Wayne Getz

University of California, Berkeley | UCB · Department of Environmental Science, Policy, and Management

Remote aerial sensing provides a non-invasive, large geographical-scale technology for avian monitoring, but the manual processing of images limits its development and applications. Artificial Intelligence (AI) methods can be used to mitigate this manual image processing requirement. The implementation of AI methods, however, has several challenges...

Background Movement is central to understanding the ecology of animals. The most robustly definable segments of an individual’s lifetime track are its diel activity routines (DARs). This robustness is due to fixed start and end points set by a 24-h clock that depends on the individual’s quotidian schedule. An analysis of day-to-day variation in the...

Resource partitioning promotes coexistence among guild members, and carnivores reduce interference competition through behavioral mechanisms that promote spatio-temporal separation. We analyzed sympatric lion and spotted hyena movements and activity patterns to ascertain the mechanisms facilitating their coexistence within semi-arid and wetland eco...

We investigated the initial outbreak rates and subsequent social distancing behaviour over the initial phase of the COVID-19 pandemic across 29 Combined Statistical Areas (CSAs) of the United States. We used the Numerus Model Builder Data and Simulation Analysis (NMB-DASA) web application to fit the exponential phase of a SCLAIV+D (Susceptible, Con...

Migration is one of the most physical and energetically demanding periods in an individual bird’s life. The composition of the bird’s gut or cloacal microbiota can temporarily change during migration, likely due to differences in diets, habitats and other environmental conditions experienced en route. However, how physiological condition, migratory...

This paper lays out a hierarchical, appropriate-complexity framework for conceptualizing movement-path segments at different spatiotemporal scales in a way that facilitates comparative analyses and bridges behavior and mathematical concepts. It then outlines a process for generating a multimode, multiscale stochastic simulation model that can be us...

We introduce an extension to Conway's Game of Life (GoL) that allows more than 2 states (dead/alive; 0/1) to be specified. State 0 is reserved for dead or lifeless cells, and states 1 to n − 1 for cells that are alive. Associated with state σ is the value vσ of cells such that v0 = 0, v1 = 1, and for σ = 2, ... , n − 1 the cell value vσ is free to...

In ecological and conservation studies, responsible researchers strive to obtain rich data while minimizing disturbance to wildlife and ecosystems. We assessed if samples collected noninvasively can be used for fecal microbiome research, comparing microbiota of noninvasively collected fecal samples to those collected from trapped common cranes at t...

Background An understanding of epidemiological dynamics, once confined to mathematical epidemiologists and applied mathematicians, can be disseminated to a non-mathematical community of health care professionals and applied biologists through simple-to-use simulation applications. We used Numerus Model Builder RAMP Ⓡ (Runtime Alterable Model Platfo...

Movement behavior is an important contributor to habitat selection and its incorporation in disease risk models has been somewhat neglected. The habitat preferences of host individuals affect their probability of exposure to pathogens. If preference behavior can be incorporated in ecological niche models (ENMs) when data on pathogen distributions a...

Proclaimed in 1907, Etosha National Park in northern Namibia is an iconic dryland system with a rich history of wildlife conservation and research. A recent research symposium on wildlife conservation in the Greater Etosha Landscape (GEL) highlighted increased concern of how intensification of global change will affect wildlife conservation based o...

Avian influenza viruses (AIV) are a worldwide threat to animal and human health. As wild waterfowl circulate and spread these viruses around the world, investigations of AIV prevalence in wild populations are critical for understanding pathogen transmission, as well as predicting disease outbreaks in domestic animals and humans. Surveillance effort...

Background. Movement is central to understanding the ecology of animals. The most easily definable segments of an individual’s lifetime track (i.e., movement path defined by a relocation data time series) are its diel activity routines (DARs). This definability is due to fixed start and end points set by a 24-hour clock that depends on the individu...

Background Interference competition among sympatric carnivores can potentially influence species viability through population reduction or extinction, and has important implications for the structure and function of large carnivore communities. Carnivores may mitigate the risk of competition through fine-scaled spatial or temporal separation that s...

Resource partitioning promotes coexistence among guild members, and carnivores reduce interference competition through behavioural mechanisms that promote spatio-temporal separation. We analyzed sympatric lion and spotted hyena movements and activity patterns to ascertain the mechanisms facilitating their coexistence within semi-arid and wetland ec...

In ecological and conservation studies, responsible researchers strive to obtain rich data while minimizing disturbance to wildlife and ecosystems. We assessed if samples collected noninvasively can be used for microbiome research, comparing microbiota of noninvasively collected fecal samples to those collected from trapped common cranes at the sam...

An understanding of epidemiological dynamics, once confined to mathematical epidemiologists and applied mathematicians, can be disseminated to a non-mathematical community of health care professionals and applied biologists through simple-to-use simulation applications. We used Numerus Model Builder RAMP ® (Runtime Alterable Model Platform) technol...

A high genetic load can negatively affect population viability and increase susceptibility to diseases and other environmental stressors. Prior microsatellite studies of two African buffalo (Syncerus caffer) populations in South Africa indicated substantial genome-wide genetic load due to high-frequency occurrence of deleterious alleles. The occurr...

We present methods for building a Java Runtime-Alterable-Model Platform (RAMP) of complex dynamical systems. We illustrate our methods by building a multivariant SEIR (epidemic) RAMP. Underlying our RAMP is an individual-based model that includes adaptive contact rates, pathogen genetic drift, waning and cross-immunity. Besides allowing parameter v...

Studies in both humans and model organisms suggest that the microbiome may play a significant role in host health, including digestion and immune function. Microbiota can offer protection from exogenous pathogens through colonization resistance, but microbial dysbiosis in the gastrointestinal tract can decrease resistance and is associated with pat...

Camera trapping is increasingly being used to monitor wildlife, but this technology typically requires extensive data annotation. Recently, deep learning has substantially advanced automatic wildlife recognition. However, current methods are hampered by a dependence on large static datasets, whereas wildlife data are intrinsically dynamic and invol...

Familiarity with the landscape increases foraging efficiency and safety. Thus, when animals are confronted with a novel environment, either by natural dispersal or translocation, establishing a home range becomes a priority. While the search for a home range carries a cost of functioning in an unfamiliar environment, ceasing the search carries a co...

In this paper, we introduce a novel method for classifying and computing the frequencies of movement modes of intraspecific and interspecific dyads, focusing in particular on distance‐mediated approach, retreat, following and side‐by‐side movement modes. Besides distance, other factors such as time of day, season, sex or age can be included in the...

SARS-Cov-2 escape mutations (EM) have been detected and are spreading. Vaccines may need adjustment to respond to these or future mutations. We designed a population level model integrating both waning immunity and EM. We also designed a set of criteria for elaborating and fitting this model to cross-neutralization and other data with a goal of min...

Human activities shape resources available to wild animals, impacting diet and likely altering their microbiota and overall health. We examined drivers shaping microbiota profiles of common cranes (Grus grus) in agricultural habitats by comparing gut microbiota and crane movement patterns (GPS‐tracking) over three periods of their migratory cycle,...

In this paper, we present methods for building a Java Runtime-Alterable-Model Platform (RAMP) of complex dynamical systems. We illustrate our methods by building a multivariant SEIR (epidemic) RAMP. Underlying our RAMP is an individual-based model that includes adaptive contact rates, pathogen genetic drift, waning and cross immunity. Besides allow...

When a transmission hotspot for an environmentally persistent pathogen establishes in otherwise high-quality habitat, the disease may exert a strong impact on a host population. However, fluctuating environmental conditions lead to heterogeneity in habitat quality and animal habitat preference, which may interrupt the overlap between selected and r...

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) the causal agent for COVID-19, is a communicable disease spread through close contact. It is known to disproportionately impact certain communities due to both biological susceptibility and inequitable exposure. In this study, we investigate the most important health, social, and environm...

Anthrax is a zoonosis caused by the spore-forming bacterium Bacillus anthracis, with potential for high fatality rate, especially in herbivores. Upon host death, spores can enter the soil surrounding the carcass and be ingested by other animals feeding in the same location. Accordingly, surveillance to quickly identify and decontaminate anthrax car...

Camera trapping is increasingly used to monitor wildlife, but this technology typically requires extensive data annotation. Recently, deep learning has significantly advanced automatic wildlife recognition. However, current methods are hampered by a dependence on large static data sets when wildlife data is intrinsically dynamic and involves long-t...

Background No versatile web app exists that allows epidemiologists and managers around the world to comprehensively analyze the impacts of COVID-19 mitigation. The http://covid-webapp.numerusinc.com/ web app presented here fills this gap. Methods Our web app uses a model that explicitly identifies susceptible, contact, latent, asymptomatic, sympto...

Scavenging of carrion shapes ecological landscapes by influencing scavenger population demography, increasing inter- and intra-specific interactions, and generating ecosystem services such as nutrient cycling and disease moderation. Previous research found the cues promoting, or the constraints limiting, an individual’s propensity or ability to sca...

Escape mutations (EM) to SARS-Cov-2 have been detected and are spreading. Vaccines may need adjustment to respond to these or future mutations. We designed a population level model integrating both waning immunity and EM. We also designed a set of criteria for elaborating and fitting this model to cross-neutralization and other data in a manner tha...

In this paper, we introduce a novel method for classifying and computing the frequencies of movement modes of intra and interspecific dyads, focusing in particular on distance-mediated approach, retreat, following and side by side movement modes. Besides distance, the method includes factors such as sex, age, time of day, or season that cause frequ...

The Arctic is undergoing the most rapid climate warming on Earth. While concerns have been raised that more frequent icing events cause die‐offs, and earlier springs generate a mismatch in phenology, the effects of warming autumns have been largely neglected. We used 25 years of individual‐based data from a growing population of wild Svalbard reind...

Environmentally mediated indirect pathogen transmission is linked to host movement and foraging in areas where pathogens are maintained in the environment. In the case of anthrax, spores of the causative bacterium Bacillus anthracis are released into the environment following host death and create locally infectious zones (LIZs) around carcass site...

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) the causal agent for COVID-19, is a communicable disease spread through close contact. It is known to disproportionately infect certain communities due to both biological susceptibility and inequitable exposure. In this study, we investigate the most important health, social,...

Animals generally benefit from their gastrointestinal microbiome, but the factors that influence the composition and dynamics of their microbiota remain poorly understood. Studies of nonmodel host species can illuminate how microbiota and their hosts interact in natural environments. We investigated the role of migratory behaviour in shaping the gu...

After 40 years of intense study on HIV/AIDS, scientists have identified, among other things, at risk populations, stages of disease progression and treatment strategies. What has received less attention is the possibility that infection might elicit an increase in sexual behavior in humans. In 2000, Starks and colleagues speculated that HIV infecti...

Background. No versatile web app exists that allows epidemiologists and managers around the world to fully analyze the impacts of COVID-19 mitigation. The NMB-DASA web app presented here fills this gap. Methods. Our web app uses a model that explicitly identifies a contact class of individuals, symptomatic and asymptomatic classes and a parallel se...

We formulate a refined SEIR epidemic model that explicitly includes a contact class C that either thwarts pathogen invasion and returns to the susceptible class S or progresses successively through a latent class L, a presymptomatic/asymptomatic class A, and a symptomatic class I. Individuals in both A and I may go directly to an immune class V, an...

We address the question of how best to fit animal movement paths, represented by point relocation time series, to a novel stochastic walk model---referred to as M-cubed---in a way that captures movement patterns at several different spatio-temporal scales. We test our approach on simulated data obtained from a high-frequency, multi-mode model const...

Concern for megafauna is increasing among scientists and non-scientists. Many studies have emphasized that megafauna play prominent ecological roles and provide important ecosystem services to humanity. But, what precisely are ‘megafauna’? Here, we critically assess the concept of megafauna and propose a goal-oriented framework for megafaunal resea...

The behavioral ecology of host species is likely to affect their microbial communities, because host sex, diet, physiology, and movement behavior could all potentially influence their microbiota. We studied a wild population of barn owls (Tyto alba) and collected data on their microbiota, movement, diet, size, coloration, and reproduction. The comp...

The risk of a zoonotic pandemic disease threatens hundreds of millions of people. Emerging infectious diseases also threaten livestock and wildlife populations around the world and can lead to devastating economic damages. China and the USA—due to their unparalleled resources, widespread engagement in activities driving emerging infectious diseases...

Animal movement paths are represented by point-location time series called relocation data. How well such paths can be simulated, when the rules governing movement depend on the internal state of individuals and environmental factors (both local and, when memory is involved, global) remains an open question. To answer this, we formulate and test mo...

Background: Understanding rhino movement behavior, especially their recursive movements, holds significant promise for enhancing rhino conservation efforts, and protecting their habitats and the biodiversity they support. Here we investigate the daily, biweekly, and seasonal recursion behavior of rhinos, to aid conservation applications and increa...

Neanderthals and modern humans both occupied the Levant for tens of thousands of years prior to the spread of modern humans into the rest of Eurasia and their replacement of the Neanderthals. That the inter-species boundary remained geographically localized for so long is a puzzle, particularly in light of the rapidity of its subsequent movement. H...

Comparative applications of animal movement path analyses are hampered by the lack of a comprehensive framework for linking structures and processes conceived at different spatio-temporal scales. Although many analyses begin by generating step-length (SL) and turning-angle (TA) distributions from relocation time-series data---some of which are link...

Animal relocation data has recently become considerably more ubiquitous, finely structured (collection frequencies measured in minutes) and co-variate rich (physiology of individuals, environmental and landscape information, and accelerometer data). To better understand the impacts of ecological interactions, individual movement and disease on glob...

Background As GPS tags and data loggers have become lighter, cheaper, and longer-lasting, there has been a growing influx of data on animal movement. Simultaneously, methods of analyses and software to apply such methods to movement data have expanded dramatically. Even so, for many interdisciplinary researchers and managers without familiarity wit...

Bovine tuberculosis (BTB) is endemic to the African buffalo (Syncerus caffer) of Hluhluwe-iMfolozi Park (HiP) and Kruger National Park, South Africa. In HiP, the disease has been actively managed since 1999 through a test-and-cull procedure targeting BTB-positive buffalo. Prior studies in Kruger showed associations between microsatellite alleles, B...

Bacillus anthracis is a spore-forming, Gram-positive bacterium responsible for anthrax, an acute infection that most significantly affects grazing livestock and wild ungulates, but also poses a threat to human health. The geographic extent of B. anthracis is poorly understood, despite multi-decade research on anthrax epizootic and epidemic dynamics...

Dynamic SEIR (Susceptible, Exposed, Infectious, Removed) compartmental models provide a tool for predicting the size and duration of both unfettered and managed outbreaks-the latter in the context of interventions such as case detection, patient isolation, vaccination and treatment. The reliability of this tool depends on the validity of key assump...

The implementation of intelligent software to identify and classify objects and individuals in visual fields is a technology of growing importance to operatives in many fields, including wildlife conservation and management. To non-experts, the methods can be abstruse and the results mystifying. Here, in the context of applying cutting edge methods...

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...

The relationship between resource availability and wildlife movement patterns is pivotal to understanding species behavior and ecology. Movement response to landscape variables occurs at multiple temporal scales, from sub‐diurnal to multiannual. Additionally, individuals may respond to both current and past conditions of resource availability. In t...

Neanderthals and modern humans both occupied the Levant for tens of thousands of years prior to modern humans' spread into the rest of Eurasia and their replacement of the Neanderthals. That the inter-species boundary remained geographically localized for so long is a puzzle, particularly in light of the rapidity of its subsequent movement. We prop...

Erlang differential equation models of epidemic processes provide more realistic disease-class transition dynamics from susceptible (S) to exposed (E) to infectious (I) and removed (R) categories than the ubiquitous SEIR model. The latter is itself is at one end of the spectrum of Erlang SEIR models with concatenated E compartments and concatenated...

Background Continued exploration of the performance of the recently proposed cross-validation-based approach for delimiting home ranges using the Time Local Convex Hull (T-LoCoH) method has revealed a number of issues with the original formulation. Main text Here we replace the ad hoc cross-validation score with a new formulation based on the tota...

In our quest to develop more intelligent machines, knowledge of the visual features used by machines to classify objects shall be helpful. The current state of the art in training machines to classify wildlife species from camera-trap data is to employ convolutional neural networks (CNN) encoded within deep learning algorithms. Here we report on re...

The sixth mass extinction poses an unparalleled quantitative challenge to conservation biologists. Mathematicians and ecologists alike face the problem of developing models that can scale predictions of extinction rates from populations to the level of a species, or even to an entire ecosystem. We review some of the most basic stochastic and analyt...

The sixth mass extinction poses an unparalleled quantitative challenge to conservation biologists. Mathematicians and ecologists alike face the problem of developing models that can scale predictions of extinction rates from populations to the level of a species, or even to an entire ecosystem. We review some of the most basic stochastic and analyt...

Novel diseases are increasingly emerging into human populations through the complex—and often, unseen—stepwise process of spillover from a combination of wildlife, livestock, vectors, and the abiotic environment. Characterizing and modeling the spillover interface are a key part of how eco-epidemiologists respond to the growing global burden of eme...

Bacillus anthracis is a spore-forming, Gram-positive bacterium responsible for anthrax, an acute and commonly lethal infection that most significantly affects grazing livestock, wild ungulates and other herbivorous mammals, but also poses a serious threat to human health. The geographic extent of B. anthracis endemism is still poorly understood, de...