Uncertainty in On-The-Fly Epidemic Fitting

Abstract. The modern world features a plethora of social, technolog-ical and biological epidemic phenomena. These epidemics now spread at unprecedented rates thanks to advances in industrialisation, trans-port and telecommunications. Effective real-time decision making and management of modern epidemic outbreaks depends on the two factors: the ability to determine epidemic parameters as the epidemic unfolds, and the ability to characterise rigorously the uncertainties inherent in these parameters. This paper presents a generic maximum-likelihood-based methodology for online epidemic fitting of SIR models from a single trace which yields confidence intervals on parameter values. The method is fully automated and avoids the laborious manual efforts tra-ditionally deployed in the modelling of biological epidemics. We present case studies based on both synthetic and real data

Global gene flow releases invasive plants from environmental constraints on genetic diversity

When plants establish outside their native range, their ability to adapt to the new environment is influenced by both demography and dispersal. However, the relative importance of these two factors is poorly understood. To quantify the influence of demography and dispersal on patterns of genetic diversity underlying adaptation, we used data from a globally distributed demographic research network comprising 35 native and 18 nonnative populations of Plantago lanceolata. Species-specific simulation experiments showed that dispersal would dilute demographic influences on genetic diversity at local scales. Populations in the native European range had strong spatial genetic structure associated with geographic distance and precipitation seasonality. In contrast, nonnative populations had weaker spatial genetic structure that was not associated with environmental gradients but with higher within-population genetic diversity. Our findings show that dispersal caused by repeated, long-distance, human-mediated introductions has allowed invasive plant populations to overcome environmental constraints on genetic diversity, even without strong demographic changes. The impact of invasive plants may, therefore, increase with repeated introductions, highlighting the need to constrain future introductions of species even if they already exist in an area

An optimal control theory approach to non-pharmaceutical interventions

<p>Abstract</p> <p>Background</p> <p>Non-pharmaceutical interventions (NPI) are the first line of defense against pandemic influenza. These interventions dampen virus spread by reducing contact between infected and susceptible persons. Because they curtail essential societal activities, they must be applied judiciously. Optimal control theory is an approach for modeling and balancing competing objectives such as epidemic spread and NPI cost.</p> <p>Methods</p> <p>We apply optimal control on an epidemiologic compartmental model to develop triggers for NPI implementation. The objective is to minimize expected person-days lost from influenza related deaths and NPI implementations for the model. We perform a multivariate sensitivity analysis based on Latin Hypercube Sampling to study the effects of input parameters on the optimal control policy. Additional studies investigated the effects of departures from the modeling assumptions, including exponential terminal time and linear NPI implementation cost.</p> <p>Results</p> <p>An optimal policy is derived for the control model using a linear NPI implementation cost. Linear cost leads to a "bang-bang" policy in which NPIs are applied at maximum strength when certain state criteria are met. Multivariate sensitivity analyses are presented which indicate that NPI cost, death rate, and recovery rate are influential in determining the policy structure. Further death rate, basic reproductive number and recovery rate are the most influential in determining the expected cumulative death. When applying the NPI policy, the cumulative deaths under exponential and gamma terminal times are close, which implies that the outcome of applying the "bang-bang" policy is insensitive to the exponential assumption. Quadratic cost leads to a multi-level policy in which NPIs are applied at varying strength levels, again based on certain state criteria. Results indicate that linear cost leads to more costly implementation resulting in fewer deaths.</p> <p>Conclusions</p> <p>The application of optimal control theory can provide valuable insight to developing effective control strategies for pandemic. Our findings highlight the importance of establishing a sensitive and timely surveillance system for pandemic preparedness.</p

Phenotypic plasticity masks range-wide genetic differentiation for vegetative but not reproductive traits in a short-lived plant

Publication history: Accepted - 19 May 2021; Published - 5 August 2021.Genetic differentiation and phenotypic plasticity jointly shape intraspecific trait variation, but their roles differ among traits. In short-lived plants, reproductive traits may be more genetically determined due to their impact on fitness, whereas vegetative traits may show higher plasticity to buffer short-term perturbations. Combining a multi-treatment greenhouse experiment with observational field data throughout the range of a widespread short-lived herb, Plantago lanceolata, we (1) disentangled genetic and plastic responses of functional traits to a set of environmental drivers and (2) assessed how genetic differentiation and plasticity shape observational trait–environment relationships. Reproductive traits showed distinct genetic differentiation that largely determined observational patterns, but only when correcting traits for differences in biomass. Vegetative traits showed higher plasticity and opposite genetic and plastic responses, masking the genetic component underlying field-observed trait variation. Our study suggests that genetic differentiation may be inferred from observational data only for the traits most closely related to fitness.Eesti Teadusagentuur, Grant/Award Number: PRG609 and PUT1409; Academy of Finland; Natural Sciences and Engineering Research Council of Canada; Science Foundation Ireland, Grant/Award Number: 15/ERCD/2803; Spanish Ministry of Science, Innovation and Universities, Grant/Award Number: IJCI-2017- 32039; European Regional Development Fun

Phenotypic plasticity masks range-wide genetic differentiation for vegetative but not reproductive traits in a short-lived plant

Genetic differentiation and phenotypic plasticity jointly shape intraspecific trait variation, but their roles differ among traits. In short-lived plants, reproductive traits may be more genetically determined due to their impact on fitness, whereas vegetative traits may show higher plasticity to buffer short-term perturbations. Combining a multi-treatment greenhouse experiment with observational field data throughout the range of a widespread short-lived herb, Plantago lanceolata, we (1) disentangled genetic and plastic responses of functional traits to a set of environmental drivers and (2) assessed how genetic differentiation and plasticity shape observational trait-environment relationships. Reproductive traits showed distinct genetic differentiation that largely determined observational patterns, but only when correcting traits for differences in biomass. Vegetative traits showed higher plasticity and opposite genetic and plastic responses, masking the genetic component underlying field-observed trait variation. Our study suggests that genetic differentiation may be inferred from observational data only for the traits most closely related to fitness

The endangered species act petitioning process: Successes and failures

The Endangered Species Act (ESA) has been a legislative tool whose critics have derided its misuse and proponents have sought to strengthen its implementation. To determine whether the ESA is ESA is being used to protect species rather than to preserve land, and if the subsequent listing is influenced by petitioner affiliation, we conducted a content analysis of listing petitions. We found that most petitions attempted to list a single species versus several species, which indicates that these petitions were concentrating on species-specific, not habitat-based, issues. Once petitioned for listing, government agencies did not bias the listing of species by taxa. However, species proposed by petitioners with a national geographic focus had a greater likelihood of being listed as compared to other petitions. This difference in effecliveness indicates listing may be influenced by petition quality or petitioner\u27s political skill and should be explored further