), totals more than doubled, reaching 738 billion to 1.12 trillion trees. We quantified uncertainty using Monte Carlo (MC) Dropout, generating pixel-level error estimates and confidence intervals. Spatial patterns reveal high tree densities in boreal and temperate forests, intermediate densities in mixed broadleaf regions, and relatively low densities in deserts, Mediterranean systems, and tundra. Compared to the global GLM-based benchmark by Crowther et al. (2015), our deep learning framework achieves markedly higher predictive accuracy, aligns more closely with national forest inventory statistics, and provides explicit uncertainty quantification, supporting applications in carbon accounting, biodiversity modeling, and ecosystem monitoring at scales through region specific calibration and validation.

  PublisherDOI

• Memories of trees past: coexistence implications of legacy conspecific density dependence

  2025-03-14

  preprintOpen accessSenior author

  The Janzen-Connell Hypothesis posits that plant species diversity is maintained by a reduction in seedling survival near living conspecific trees relative to heterospecifics –known as negative conspecific density dependence (CDD). CDD facilitates coexistence if stronger than heterospecific density dependence (HDD). However, whether and how long CDD persists after trees die is unknown. In a three-year study across three forests, we monitored seedling survival near living and dead trees, both conspecific and heterospecific, across a seven-year chrono-sequence since tree death. CDD persisted for at least five years after tree death (‘legacy CDD’), and most species showed increasingly stronger CDD relative to HDD through time. We used our empirical findings to parametrize a theoretical community dynamics model. Our model suggests that both stabilizing niche differences and fitness differences persist after tree death. While legacy CDD can facilitate coexistence, fitness differences often overwhelmed niche differences, making competitive exclusion the most likely outcome.

  PublisherOA PDFDOI

• Aboveground Biomass and Tree Mortality Revealed Through Multi-Scale LiDAR Analysis

  Remote Sensing · 2025-02-25 · 1 citations

  articleOpen accessSenior author

  Accurately monitoring aboveground biomass (AGB) and tree mortality is crucial for understanding forest health and carbon dynamics. LiDAR (Light Detection and Ranging) has emerged as a powerful tool for capturing forest structure across different spatial scales. However, the effectiveness of LiDAR for predicting AGB and tree mortality depends on the type of instrument, platform, and the resolution of the point cloud data. We evaluated the effectiveness of three distinct LiDAR-based approaches for predicting AGB and tree mortality in a 25.6 ha North American temperate forest. Specifically, we evaluated the following: GEDI-simulated waveforms from airborne laser scanning (ALS), grid-based structural metrics derived from unmanned aerial vehicle (UAV)-borne lidar data, and individual tree detection (ITD) from ALS data. Our results demonstrate varying levels of performance in the approaches, with ITD emerging as the most accurate for AGB modeling with a median R2 value of 0.52, followed by UAV (0.38) and GEDI (0.11). Our findings underscore the strengths of the ITD approach for fine-scale analysis, while grid-based forest metrics used to analyze the GEDI and UAV LiDAR showed promise for broader-scale monitoring, if more uncertainty is acceptable. Moreover, the complementary strengths across scales of each LiDAR method may offer valuable insights for forest management and conservation efforts, particularly in monitoring forest dynamics and informing strategic interventions aimed at preserving forest health and mitigating climate change impacts.

  PublisherOA PDFDOI

• Memories of Trees Past: Coexistence Implications of Legacy Conspecific Density Dependence

  Ecology Letters · 2025-10-01

  articleOpen accessSenior author

  The Janzen-Connell Hypothesis posits that plant species diversity is maintained by a reduction in seedling survival near living conspecific trees relative to heterospecifics-known as negative conspecific density dependence (CDD). CDD facilitates coexistence if stronger than heterospecific density dependence (HDD). However, whether and how long CDD persists after trees die is unknown. In a three-year study across three forests, we monitored seedling survival near living and dead trees, both conspecific and heterospecific, across a seven-year chrono-sequence since tree death. CDD persisted for at least 5 years after tree death ('legacy CDD'), and most species showed stronger CDD relative to HDD through time. We used our empirical findings to parametrize a theoretical community dynamics model. Our model suggests that both stabilising niche differences and fitness differences persist after tree death. While legacy CDD can facilitate coexistence, fitness differences often overwhelmed niche differences, making competitive exclusion the most likely outcome.

  PublisherOA PDFDOI

• Seedling passage times in gaps and closed canopies reveal decades of understory persistence in a New England forest

  Ecosphere · 2025-05-01 · 7 citations

  articleOpen access

  Abstract The duration of tree seedling persistence in the understory varies greatly between forests and across environmental conditions within a forest ecosystem. To examine species‐level variation in understory persistence and passage to the sapling life stage, we followed 5236 seedlings in single‐tree canopy gaps and closed canopy conditions over three years and simulated seedling passage times and the number of seedlings required to produce one 1.5‐m tall sapling of five common tree species in a hemlock–hardwood forest of Massachusetts, USA. Averaged across species, it took 26 years in gaps and 31 years under closed canopies to go from a first‐year seedling to a 1.5‐m sapling. Across species, the average number of seedlings needed for one sapling was 294 in gaps and 2674 in closed canopy environments. We observed high interspecific variation in passage times and number required for one sapling. Betula congeners and Pinus strobus took less time and significantly fewer individuals than Acer rubrum and Tsuga canadensis , which are generally regarded as more tolerant of understory conditions. The largest intraspecific difference in gaps versus closed canopy environments was for Quercus rubra , where we estimated the number of seedlings required to produce one sapling in closed canopies to be 172 times higher than in gaps. Stem breakage also increased the number of seedlings needed per sapling, especially in closed canopy environments. We evaluated our estimates in the lab by aging cross‐sections obtained from seedlings in gap and closed canopy conditions. Compared to our empirical age‐to‐height relationships, most simulations tended to underpredict seedling age for a given height, suggesting that passage times may be even longer than our simulations indicated. Our study shows that trees can persist for decades in the seedling life stage, highlighting a need for better‐parameterized recruitment processes in demographic forecasting.

  PublisherOA PDFDOI

• Cyclones reduce growth and mortality differences between liana‐laden and liana‐free trees in Belize

  Journal of Ecology · 2025-07-16 · 2 citations

  articleOpen accessSenior author

  Abstract Lianas—woody vines—are often abundant and strong competitors in tropical forests, shaping forest structure and diversity by affecting tree growth and mortality. Tropical cyclones damage trees and create canopy openings that favour lianas, but the combined effects of lianas and cyclones on tree dynamics remain largely unexplored. Using long‐term forest inventory data from Belize along with estimates of cyclone wind exposure, we assessed how cyclone disturbances influence liana prevalence (i.e. the proportion of liana‐laden trees in a stand) and how cyclone–liana interactions modulate tree growth and mortality patterns. Cyclone wind exposure reduced liana prevalence in the short term (5‐ and 10‐year intervals) but increased it over a longer timeframe (20 years). Precipitation also strongly influenced liana prevalence, with drier conditions promoting tree infestation by lianas. Lianas typically suppressed tree growth and increased mortality risk. However, increasing wind exposure diminished these effects, causing growth rates and mortality risk of liana‐free and liana‐laden trees to converge. Liana‐free tree mortality risk rose more steeply, showing a trend towards higher mortality risk than liana‐laden trees under high wind exposure, potentially due to the stabilising benefits of lianas and their association with cyclone‐resistant tree species. Synthesis . Our findings reveal a time‐dependent influence of cyclones on liana prevalence and demonstrate that cyclones moderate liana effects on growth and mortality by favouring liana‐prone, cyclone‐resistant species while disproportionately impacting liana‐free trees. These insights highlight the importance of considering cyclone disturbances when predicting liana‐tree interactions and their impacts on forest dynamics and carbon storage in tropical forests.

  PublisherOA PDFDOI

• Mosaic of Size‐Dependent Mortality in Three Ecologically and Economically Important Pine Species Reveals Patterns Across Space and Time

  Global Ecology and Biogeography · 2025-10-01 · 1 citations

  articleOpen accessSenior author

  ABSTRACT Aim Global forests face increasing stresses from novel climate states, altered disturbance regimes and the spread of pests and pathogens. Understanding where and when mortality occurs across species' ranges—and identifying associated mortality agents—can improve predictions of forest shifts, inform management and enhance vegetation model carbon cycle components. Location USA. Time Period 2003–2023. Taxa Studied Pinus elliottii , Pinus palustris and Pinus taeda . Methods Using inventory data on 129,970 trees from 14,517 forest plots censused two to five times, recorded agents of mortality (competition, weather events, fire, animals, insects and pathogens), and applied Bayesian size‐dependent survival models, multinomial regressions and spatial eigenvector‐based analyses to assess spatial and temporal variation in the survival of three major US pine species. Results Species varied ontogenetically, spatially and temporally in survival. Most interspecific differences occurred in saplings and small trees (< 10 cm diameter), and near species' maximum stature. Pinus taeda showed a marked decline in survival across the natural populations over the last two decades. Spatially, survival patterns were significant for all three species; P. taeda showed consistent spatial structuring at all three spatially examined resolutions, with mortality associated primarily with weather, insects and competition. Pinus elliottii and P. palustris showed spatial structures at one resolution each. As expected, competition dominated in low‐mortality areas, consistent with background mortality from succession and gap‐phase dynamics. High mortality patches were dominated by disturbance agents such as weather events and insects. Main Conclusions Exploring range‐wide demography while jointly accounting for ontogenetic, spatial and temporal variations is essential in determining species vulnerability to environmental and anthropogenic changes. Models to predict future trends in mortality need to include mechanisms beyond climate envelopes (such as fire, storms, pests and pathogens) in order to properly capture species' whole‐range responses to global change.

  PublisherDOI

• Author response for "Memories of Trees Past: Coexistence Implications of Legacy Conspecific Density Dependence"

  2025-06-13

  peer-reviewSenior author
  PublisherDOI

Frequent coauthors

• M. Meghan Miller

  University of Concepción

  48 shared

• Kristina J. Anderson‐Teixeira

  ForestGEO

  47 shared

• Norman A. Bourg

  National Zoological Park

  40 shared

• William J. McShea

  National Zoological Park

  38 shared

• Timothy H. Dixon

  38 shared

• Roy K. Dokka

  36 shared

• Sean M. McMahon

  ForestGEO

  33 shared

• H. S. Dattaraja

  Indian Institute of Science Bangalore

  31 shared

Education

• PhD Evolution, Ecology and Behavior, Biology

  Indiana University Bloomington

  2013

• MS Environmental Science, School of Public and Environmental Affairs

  Indiana University Bloomington

  2008

• BS Forestry, Forestry

  Purdue University

  1996