Robert D. Holt's research while affiliated with University of Florida and other places

Publications (340)

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All individuals transition through various life stages over the course of their development and nearly all organisms must contend with infectious disease at some point in their lives. Yet the intersection of these two universal features of life—stage structure and infectious disease—and their joint effects on population dynamics are poorly understo...
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Invasive plants, which cause substantial economic and ecological impacts, acquire both pathogens and beneficial microbes in their introduced ranges. Communities of fungal endophytes are known to mediate impacts of pathogens on plant fitness, but few studies have examined the temporal dynamics of fungal communities on invasive plants. The annual gra...
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Genetic connectivity lies at the heart of evolutionary theory, and landscape genetics has rapidly advanced to understand how gene flow can be impacted by the environment. Isolation by landscape resistance, often inferred through the use of circuit theory, is increasingly identified as being critical for predicting genetic connectivity across comple...
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Community structure depends jointly on species' responses to, and effects on, environmental factors. Many such factors, including detritus, are studied in ecosystem ecology. Detritus in terrestrial ecosystems is dominated by plant litter (nonliving organic material), which, in addition to its role in material cycling, can act as a niche factor modu...
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Environmental fluctuations are pervasive in nature, but the influence of non-directional temporal variation on range limits has received scant attention. We synthesize insights from the literature and use simple models to make conceptual points about the potentially wide range of ecological and evolutionary effects of temporal variation on range li...
Preprint
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Invasive species impact ecosystems through their large abundances and strong per capita effects. Enemies can regulate abundances and per capita effects, but are notably absent for many new invaders. However, invaders acquire enemies over time and as they spread; processes hypothesized to mitigate negative invader impacts by reducing abundance or pe...
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Predator-prey interactions are ubiquitous and powerful forces that structure ecological communities.1, 2, 3 Habitat complexity has been shown to be particularly important in regulating the strength of predator-prey interactions.4, 5, 6 While it is well established that changes in habitat structure can alter the efficacy of predatory and anti-predat...
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Adaptive habitat construction is a process by which individuals alter their environment so as to increase their (inclusive) fitness. Such alterations are a subset of the myriad ways that individuals condition their environment. We present an individual‐based model of habitat construction to explore what factors might favor selection when the benefi...
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Abstract Plant litter can alter ecosystems and promote plant invasions by altering resource availability, depositing phytotoxins, and transmitting microorganisms to living plants. Transmission of microorganisms from invasive plant litter to live plants may gain importance as invasive plants, which often escape pathogens upon introduction to a new r...
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Understanding Batesian mimicry is a classic problem in evolutionary biology. In Batesian mimicry, a defended species (the model) is mimicked by an undefended species (the mimic). Prior theories have emphasized the role of predator behavior and learning as well as evolution in model-mimic complexes but have not examined the role of population dynami...
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Trait adaptation to a heterogeneous environment can occur through six modes: genetic differentiation of those traits, a jack-of-all-trades phenotypic uniformity, diversified bet-hedging, phenotypic plasticity, habitat choice, and habitat construction. A key question is what circumstances favor one mode over another, and how they might interact if a...
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Significance Understanding the persistence of populations in fragmented landscapes is critical for predicting the consequences of habitat destruction, yet analytical tools are largely lacking. Metapopulation capacity provides one such tool, because it summarizes the influences of habitat area and distribution on population persistence in a single m...
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Warning signals are a striking example of natural selection present in almost every ecological community – from Nordic meadows to tropical rainforests, defended prey species and their mimics ward off potential predators before they attack. Yet despite the wide distribution of warning signals, they are relatively scarce as a proportion of the total...
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Emigration propensity (i.e., the tendency to leave undisturbed patches) is a key life‐history trait of organisms in metapopulations with local extinctions and colonizations. Metapopulation models of dispersal evolution typically assume that patch disturbance kills all individuals within the patch, thus causing local extinction. However, individuals...
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Aim: The positive relationship between species richness and area-the species-area relationship (SAR)-is a key principle in ecology. Previous studies show large variation in the SAR across taxa collectively indicating the necessity of a taxon-focused approach to accurately evaluate biodiversity scaling patterns. Ants are ideal for this given their g...
Preprint
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Plant litter can alter ecosystems and promote plant invasions by changing resource acquisition, depositing toxins, and transmitting microorganisms to living plants. Transmission of microorganisms from invasive litter to live plants may gain importance as invasive plants accumulate pathogens over time since introduction. It is unclear, however, if i...
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Habitat construction and phenotypic plasticity are alternative responses to variable environments. We explored evolution along an environmental gradient of habitat construction alone and in combination with phenotypic plasticity using individual‐based simulations that manipulated the fitness benefit of construction and whether construction maintain...
Chapter
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The species–area relationship (SAR) describes a range of related phenomena that are fundamental to the study of biogeography, macroecology and community ecology. While the subject of ongoing debate for a century, surprisingly, no previous book has focused specifically on the SAR. This volume addresses this shortfall by providing a synthesis of the...
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Evolutionary rescue occurs when genetic change allows a population to persist in response to an environmental change that would otherwise have led to extinction. Most studies of evolutionary rescue assume that species have either fully clonal or fully sexual reproduction; however, many species have partially clonal reproductive strategies in which...
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1. Threshold non‐linearities in the relationship between island area and species richness can result in dramatic declines in richness with a seemingly small decline in area near the threshold. What is not known, is whether threshold declines in richness are also accompanied by non‐linear changes in functional trait space and non‐random shifts of tr...
Chapter
This book contains 23 chapters divided into seven parts. Part I reviews the key hypotheses in invasion ecology that invoke biotic interactions to explain aspects of plant invasion dynamics; and reviews models, theories and hypotheses on how invasion performance and impact of introduced species in recipient ecosystems can be conjectured according to...
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Successful public health regimes for COVID-19 push below unity long-term regional R t -the average number of secondary cases caused by an infectious individual. We use a susceptible-infectious-recovered (SIR) model for two coupled populations to make the conceptual point that asynchronous, variable local control, together with movement between popu...
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Hyperparasitism denotes the natural phenomenon where a parasite infecting a host is in turn infected by its own parasite. Hyperparasites can shape the dynamics of host-parasite interactions and often have a deleterious impact on pathogens, an important class of parasites, causing a reduction in their virulence and transmission rate. Hyperparasitism...
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Non-native invasive plants can establish in natural areas, where they can be ecologically damaging and costly to manage. Like cultivated plants, invasive plants can experience a relatively disease-free period upon introduction and accumulate pathogens over time. Diseases of invasive plant populations are infrequently studied compared to diseases of...
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Substantial environmental change can force a population onto a path towards extinction, but under some conditions, adaptation by natural selection can rescue the population and allow it to persist. This process, known as evolutionary rescue, is believed to be less likely to occur with greater magnitudes of random environmental fluctuations because...
Preprint
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Successful public health regimes for COVID-19 push below unity long-term global R t -- the average number of secondary cases caused by an infectious individual. Most assessments use local information. Populations differ in R t , amongst themselves and over time. We use a SIR model for two populations to make the conceptual point that even if each l...
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Aim We evaluated different facets of beta diversity (taxonomic, phylogenetic and functional), and its components (spatial turnover and nestedness), of a stream macroalgal metacommunity, as well as the effect of local environmental variables, types of biome and spatial factors on these facets and components. Location Ten natural areas of southern B...
Preprint
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Latin America is experiencing severe impacts of the SARS-CoV-2 pandemic, but poverty and weak public health institutions hamper gathering the kind of refined data needed to inform classical SEIR models of epidemics. We present an alternative approach that draws on advances in statistical ecology and conservation biology to enhance the value of spar...
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The world is changing at a rapid rate, threatening extinction for a large part of the world's biota. One potential response to those altered conditions is to evolve so as to be able to persist in place. Such evolution includes not just traits themselves, but also the phenotypic plasticity of those traits. We used individual‐based simulations to exp...
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Dr. Luis Escobar asked me to provide a joint review of the submissions by Stephens et al. (2019, this issue) and Peterson et al. (2019, this issue). I pulled thoughts together, but by the time I sent them along, he had received other reviews and made an editorial decision. He felt my perspective might nevertheless warrant publishing as a commentary...
Chapter
This book contains 23 chapters divided into seven parts. Part I reviews the key hypotheses in invasion ecology that invoke biotic interactions to explain aspects of plant invasion dynamics; and reviews models, theories and hypotheses on how invasion performance and impact of introduced species in recipient ecosystems can be conjectured according to...
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Vulnerability to habitat fragmentation Habitat fragmentation caused by human activities has consequences for the distribution and movement of organisms. Betts et al. present a global analysis of how exposure to habitat fragmentation affects the composition of ecological communities (see the Perspective by Hargreaves). In a dataset consisting of 448...
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Contemporary and historical factors influence assemblage structure. The environmental and spatial influences acting on fish organization of rain forest coastal streams in the Atlantic rain forest of Brazil were examined. Fish (and functional traits such as morphology, diet, velocity preference, body size), environmental variables (pH, water conduct...
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Conservation biology was founded on the idea that efforts to save nature depend on a scientific understanding of how it works. It sought to apply ecological principles to conservation problems. We investigated whether the relationship between these fields has changed over time through machine reading the full texts of 32,000 research articles publi...
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Environmental factors control spatial distributions and local abundances in distinct – but overlapping – ways. Osorio‐Olivera et al. examine when environments near the geometric center of a species' ecological niche – which they assume to be optimal for growth when rare – also harbor the greatest number of individuals on average at equilibrium, and...
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1.The role of biotic interactions in shaping the distribution and abundance of species should be particularly pronounced in symbionts. Indeed, symbionts have a dual niche composed of traits of their individual hosts and the abiotic environment external to the host, and often combine active dispersal at finer scales with host‐mediated dispersal at b...
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Evidential statistics is an important advance in model and theory testing, and scientific reasoning in general, combining and extending key insights from other philosophies of statistics. A key desiderata in evidential statistics is the rigorous and objective comparison of alternative models against data. Scientific theories help to define the rang...
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Exotic species are often predicted to successfully invade when their functional traits differ from species in recipient communities. Many studies have related trait differences among natives and invaders to competitive outcomes. Few studies, however, have tested whether functionally similar invaders have similar competitive impacts on natives. We i...
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In nature, rates of dispersal vary greatly over time, yet most theoretical explorations of ecological and evolutionary dynamics to date have assumed constant movement rates. Here we examine how a particular pattern of temporal variation-periodic pulses of immigration-influences adaptation to a harsh environment, in which a species experiences condi...
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A large array of species distribution model (SDM) approaches have been developed for explaining and predicting the occurrences of individual species or species assemblages. Given the wealth of existing models, it is unclear which models perform best for interpolation or extrapolation of existing data sets, particularly when one is concerned with sp...
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How a disease is transmitted affects our ability to determine R0, the average number of new cases caused by an infectious host at the onset of an epidemic. R0 becomes progressively more difficult to compute as transmission varies from directly transmitted diseases to diseases that are vector-borne to environmentally transmitted diseases. Pathogens...
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Significance Biologists have long sought to explain how tropical forests can support as many as 1,000 tree species at a single site. Such high diversity presents a paradox in that two well-documented mechanisms, competition and drift, both erode diversity over time. Much imagination has gone into the quest to find a countervailing force of sufficie...
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This paper introduces a novel partial differential equation immuno-eco-epidemiological model of competition in which one species is affected by a disease while another can compete with it directly and by lowering the first species' immune response to the infection, a mode of competition termed stress-induced competition. When the disease is chronic...
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Populations subject to substantial environmental change that decreases absolute fitness (expected number of offspring per individual) to less than one must adapt to persist. The probability of adaptive evolutionary rescue may be influenced by factors intrinsic to the organism itself, or by features specific to the individual population and its envi...
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Natural enemies, that is, species that inflict harm on others to feed on them, are fundamental drivers of biodiversity dynamics and represent a substantial portion of it. Along the life history of the Earth, natural enemies have been involved in probably some of the most productive mechanisms of biodiversity genesis; that is, adaptive radiation med...
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Aim: The species–area (SAR) and species–time relationships (STR) are of vital importance in community ecology. Previous studies suggest that a unified, general species–time–area relationship (STAR) may hold, with non-independent scaling of richness across space and time. Most STAR studies to date have considered species accumulation curves in relat...
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Most species have one or more natural enemies, e.g., predators, parasites, pathogens, and herbivores, among others. These species in turn typically attack multiple victim species. This leads to the possibility of indirect interactions among those victims, both positive and negative. The term apparent competition commonly denotes negative indirect i...
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We used an individual-based simulation model to examine the role of phenotypic plasticity on persistence and adaptation to two patterns of environmental variation, a single, abrupt step change and continual, linear change. Our model tested the assumptions and predictions of the theory of genetic assimilation, explored the evolutionary dynamics of t...
Chapter
In this chapter, we analyze environmentally growing opportunistic diseases, which are a growing threat to human health, food production, and wildlife. The traditional treatment methods for opportunist diseases often fail because environmentally growing opportunist pathogens can utilize outside-host environmental resources for growth and can reside...
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Evolutionary lag-the difference between mean and optimal phenotype in the current environment-is of keen interest in light of rapid environmental change. Many ecologically important organisms have life histories that include stage structure and both sexual and clonal reproduction, yet how stage structure and clonality interplay to govern a populati...
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Herbivory has long been recognized as a significant driver of plant population dynamics, yet its effects along environmental gradients are unclear. Understanding how weather modulates plant–insect interactions can be particularly important for predicting the consequences of exotic insect invasions, and an explicit consideration of weather may help...
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FULL TEXT FREELY AVAILABLE AT http://escholarship.org/uc/item/8r20x7qz There is a great deal of interest in the effects of biotic interactions on geographic distributions. Nature contains many different types of biotic interactions (notably mutualism, commensalism, predation, amensalism, and competition), and it is difficult to compare the effects...
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Ilkka Hanski is most widely known for his seminal contributions to metapopulation ecology, both theoretical and empirical. But he also made many important and wide-ranging contributions to other arenas of ecological inquiry, including in particular predator-prey, host-parasitoid, and host-pathogen interactions. This paper provides an overview of hi...
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There is no consensus on when biotic interactions impact the range limits of species. Starting from MacArthur's use of invasibility to understand how biotic interactions influence coexistence, here we examine how biotic interactions shape species distributions. Range limits emerge from how birth, death, and movement rates vary with the environment....
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It is widely recognized that ecological dynamics influence evolutionary dynamics, and conversely that evolutionary changes alter ecological processes. Because fragmentation impacts all biological levels (from individuals to ecosystems) through isolation and reduced habitat size, it strongly affects the links among evolutionary and ecological proces...
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This paper introduces a time-since-recovery structured, multi-strain, multi-population model of avian influenza. Influenza A viruses infect many species of wild and domestic birds and are classified into two groups based on their ability to cause disease: low pathogenic avian influenza (LPAI) and high pathogenic avian influenza (HPAI). Prior infect...