John Drake

John Drake
University of Georgia | UGA · Odum School of Ecology

PhD

About

315
Publications
49,415
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15,866
Citations

Publications

Publications (315)
Article
Timely forecasts of the emergence, re-emergence and elimination of human infectious diseases allow for proactive, rather than reactive, decisions that save lives. Recent theory suggests that a generic feature of dynamical systems approaching a tipping point—early warning signals (EWS) due to critical slowing down (CSD)—can anticipate disease emerge...
Article
El orden Carnivora incluye más de 300 especies que varían en tamaño en muchos órdenes de magnitud y habitan en todos los biomas principales, desde las selvas tropicales hasta los mares polares. La gran diversidad de parásitos carnívoros representa una fuente de posibles enfermedades emergentes en humanos. El riesgo zoonótico de este grupo puede deb...
Article
Full-text available
Deforestation alters wildlife communities and modifies human–wildlife interactions, often increasing zoonotic spillover potential. When deforested land reverts to forest, species composition differences between primary and regenerating (secondary) forest could alter spillover risk trajectory. We develop a mathematical model of land-use change, wher...
Article
Many livestock diseases rely on wildlife for the transmission or maintenance of the pathogen, and the wildlife-livestock interface represents a potential site of disease emergence for novel pathogens in livestock. Predicting which pathogen species are most likely to emerge in the future is an important challenge for infectious disease surveillance...
Article
Full-text available
Abstract Urban environments are heterogeneous landscapes of social and environmental features, with important consequences for human–nature entanglements, such as that of mosquito‐borne disease. Investigations into this intra‐urban heterogeneity in mosquito dynamics find conflicting results, likely due to the complex socio‐ecological interactions a...
Article
Early warning indicators based on critical slowing down have been suggested as a model-independent and low-cost tool to anticipate the (re)emergence of infectious diseases. We studied whether such indicators could reliably have anticipated the second COVID-19 wave in European countries. Contrary to theoretical predictions, we found that characteris...
Article
Full-text available
Ecological theory suggests that predators can either keep prey populations healthy by reducing parasite burdens or alternatively, increase parasitism in prey. To quantify the overall magnitude and direction of the effect of predation on parasitism in prey observed in practice, we conducted a meta-analysis of 47 empirical studies. We also examined h...
Article
Short-term forecasts of the dynamics of coronavirus disease 2019 (COVID-19) in the period up to its decline following mass vaccination was a task that received much attention but proved difficult to do with high accuracy. However, the availability of standardized forecasts and versioned datasets from this period allows for continued work in this ar...
Article
Zoonotic disease outbreaks are an important threat to human health and numerous drivers have been recognized as contributing to their increasing frequency. Identifying and quantifying relationships between drivers of zoonotic disease outbreaks and outbreak severity is critical to developing targeted zoonotic disease surveillance and outbreak preven...
Article
Full-text available
Helminths are parasites that cause disease at considerable cost to public health and present a risk for emergence as novel human infections. Although recent research has elucidated characteristics conferring a propensity to emergence in other parasite groups (e.g. viruses), the understanding of factors associated with zoonotic potential in helminth...
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Full-text available
Background Globally, tuberculosis disease (TB) is more common among males than females. Recent research proposes that differences in social mixing by sex could alter infection patterns in TB. We examine evidence for two mechanisms by which social-mixing could increase men’s contact rates with TB cases. First, men could be positioned in social netwo...
Preprint
Full-text available
Urban environments are heterogeneous landscapes of social and environmental features, with important consequences for human-nature entanglements, such as that of mosquito-borne disease. Investigations into this intra-urban heterogeneity in mosquito dynamics find conflicting results, likely due to the complex socio-ecological interactions and the im...
Preprint
Full-text available
Short-term forecasts of the dynamics of COVID-19 in the period up to its decline following mass vaccination was a task that received much attention but proved difficult to do with high accuracy. A major obstacle has been capturing variations in the underlying kinetics of transmission resulting from changes in public policy, individual behaviors, an...
Article
Full-text available
The order Carnivora includes over 300 species that vary many orders of magnitude in size and inhabit all major biomes, from tropical rainforests to polar seas. The high diversity of carnivore parasites represents a source of potential emerging diseases of humans. Zoonotic risk from this group may be driven in part by exceptionally high functional d...
Article
Full-text available
Measurement of traffic flow stability and resilience is a critical step toward evaluating the performance of transportation systems and implementing appropriate management strategies. Quantifying changes in the stability and resilience of transportation systems, however, is hampered by the complexity of real traffic dynamics and the diversity of in...
Article
Resilience of ecosystems to the sudden decline of large‐bodied species is dependent on characteristics of surviving guild members. However, that response may also be mediated by local habitat conditions. Here, we examine the mechanisms behind the observed lack of functional compensation in the algal‐grazing guild by insect grazers following the dec...
Article
Full-text available
The pandemic of COVID-19 has become one of the greatest threats to human health, causing severe disruptions in the global supply chain, and compromising health care delivery worldwide. Although government authorities sought to contain the spread of SARS-CoV-2, by restricting travel and in-person activities, failure to deploy time-sensitive strategi...
Article
Full-text available
There are many outstanding questions about how to control the global COVID-19 pandemic. The information void has been especially stark in the World Health Organization Africa Region, which has low per capita reported cases, low testing rates, low access to therapeutic drugs, and has the longest wait for vaccines. As with all disease, the central ch...
Article
Full-text available
Background During outbreaks of emerging and re-emerging infections, the lack of effective drugs and vaccines increases reliance on non-pharmacologic public health interventions and behavior change to limit human-to-human transmission. Interventions that increase the speed with which infected individuals remove themselves from the susceptible popula...
Article
Initial efforts to mitigate transmission of SARS-CoV-2 relied on intensive social distancing measures such as school and workplace closures, shelter-in-place orders and prohibitions on the gathering of people. Other non-pharmaceutical interventions for suppressing transmission include active case finding, contact tracing, quarantine, immunity or he...
Preprint
Full-text available
Helminths are parasites that cause disease at considerable cost to public health and present a risk for emergence as novel human infections. Although recent research has elucidated characteristics conferring a propensity to emergence in other parasite groups (e.g. viruses), the understanding of factors associated with zoonotic potential in helminth...
Article
Invasive mosquitoes are expanding their ranges into new geographic areas and interacting with resident mosquito species. Understanding how novel interactions can affect mosquito population dynamics is necessary to predict transmission risk at invasion fronts. Mosquito life‐history traits are extremely sensitive to temperature and this can lead to t...
Article
Full-text available
Precision health mapping is a technique that uses spatial relationships between socio-ecological variables and disease to map the spatial distribution of disease, particularly for diseases with strong environmental signatures, such as diarrhoeal disease (DD). While some studies use GPS-tagged location data, other precision health mapping efforts re...
Preprint
Full-text available
The pandemic of COVID-19 has become one of the greatest threats to human health, causing severe disruptions in the global supply chain, and compromising health care delivery worldwide. Although government authorities sought to contain the spread of SARS-CoV-2, the virus that causes COVID-19, by restricting travel and in-person activities, failure t...
Preprint
Full-text available
White-nose syndrome has caused massive mortality in multiple bat species and spread across much of North America, making it one of the most destructive wildlife diseases on record. This has also resulted in it being one of the most well-documented wildlife disease outbreaks, making it possible to look for changes in the pattern of spatial spread ov...
Preprint
Full-text available
Historically, emerging and re-emerging infectious diseases have caused large, deadly, and expensive multi-national outbreaks. Often outbreak investigations aim to identify who infected whom by reconstructing the outbreak transmission tree, which visualizes transmission between individuals as a network with nodes representing individuals and branche...
Chapter
The size of annual outbreaks in seasonally forced host-pathogen systems is poorly understood. We studied contributing factors to the six-fold observed variation in the number of human cases of West Nile virus in New York City in the years 2000–2008. Sampling error and intrinsic noise (demographic stochasticity) explain roughly half of the observed...
Article
Full-text available
COVID-19 has wreaked havoc globally with particular concerns for sub-Saharan Africa (SSA), where models suggest that the majority of the population will become infected. Conventional wisdom suggests that the continent will bear a higher burden of COVID-19 for the same reasons it suffers from other infectious diseases: ecology, socioeconomic conditi...
Article
The majority of known early warning indicators of critical transitions rely on asymptotic resilience and critical slowing down. In continuous systems, critical slowing down is mathematically described by a decrease in magnitude of the dominant eigenvalue of the Jacobian matrix on the approach to a critical transition. Here, we show that measures of...
Article
Full-text available
Our understanding of ecological processes is built on patterns inferred from data. Applying modern analytical tools such as machine learning to increasingly high dimensional data offers the potential to expand our perspectives on these processes, shedding new light on complex ecological phenomena such as pathogen transmission in wild populations. H...
Preprint
Full-text available
The COVID-19 pandemic has wreaked havoc globally, and there has been a particular concern for sub-Saharan Africa (SSA), where models suggest that the majority of the population will become infected. Conventional wisdom suggests that the continent will bear a higher burden of COVID-19 for the same reasons it suffers high burdens of other infectious...
Preprint
Full-text available
Invasive mosquitoes are expanding their ranges into new geographic areas and interacting with resident mosquito species. Understanding how novel interactions can affect mosquito population dynamics is necessary to predict transmission risk at invasion fronts. Mosquito life-history traits are extremely sensitive to temperature and this can lead to t...
Article
Full-text available
Understanding the drivers of biodiversity is important for forecasting changes in the distribution of life on earth. However, most studies of biodiversity are limited by uneven sampling effort, with some regions or taxa better sampled than others. Numerous methods have been developed to account for differences in sampling effort, but most methods w...
Chapter
Ecological systems are prone to dramatic shifts between alternative stable states. In reality, these shifts are often caused by slow forces external to the system that eventually push it over a tipping point. Theory predicts that when ecological systems are brought close to a tipping point, the dynamical feedback intrinsic to the system interact wi...
Preprint
Full-text available
Diarrheal disease (DD) is responsible for over 700,000 child deaths annually, the majority in the tropics. Due to its strong environmental signature, DD is amenable to precision health mapping, a technique that leverages spatial relationships between socio-ecological variables and disease to predict hotspots of disease risk. However, precision heal...
Article
Full-text available
Campaigns to eliminate infectious diseases could be greatly aided by methods for providing early warning signals of resurgence. Theory predicts that as a disease transmission system undergoes a transition from stability at the disease-free equilibrium to sustained transmission, it will exhibit characteristic behaviours known as critical slowing dow...
Article
Full-text available
Despite medical advances, the emergence and re-emergence of infectious diseases continue to pose a public health threat. Low-dimensional epidemiological models predict that epidemic transitions are preceded by the phenomenon of critical slowing down (CSD). This has raised the possibility of anticipating disease (re-)emergence using CSD-based early-...
Preprint
Full-text available
During outbreaks of emerging infections, the lack of effective drugs and vaccines increases reliance on non-pharmacologic public health interventions and behavior change to limit human-to-human transmission. Interventions that increase the speed with which infected individuals remove themselves from the susceptible population are paramount, particu...
Article
Full-text available
Schistosomiasis control programs rely heavily on mass drug administration (MDA) campaigns with praziquantel for preventative chemotherapy. Areas where the prevalence and/or intensity of schistosomiasis infection remains high even after several rounds of treatment, termed “persistent hotspots” (PHSs), have been identified in trials of MDA effectiven...
Article
Full-text available
Much of the basic ecology of Ebolavirus remains unresolved despite accumulating disease outbreaks, viral strains and evidence of animal hosts. Because human Ebolavirus epidemics have been linked to contact with wild mammals other than bats, traits shared by species that have been infected by Ebolavirus and their phylogenetic distribution could sugg...
Article
Full-text available
The introduced fungal pathogen Pseudogymnoascus destructans is causing decline of several species of bats in North America, with some even at risk of extinction or extirpation. The severity of the epidemic of white‐nose syndrome caused by P. destructans has prompted investigation of the transmission and virulence of infection at multiple scales, bu...
Article
Full-text available
The Asian tiger mosquito, Aedes albopictus, transmits several arboviruses of public health importance, including chikungunya and dengue. Since its introduction to the United States in 1985, the species has invaded more than 40 states, including temperate areas not previously at risk of Aedes-transmitted arboviruses. Mathematical models incorporate...
Article
Full-text available
Emerging and re-emerging pathogens exhibit very complex dynamics, are hard to model and difficult to predict. Their dynamics might appear intractable. However, new statistical approaches—rooted in dynamical systems and the theory of stochastic processes—have yielded insight into the dynamics of emerging and re-emerging pathogens. We argue that thes...
Preprint
Full-text available
The Asian tiger mosquito, Aedes albopictus, transmits several arboviruses of public health importance, including chikungunya and Zika. Since its introduction to the United States in 1985, the species has invaded over forty states, including temperate areas not previously at risk of Aedes-transmitted arboviruses. Mathematical models incorporate clim...
Article
Full-text available
Second-order statistics such as the variance and autocorrelation can be useful indicators of the stability of randomly perturbed systems, in some cases providing early warning of an impending, dramatic change in the system’s dynamics. One specific application area of interest is the surveillance of infectious diseases. In the context of disease (re...
Article
Full-text available
Many ecological systems are subject critical transitions, which are abrupt changes to contrasting states triggered by small changes in some key component of the system. Temporal early warning signals such as the variance of a time series, and spatial early warning signals such as the spatial correlation in a snapshot of the system’s state, have bee...
Article
Full-text available
Aim We examined body size scaling relationships for two developmental life stages of parasitic helminths (egg and adult) separately in relationship to latitude (i.e. Bergmann's rule), temperature and temperature seasonality. Given that helminth eggs experience environmental conditions more directly, whereas adults live inside infected host individu...
Article
Full-text available
Effective public health research and preparedness requires an accurate understanding of which virus species possess or are at risk of developing human transmissibility. Unfortunately, our ability to identify these viruses is limited by gaps in disease surveillance and an incomplete understanding of the process of viral adaptation. By fitting booste...
Data
Descriptions of the predictor variables included in our models. (XLSX)
Data
Variable partial dependence plots, supplementary models with study effort. Partial dependence plots show how the model-predicted probability that a virus is able to spread between humans is affected by individual viral traits when the effects all other predictors are controlled for. These models include the log10-transformed number of PubMed citati...
Data
A ranking of virus species by their mean predicted response probability in the primary GBM model ensemble. Viruses for which there is evidence of human-to-human transmission are given a value of 1 in the column Actual.Response, while viruses which are no known to be transmissible have a value of 0. (CSV)
Data
Family characteristics of false-negative virus species. Each point represents a virus family that contains one or more species known to infect humans. Points represent the families of viruses included in our dataset (those known to infect humans). Red points are the 5 virus families containing the ten known-transmissible species with the lowest mod...
Data
Information on the parameters, AUC scores, and variable relative influence scores of the primary and secondary models. (XLSX)
Data
Variable partial dependence plots, supplementary models with a modified response definition. Partial dependence plots show how the model-predicted probability that a virus is able to spread between humans is affected by individual viral traits when the effects all other predictors are controlled for. In these models, we modified our definition of t...
Article
Full-text available
Methods for modeling species’ distributions in nature are typically evaluated empirically with respect to data from observations of species occurrence and, occasionally, absence at surveyed locations. Such models are relatively “theory‐free.” In contrast, theories for explaining species’ distributions draw on concepts like fitness, niche, and envir...
Article
Full-text available
Background: Yellow fever virus is a mosquito-borne flavivirus that persists in an enzoonotic cycle in non-human primates (NHPs) in Brazil, causing disease in humans through spillover events. Yellow fever (YF) re-emerged in the early 2000s, spreading from the Amazon River basin towards the previously considered low-risk, southeastern region of the...