Leah R. Johnson

• PhD
• Professor (Associate) at Virginia Tech

Mapping the distribution of malaria has received substantial attention because the disease is a major source of illness and mortality in humans, especially in developing countries. It also has a defined temporal and spatial distribution. The distribution of malaria is most influenced by its mosquito vector, which is sensitive to extrinsic environme...

Dynamic energy budget (DEB) theory provides a sophisticated, mechanistic framework for understanding the full life cycles of individuals within a complex environment. By relating environmental conditions, notably food availability, to individual life histories, DEB theory makes it possible, in principle, to make predictions for individuals and popu...

Extrinsic environmental factors influence the distribution and population dynamics of many organisms, including insects that are of concern for human health and agriculture. This is particularly true for vector-borne infectious diseases, like malaria, which is a major source of morbidity and mortality in humans. Understanding the mechanistic links...

The ecology of mosquito vectors and malaria parasites affect the incidence, seasonal transmission and geo-graphical range of malaria. Most malaria models to date assume constant or linear responses of mosquito and parasite life-history traits to temperature, predicting optimal transmission at 31 °C. These models are at odds with field observations...

Individual based models (IBMs) and Agent based models (ABMs) have become widely used tools to understand complex biological systems. However, general methods of parameter inference for IBMs are not available. In this paper we show that it is possible to address this problem with a traditional likelihood-based approach, using an example of an IBM de...

Invasive Aedes mosquitoes are major vectors of arboviral diseases such as dengue, Zika, and chikungunya, posing an increasing threat to global public health. Their recent geographic expansion calls for predictive models to simulate population dynamics and transmission risk. Temperature is a key driver in these models, influencing traits that affect...

Reliable predictions of ectotherm responses to climatic warming are important because many of these organisms perform important roles that can directly impact human society. Thermal performance curves (TPCs) provide useful information on the physiological constraints that limit the capacity of these temperature‐sensitive organisms to exist and grow...

Vector-borne diseases pose a persistent and increasing challenge to human, animal, and agricultural systems globally. Mathematical modeling frameworks incorporating vector trait responses are powerful tools to assess risk and predict vector-borne disease impacts. Developing these frameworks and the reliability of their predictions hinge on the avai...

The temperature dependence of population fitness ( r m ) is key to predicting ectotherm responses to climatic change. Discrete-time matrix projection models (MPMs) are used to calculate r m because they capture variation in its underlying life-history trait values and time delays inherent in those traits. However, MPM calculations can be laborious...

Climate change poses significant challenges to agriculture and food security, particularly through its effects on insect vector populations and the pathogens they transmit. Aphids are one of the biggest group of ectotherms that transmit viruses to plants; more than 200 species have been identified as pathogen vectors. These aphids are responsible f...

Aphids are highly sensitive to temperature changes and play a crucial role in transmitting plant viruses, accounting for the transmission of more than 50% of viruses that cause disease in crops. Among them, Myzus persicae is a major global pest, affecting over 400 plant species and transmitting more than 100 plant viruses, including potato virus Y...

The temperature dependence of maximal population growth rate ( r m ) is key to predicting how organisms respond and adapt to natural and anthropogenic changes in climate. For organisms with complex life histories, discrete-time matrix projection models (MPMs) can be used to calculate temperature-dependent r m because they directly capture variation...

The interactions of environmental, geographic, socio-demographic, and epidemiological factors in shaping mosquito-borne disease transmission dynamics are complex and changeable, influencing the abundance and distribution of vectors and the pathogens they transmit. In this study, 27 years of cross-sectional malaria survey data (1990–2017) were used...

1. Reliable predictions of arthropod responses to climatic warming are important because many of these species perform important roles that can directly impact human society. 2. Thermal performance curves (TPCs) provide useful information on the physiological constraints that limit the capacity of temperature-sensitive organisms (like arthropods) t...

The capacity of arthropod populations to adapt to long-term climatic warming is currently uncertain. Here we combine theory and extensive data to show that the rate of their thermal adaptation to climatic warming will be constrained in two fundamental ways. First, the rate of thermal adaptation of an arthropod population is predicted to be limited...

Most models exploring the effects of climate change on mosquito‐borne disease ignore thermal adaptation. However, if local adaptation leads to changes in mosquito thermal responses, “one size fits all” models could fail to capture current variation between populations and future adaptive responses to changes in temperature. Here, we assess phenotyp...

Background: The interactions of environmental, geographic, socio-demographic, and epidemiological factors in shaping mosquito-borne disease transmission dynamics are complex and changeable, influencing the abundance and distribution of vectors and the pathogens they transmit. In this study, 27 years of prevalence data (1990-2017) were used to exami...

In ecology, it is common for processes to be bounded based on physical constraints of the system. One common example is the positivity constraint, which applies to phenomena such as duration times, population sizes, and total stock of a system’s commodity. In this paper, we propose a novel method for parameterizing Lognormal state space models usin...

Skin microbial communities are an essential part of host health and can play a role in mitigating disease. Host and environmental factors can shape and alter these microbial communities and, therefore, we need to understand to what extent these factors influence microbial communities and how this can impact disease dynamics. Microbial communities h...

The capacity of arthropod populations to adapt to long-term climatic warming is uncertain. Here, we combine theory and extensive data on diverse arthropod taxa to show that their rate of thermal adaptation to climatic warming will be constrained in two fundamental ways. First, the rate of thermal adaptation is predicted to be limited by the rate of...

Vector‐borne diseases cause significant financial and human loss, with billions of dollars spent on control. Arthropod vectors experience a complex suite of environmental factors that affect fitness, population growth and species interactions across multiple spatial and temporal scales. Temperature and water availability are two of the most importa...

Vector-borne diseases cause significant financial and human loss, with billions of dollars spent on control. Arthropod vectors experience a complex suite of environmental factors that affect fitness, population growth, and species interactions across multiple spatial and temporal scales. Temperature and water availability are two of the most import...

Background Anopheles stephensi is a malaria-transmitting mosquito that has recently expanded from its primary range in Asia and the Middle East, to locations in Africa. This species is a competent vector of both Plasmodium falciparum and Plasmodium vivax malaria. Perhaps most alarming, the characteristics of An. stephensi, such as container breedin...

Hierarchical probability models are being used more often than non-hierarchical deterministic process models in environmental prediction and forecasting, and Bayesian approaches to fitting such models are becoming increasingly popular. In particular, models describing ecosystem dynamics with multiple states that are autoregressive at each step in t...

The degree to which arthropod populations will be able to adapt to climatic warming is uncertain. Here, we report that arthropod thermal adaptation is likely to be constrained in two fundamental ways. First, maximization of population fitness with warming is predicted to be determined predominantly by the temperature of peak performance of juvenile...

In ecology it is common for processes to be bounded based on physical constraints of the system. One common example is the positivity constraint, which applies to phenomena such as duration times, population sizes, and total stock of a system's commodity. In this paper, we propose a novel method for embedding these dynamical systems into a lognorma...

Background: Anopheles stephensi is a malaria-transmitting mosquito that has recently expanded from its primary range in Asia and the Middle East, to locations in Africa. This species is a competent vector of both P. falciparum (PF) and P. vivax (PV) malaria. Perhaps most alarming, the characteristics of An. stephensi, such as container breeding and...

Extrinsic environmental factors influence the spatiotemporal dynamics of many organisms, including insects that transmit the pathogens responsible for vector‐borne diseases (VBDs). Temperature is an especially important constraint on the fitness of a wide variety of ectothermic insects. A mechanistic understanding of how temperature impacts traits...

[This corrects the article DOI: 10.1371/journal.pntd.0005568.].

Environmental temperature is a crucial abiotic factor that influences the success of ectothermic organisms, including hosts and pathogens in disease systems. One example is the amphibian chytrid fungus, Batrachochytrium dendrobatidis (Bd), which has led to widespread amphibian population declines. Understanding its thermal ecology is essential to e...

Bayesian methods are increasingly being applied to parameterize mechanistic process models used in environmental prediction and forecasting. In particular, models describing ecosystem dynamics with multiple states that are linear and autoregressive at each step in time can be treated as statistical state space models. In this paper we examine this...

The transmission of vector-borne diseases is governed by complex factors including pathogen characteristics, vector–host interactions, and environmental conditions. Temperature is a major driver for many vector-borne diseases including Bluetongue viral (BTV) disease, a midge-borne febrile disease of ruminants, notably livestock, whose etiology rang...

In the aftermath of the 2015 pandemic of Zika virus (ZIKV), concerns over links between climate change and emerging arboviruses have become more pressing. Given the potential that much of the world might remain at risk from the virus, we used a previously established temperature‐dependent transmission model for ZIKV to project climate change impact...

Delta smelt is an endangered fish species in the San Francisco estuary that have shown an overall population decline over the past 30 years. Researchers have developed a stochastic, agent-based simulator to virtualize the system, with the goal of understanding the relative contribution of natural and anthropogenic factors suggested as playing a rol...

The temperature-dependence of many important mosquito-borne diseases has never been quantified. These relationships are critical for understanding current distributions and predicting future shifts from climate change. We used trait-based models to characterize temperature-dependent transmission of 10 vector-pathogen pairs of mosquitoes (Culex pipi...

The temperature-dependence of many important mosquito-borne diseases has never been quantified. These relationships are critical for understanding current distributions and predicting future shifts from climate change. We used trait-based models to characterize temperature-dependent transmission of 10 vector–pathogen pairs of mosquitoes (Culex pipi...

The temperature-dependence of many important mosquito-borne diseases has never been quantified. These relationships are critical for understanding current distributions and predicting future shifts from climate change. We used trait-based models to characterize temperature-dependent transmission of 10 vector–pathogen pairs of mosquitoes (Culex pipi...

Models predicting disease transmission are vital tools for long-term planning of malaria reduction efforts, particularly for mitigating impacts of climate change. We compared temperature-dependent malaria transmission models when mosquito life-history traits were estimated from a truncated portion of the lifespan (a common practice) versus traits m...

Many important endemic and emerging diseases are transmitted by vectors that are biting arthropods. The functional traits of vectors can affect pathogen transmission rates directly and also through their effect on vector population dynamics. Increasing empirical evidence shows that vector traits vary significantly across individuals, populations, a...

Transmission of malaria and other vector-borne diseases (VBDs) is greatly influenced by environmental factors, especially temperature, due to the ectothermic nature of insect and arthropod vectors. However, the response of transmission to temperature and other drivers is complex, as thermal traits of ectotherms are typically non-linear, and they in...

In the aftermath of the 2015 pandemic of Zika virus, concerns over links between climate change and emerging arboviruses have become more pressing. Given the potential that much of the world might remain at risk from the virus, we use a model of thermal bounds on Zika virus (ZIKV) transmission to project climate change impacts on transmission suita...

The temperature-dependence of many important mosquito-borne diseases has never been quantified. These relationships are critical for understanding current distributions and predicting future shifts from climate change. We used trait-based models to characterize temperature-dependent transmission of 10 vector–pathogen pairs of mosquitoes ( Culex pip...

In modern science, deterministic computer models are often used to understand complex phenomena, and a thriving statistical community has grown around effectively analysing them. This review aims to bring a spotlight to the growing prevalence of stochastic computer models --- providing a catalogue of statistical methods for practitioners, an introd...

Background: The lack of a continuous long-term in vitro culture system for Plasmodium vivax severely limits our knowledge of pathophysiology of the most widespread malaria parasite. To gain direct understanding of P. vivax human infections, we used Next Generation Sequencing data mining to unravel parasite in vivo expression profiles for P. vivax,...

A wide range of research has promised new tools for forecasting infectious disease dynamics, but little of that research is currently being applied in practice, because tools do not address key public health needs, do not produce probabilistic forecasts, have not been evaluated on external data, or do not provide sufficient forecast skill to be use...

Mosquito density plays an important role in the spread of mosquito-borne diseases such as dengue and Zika. While it remains very challenging to estimate the density of mosquitoes, modelers have tried different methods to represent it in mathematical models. The goal of this paper is to investigate the various ways mosquito density has been quantifi...

The Cort-Fitness Hypothesis has generated much interest from investigators integrating field endocrinology with evolutionary biology, ecology, and conservation. The hypothesis was developed to test the assumption that if glucocorticoid levels increase with environmental challenges and fitness decreases with environmental challenges, then there shou...

The transmission of vector-borne diseases is governed by complex factors including pathogen characteristics, vector-host interactions, and environmental conditions. Temperature is a major driver for many vector-borne diseases including Bluetongue viral (BTV) disease, a midge-borne febrile disease of ruminants, notably livestock, whose etiology rang...

Mosquito‐borne diseases cause a major burden of disease worldwide. The vital rates of these ectothermic vectors and parasites respond strongly and nonlinearly to temperature and therefore to climate change. Here, we review how trait‐based approaches can synthesise and mechanistically predict the temperature dependence of transmission across vectors...

Predicting where crop pests and diseases can occur, both now and in the future under different climate change scenarios, is a major challenge for crop management. One solution is to estimate the fundamental thermal niche of the pest/disease to indicate where establishment is possible. Here, we develop methods for estimating and displaying the funda...

The observed dynamics of infectious diseases are driven by processes across multiple scales. Here we focus on two: within-host, that is, how an infection progresses inside a single individual (for instance viral and immune dynamics), and between-host, that is, how the infection is transmitted between multiple individuals of a host population. The d...

Forecasting the impacts of climate change on Aedes-borne viruses—especially dengue, chikungunya, and Zika—is a key component of public health preparedness. We apply an empirically parameterized model of viral transmission by the vectors Aedes aegypti and Ae. albopictus, as a function of temperature, to predict cumulative monthly global transmission...

Changing year-round (12 month) population at risk due to temperature suitability for Aedes aegypti virus transmission. All values are given in millions; future projections are averaged across GCMs, broken down by year (2050, 2080) and RCP (2.6, 4.5, 6.0, 8.5), and are given as net change from current population at risk. 0+/0- denote the sign of sma...

Global health regions. We adopt the same system as the Global Burden of Disease Study in our regional breakdown. (TIF)

Changing year-round (12 month) population at risk due to temperature suitability for Aedes albopictus virus transmission. All values are given in millions; future projections are averaged across GCMs, broken down by year (2050, 2080) and RCP (2.6, 4.5, 6.0, 8.5), and are given as net change from current population at risk. 0+/0- denote the sign of...

Top 10 regional increases in populations experiencing year-round temperature suitability for transmission (12 months). Regions are ranked based on millions of people exposed for the first time to any transmission risk; parentheticals give the net change (first exposures minus populations escaping transmission risk). All values are given for the wor...

Forecasting the impacts of climate change on Aedes-borne viruses—especially dengue, chikungunya, and Zika—is a key component of public health preparedness. We apply an empirically parameterized model of viral transmission by the vectors Aedes aegypti and Ae. albopictus , as a function of temperature, to predict cumulative monthly global transmissio...

The observed dynamics of infectious diseases are driven by processes across multiple scales. First is within-host, that is how an infection progresses inside a single individual (for instance viral and immune dynamics). Second is how the infection is transmitted between multiple individuals of a host population. The dynamics of each of these may be...

The observed dynamics of infectious diseases are driven by processes across multiple scales. First is within-host, that is how an infection progresses inside a single individual (for instance viral and immune dynamics). Second is how the infection is transmitted between multiple individuals of a host population. The dynamics of each of these may be...

Vectors are responsible for the transmission of many important endemic and emerging diseases. The functional traits of these animals have important consequences for pathogen transmission, but also for fitness and population dynamics of the vectors themselves. Increasing empirical evidence suggests that vector traits vary significantly at time scale...

The Cort-Fitness hypothesis has generated much interest from investigators integrating field endocrinology with evolutionary biology, ecology, and conservation. The hypothesis was developed on the assumption that if glucocorticoid levels increase with environmental challenges and fitness decreases with environmental challenges, then there should be...

Tolerance, or the maintenance of host health or fitness at a given parasite burden, has often been studied in evolutionary and medical contexts, particularly with respect to effects on the evolution of parasite virulence and individual patient outcomes. These bodies of work have provided insight about tolerance for evolutionary phenomena (e.g., vir...

Mechanistic representations of individual life-history trajectories are powerful tools for the prediction of organismal growth, reproduction and survival under novel environmental conditions. Dynamic energy budget (DEB) theory provides compact models to describe the acquisition and allocation of energy by organisms over their full life cycle. Howev...

Epidemiological dynamics depend on the traits of hosts and parasites, but hosts and parasites are heterogeneous entities that exist in dynamic environments. Resource availability is a particularly dynamic and potent environmental driver of within-host infection dynamics (temporal patterns of growth, reproduction, parasite production and survival)....

In 2015 the US federal government sponsored a dengue forecasting competition using historical case data from Iquitos, Peru and San Juan, Puerto Rico. Competitors were evaluated on several aspects of out-of-sample forecasts including the targets of peak week, peak incidence during that week, and total season incidence across each of several seasons....

Mechanistic representations of individual life-history trajectories are powerful tools for the prediction of organismal growth, reproduction and survival under novel environmental conditions. Dynamic energy budget (DEB) theory provides compact models to describe the acquisition and allocation of energy by organisms over their full life cycle. Howev...

Knowledge of thermal traits is essential for understanding and modelling physiological responses to environmental change. Egg temperatures are poorly studied in most tubenose species. We employed a contactless infrared thermometer to measure egg and nest surface temperatures throughout the incubation period for four albatross species at Bird Island...

Animal movement patterns contribute to our understanding of variation in breeding success and survival of individuals, and the implications for population dynamics. Over time, sensor technology for measuring movement patterns has improved. Although older technologies may be rendered obsolete, the existing data are still valuable, especially if new...

The lack of a continuous in vitro culture system for Plasmodium vivax severely limits our knowledge of pathophysiology of the most widespread malaria parasite. To gain direct understanding of P. vivax human infections, we used Next Generation Sequencing data mining to unravel parasite in vivo expression profiles for P. vivax, and P. falciparum as c...

The thermal sensitivities of organisms regulate a wide range of ecological interactions, including host–parasite dynamics. The effect of temperature on disease ecology can be remarkably complex in disease systems where the hosts are ectothermic and where thermal conditions constrain pathogen reproductive rates. Amphibian chytridiomycosis, caused by...

Recent epidemics of Zika, dengue, and chikungunya have heightened the need to understand the seasonal and geographic range of transmission by Aedes aegypti and Ae. albopictus mosquitoes. We use mechanistic transmission models to derive predictions for how the probability and magnitude of transmission for Zika, chikungunya, and dengue change with me...

Supplementary Results, References, and Figures A-O. (PDF)

Supplementary Tables A-D. (PDF)