Daijiang Li

University of Florida | UF · Department of Wildlife Ecology and Conservation

Global climate change has led to the decline of species and functional diversity in ecosystems, changing community composition and ecosystem functions. However, we still know little about how species with different resource-use strategies (different types of resource usage and plant growth of plants as indicated by the spectrum of plant economic tr...

Aim. Environmental conditions strongly affect the distribution and abundance of species via complex forces. Shifts in environmental conditions and differences in the speed and scale of these effects complicate our efforts to infer how species will respond to future environmental change. We test how 18 functional traits affect plant species response...

Despite the increasingly available phylogenetic hypotheses for multiple taxonomic groups, most of them do not include all species. In phylogenetic ecology, there is still a strong demand to have phylogenies with all species in a study included. The existing software tools to graft species to backbone megatrees, however, are mostly limited to a spec...

Resumen extendido en español

Grass species are often included during restoration to reinstate feedbacks with fire. In biodiverse pine savannas of the southeastern U.S., wiregrass (Aristida beyrichiana) is the preferred candidate for restoring low intensity fires through the understory. Less common but locally co‐dominant in dry pine savannas, pineywoods dropseed (Sporobolus ju...

Aim Raptors, a highly threatened but ecologically important group of birds, have been recognized as a good proxy for overall biodiversity in conservation planning. However, previous work on raptor diversity focused predominantly on taxonomic diversity. Here, we assess the global patterns of raptor taxonomic, phylogenetic and functional diversity an...

Aim Most studies focusing on terrestrial ecosystems have shown that non‐native species are more likely to invade phylogenetically clustered communities, that the introduction of non‐native species increases phylogenetic clustering in the recipient communities, and that the latter is more conspicuous for recipient communities at a larger spatial sca...

Premise Numerous processes influence plant distributions and co‐occurrence patterns, including ecological sorting, limiting similarity, and stochastic effects. To discriminate among these processes and determine the spatial scales at which they operate, we investigated how functional traits and phylogenetic relatedness influence the distribution of...

The underlying causes of biodiversity disparities among geographic regions have long been a fundamental theme in ecology and evolution. However, the patterns of phylogenetic diversity (PD) and phylogenetic beta diversity (PBD) of congeners that are disjunctly distributed between eastern Asia–eastern North America (EA−ENA disjuncts) and their associ...

Natural history collections (NHCs) have been indispensable to understanding longer‐term trends of the timing of seasonal events. Massive‐scale digitization of specimens promises to further enable phenological research, especially the ability to move towards a deeper understanding of drivers of change and how trait–environment interactions shape phe...

Soil microbes have a major impact on microbial function in extreme environments, such as deserts, where environmental factors such as salinity and soil water act as strong filters to community structure. In fact, environmental filtering in these extreme environments can occur over even small gradients in soil depth, which is often overlooked, but i...

Understanding patterns and drivers of species distribution and abundance, and thus biodiversity, is a core goal of ecology. Despite advances in recent decades, research into these patterns and processes is currently limited by a lack of standardized, high‐quality, empirical data that span large spatial scales and long time periods. The NEON fills t...

Aim Nitrogen (N)‐fixing plants are an important component of global plant communities, but the drivers of N‐fixing plant diversity, especially in temperate regions, remain underexplored. Here, we examined broad‐scale patterns of N‐fixing and non‐fixing plant phylogenetic diversity (PD) and species richness (SR) across a wide portion of temperate No...

Understanding the drivers of community stability in times of increasing anthropogenic pressure is an urgent issue. Biodiversity is known to promote community stability, but studies of the biodiversity–stability relationship rarely consider the full complexity of biodiversity change. Furthermore, finding generalities that hold across taxonomic group...

Abstract In recent decades, the use of satellite sensors, near‐surface cameras, and other remote methods for monitoring vegetation phenology at landscape and higher scales has become increasingly common. These technologies provide a means to determine the timing of phenophases and growing season length at different spatial resolutions; coverage tha...

Structural diversity is an emerging dimension of biodiversity that accounts for size variations in organs among individuals in a community. Previous studies show significant effects of structural diversity on forest growth, but its effects on forest mortality are not known, particularly at a large scale. To address this knowledge gap, we quantified...

It is a critical time to reflect on the National Ecological Observatory Network (NEON) science to date as well as envision what research can be done right now with NEON (and other) data and what training is needed to enable a diverse user community. NEON became fully operational in May 2019 and has pivoted from planning and construction to operatio...

Aim Urbanization is becoming one of the most important drivers of global environmental change as human population and economic development rapidly increase. However, the effects of urbanization on plant phenology are still poorly understood, especially for leaf senescence and growing season length across large spatial scales. We aimed to fill this...

Yucca in the American desert Southwest typically flowers in early spring, but a well-documented anomalous bloom event occurred during an unusually cold and wet late fall and early winter 2018–2019. We used community science photographs to generate flowering presence and absence data. We fit phenoclimatic models to determine which climate variables...

Insect phenological lability is key for determining which species will adapt under environmental change. However, little is known about when adult insect activity terminates and overall activity duration. We used community-science and museum specimen data to investigate the effects of climate and urbanisation on timing of adult insect activity for...

Wisconsin’s plant communities are responding to shifting disturbance regimes, habitat fragmentation, aerial nitrogen deposition, exotic species invasions, ungulate herbivory, and successional processes. To better understand how plant functional traits mediate species’ responses to changing environmental conditions, we collected a large set of funct...

Understanding patterns and drivers of species distributions and abundances, and thus biodiversity, is a core goal of ecology. Despite advances in recent decades, research into these patterns and processes is currently limited by a lack of standardized, high-quality, empirical data that spans large spatial scales and long time periods. The National...

Anthropogenically-driven climate warming is a hypothesized driver of animal body size reductions. Less understood are effects of other human-caused disturbances on body size, such as urbanization. We compiled 140,499 body size records of over 100 North American mammals to test how climate and human population density, a proxy for urbanization, and...

Aim A full understanding of the origin and maintenance of β-diversity patterns in a region requires understanding of: (1) the relationships of both taxonomic and phylogenetic β-diversity (TBD and PBD, respectively) and their respective turnover and nestedness components with geographical and environmental distances; (2) the relative importance of t...

Yucca in the American desert Southwest typically flowers in early spring, but a well-documented anomalous bloom event occurred during an unusually cold and wet late fall and early winter 2018–2019. We used citizen science photographs as a means to generate flowering presence and absence data. We fit phenoclimatic models to determine which climate v...

Insect phenological lability is key for determining which species will adapt under environmental change. However, little is known about when adult insect activity terminates, and overall activity duration. We used community-science and museum specimen data to investigate the effects of climate and urbanization on timing of adult insect activity for...

Understanding the determinants of species distributions is a central topic in ecology. Competition, stress tolerance and colonization, respectively represented by Grime's competitor (C), stress‐tolerator (S) and ruderal (R) schemes, are three important functions that interactively influence plant distributions. In this study, we compiled a dataset...

A wave of green leaves and multi‐colored flowers advances from low to high latitudes each spring. However, little is known about how flowering offset (i.e., ending of flowering) and duration of populations of the same species vary along environmental gradients. Understanding these patterns is critical for predicting the effects of future climate an...

Anthropogenically-driven climate warming is a hypothesized driver of animal body size reductions. Less understood are effects of other human-caused disturbances on body size, such as urbanization. We compiled 140,499 body size records of over 100 North American mammals to test how climate and urbanization, and their interactions with species traits...

Despite advances in community assembly theory, uncertainties remain regarding how ecological and evolutionary processes shape species distributions and communities. We analyzed patterns of occurrence for 139 herbaceous plant species across 257 forest stands in Wisconsin (USA) to test predictions from community assembly theory. Specifically, we appl...

The tropical niche conservatism hypothesis suggests that most groups should be most phylogenetically clustered in cold, dry environments. This idea has been well‐tested in plants and some animal groups, but not for fishes. We assess the geographic patterns of freshwater fish phylogenetic structure and investigate the relationships between these pat...

Model‐based approaches are increasingly popular in ecological studies. A good example of this trend is the use of joint species distribution models to ask questions about ecological communities. However, most current applications of model‐based methods do not include phylogenies despite the well‐known importance of phylogenetic relationships in sha...

To better understand how ecosystems are changing, a multifaceted approach to measuring biodiversity that considers species richness (SR) and evolutionary history across spatial scales is needed. Here, we compiled 162 datasets for fish, bird and plant assemblages across the globe and measured how taxonomic and phylogenetic diversity changed at diffe...

Body size decline is hypothesized to be a key response to climate warming, including warming driven by urban heat islands. However, urbanization may also generate selective gradients for body size increases in smaller endotherms via habitat fragmentation. Here we utilize a densely sampled, multi-source dataset to examine how climate and urbanizatio...

Climate strongly shapes plant diversity over large spatial scales, with relatively warm and wet (benign, productive) regions supporting greater numbers of species. Unresolved aspects of this relationship include what causes it, whether it permeates to community diversity at smaller spatial scales, whether it is accompanied by patterns in functional...

Model-based approaches are increasingly popular in ecological studies. A good example of this trend is the use of joint species distribution models to ask questions about ecological communities. However, most current applications of model-based methods do not include phylogenies despite the well-known importance of phylogenetic relationships in sha...

Premise: Citizen science platforms for sharing photographed digital vouchers, such as iNaturalist, are a promising source of phenology data, but methods and best practices for use have not been developed. Here we introduce methods using Yucca flowering phenology as a case study, because drivers of Yucca phenology are not well understood despite th...

Plant and animal phenology is shifting in response to urbanization, with most hypotheses focusing on the ‘urban heat island’ (UHI) effect as the driver. However, generalities regarding the direction and magnitude of phenological response to urbanization have not yet emerged because most studies have focused on remote-sensed vegetative phenologies o...

While climate change has already profoundly influenced biodiversity through local extinctions, range shifts, and altered interactions, its effects on the evolutionary history contained within sets of coexisting species—or phylogenetic community diversity—have yet to be documented. Phylogenetic community diversity may be a proxy for the diversity of...

Broad-scale plant flowering phenology data has predominantly come from geographically and taxonomically restricted monitoring networks. However, platforms such as iNaturalist, where citizen scientists upload photographs and curate identifications, provide a promising new source of data. Here we develop a general set of best practices for scoring iN...

1. Effects of climate change on plant community functional diversity are of interest since experiments have found functional diversity to predict ecosystem function. Functional diversity has been hypothesized to confer resilience to plant communities (as a “driver” of community change), but in unmanipulated natural communities, it might alternative...

Should we build our own phylogenetic trees based on gene sequence data, or can we simply use available synthesis phylogenies? This is a fundamental question that any study involving a phylogenetic framework must face at the beginning of the project. Building a phylogeny from gene sequence data (purpose-built phylogeny) requires more effort, experti...

Aim How do factors such as space, time, climate and other ecological drivers influence food web structure and dynamics? Collections of well‐studied food webs and replicate food webs from the same system that span biogeographical and ecological gradients now enable detailed, quantitative investigation of such questions and help integrate food web ec...

The goal of this paper is to present the Rlda package for mixed-membership clustering analysis based on the Latent Dirichlet Allocation model adapted to different types of data (i.e., Multinomial, Bernoulli, and Binomial entries). We present the corresponding statistical models and illustrate their use with several examples using the Rlda package....

The species–area relationship (SAR) is one of the most general patterns in ecology. Recently, SARs have been employed as tools for comparing the ecology and biogeography of native and exotic species across spatial scales and exploring the influence of invasive species on native biodiversity. Here, we assess published studies to determine if SARs di...

Aim Ecological communities are composed of both species and the biotic relationships (interactions or spatial associations) among them. Biotic homogenization in species composition (i.e., increased site‐to‐site similarity) is recognized as a common consequence of global change, but less is known about how the similarity of species relationships ch...

Premise of the Study Community phylogenetic methods incorporate information on evolutionary relationships into studies of organismal assemblages. We used a community phylogenetic framework to investigate relationships and biogeographic affinities and to calculate phylogenetic signal of endemism and invasiveness for the flora of the pine rocklands—a...

AimsEcological forest succession can be influenced by plant-plant interactions that exert contrasting effects on early- and late-successional species. In this study, we explored the role of indirect plant-plant interactions and the underlying microbial mechanisms in forest succession. Methods In a mesocosm experiment, we used Schima superba, a wide...

Should we build our own phylogenetic trees based on gene sequence data or can we simply use available synthesis phylogenies? This is a fundamental question that any study involving a phylogenetic framework must face at the beginning of the project. Building a phylogeny from gene sequence data (purpose-built phylogeny) requires more effort and exper...

Understorey communities can dominate forest plant diversity and strongly affect forest ecosystem structure and function. Understoreys often respond sensitively but inconsistently to drivers of ecological change, including nitrogen (N) deposition. Nitrogen deposition effects, reflected in the concept of critical loads, vary greatly not only among sp...

Premise of the study: Many ecological and evolutionary processes shape the assembly of organisms into local communities from a regional pool of species. We analyzed phylogenetic and functional diversity to understand community assembly of the ferns of Florida at two spatial scales. Methods: We built a phylogeny for 125 of the 141 species of fern...

The contemporary state of functional traits and species richness in plant communities depends on legacy effects of past disturbances. Whether temporal responses of community properties to current environmental changes are altered by such legacies is, however, unknown. We expect global environmental changes to interact with land-use legacies given d...

Aim To test whether native and non‐native species have similar diversity–area relationships (species–area relationships [ SAR s] and phylogenetic diversity–area relationships [ PDAR s]) and whether they respond similarly to environmental variables. Location United States. Methods Using lists of native and non‐native species as well as environment...

Ecological communities are comprised of both species and the biotic relationships among them. Biotic homogenization in species composition (i.e. increased site-to-site similarity) is recognized a common consequence of global change, but less is known about how species relationships change over space and time. Does homogenization of species composit...

US national parks are firmly engrained into the culture of the country. Since the first national park was established in 1872, these protected areas have been central to biodiversity conservation, education, and recreation in the United States. However, national parks face many of the same threats to biodiversity as non-protected areas, including n...

Plant functional traits allow us to mechanistically link changes in species composition to changes in ecosystem functions. Understanding how and why changes occur in functional composition of plant communities can thus help us better conserve and restore biodiversity. We aim to examine long-term effects of fire exclusion and climate change on the f...

Describes the Bayesian LDA model for mixed-membership clustering based on different types of data (i.e., Multinomial, Bernoulli, and Binomial entries).

A growing number of studies incorporate functional trait information to analyse patterns and processes of community assembly. These studies of trait–environment relationships generally ignore phylogenetic relationships among species. When functional traits and the residual variation in species distributions among communities have phylogenetic signa...

Phylogenetic and functional trait‐based analyses inform our understanding of community composition, yet methods for quantifying the overlap in information derived from functional traits and phylogenies remain underdeveloped. Does adding traits to analyses of community composition reduce the phylogenetic signal in the residual variation? If not, the...

More and more ecologists have started to resurvey communities sampled in earlier decades to determine long-term shifts in community composition and infer the likely drivers of the ecological changes observed. However, to assess the relative importance of and interactions among multiple drivers, joint analyses of resurvey data from many regions span...

1. A growing number of studies incorporate functional trait information to analyse patterns and processes of community assembly. These studies of trait-environment relationships generally ignore phylogenetic relationships among species. When functional traits and the residual variation in species distributions among communities have phylogenetic si...

Plant species co-occur within communities in response to variation in environmental conditions, limited species dispersal and biotic interactions. We used surveys and resurveys of the same sites of three temperate forest plant communities to study patterns of association between co-occurring species pairs and to infer how these mechanisms contribut...

Now it has taxonomic and functional diversity functions.

Fire suppression throughout the twentieth century greatly altered plant communities in fire-dominated systems across North America. Our ability to assess these effects over the long-term, however, is handicapped by the paucity of baseline data. Here, we used detailed baseline data from the 1950s to track changes in the over- and understory composit...

Background/Question/Methods Fire can strongly affect plant community structure and composition. Fire suppression through the 20thcentury has thus greatly shaped plant community structure and composition in fire-dominated systems across North America. The lack of baseline data limits our ability to infer the long-term effects of fire suppression o...

A common hypothesis to explain the effect of litter mixing is based on the difference in litter N content between mixed species. Although many studies have shown that litter of invasive non-native plants typically has higher N content than that of native plants in the communities they invade, there has been surprisingly little study of mixing effec...

Overall results of mixing effect on litter mass loss, N release and C release between litter mixing types, between mixing ratios, between decay time. (DOCX)

Pearson coefficients between mixing effect of litter mass loss, N, C release with the difference in initial single litter N content and C/N ratio. (DOCX)

Observed litter N release. (DOCX)

Observed litter C release. (DOCX)