One of the key questions regarding the underlying mechanisms of mammalian land migrations is how animals select where to go. Most studies assume perception of resources as the navigational mechanism. ...The possible role of memory that would allow forecasting conditions at distant locations and times based on information about environmental conditions from previous years has been little studied. We study migrating zebra in Botswana using an individual-based simulation model, where perceptually guided individuals use currently sensed resources at different perceptual ranges, while memory-guided individuals use long-term averages of past resources to forecast future conditions. We compare simulated individuals guided by perception or memory on resource landscapes of remotely sensed vegetation data to trajectories of GPS-tagged zebras. Our results show that memory provides a clear signal that best directs migrants to their destination compared to perception at even the largest perceptual ranges. Zebras modelled with memory arrived two to four times, or up to 100 km, closer to the migration destination than those using perception. We suggest that memory in addition to perception is important for directing ungulate migration. Furthermore, our findings are important for the conservation of migratory mammals, as memory informing direction suggests migration routes could be relatively inflexible.
Animals regularly return to locations such as foraging patches, nests, dens, watering holes, or movement corridors, and these revisited locations are often sites of ecological significance. Analyzing ...the temporal and spatial pattern of revisitation can lead to important insights into the life history and ecology of populations. We introduce the R package ‘recurse’ to calculate revisitations to locations in the movement trajectory or other locations for one or multiple individuals. The package also calculates metrics such as residence time and time between visits. It can be used to quantitatively identify frequently used sites (e.g. dens, nests, foraging locations), to examine patterns of revisitation and link them with covariates such as habitat features or climatic data, and to address conservation questions of interest about specific locations. We present an example application with movement trajectory data from a turkey vulture Cathartes aura during the breeding season and demonstrate analyzing recursions, specific locations, seasonal and daily temporal patterns, and visit timing. The ‘recurse’ package should be of interest both to ecologists looking to analyze their movement data and to conservationists needing site‐specific information for management and conservation actions.
Trial results for two COVID-19 vaccines suggest at least 90% efficacy against symptomatic disease (VE
). It remains unknown whether this efficacy is mediated by lowering SARS-CoV-2 infection ...susceptibility (VE
) or development of symptoms after infection (VE
). We aim to assess and compare the population impact of vaccines with different efficacy profiles (VE
and VE
) satisfying licensure criteria. We developed a mathematical model of SARS-CoV-2 transmission, calibrated to data from King County, Washington. Rollout scenarios starting December 2020 were simulated with combinations of VE
and VE
resulting in up to 100% VE
. We assumed no reduction of infectivity upon infection conditional on presence of symptoms. Proportions of cumulative infections, hospitalizations and deaths prevented over 1 year from vaccination start are reported. Rollouts of 1 M vaccinations (5000 daily) using vaccines with 50% VE
are projected to prevent 23-46% of infections and 31-46% of deaths over 1 year. In comparison, vaccines with 90% VE
are projected to prevent 37-64% of infections and 46-64% of deaths over 1 year. In both cases, there is a greater reduction if VE
is mediated mostly by VE
. The use of a "symptom reducing" vaccine will require twice as many people vaccinated than a "susceptibility reducing" vaccine with the same 90% VE
to prevent 50% of the infections and death over 1 year. Delaying the start of the vaccination by 3 months decreases the expected population impact by more than 50%. Vaccines which prevent COVID-19 disease but not SARS-CoV-2 infection, and thereby shift symptomatic infections to asymptomatic infections, will prevent fewer infections and require larger and faster vaccination rollouts to have population impact, compared to vaccines that reduce susceptibility to infection. If uncontrolled transmission across the U.S. continues, then expected vaccination in Spring 2021 will provide only limited benefit.
An individual's choices are shaped by its experience, a fundamental property of behavior important to understanding complex processes. Learning and memory are observed across many taxa and can drive ...behaviors, including foraging behavior. To explore the conditions under which memory provides an advantage, we present a continuous-space, continuous-time model of animal movement that incorporates learning and memory. Using simulation models, we evaluate the benefit memory provides across several types of landscapes with variable-quality resources and compare the memory model within a nested hierarchy of simpler models (behavioral switching and random walk). We find that memory almost always leads to improved foraging success, but that this effect is most marked in landscapes containing sparse, contiguous patches of high-value resources that regenerate relatively fast and are located in an otherwise devoid landscape. In these cases, there is a large payoff for finding a resource patch, due to size, value, or locational difficulty. While memory-informed search is difficult to differentiate from other factors using solely movement data, our results suggest that disproportionate spatial use of higher value areas, higher consumption rates, and consumption variability all point to memory influencing the movement direction of animals in certain ecosystems.
Predator reintroductions are often used as a means of restoring the ecosystem services that these species can provide. The ecosystem consequences of predator reintroduction depend on how prey species ...respond. Yet, to date, we lack a general framework for predicting these responses. To address this knowledge gap, we modeled the impacts of predator reintroduction on foragers as a function of predator characteristics (habitat domain; i.e., area threatened) and prey characteristics (knowledge of alternative habitat and exploratory tendency). Foraging prey had the capacity to both remember and return to good habitat and to remember and avoid predators. In general, we found that forager search time increased and consumption decreased after predator introduction. However, predator habitat domain played a key role in determining how much prey habitat use changed following reintroduction, and the forager's knowledge of alternative habitats and exploratory inclinations affected what types of habitat shifts occurred. Namely, habitat shifts and consumption sacrifices by prey were extreme in some cases, particularly when they were pushed far from their starting locations by broad-domain predators, whereas informed foragers spent less time searching and displayed smaller reductions to consumption than their naïve counterparts following predator exposure. More exploratory foragers exhibited larger habitat shifts, thereby sacrificing consumption but reducing encounters by relocating to refugia, whereas less exploratory foragers managed risk in place and consequently suffered increased encounters while consuming more resources. By implication, reintroductions of predators with broad habitat domains are especially likely to impose foraging and movements costs on prey, but forager spatial memory state can mitigate these effects, as informed foragers can better access alternate habitat and avoid predators with smaller reductions in consumption.
•We review literature of climate change impacts on migratory marine species.•Emphasized phenology adaption by genetic and phenotypic plasticity processes.•Modeled climate change effects on population ...dynamics and phenology with IBM.•Extinction depends on bioclimate envelope size and rate of phenology adaptation.•High variability in body condition may be an indicator of extinction potential.
We review literature concerning the impacts of climate change on the migration of marine species, with an emphasis on the adaptation of migration phenology through genetic tracking and phenotypic plasticity. We then develop an individual-based modeling framework characterizing the effects of climate change on phenology and population dynamics. In the framework, an animal's ability to match its environmental preferences, its bioclimate envelope, to the environmental conditions by adjusting its migration timing between foraging and breeding habitats determines its condition, survival, and fecundity. Climate-induced changes in the envelope produce timing mismatches that result in a population adapting its phenology through both genetic and plastic processes. Model results suggest: (1) the temporal size of the bioclimate envelope is an important determinant of a population's sensitivity to climate change and susceptibility to extinction, (2) population extinction can occur if the rate of change in the timing of the envelope exceeds the rate its phenology changes or if the variability in the envelope exceeds the population's inherent capacity for variability, (3) a population with migration timing cued by photoperiod is expected to exhibit weaker phenotypic plasticity than one cued by temperature, and (4) population extinction in response to climate change follows a threshold pattern such that population size may not be a reliable indicator of extinction threat, although variability in average individual condition across years may be an extinction threat indicator. Finally, while the model is intentionally simplistic, we discuss how it can be extended to cover more complex interactions.
In late March 2020, a “Stay Home, Stay Healthy” order was issued in Washington State in response to the COVID-19 pandemic. On May 1, a 4-phase reopening plan began. We investigated whether adjunctive ...prevention strategies would allow less restrictive physical distancing to avoid second epidemic waves and secure safe school reopening.
We developed a mathematical model, stratifying the population by age, infection status and treatment status to project SARS-CoV-2 transmission during and after the reopening period. The model was parameterized with demographic and contact data from King County, WA and calibrated to confirmed cases, deaths and epidemic peak timing. Adjunctive prevention interventions were simulated assuming different levels of pre-COVID physical interactions (pC_PI) restored.
The best model fit estimated ~35% pC_PI under the lockdown which prevented ~17,000 deaths by May 15. Gradually restoring 75% pC_PI for all age groups between May 15-July 15 would have resulted in ~350 daily deaths by early September 2020. Maintaining <45% pC_PI was required with current testing practices to ensure low levels of daily infections and deaths. Increased testing, isolation of symptomatic infections, and contact tracing permitted 60% pC_PI without significant increases in daily deaths before November and allowed opening of schools with <15 daily deaths. Inpatient antiviral treatment was predicted to reduce deaths significantly without lowering cases or hospitalizations.
We predict that widespread testing, contact tracing and case isolation would allow relaxation of physical distancing, as well as opening of schools, without a surge in local cases and deaths.
SARS-CoV-2 vaccine clinical trials assess efficacy against disease (VE
), the ability to block symptomatic COVID-19. They only partially discriminate whether VE
is mediated by preventing infection ...completely, which is defined as detection of virus in the airways (VE
), or by preventing symptoms despite infection (VE
). Vaccine efficacy against transmissibility given infection (VE
), the decrease in secondary transmissions from infected vaccine recipients, is also not measured. Using mathematical modeling of data from King County Washington, we demonstrate that if the Moderna (mRNA-1273QS) and Pfizer-BioNTech (BNT162b2) vaccines, which demonstrated VE
> 90% in clinical trials, mediate VE
by VE
, then a limited fourth epidemic wave of infections with the highly infectious B.1.1.7 variant would have been predicted in spring 2021 assuming rapid vaccine roll out. If high VE
is explained by VE
, then high VE
would have also been necessary to limit the extent of this fourth wave. Vaccines which completely protect against infection or secondary transmission also substantially lower the number of people who must be vaccinated before the herd immunity threshold is reached. The limited extent of the fourth wave suggests that the vaccines have either high VE
or both high VE
and high VE
against B.1.1.7. Finally, using a separate intra-host mathematical model of viral kinetics, we demonstrate that a 0.6 log vaccine-mediated reduction in average peak viral load might be sufficient to achieve 50% VE
which suggests that human challenge studies with a relatively low number of infected participants could be employed to estimate all three vaccine efficacy metrics.
Although evidence indicates that salmon could use geomagnetic cues in their high seas homing migration, the underlying behavioral strategy salmon apply to navigation cues is poorly understood. In one ...hypothesis, salmon imprint on the magnetic field when entering the ocean as juveniles and use the difference between the local and imprinted fields to navigate home. In this paper we demonstrate that simple behaviors incorporating this cue difference, to approach the isoline matching the imprinted magnetic value and then to follow along the isoline to the river mouth, are sufficient to guide spring Chinook salmon (Oncorhynchus tshawytscha) to the Columbia River. We model homing trajectories of salmon, combining ocean currents and fish swimming behaviors. Although the magnetic field inclination angle is a more robust cue than magnetic field intensity, both are sufficient to direct fish to the river mouth from a wide region of the Northeastern Pacific. The threshold defining the transition between the isoline approach and follow behaviors is the main factor determining successful homing trajectories. Small thresholds are more successful, meaning the approach behavior predominates until the fish is near the isoline intersecting the river mouth. The follow behavior swim heading can compensate for magnetic field changes, and the directed migration start date determines the longitudinal center of successful starting locations. This analysis suggests that salmon from ocean habitats may approach their home river in a narrow migration corridor along a magnetic field isoline.
The rapid spread of highly transmissible SARS-CoV-2 variants combined with slowing pace of vaccination in Fall 2021 created uncertainty around the future trajectory of the epidemic in King County, ...Washington, USA. We analyzed the benefits of offering vaccination to children ages 5-11 and expanding the overall vaccination coverage using mathematical modeling. We adapted a mathematical model of SARS-CoV-2 transmission, calibrated to data from King County, Washington, to simulate scenarios of vaccinating children aged 5-11 with different starting dates and different proportions of physical interactions (PPI) in schools being restored. Dynamic social distancing was implemented in response to changes in weekly hospitalizations. Reduction of hospitalizations and estimated time under additional social distancing measures are reported over the 2021-2022 school year. In the scenario with 85% vaccination coverage of 12+ year-olds, offering early vaccination to children aged 5-11 with 75% PPI was predicted to prevent 756 (median, IQR 301-1434) hospitalizations cutting youth hospitalizations in half compared to no vaccination and largely reducing the need for additional social distancing measures over the school year. If, in addition, 90% overall vaccination coverage was reached, 60% of remaining hospitalizations would be averted and the need for increased social distancing would almost certainly be avoided. Our work suggests that uninterrupted in-person schooling in King County was partly possible because reasonable precaution measures were taken at schools to reduce infectious contacts. Rapid vaccination of all school-aged children provides meaningful reduction of the COVID-19 health burden over this school year but only if implemented early. It remains critical to vaccinate as many people as possible to limit the morbidity and mortality associated with future epidemic waves.
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