About

Robert Holt is an Eminent Scholar and the Arthur R. Marshall Jr. Chair in Ecology at the University of Florida's Department of Biology. His research interests focus on Theoretical Ecology. Further profile details can be found at https://biology.ufl.edu/directory/robert-holt/ and https://people.clas.ufl.edu/rdholt/.

Research topics

• Computer Science
• Biology
• Ecology
• Geography
• Medicine
• Environmental science
• Cartography
• Virology
• Engineering
• Physical medicine and rehabilitation
• Environmental resource management
• Data science
• Telecommunications

Selected publications

• Modeling and inferring metacommunity dynamics with Maximum Caliber

  Proceedings of the National Academy of Sciences · 2026-01-02

  articleOpen access

  A major challenge for community ecology is using spatiotemporal data to infer parameters of dynamical models without conducting laborious experiments. We present a framework from statistical physics—Maximum Caliber—to characterize the temporal dynamics of complex ecological systems in spatially extended landscapes and infer parameters from empirical data. As an extension of Maximum Entropy modeling, Maximum Caliber aims at modeling the probability of possible trajectories of a stochastic system, rather than focusing on system states. We demonstrate the ability of the Maximum Caliber framework to capture ecological processes ranging from near to far from equilibrium, using an array of species interaction motifs including random interactions, apparent competition, intraguild predation, and nontransitive competition, along with dispersal among multiple patches. For spatiotemporal data of species occupancy in a metacommunity, the parameters of a Maximum Caliber model can be estimated through a simple logistic regression to reveal migration rates between patches, interactions between species, and local environmental suitabilities. We test the accuracy of the method over a range of system sizes and time periods and find that these parameters can be estimated without bias. We introduce “entropy production” as a measure of irreversibility in system dynamics, and use “pseudo- R 2 ” to characterize predictability of future states. We show that our model can predict the dynamics of metacommunities that are far from equilibrium. The capacity to estimate basic parameters of dynamical metacommunity models from spatiotemporal data represents an important breakthrough for the study of metacommunities with application to practical problems in conservation and restoration ecology.

  PublisherOA PDFDOI

• Slow and fast dispersers competing in heterogeneous landscapes: a comparative study of modeling perspectives

  Journal of Theoretical Biology · 2026-03-22

  article
  PublisherDOI

• Foliar pathogen epidemic slows decomposition of invasive plant litter

  Ecology · 2026-04-01

  articleOpen access

  Decomposition of plant litter, facilitated primarily by microbial decomposers, plays a critical role in biogeochemical cycling and ecosystem function. The rate of litter decomposition can determine its environmental impact, where accelerated decomposition alters the timing and rate of nutrient release and may promote nutrient leaching, whereas slowed decomposition can result in litter accumulation, which impacts seedling recruitment, fire regimes, perennation of microbial communities, and slows nutrient release. Mutualistic endophytes are known to slow litter decomposition, but less is known about the impact that plant pathogens, present in diseased litter, have on decomposition rates. We compared litter decomposition of the invasive annual grass Microstegium vimineum with Bipolaris leaf spot symptoms, a fungal disease, to litter without symptoms of the disease in a year-long common garden experiment. We found leaf tissue with disease symptoms decomposed later in the year compared to litter without symptoms. By summer, 54% of leaf tissue from healthy sites remained compared to 80% of leaf material from diseased litter. Fungal infection did not impact the lignin or C:N content of the litter. There were significant differences in fungal community composition between infected and healthy litter at the start of the experiment that persisted until the end of summer. Disease epidemics prior to senescence contributed to the persistence of infected tissue, which could slow the return of nutrients to the environmental pool and promote the survival and dispersal of pathogen inoculum the following season.

  PublisherDOI

• Modeling and Inferring Metacommunity Dynamics with Maximum Caliber

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-06-26

  preprintOpen access

  Abstract A major challenge for community ecology is using spatio-temporal data to infer parameters of dynamical models without conducting laborious experiments. We present a novel framework from statistical physics – Maximum Caliber – to characterize the temporal dynamics of complex ecological systems in spatially extended landscapes and infer parameters from empirical data. As an extension of Maximum Entropy modeling, Maximum Caliber aims at modeling the probability of possible trajectories of a stochastic system, rather than focusing on system states. We demonstrate the ability of the Maximum Caliber framework to capture ecological processes ranging from near-to far from-equilibrium, using an array of species interaction motifs including random interactions, apparent competition, intraguild predation, and non-transitive competition, along with dispersal among multiple patches. For spatio-temporal data of species occupancy in a metacommunity, the parameters of a Maximum Caliber model can be estimated through a simple logistic regression to reveal migration rates between patches, interactions between species, and local environmental suitabilities. We test the accuracy of the method over a range of system sizes and time periods, and find that these parameters can be estimated without bias. We introduce “entropy production” as a measure of irreversibility in system dynamics, and use “pseudo- R 2 ” to characterize predictability of future states. We show that our model can predict the dynamics of metacommunities that are far from equilibrium. The capacity to estimate basic parameters of dynamical metacommunity models from spatio-temporal data represents an important breakthrough for the study of metacommunities with application to practical problems in conservation and restoration ecology.

  PublisherOA PDFDOI

• Slow and Fast Dispersers Competing in Heterogeneous Landscapes: A Comparative Study of Modeling Perspectives

  SSRN Electronic Journal · 2025-01-01

  preprintOpen access
  PublisherDOI

• Dispersal and Competition in Heterogeneous Landscapes: A Comparative Study of Modeling Perspectives

  SSRN Electronic Journal · 2025-01-01

  preprintOpen access
  PublisherDOI

• Fast‐growing annual plants drive disease spillover in multi‐host communities

  Journal of Ecology · 2025-02-10

  articleOpen accessSenior author

  Abstract Emerging infectious plant diseases threaten natural, agricultural and urban systems. Predicting pathogen spillover from one host species to another can reduce disease impacts, but traditional compartment models poorly explain plant disease because plants often experience localized rather than systemic disease. Thus, the amount of infection should be tracked within each host individual, rather than characterizing a host as infected or uninfected. Additionally, annual plants can grow and complete their life cycle on timescales comparable to disease progression, thereby creating potential for feedbacks between tissue growth and pathogen spread that could be important to disease spillover. We hypothesized that, for two plant species that differ in individual‐level growth rates and share a pathogen, the faster‐growing host supports higher pathogen levels that spill onto, and negatively affect, the slower‐growing host. This prediction follows classical apparent competition theory in which prey species with high intrinsic growth rates sustain greater predator abundances, which then suppress other, slower‐growing, prey in the community. We explored whether this theory applies to plants sharing pathogens by developing an intra‐annual host–pathogen model tracking size structure of, and degree of infection in, plant hosts. We asked how growth rates of annual plant species alter spillover from a reservoir host to focal host species, and disease amplification or dilution in annual plant communities. We found that faster‐growing host individuals supported the greatest pathogen loads compared with slower‐growing host individuals, yet they experienced smaller pathogen‐driven reductions in end‐of‐season biomass. Consistent with apparent competition predictions, pathogen spillover from reservoir to focal host species caused greatest declines in end‐of‐season biomass in focal individuals when the reservoir host was fast‐growing and focal host was slow‐growing. In communities with both fast and slow‐growing species, slower‐growing hosts generally diluted disease, while faster hosts amplified it. Synthesis . The model predicts that faster‐growing hosts are likely to be high impact reservoirs for spillover and could amplify disease in multi‐host communities. Slower‐growing hosts are likely to bear the greater impact of pathogen spillover via reduced end‐of‐season biomass. Thus, plant growth rates could be an important factor in driving outcomes of infectious disease spillover in multi‐host annual plant communities.

  PublisherOA PDFDOI

• Ecological Services of Bird Communities in Atlantic Forest Follow the Pareto 80-20 Rule

  SSRN Electronic Journal · 2025-01-01

  preprintOpen access
  PublisherDOI

• Landscape composition and configuration drive bird richness, abundance, and functional diversity in Neotropical forest fragments

  Biodiversity and Conservation · 2025-10-11 · 2 citations

  article
  PublisherDOI

• An invasive prey alters local and landscape contributions of sources and sinks for an endangered predator

  Ecology · 2025-11-01

  articleOpen access

  Source-sink dynamics are a cornerstone of theory for spatially structured populations. Despite long-standing interest, understanding temporal variation in source-sink dynamics in wild populations remains rare. Biological invasions have the potential to alter source-sink dynamics for native species, which may change over time as invasions proceed. We used 28 years of data on reproduction, movement, and survival to estimate annual source-sink dynamics across the entire range of the endangered Everglade snail kite (Rostrhamus sociabilis plumbeus) during the invasion of a novel prey species, the island apple snail (Pomacea maculata). Snail kite populations underwent striking changes in source-sink dynamics with time since invasion, and no population was consistently a source or sink over time. Some initial benefits of increased prey availability on snail kite demography were diminished in the long term. Populations invaded by P. maculata impacted uninvaded populations via changes in snail kite retention (i.e., lack of movement) and emigration across the metapopulation. Our findings illustrate how effects of biological invasions can change over time and may take decades to fully emerge, and they emphasize how an invasive species can have distant impacts on uninvaded populations via fluctuations in native species' local retention and emigration. In addition, our results demonstrate how fluctuating emigration and retention alter long-term interpretations of source-sink dynamics through variation in local versus landscape contributions of populations to the metapopulation, highlighting that the status of "source" or "sink" can be highly variable through time.

  PublisherDOI

Recent grants

• Collaborative Research: Coevolution of Hosts and Parasitoids Within a Geographic Mosaic

  NSF · $90k · 2005–2010

• Collaborative Research: SG: Clonality and the scope for adaptation in heterogeneous environments

  NSF · $38k · 2019–2024

Frequent coauthors

• Michael Barfield

  University of Florida

  74 shared

• Ricardo M. Holdø

  University of Georgia

  25 shared

• Gary A. Polis

  24 shared

• Richard S. Ostfeld

  Cary Institute of Ecosystem Studies

  23 shared

• Michael Hochberg

  Institut de Recherche pour le Développement

  22 shared

• William M. Cook

  20 shared

• Bryan L. Foster

  University of Kansas

  20 shared

• Andrea H. Lloyd

  De la Préhistoire à l'Actuel : Culture, Environnement et Anthropologie

  16 shared

Awards & honors

• Eminent Scholar & Arthur R. Marshall Jr. Chair in Ecology