Daniel J Johnson

Daniel J Johnson
University of Florida | UF · School of Forest Fisheries and Geomatics Sciences

Ph.D.
Science

About

72
Publications
39,549
Reads
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3,077
Citations
Introduction
Additional affiliations
July 2018 - present
University of Florida
Position
  • Professor (Assistant)
August 2017 - February 2018
Utah State University
Position
  • PostDoc Position
June 2015 - August 2017
Los Alamos National Laboratory
Position
  • Fellow

Publications

Publications (72)
Article
Full-text available
Survival rates of large trees determine forest biomass dynamics. Survival rates of small trees have been linked to mechanisms that maintain biodiversity across tropical forests. How species survival rates change with size offers insight into the links between biodiversity and ecosystem function across tropical forests. We tested patterns of size-de...
Article
Longleaf pine once dominated much of the forested area of the Coastal Plain of the southeastern United States and is a focal forest type for restoration efforts. In these forests, two species dominate the canopy which may influence tree regeneration. Ultimately, the outcomes of habitat filtering, competition, and disturbance manifest in spatial pat...
Article
The growth and survival of individual trees determine the physical structure of a forest with important consequences for forest function. However, given the diversity of tree species and forest biomes, quantifying the multitude of demographic strategies within and across forests and the way that they translate into forest structure and function rem...
Article
Mechanisms such as conspecific negative density dependence (CNDD) and niche partitioning have been proposed to explain species coexistence and community diversity. However, as a potentially important axis of niche partitioning, the role of interannual climate variability in driving local community dynamics remains largely unknown. We here use a 15‐...
Article
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Determining mechanisms of plant establishment in ecological communities can be particularly difficult in disturbance-dominated ecosystems. Longleaf pine (Pinus palustris Mill.) and its associated plant community exemplify systems that evolved with disturbances, where frequent, widespread fires alter the population dynamics of longleaf pine within d...
Article
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The effects of forest fires on tree recruitment dynamics in tropical forests is important for predicting forest dynamics and ecosystem function in Southeast Asia. To our knowledge, no studies have examined the effects of fire intensity on community-level recruitment patterns in tropical forests due to the rarity of long-term observation datasets in...
Article
Allometric equations for calculation of tree aboveground biomass (AGB) form the basis for estimates of forest carbon storage and exchange with the atmosphere. While standard models exist to calculate forest biomass across the tropics, we lack a standardized tool for computing AGB across boreal and temperate regions that comprise the global extratro...
Article
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Applications of unmanned aerial vehicles (UAVs) have proliferated in the last decade due to the technological advancements on various fronts such as structure-from-motion (SfM), machine learning, and robotics. An important preliminary step with regard to forest inventory and management is individual tree detection (ITD), which is required to calcul...
Article
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Large vertebrates are rarely considered important drivers of conspecific negative density-dependent mortality (CNDD) in plants because they are generalist consumers. However, disturbances like trampling and nesting also cause plant mortality, and their impact on plant diversity depends on the spatial overlap between wildlife habitat preferences and...
Article
Negative intraspecific interactions could provide opportunities for heterospecific regeneration, thereby maintaining species coexistence in forest communities. Increasing conspecific tree and seedling neighbor densities often have negative correlations with seedling survival. If and how the strength of interactions change with seedling age remains...
Article
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ForestGEO is a network of scientists and long-term forest dynamics plots (FDPs) spanning the Earth's major forest types. ForestGEO's mission is to advance understanding of the diversity and dynamics of forests and to strengthen global capacity for forest science research. ForestGEO is unique among forest plot networks in its large-scale plot dimens...
Article
Recent years have witnessed an increased interest in managing and restoring southern pine stands using uneven-aged silvicultural strategies, that rely on natural regeneration. Group selection harvests are regarded as an effective approach to induce natural regeneration and convert pine plantations to uneven-aged stands. In a wet flatwoods site in n...
Preprint
Large vertebrates are rarely considered important drivers of conspecific negative density-dependent mortality (CNDD) in plants because they are generalist consumers. However, disturbances like trampling also cause plant mortality, and their impact on plant diversity depends on the spatial overlap between wildlife habitat preferences and plant speci...
Article
Full-text available
Conspecific negative density dependence (CNDD) could be one of the most important local-scale mechanisms shaping plant species coexistence. However, the spatial and temporal changes in the strength CNDD and the implications for the plant diversity remain unknown. We used 10 years of seedling data, in a seasonal tropical rainforest, to discover how...
Article
BACKGROUND: Forest dynamics arise from the interplay of chronic drivers and transient disturbances with the demographic processes of recruitment, growth, and mortality. The resulting trajectories of vegetation development drive the biomass and species composition of terrestrial ecosystems. Forest dynamics are changing because of anthropogenic-drive...
Article
Forest dynamics arise from the interplay of environmental drivers and disturbances with the demographic processes of recruitment, growth, and mortality, subsequently driving biomass and species composition. However, forest disturbances and subsequent recovery are shifting with global changes in climate and land use, altering these dynamics. Changes...
Article
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Vegetation plays an important role in regulating global carbon cycles and is a key component of the Earth system models (ESMs) that aim to project Earth's future climate. In the last decade, the vegetation component within ESMs has witnessed great progress from simple “big-leaf” approaches to demographically structured approaches, which have a bett...
Article
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Plant‐soil feedback (PSF) theory provides a powerful framework for understanding plant dynamics by integrating growth assays into predictions of whether soil communities stabilise plant–plant interactions. However, we lack a comprehensive view of the likelihood of feedback‐driven coexistence, partly because of a failure to analyse pairwise PSF, the...
Article
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Symbiotic nitrogen (N)‐fixing trees can provide large quantities of new N to ecosystems, but only if they are sufficiently abundant. The overall abundance and latitudinal abundance distributions of N‐fixing trees are well characterised in the Americas, but less well outside the Americas. Here, we characterised the abundance of N‐fixing trees in a n...
Article
Full-text available
Vegetation plays a key role in regulating global carbon cycles and is a key component of the Earth System Models (ESMs) aimed to project Earth's future climates. In the last decade, the vegetation component within ESMs has witnessed great progresses from simple 'big-leaf' approaches to demographically-structured approaches, which has a better repre...
Article
Full-text available
Ecological theory suggests that coexistence of many species within communities requires negative frequency-dependent feedbacks to prevent exclusion of the least fit species. For plant communities, empirical evidence of negative frequency dependence driving species coexistence and diversity patterns is rapidly accumulating, but connecting these find...
Article
Full-text available
Aim Understanding how spatial distributions of rare and common species are associated with environmental and spatial processes is essential to understanding community assembly. We addressed the following questions: (a) does the relative importance of space and topography vary from rare to common tree species? (b) Are the contributions of topography...
Article
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As cyclonic wind storms (hurricanes and typhoons) increase in frequency and intensity with climate change, it is important to understand their effects on the populations and communities of tropical trees they impact. Using tree demographic data from four large, tropical forest dynamics plots that differ in cyclonic storm frequency, we compare tree...
Article
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The fate of tropical forests under climate change is unclear as a result, in part, of the uncertainty in projected changes in precipitation and in the ability of vegetation models to capture the effects of drought‐induced mortality on aboveground biomass (AGB). We evaluated the ability of a terrestrial biosphere model with demography and hydrodynam...
Article
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Hülsmann and Hartig suggest that ecological mechanisms other than specialized natural enemies or intraspecific competition contribute to our estimates of conspecific negative density dependence (CNDD). To address their concern, we show that our results are not the result of a methodological artifact and present a null-model analysis that demonstrat...
Article
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Chisholm and Fung claim that our method of estimating conspecific negative density dependence (CNDD) in recruitment is systematically biased, and present an alternative method that shows no latitudinal pattern in CNDD. We demonstrate that their approach produces strongly biased estimates of CNDD, explaining why they do not detect a latitudinal patt...
Article
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Wood decomposition is a major component of the global carbon cycle. Decomposition rates vary across climate gradients, which is thought to reflect the effects of temperature and moisture on the metabolic kinetics of decomposers. However, decomposition rates also vary with wood traits, which may reflect the influence of stoichiometry on decomposer m...
Article
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Questions Density‐dependent processes may promote species diversity in plant communities. Here, we tested whether seedling survival was density‐dependent and varied by seedling size, species, and climatic factors. Location Tropical rainforest, Xishuangbanna, southwestern China. Methods Generalized linear mixed‐effects models were used to examine...
Article
Aim To examine the contribution of large‐diameter trees to biomass, stand structure, and species richness across forest biomes. Location Global. Time period Early 21st century. Major taxa studied Woody plants. Methods We examined the contribution of large trees to forest density, richness and biomass using a global network of 48 large (from 2 t...
Article
Forest soils store large amounts of carbon (C) and nitrogen (N), yet how predicted shifts in forest composition will impact long‐term C and N persistence remains poorly understood. A recent hypothesis predicts that soils under trees associated with arbuscular mycorrhizas (AM) store less C than soils dominated by trees associated with ectomycorrhiza...
Article
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Tree mortality rates appear to be increasing in moist tropical forests (MTFs) with significant carbon cycle consequences. Here, we review the state of knowledge regarding MTF tree mortality, create a conceptual framework with testable hypotheses regarding the drivers, mechanisms and interactions that may underlie increasing MTF mortality rates, and...
Article
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Plant-soil feedbacks are known to play a central role in species co-existence, but conceptual frameworks for predicting their magnitude and direction are lacking. We ask whether co-occurring trees that associate with different types of mycorrhizal fungi, which are hypothesized to differ in terms of nutrient use and plant-soil feedbacks, differ in s...
Article
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In tropical tree communities, processes occurring during early life stages play a critical role in shaping forest composition and diversity through differences in species' performance. Predicting the future of tropical forests depends on a solid understanding of the drivers of seedling survival. At the same time, factors determining spatial and tem...
Article
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Local tree species diversity is maintained in part by conspecific negative density dependence (CNDD). This pervasive mechanism occurs in a variety of forms and ecosystems, but research to date has been heavily skewed toward tree seedling survival in tropical forests. To evaluate CNDD more broadly, we investigated how sapling growth rates were affec...
Article
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Theory predicts that higher biodiversity in the tropics is maintained by specialized interactions among plants and their natural enemies that result in conspecific negative density dependence (CNDD). By using more than 3000 species and nearly 2.4 million trees across 24 forest plots worldwide, we show that global patterns in tree species diversity...
Article
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Determining the drivers of species rarity is fundamental for understanding and conserving biodiversity. Rarity of a given species within its community may arise due to exclusion by other ecologically similar species. Conversely, rare species may occupy habitats that are rare in the landscape or they may be ill-suited to all available habitats. The...
Article
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Quantifying the duration and drivers of seedling persistence is critical for understanding seedling dynamics and species co-existence in plant communities. In this study, we incorporated data from multiple seedling censuses to characterize patterns of seedling persistence in a tropical karst forest. Specifically, we evaluated the effects of density...
Article
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http://www.sciencejournalforkids.org/articles/what-kind-of-fungus-are-you
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A central challenge in global ecology is the identification of key functional processes in ecosystems that scale, but do not require, data for individual species across landscapes. Given that nearly all tree species form symbiotic relationships with one of two types of mycorrhizal fungi—arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) fungi—an...
Conference Paper
Background/Question/Methods: Forest species composition can influence forest ecosystem functions. Species can be classified into function guilds to simplify communities for more efficient modelling. Mycorrhizal association encapsulates a suite of functional traits that can be useful for understanding forest dynamics. Shared mycorrhizal networks and...
Article
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Global change is impacting forests worldwide, threatening biodiversity and ecosystem services including climate regulation. Understanding how forests respond is critical to forest conservation and climate protection. This review describes an international network of 59 long-term forest dynamics research sites (CTFS-ForestGEO) useful for characteriz...
Article
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Aims Seedlings are vulnerable to many kinds of fatal abiotic and biotic agents, and examining the causes of seedling dynamics can help understand mechanisms of species coexistence. To disentangle the relative importance of neighborhood densities, habitat factors and phylogenetic relatedness on focal seedling survival, we monitored the survival of 5...
Article
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Advances in forest carbon mapping have the potential to greatly reduce uncertainties in the global carbon budget and to facilitate effective emissions mitigation strategies such as REDD+ (Reducing Emissions from Deforestation and Forest Degradation). Though broad-scale mapping is based primarily on remote sensing data, the accuracy of resulting for...
Article
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1.Invasive plants, herbivores and site management history can play crucial roles in determining plant community composition. The net effects of invasive species on plant communities are well known, but we have a poor understanding of the relative contributions of direct competitive effects of invasive species and their interactions with herbivores...
Article
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Factors that control tree seedling dynamics are critical determinants of forest diversity. We examined the role of density-dependent mortality and abiotic factors in the differential establishment and survival of tree seedlings at three, large, mapped forest plots in Indiana, Virginia, and Wisconsin, USA. We tested whether seedling densities and se...
Conference Paper
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Background/Question/Methods Future forest composition is dependent on the dynamics and identity of tree seedlings during recruitment into the understory. The realized regeneration niche of tree species can be influenced by both biotic factors and abiotic factors that may change over time. The relative importance of those factors has not been well...
Article
Advances in forest carbon mapping have the potential to greatly reduce uncertainties in the global carbon budget and to facilitate effective emissions mitigation strategies such as REDD+. Though broad scale mapping is based primarily on remote sensing data, the accuracy of resulting forest carbon stock estimates depends critically on the quality of...
Article
Predicted decreases in water availability across the temperate forest biome have the potential to offset gains in carbon (C) uptake from phenology trends, rising atmospheric CO2 , and nitrogen deposition. While it is well-established that severe droughts reduce the C sink of forests by inducing tree mortality, the impacts of mild but chronic water...
Article
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One goal of postsecondary education is to assist students in developing expert-level understanding. Previous attempts to encourage expert-level understanding of phylogenetic analysis in college science classrooms have largely focused on isolated, or "one-shot," in-class activities. Using a deliberate practice instructional approach, we designed a s...
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National-scale forest inventories have endeavoured to include holistic measurements of forest health inclusive of attributes such as downed dead wood and tree regeneration that occur in the forest understory. Inventories may require year-round measurement of inventory plots with some of these measurements being affected by seasonal obstructions (e....
Conference Paper
Background/Question/Methods An emerging theme in the search for mechanisms that structure and maintain forest diversity is conspecific negative density dependence. Theory predicts that negative density dependence could be an important process in maintaining diversity and recent empirical evidence supports that prediction. Building on our previous...
Article
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Dickie, Hurst, and Bellingham question some of the methods of our recent study on conspecific density dependence in forests. Here, we reanalyze our data set with the inclusion of joint absence plots of each species. We find that our results are robust to further analyses and that patterns of abundance and richness correlate with our measure of dens...
Conference Paper
Background/Question/Methods Forests are dynamic systems and their composition can have a great impact on the sustainability of natural and anthropogenic ecosystems. Regeneration of tree seedlings determines the successional trajectory of forests. We examined the role of density dependence in shaping the tree seedling communities in three large fo...
Conference Paper
Background/Question/Methods High rates of species loss have motivated intensive research into how the numbers of species in ecosystems (species richness) influences their functioning. To date, most species richness-ecosystem function research has focused on grasslands, partly because of their global importance, but also because grassland species’...
Article
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Many tree species have seedling recruitment patterns suggesting that they are affected by non-competitive distance-dependent sources of mortality. We conducted an experiment, with landscape-level replication, to identify cases of negative distance-dependent effects and whether variation in these effects corresponded with tree recruitment patterns i...