Daniel J Johnson

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

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...

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...

Protecting and enhancing forest carbon sinks is considered a natural solution for mitigating climate change. However, the increasing frequency, intensity, and duration of droughts due to climate change can threaten the stability and growth of existing forest carbon sinks. Extreme droughts weaken plant hydraulic systems, can lead to tree mortality e...

Aim: Global forests and their structural and functional features are shaped by many mechanisms that impact tree vital rates. Although many studies have tried to quantify how specific mechanisms influence vital rates, their relative importance among forests remains unclear. We aimed to assess the patterns of variation in vital rates among species an...

The longleaf pine ( Pinus palustris Mill.) and related ecosystem is an icon of the southeastern United States (US). Once covering an estimated 37 million ha from Texas to Florida to Virginia, the near-extirpation of, and subsequent restoration efforts for, the species has been well-documented over the past ca. 100 years. Although longleaf pine is o...

Measuring forest biodiversity using terrestrial surveys is expensive and can only capture common species abundance in large heterogeneous landscapes. In contrast, combining airborne imagery with computer vision can generate individual tree data at the scales of hundreds of thousands of trees. To train computer vision models, ground-based species la...

Our understanding of broad-scale forest disturbances under climatic extremes remains incomplete. Drought, as a typical extreme event, is a key driver of forest mortality but there have been no reports on continental-scale quantification of its impact on forest mortality or how it compares to other natural or anthropogenic drivers. Thus, our ability...

An important mechanism promoting species coexistence is conspecific negative density dependence (CNDD), which inhibits conspecific neighbors by accumulating host-specific enemies near adult trees. Natural enemies may be genotype-specific and regulate offspring dynamics more strongly than non-offspring, which is often neglected due to the difficulty...

Accurate field data are essential to understanding ecological systems and forecasting their responses to global change. Yet, data collection errors are common, and data analysis often lags far enough behind its collection that many errors can no longer be corrected, nor can anomalous observations be revisited. Needed is a system in which data quali...

The recent developments of new deep learning architectures create opportunities to accurately classify high-resolution unoccupied aerial system (UAS) images of natural coastal systems and mandate continuous evaluation of algorithm performance. We evaluated the performance of the U-Net and DeepLabv3 deep convolutional network architectures and two t...

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...

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‐...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

Shifting forest dynamics Forest dynamics are the processes of recruitment, growth, death, and turnover of the constituent tree species of the forest community. These processes are driven by disturbances both natural and anthropogenic. McDowell et al. review recent progress in understanding the drivers of forest dynamics and how these are interactin...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

Maintaining tree diversity Negative interaction among plant species is known as conspecific negative density dependence (CNDD). This ecological pattern is thought to maintain higher species diversity in the tropics. LaManna et al. tested this hypothesis by comparing how tree species diversity changes with the intensity of local biotic interactions...

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...

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...

http://www.sciencejournalforkids.org/articles/what-kind-of-fungus-are-you

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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....