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Neutral competition in a deterministically changing environment: revisiting continuum approachesSep 17 2019Environmental variation can play an important role in ecological competition by influencing the relative advantage between competing species. Here, we consider such effects by extending a classical, competitive Moran model to incorporate an environment ... More
Bayesian inference of species trees using diffusion modelsSep 16 2019We describe a new and computationally efficient Bayesian methodology for inferring species trees and demographics from unlinked binary markers. Likelihood calculations are carried out using diffusion models of allele frequency dynamics combined with a ... More
Bayesian inference of species trees using diffusion modelsSep 16 2019Sep 17 2019We describe a new and computationally efficient Bayesian methodology for inferring species trees and demographics from unlinked binary markers. Likelihood calculations are carried out using diffusion models of allele frequency dynamics combined with a ... More
Replicator population dynamics of group ($n$-agent) interactions. Broken symmetry, thresholds for metastability and macroscopic behaviorSep 15 2019We analyze from basic physical considerations the Darwinian competition for reproduction (evolutionary dynamics) of strategists in a Public Goods Game, the archetype for $n$-agent (group) economical and biological interactions. In the proposed setup, ... More
Preliminary study of mortality by cause and sociodemographic characteristics, municipality of San Francisco, Antioquia (Columbia), 2001-2010Sep 15 2019Objective: Determining the structure of mortality from causes and sociodemographic characteristics, in the municipality of San Francisco, Antioquia, 2001-2010. Methodology: Quantitative descriptive study with retrospective longitudinal data obtained from ... More
The human monogamy behavior can influence the transmission of AIDSSep 14 2019In this letter, we mainly consider an MSM (men have sex with men) network to analysis how monogamy behavior can influence the transmission of HIV. By calculating and analyzing the basic reproductive number of that network, we find the condition for when ... More
Repulsion in controversial debate drives public opinion into fifty-fifty stalemateSep 13 2019Opinion formation is a process with strong implications for public policy. In controversial debates with large consequences, the public opinion is often trapped in a fifty-fifty stalemate, jeopardizing broadly accepted political decisions. Emergent effects ... More
High Resolution Forecasting of Heat Waves impacts on Leaf Area Index by Multiscale Multitemporal Deep LearningSep 13 2019Climate change impacts could cause progressive decrease of crop quality and yield, up to harvest failures. In particular, heat waves and other climate extremes can lead to localized food shortages and even threaten food security of communities worldwide. ... More
An adaptive voter model on simplicial complexesSep 12 2019Collective decision making processes lie at the heart of many social, political and economic challenges. The classical voter model is a well-established conceptual model to study such processes. In this work, we define a new form of adaptive (or co-evolutionary) ... More
Ecological communities from random Lotka-Volterra dynamics with nonlinear functional responseSep 12 2019We investigate the outcome of Lotka-Volterra dynamics of ecological communities with random interaction coefficients and non-linear functional response. We show in simulations that the saturation of Holling type-II response stabilises the dynamics. This ... More
Stationary distributions of continuous-time Markov chains: a review of theory and truncation-based approximationsSep 12 2019Computing the stationary distributions of a continuous-time Markov chain involves solving a set of linear equations. In most cases of interest, the number of equations is infinite or too large, and cannot be solved analytically or numerically. Several ... More
The Emergence of Innovation Complexity at Different Geographical and Technological ScalesSep 12 2019We define a novel quantitative strategy inspired by the ecological notion of nestedness to single out the scale at which innovation complexity emerges from the aggregation of specialized building blocks. Our analysis not only suggests that the innovation ... More
Ecosystem-level stabilizing effects of biodiversity via nutrient-diversity feedbacks in multitrophic systemsSep 12 2019Statistical averaging and asynchronous population dynamics as portfolio mechanisms are considered as the most important processes with which biodiversity contributes to ecosystem stability. However, portfolio theories usually regard biodiversity as a ... More
Tree congruence: quantifying similarity between dendrogram topologiesSep 11 2019Tree congruence metrics are typically global indices that describe the similarity or dissimilarity between dendrograms. This study principally focuses on topological congruence metrics that quantify similarity between two dendrograms and can give a normalised ... More
A sub-critical branching process model for application to analysing Y haplotype DNA mixturesSep 11 2019The treatment of short-tandem-repeat (STR) loci on the Y chromosome presents special problems in the forensic analysis of DNA mixtures, chiefly but not exclusively relating to the linkage of Y-STR loci which precludes the use of the `product rule' for ... More
Digital Beings as an option to study gut flora evolution and adaptationSep 10 2019In this work, we introduce a computational model for the study of the host-bacteria interaction and the influence of the intestinal microbiota on the behavior and feeding pattern of an individual. The model is based on digital entities, which we've called ... More
Quasi-steady uptake and bacterial community assembly in a mathematical model of soil-phosphorus mobilitySep 10 2019We mathematically model the uptake of phosphorus by a soil community consisting of a plant and two bacterial groups: copiotrophs and oligotrophs. Four equilibrium states emerge, one for each of the species monopolising the resource and dominating the ... More
Boltzmann machine learning and regularization methods for inferring evolutionary fields and couplings from a multiple sequence alignmentSep 10 2019The inverse Potts problem to infer the Boltzmann distribution for homologous protein sequences from their single-site and pairwise frequencies recently attracts a great deal of attention due to its capacity to accurately predict residue-residue contacts ... More
Stirring, mixing, growing: modeling microscale processes that change larger scale phytoplankton dynamicsSep 10 2019The quantitative description of marine systems is constrained by a major issue of scale separation: most marine biochemical processes occur at sub-centimeter scales, while the contribution to the Earth's biogeochemical cycles is expressed at much larger ... More
Influenza-associated mortality for different causes of death during the 2010-2011 through the 2014-2015 influenza seasons in RussiaSep 06 2019Sep 09 2019Background: There is limited information on the volume of influenza-associated mortality in Russia. Methods: Using previously developed methodology (Goldstein et al., Epidemiology 2012), we regressed the monthly rates of mortality for respiratory causes, ... More
Influenza-associated mortality for various causes of death during the 2010-2011 through the 2014-2015 influenza seasons in RussiaSep 06 2019Background: There is limited information on the volume of influenza-associated mortality in Russia. Methods: Using previously developed methodology (Goldstein et al., Epidemiology 2012), we regressed the monthly rates of mortality (available from the ... More
Stochastic models for adaptive dynamics: Scaling limits and diversitySep 05 2019I discuss the so-called stochastic individual based model of adaptive dynamics and in particular how different scaling limits can be obtained by taking limits of large populations, small mutation rate, and small effect of single mutations together with ... More
Irrelevance of linear controllability to nonlinear dynamical networksSep 03 2019There has been tremendous development of linear controllability of complex networks. Real-world systems are fundamentally nonlinear. Is linear controllability relevant to nonlinear dynamical networks? We identify a common trait underlying both types of ... More
Fast computation of kernel statistics using genotype value decompositionSep 03 2019Sep 04 2019Because of the recent advances of genome sequences, a large number of human genome sequences are available for the study of human genetics. Genome-wide association studies typically focus on associations between single-nucleotide polymorphisms and traits ... More
Inferring species interactions using Granger causality and convergent cross mappingSep 02 2019Identifying directed interactions between species from time series of their population densities has many uses in ecology. This key statistical task is equivalent to causal time series inference, which connects to the Granger causality (GC) concept: $x$ ... More
Theoretical and numerical considerations of the assumptions behind triple closures in epidemic models on networksSep 02 2019Networks are widely used to model the contact structure within a population and in the resulting models of disease spread. While networks provide a high degree of realism, the analysis of the exact model is out of reach and even numerical methods fail ... More
Percolation theory suggests some universal features in range margins across environmental gradientsSep 02 2019The margins within the geographic range of species are often specific in terms of ecological and evolutionary processes, and can strongly influence the species' reaction to climate change. One of the frequently observed features at range margins is fragmentation, ... More
Seasonal payoff variations and the evolution of cooperation in social dilemmasAug 30 2019Varying environmental conditions affect relations between interacting individuals in social dilemmas, thus affecting also the evolution of cooperation. Oftentimes these environmental variations are seasonal and can therefore be mathematically described ... More
Evidence for a multi-level trophic organization of the human gut microbiomeAug 28 2019The human gut microbiome is a complex ecosystem, in which hundreds of microbial species and metabolites coexist, in part due to an extensive network of cross-feeding interactions. However, both the large-scale trophic organization of this ecosystem, and ... More
Mathematically Modeling Spillover Dynamics of Emerging Zoonoses with Intermediate HostsAug 28 2019The World Health Organization describes zoonotic diseases as a major pandemic threat, and modeling the behavior of such diseases is a key component of their control. Many emerging zoonoses, such as SARS, Nipah, and Hendra, mutated from their wild type ... More
Machine learning algorithms to infer trait matching and predict species interactions in ecological networksAug 26 2019Ecologists have long suspected that species are more likely to interact if their traits match in a particular way. For example, a pollination interaction may be particularly likely if the proportions of a bee's tongue match flower shape in a beneficial ... More
An Age-Dependent Model for Dengue Transmission: Analysis and Comparison to Field Data from Semarang, IndonesiaAug 25 2019Medical statistics reveal a significant dependence of hospitalized dengue patient on the patient's age. To incorporate an age-dependence into a mathematical model, we extend the classical ODE system of disease dynamics to a PDE system. The equilibrium ... More
A simple stochastic model to describe the evolution over time of core genome SNP GC content in prokaryotesAug 24 2019Genomes in living organisms consist of the nucleotides adenine (A), guanine (G), cytosine (C) and thymine (T). All prokaryotes have genomes consisting of double-stranded DNA, where the A's and G's (purines) of one strand bind respectively to the T's and ... More
Extinction risk of a Metapopulation under the Allee EffectAug 23 2019We study the extinction risk of a fragmented population residing on a network of patches coupled by migration, where the local patch dynamics include the Allee effect. We show that mixing between patches dramatically influences the population's viability. ... More
Tree-metrizable HGT networksAug 23 2019Phylogenetic trees are often constructed by using a metric on the set of taxa that label the leaves of the tree. While there are a number of methods for constructing a tree using a given metric, such trees will only display the metric if it satisfies ... More
A phylogenetic approach disentangles interlocus gene conversion tract length and initiation rateAug 22 2019Interlocus gene conversion (IGC) homogenizes paralogs. Little is known regarding the mutation events that cause IGC and even less is known about the IGC mutations that experience fixation. To disentangle the rates of fixed IGC mutations from the tract ... More
Revisiting the R* theory: preemption enables multispecies coexistence on a single resourceAug 22 2019Resource competition theory (R* theory) predicts that the species with the highest efficiency (lowest resource requirements) will exclude all other species when competing over a single resource. This prediction contrasts the vast diversity in natural ... More
Outgroup Homogeneity Bias Causes Ingroup FavoritismAug 22 2019Ingroup favoritism, the tendency to favor ingroup over outgroup, is often explained as a product of intergroup conflict, or correlations between group tags and behavior. Such accounts assume that group membership is meaningful, whereas human data show ... More
Diversity in Biology: definitions, quantification, and modelsAug 22 2019Diversity indices are useful single-number metrics for characterizing a complex distribution of a set of attributes across a population of interest. The utility of these different metrics or set of metrics depend on the context and application, and whether ... More
The agreement distance of unrooted phylogenetic networksAug 22 2019A rearrangement operation makes a small graph-theoretical change to a phylogenetic network to transform it into another one. For unrooted phylogenetic trees and networks, popular rearrangement operations are tree bisection and reconnection (TBR) and prune ... More
Deterministic Epidemic Models For Ebola Infection With Time-dependent ControlsAug 21 2019Aug 22 2019In this paper, we have studied epidemiological models for Ebola infection using nonlinear ordinary differential equations and optimal control theory. We considered optimal control analysis of SIR and SEIR models for the deadly Ebola infection using vaccination, ... More
Deterministic epidemic models for ebola infection with time-dependent controlsAug 21 2019In this paper, we have studied epidemiological models for Ebola infection using nonlinear ordinary differential equations and optimal control theory. We considered optimal control analysis of SIR and SEIR models for the deadly Ebola virus infection using ... More
Toward a trait-based species pool hypothesisAug 21 2019The species pool hypothesis highlights the effects of historical processes and past adaptation on contemporary patterns of species diversity. This hypothesis has been contentious because it is difficult to test. Here we argue that a trait-based approach ... More
Evolution of specialization in dynamic fluidsAug 21 2019Previously we found mechanical factors involving diffusion and fluid shear promote evolution of social behavior in microbial populations (Uppal and Vural 2018). Here, we extend this model to study the evolution of specialization using realistic physical ... More
Mapping the bacterial ways of lifeAug 20 2019The rise in the availability of bacterial genomes defines a need for synthesis: abstracting from individual taxa, to see the larger patterns of bacterial lifestyles across microbial systems. In community ecology, a central organising theory is the niche ... More
Singular Lagrangians and the dynamics of the "Kill the Winner" model and its descendantsAug 20 2019We consider certain analytical features of the "Kill the Winner" model which is a stochastic model that can explain among other things competition among species and simultaneous predation on the competing species. The model equations are shown to admit ... More
Mathematical analysis of a two-strain disease model with amplificationAug 19 2019We investigate a two-strain disease model with amplification to simulate the prevalence of drug-susceptible (s) and drug-resistant (m) disease strains. We model the emergence of drug resistance as a consequence of inadequate treatment, i.e. amplification. ... More
Spectral theory for the stability of dynamical systems on large oriented locally tree-like graphsAug 19 2019We develop a mathematical theory for the linear stability of stationary states in large dynamical systems modelled by a set of randomly coupled differential equations on a locally tree-like network. Our approach provides analytical expressions for the ... More
Drift, stabilizing and destabilizing for a Keller-Siegel's system with the short-wavelength external signalAug 19 2019This article aims at exploring the short-wavelength stabilization and destabilization of the advection-diffusion systems formulated using the Patlak-Keller-Segel cross-diffusion. We study a model of the taxis partly driven by an external signal. We address ... More
Drift, stabilizing and destabilizing for a Keller-Siegel's system with the short-wavelength external signalAug 19 2019Sep 02 2019This article aims at exploring the short-wavelength stabilization and destabilization of the advection-diffusion systems formulated using the Patlak-Keller-Segel cross-diffusion. We study a model of the taxis partly driven by an external signal. We address ... More
Modeling Major Transitions in Evolution with the Game of LifeAug 19 2019Maynard Smith and Szathm\'ary's book, The Major Transitions in Evolution, describes eight major events in the evolution of life on Earth and identifies a common theme that unites these events. In each event, smaller entities came together to form larger ... More
Controlling distant contacts to reduce disease spreading on disordered complex networksAug 16 2019Disorder is a characteristic of real social networks generated by heterogeneity in person-to-person interactions. This property affects the way a disease spreads through a population, reaches a tipping point in the fraction of infected individuals, and ... More
A Low-Profile, Self-Contained System for Atmospheric Monitoring and Mid-flight Collection of Viable Microbiological Samples at High AltitudeAug 16 2019The prevalence of bacteria in the atmosphere has been well established in relevant literature, suggesting that airborne bacteria can influence atmospheric characteristics including the development of clouds. Studies have also demonstrated that the atmospheric ... More
Generalized group-based epidemic model for spreading processes on networks: GgroupEMAug 16 2019We develop a generalized group-based epidemic model (GgroupEM) framework for any compartmental epidemic model (for example; susceptible-infected-susceptible, susceptible-infected-recovered, susceptible-exposed-infected-recovered). Here, a group consists ... More
Turbulent coherent structures and early life below the Kolmogorov scaleAug 16 2019A great number of biological organisms live in aqueous environments. Major evolutionary transitions, including the emergence of life itself, likely occurred in such environments. While the chemical aspects of the role of water in biology are well-studied, ... More
Evolution of cooperation in networks: well-connected cooperators can enhance cooperation but are counteracted by Trojan horsesAug 16 2019Cooperative behaviour is widespread in nature, but explaining how cooperation evolves constitutes a major scientific challenge. Simulation models has shown that social network structure plays a key role in rendering cooperation evolutionarily stable. ... More
Geographically-dependent individual-level models for infectious diseases transmissionAug 15 2019Infectious disease models can be of great use for understanding the underlying mechanisms that influence the spread of diseases and predicting future disease progression. Modeling has been increasingly used to evaluate the potential impact of different ... More
Deep learning on butterfly phenotypes tests evolution's oldest mathematical modelAug 15 2019Traditional anatomical analyses captured only a fraction of real phenomic information. Here, we apply deep learning to quantify total phenotypic similarity across 2468 butterfly photographs, covering 38 subspecies from the polymorphic mimicry complex ... More
Epidemic models on social networks -- with inferenceAug 15 2019Consider stochastic models for the spread of an infection in a structured community, where this structured community is itself described by a random network model. Some common network models and transmission models are defined and large population proporties ... More
When very slow is too fast -- collapse of a predator-prey systemAug 15 2019Critical transitions or regime shifts are sudden and unexpected changes in the state of an ecosystem, that are usually associated with dangerous levels of environmental change. However, recent studies show that critical transitions can also be triggered ... More
Laboratory biases hinder Eco-Evo-Devo integration: hints from the microworldAug 14 2019How specific environmental contexts contribute to the robustness and variation of developmental trajectories and evolutionary transitions is a central point in Eco-Evo-Devo. However, the articulation of ecological, evolutionary and developmental processes ... More
Mobility restrictions for the control of epidemics: When do they work?Aug 14 2019Mobility restrictions - travel advisories, trade and travel bans, border closures and, in extreme cases, area quarantines or cordons sanitaires - are among the most widely used measures to control infectious diseases. Restrictions of this kind were important ... More
A simple model for pattern formation in clonal-growth plantsAug 13 2019Clonal plants reproduce by generating new plants from a piece of an existing one without the need of producing seeds or spores. They form a whole family of plants, including terrestrial and marine species. However, the specific features of clonal growth ... More
Estimation of the excess mortality in chronic diseases from prevalence and incidence dataAug 12 2019Aggregated health data such as claims data from health insurances become more and more available for research purposes. Estimates of excess mortality from prevalence and incidence of a chronic condition have only been possible for ages 50 years and older ... More
Fixation probabilities in evolutionary dynamics under weak selectionAug 10 2019In evolutionary dynamics, a key measure of a mutant trait's success is the probability that it takes over the population given some initial mutant-appearance distribution. Under weak selection, meaning a small perturbation of the neutral model, we give ... More
Inferring differentiation order in adaptive immune responses from population level dataAug 09 2019A hallmark of the adaptive immune response is the proliferation of pathogen-specific lymphocytes that leave in their wake a long lived population of cells that provide lasting immunity. A subject of ongoing investigation is when during an adaptive immune ... More
Can endogenous fluctuations persist in high-diversity ecosystems?Aug 09 2019When can complex ecological interactions drive an entire ecosystem into a persistent non-equilibrium state, where species abundances keep fluctuating without going to extinction? We show that high-diversity spatially-extended systems, in which conditions ... More
Can endogenous fluctuations persist in high-diversity ecosystems?Aug 09 2019Aug 26 2019When can complex ecological interactions drive an entire ecosystem into a persistent non-equilibrium state, where species abundances keep fluctuating without going to extinction? We show that high-diversity spatially-extended systems, in which conditions ... More
Preferences for efficiency, rather than preferences for morality, drive cooperation in the one-shot Stag-Hunt GameAug 08 2019Recent work highlights that cooperation in the one-shot Prisoner's dilemma (PD) is primarily driven by moral preferences for doing the right thing, rather than social preferences for equity or efficiency. By contrast, little is known on what motivates ... More
Hospitalization in the transmission of dengue dynamics: The impact on public health policiesAug 08 2019Dengue virus has caused major problems for public health officials for decades in tropical and subtropical countries. We construct a compartmental model that includes the risk of hospitalization and its impact on public health policies. The basic reproductive ... More
Population collapse in Elite-dominated societies: A differential equations model without differential equationsAug 07 2019The HANDY model of Motesharrei, Rivas, and Kalnay examines interactions with the environment by human populations, both between poor and rich people, i.e., "Commoners" and "Elites". The Elites control the society's wealth and consume it at a higher rate ... More
Invariant predictions of epidemic patterns from radically different forms of seasonal forcingAug 07 2019Seasonal variation in environmental variables, and in rates of contact among individuals, are fundamental drivers of infectious disease dynamics. Unlike most periodically-forced physical systems, for which the precise pattern of forcing is typically known, ... More
Subpopulations and Stability in Microbial CommunitiesAug 07 2019In microbial communities, each species may have multiple, distinct phenotypes. How do these subpopulations affect the stability of the community? Here, we address this question theoretically, showing that simple models with subpopulation structure and ... More
Environmental Disorder Regulation of Invasion and Genetic LossAug 07 2019Many physical and natural systems, including the population of species, evolve in habitats with spatial stochastic variations of the individuals' motility. We study here the effect of those fluctuations on invasion and genetic loss. A Langevin equation ... More
Plant coexistence mediated by adaptive foraging preferences of exploiters or mutualistsAug 07 2019Coexistence of plants depends on their competition for common resources and indirect interactions mediated by shared exploiters or mutualists. These interactions are driven either by changes in animal abundance (density-mediated interactions, e.g., apparent ... More
Dengue model with early-life stage of vectors and age-structure within hostAug 07 2019We construct an epidemic model for the transmission of dengue fever with early-life stage in the vector dynamics and age-structure within hosts. The early-life stage of the vector is modeled via a general function that supports multiple vector densities. ... More
Diverse interactions and ecosystem engineering stabilize community assemblyAug 06 2019The complexity of an ecological community can be distilled into a network, where diverse interactions connect species in a web of dependencies. Species interact not only with each other but indirectly through environmental effects, however the role of ... More
A mechanistic model of disjunctive metabolic symbioses in microbesAug 06 2019Lately, experimental research on microbial symbioses based on nutrient exchange and interdependence has yielded a number of interesting findings, however an in-depth mathematical description of the exact underlying dynamics of such symbiotic associations ... More
Multi-Strain Age-Structured Dengue Transmission Model: Analysis and Optimal ControlAug 06 2019Dengue is a serious health problem in the Philippines. In 2016, the Department of Health of the country launched a dengue vaccination campaign using Dengvaxia. However, the campaign was mired with controversy and the use of Dengvaxia was banned in the ... More
Counting Tree-Child Networks and Their SubclassesAug 06 2019Galled trees are studied as a recombination model in population genetics. This class of phylogenetic networks is generalized into tree-child, galled and reticulation-visible network classes by relaxing a structural condition imposed on galled trees. We ... More
Counting Tree-Child Networks and Their SubclassesAug 06 2019Aug 07 2019Galled trees are studied as a recombination model in population genetics. This class of phylogenetic networks is generalized into tree-child, galled and reticulation-visible network classes by relaxing a structural condition imposed on galled trees. We ... More
Antioxidant capacity is repeatable across years but does not consistently correlate with a marker of peroxidation in a free-living passerine birdAug 05 2019Oxidative stress occurs when reactive oxygen species (ROS) exceed antioxidant defences, which can have deleterious effects on cell function, health and survival. Therefore, organisms are expected to finely regulate pro-oxidant and antioxidant processes. ... More
Testing Multispecies Coalescent Simulators using Summary StatisticsAug 04 2019As genomic scale datasets motivate research on species tree inference, simulators of the multispecies coalescent (MSC) process are essential for the testing and evaluation of new inference methods. However, the simulators themselves must be tested to ... More
Could short-lasting non-specific immunity explain seasonal spacing of epidemic diseases?Aug 02 2019Common respiratory viruses cause seasonal epidemics in sequential patterns. The underlying mechanisms for this pattern have been debated for some time. For influenza, contenders include temperature, humidity, and vitamin D levels. While such seasonal ... More
Monotonic and nonmonotonic immune responses in viral infection systemsAug 02 2019In this paper, we study two-dimensional, three-dimensional monotonic and nonmonotonic immune responses in viral infection systems. Our results show that the viral infection systems with monotonic immune response has no bistability appear. However, the ... More
Statistical tools for seed bank detectionJul 31 2019Sep 09 2019In this article, we derive statistical tools to analyze and distinguish the patterns of genetic variability produced by classical and recent population genetic models related to seed banks. In particular, we are concerned with models described by the ... More
Statistical tools for seed bank detectionJul 31 2019In this article, we derive statistical tools to analyze and distinguish the patterns of genetic variability produced by classical and recent population genetic models related to seed banks. In particular, we are concerned with models described by the ... More
Climate-driven statistical models as effective predictors of local dengue incidence in Costa Rica: A Generalized Additive Model and Random Forest approachJul 30 2019Climate has been an important factor in shaping the distribution and incidence of dengue cases in tropical and subtropical countries. In Costa Rica, a tropical country with distinctive micro-climates, dengue has been endemic since its introduction in ... More
An artifcial life approach to studying niche differentiation in soundscape ecologyJul 30 2019Artificial life simulations are an important tool in the study of ecological phenomena that can be difficult to examine directly in natural environments. Recent work has established the soundscape as an ecologically important resource and it has been ... More
Seed Banks, Entropy and GaiaJul 29 2019In this paper we discuss the Gaia hypothesis and the idea of sequential selection. Building on previous work using the Tangled Nature Model of co-evolution we elaborate on Gaia as an example of an entropic hierarchy. We argue that sequential selection ... More
The Effect of Social Information in the Dictator Game with a Taking OptionJul 29 2019We experimentally study how redistribution choices are affected by positive and negative information regarding the behaviour of a previous participant in a dictator game with a taking option. We use the strategy method to identify behavioural "types", ... More
Trait-space patterning and the role of feedback in antigen-immunity coevolutionJul 29 2019Coevolutionary arms races form between interacting populations that constitute each other's environment and respond to mutual changes. This inherently far-from-equilibrium process finds striking manifestations in the adaptive immune system, where highly ... More
Fast Diffusion Inhibits Disease OutbreaksJul 29 2019We show that the basic reproduction number of an SIS patch model with standard incidence is either strictly decreasing and strictly convex with respect to the diffusion coefficient of infected subpopulation if the patch reproduction numbers of at least ... More
Effects of resource competition on evolution and adaptive radiationJul 28 2019The entanglement of population dynamics, evolution and adaptive radiation for the species sharing common resources is studied. For the population dynamics we modify the competitive Lotka-Volterra equations introducing a new resource contest principles. ... More
Calculating Germinal Centre ReactionsJul 28 2019Germinal centres are anatomically defined lymphoid organ structures that mediate B cell affinity maturation and affect the quality of humoral immune responses. Mathematical models based on differential equations or agent-based simulations have been widely ... More
Predominance of the weakest species in Lotka-Volterra and May-Leonard implementations of the rock-paper-scissors modelJul 25 2019We revisit the problem of the predominance of the 'weakest' species in the context of Lotka-Volterra and May-Leonard implementations of a spatial stochastic rock-paper-scissors model in which one of the species has its predation probability reduced by ... More
Complete maximum likelihood estimation for SEIR epidemic models: theoretical developmentJul 24 2019Jul 29 2019We present a class of SEIR Markov chain models for infectious diseases observed over discrete time in a random human population living in a closed environment. The population changes over time through random births, deaths, and transitions between states ... More
Complete maximum likelihood estimation for SEIR epidemic models: theoretical developmentJul 24 2019We present a class of SEIR Markov chain models for infectious diseases observed over discrete time in a random human population living in a closed environment. The population changes over time through random births, deaths, and transitions between states ... More
Simulating an infinite mean waiting timeJul 23 2019Aug 30 2019We consider a hybrid method to simulate the return time to the initial state in a critical-case birth--death process. The expected value of this return time is infinite, but its distribution asymptotically follows a power-law. Hence, the simulation approach ... More
Simulating an infinite mean waiting timeJul 23 2019We consider a hybrid method to simulate the return time to the initial state in a critical-case birth--death process. The expected value of this return time is infinite, but its distribution asymptotically follows a power-law. Hence, the simulation approach ... More